From nih-image-request@io.ece.drexel.edu Thu Jun 25 14:46 EDT 1998 X-UIDL: 82e9e0dd82e906ad8903b103d48111e2 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA12655 for cshtest; Thu, 25 Jun 1998 14:46:23 -0400 (EDT) Resent-Date: Thu, 25 Jun 1998 14:46:23 -0400 (EDT) Date: Thu, 25 Jun 1998 13:42:41 -0500 (CDT) Message-Id: Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu From: Ty Wilson To: Multiple recipients of list Subject: NIH-IMAGE Mailing List Move X-Listprocessor-Version: 6.0c -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List MIME-Version: 1.0 Resent-Message-ID: <"c0nNh2.0.g53._hfar"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/10 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 3903 Status: RO To all members of the nih-image mailing list - The current list-owners, Ty Wilson, John Ladwig, and Ed Nater, are pleased to announce: THE NIH-IMAGE MAILING LIST IS MOVING TO A NEW LOCATION Jonathan Nissanov and Vaughn Adams of the Computer Vision Center for Vertebrate Brain Mapping at Drexel University have graciously and generously volunteered to host the nih-image mailing list in the future. We ask you to support them in this effort and show them the same patience and kindness you have shown us over the last few years. The proposed date and time of the move will be Monday, 29 June, 1998. We apologize in advance for any inconvenience this changeover will cause to list members; we have taken several steps (detailed below) to reduce this inconvenience as much as possible. =-=-=-=-=-=-=-= ABOUT THE CHANGEOVER To facilitate the move and to clean up the membership list, we are asking all members to subscribe to the new mailing list and to unsubscribe from the old one. PLEASE NOTE: You need to make this change yourself; we will *not* do it for you. Members may make the change to the new list at anytime as of the posting of this message. Instructions for subscribing to the new mailing list and unsubscribing from the old one follow at the end of this message. Prior to the changeover date, we will forward all messages sent to the old list to the members of the new list. However, until the time of the changeover, all postings must be sent to the old list. Consequently, those individuals interested in posting to the list should maintain membership in the old list until the changeover date and then change their subscriptions after the changeover has been made. At the changeover date we will reverse the message flow. From that date, and for a one week period thereafter, we will forward all messages sent from the new list to the membership remaining on the old list. After the changeover date, however, all postings will have to be sent to the new list; messages sent to the old mailing list will not be forwarded to the new list in order to avoid the potential for looping messages. =-=-=-=-=-=-=-= HOW TO SUBSCRIBE TO THE NEW NIH-IMAGE MAILING LIST: To subscribe to the new nih-image mailing list, you need to do one of the following, depending on whether you wish to receive regular postings (each posting is sent individually) or a digested version (where you receive one composite posting per day). **Please note** that the commands are somewhat different from the old list.: To SUBSCRIBE to the REGULAR LIST, send E-mail to: nih-image-request@biomed.drexel.edu The Subject of the message should contain "Subscribe" As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe To SUBSCRIBE to A DIGESTED VERSION of the list, send E-mail to: nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe =-=-=-=-=-=-=-= HOW TO UNSUBSCRIBE FROM THE OLD NIH-IMAGE MAILING LIST: To unsubscribe, send an email message to: listproc@soils.umn.edu with the message body: unsubscribe nih-image If you have difficulties in unsubscribing, please notify the list-owner at: owner-nih-image@soils.umn.edu and provide a copy of the message returned by the list processor following the unsuccessful attempt as well as your full name and, if possible, the exact email address by which you originally subscribed to nih-image. We will gladly remove you from the list. =-=-=-=-=-=-=-= PLEASE REMEMBER: The old mailing list will be shut down on Monday, 6 July, 1998 (or sooner if all members have unsubscribed before then). Message forwarding to the old list will cease at that time. Those individuals who have failed to subscribe to the new mailing list at that time will no longer receive postings from the mailing list. From nih-image-request@io.ece.drexel.edu Fri Jun 26 00:38 EDT 1998 X-UIDL: 84ba265a9f0fb37d8ca46162868140ef Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id AAA29345 for cshtest; Fri, 26 Jun 1998 00:38:29 -0400 (EDT) Resent-Date: Fri, 26 Jun 1998 00:38:29 -0400 (EDT) Date: Thu, 25 Jun 1998 23:38:01 -0500 (CDT) Message-Id: <199806260439.MAA12394@nero.rph.health.wa.gov.au> Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu From: "Robert Day" To: Multiple recipients of list Subject: Re: Sony LANC protocol X-Listprocessor-Version: 6.0c -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List In-reply-to: <1.5.4.16.19980625075403.561788ea@31d.marlab.ac.uk> Content-transfer-encoding: 7BIT MIME-Version: 1.0 Resent-Message-ID: <"FLHh7.0._97.vMoar"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/11 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 350 Status: RO > > I am looking for information about the LANC or Control-L protocol > which is used to control video recorders. > Chris, try the Sony LANC/Control-L page at: Rob Day -- Robert Day rob.day@nero.rph.health.wa.gov.au Project Bioengineer ph +61 8 9224 3227 Royal Perth Hospital fax +61 8 9224 1138 From nih-image-request@io.ece.drexel.edu Fri Jun 26 12:32 EDT 1998 X-UIDL: f431754d23698ef7fbe5f358fc4466ea Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA01752 for cshtest; Fri, 26 Jun 1998 12:32:30 -0400 (EDT) Resent-Date: Fri, 26 Jun 1998 12:32:30 -0400 (EDT) Date: Fri, 26 Jun 1998 11:29:07 -0500 (CDT) Message-Id: <3593CBE0.322AB815@soils.umn.edu> Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu From: Ed Nater To: Multiple recipients of list Subject: IMPORTANT: The NIH-Image mailing list is moving X-Listprocessor-Version: 6.0c -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List MIME-Version: 1.0 X-Mailer: Mozilla 4.05 (Macintosh; U; PPC) Resent-Message-ID: <"AHEOe.0.IP.8pyar"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/12 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2858 Status: RO Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit !! IMPORTANT ANNOUNCEMENT !! The email mailing list, nih-image, has moved to a new location. The old list will cease operation on the 29th of June, 1998, but will continue to forward messages from the new list until 6 July, 1998. To continue as a list member, you will have to subscribe to the new list. To do so, you need to do one of the following, depending on whether you wish to receive regular postings (each posting is sent individually) or a digested version (where you receive one composite posting per day). Please note that the commands are somewhat different from the old list.: To SUBSCRIBE to the REGULAR LIST, send E-mail to: nih-image request@biomed.drexel.edu The Subject of the message should contain "Subscribe" As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe To SUBSCRIBE to A DIGESTED VERSION of the list, send E-mail to: nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe IF YOU HAVE TROUBLE subscribing to the new list, please send an email message explaining the problem to nih-image-owner@biomed.drexel.edu. IN ADDITION, please unsubscribe from the old list. It will help us keep track of the changeover and it will prevent you from receiving additional messages like this one. To unsubscribe, send an email message to: listproc@soils.umn.edu with the message body: unsubscribe nih-image If you have difficulties in unsubscribing, please notify the list-owner at: owner-nih-image@soils.umn.edu and provide a copy of the message returned by the list processor following the unsuccessful attempt and your full name and, if possible, the exact email address by which you originally subscribed to nih-image. Thank you all for the patience, kindness, and respect you have shown us (John Ladwig, Ty Wilson, and Ed Nater) in the past. It has been an honor hosting this list and, although we take justifiable pride in the quality and usefulness of this list, it is you, the members, who have made it the high quality resource it has become. Please afford Jonathan Nissanov and Vaughn Adams the same degree of respect you have shown us and you will ensure its continued success. This message will be sent on a daily basis until the list closes. Thank you all. Ed List-owner -- Edward A. Nater phone: 612-625-1725 Professor and fax: 612-624-4223 Director of Graduate Studies email: ed.nater@soils.umn.edu Department of Soil, Water, and Climate, 439 Borlaug Hall University of Minnesota, St. Paul, MN 55108-6028 USA "Science advances one funeral at a time." - Niels Bohr From nih-image-request@io.ece.drexel.edu Fri Jun 26 14:00 EDT 1998 X-UIDL: aa8861522426dd7b73ff04fba5501c55 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA08642 for cshtest; Fri, 26 Jun 1998 14:00:36 -0400 (EDT) Resent-Date: Fri, 26 Jun 1998 14:00:36 -0400 (EDT) X-Sender: h1345emq@popserv.rz.hu-berlin.de Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Fri, 26 Jun 1998 19:52:58 +0100 To: nih-image@io.ece.drexel.edu From: Peter Bramlage Subject: Website / Mailing List Resent-Message-ID: <"2lVyS2.0.K32.V5-ar"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/13 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1344 Status: RO I hope you don't mind if I bother this list once with a mail that is way off topic. But I believe it could be interesting for some of you. As some of you may know, I own a small website that deals with the primary topic of methods in the area of Heart & Vessel Research. I am writing you to tell you that I added a mailing list just for the topic of Heart & Vessel Research to my Internetserver (http://www.hvresearch.com). I had the impression that people are interested in communicating, but are not willing to use the guestbook for this purpose. Since I believe that communication is the most important issue in our business I installed this Listserver. I would like to ask you to help me with the initial etablishment of the list. For most of us it is nice to subscribe to a mailing list and read the mails coming in for a while, before participating actively in the discussion. That is may main concern. People will probably unsubscribe before a proper discussion can develop. Your task would be to have an open ear for people on the list and to help when you think help is possible. To subscribe to the list just send an email to requests@hvresearch.com with subscribe listserv as the body of the message. I appreciate your help ! ... and feel free to give this adress to as many people as you can ;-) Best Regards, Peter From nih-image-request@io.ece.drexel.edu Sun Jun 28 02:56 EDT 1998 X-UIDL: b051232c3129d443902eeab47bc5252e Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA08511; Sun, 28 Jun 1998 02:54:26 -0400 (EDT) Resent-Date: Sun, 28 Jun 1998 02:54:26 -0400 (EDT) Date: Sun, 28 Jun 1998 01:50:54 -0500 (CDT) Message-Id: <199806280611.BAA08392@catena.soils.umn.edu> Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu From: John Ladwig To: Multiple recipients of list Subject: Administrivia: Getting on, off and around the list X-Listprocessor-Version: 6.0c -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List Resent-Message-ID: <"rfqb33.0.s_1.dVUbr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/14 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 3701 Status: RO This message is automatically posted once per month, on the 28th of the month. It contains information about list mechanics (subscribing, subscribing, digests, message archive access, and program distribution points. -jml NIH-Image mailing list coordinator [UN]SUBSCRIBING: ================ [Un]Subscription requests should be sent to: listproc@soils.umn.edu with one of the following commands in the *body* of the message: subscribe nih-image Your Realname unsubscribe nih-image and *no* Subject: line. Placing commands in the Subject line will only get them rejected by the automated list manager, and handed to a human, who is *no doubt* slower to respond than the list manager. DIGESTS: ======== Send the following in the body of a message to set nih-image mail digest to go back to message-at-a-time mode, send set nih-image mail ack to the same address. SUSPENDING: =========== To temporarily suspend your subscription, send the following in the body of a message to set nih-image mail postpone to go back to message-at-a-time or digest mode, send set nih-image mail ack or set nih-image mail digest ADDRESS CHANGES =============== If your email address has changed, please send mail to owner-nih-image@soils.umn.edu and ask the human there to change things around for you. If you have received an error message regarding your changed address, be assured that a human being *will* see that error message, and will handle the changeover. It may or may not be immediate, but it's usually handled within a few days. MESSAGE ARCHIVE ACCESS ====================== Best would be to point your web browser to: Next best, if you have access to gopher, you can connect to gopher.soils.umn.edu at port 70 (which can be found under the University of Minnesota "All the Gophers in the World" listing), and look under: Computer Information/ General Information/ Search Nih-Image Mailing List Current Month's Articles Search Nih-Image Mailing List Archives to search the archived messages for keywords. The Current Month's Articles are indexed on an hourly basis, the Archives on a daily basis. You can also browse the monthly archives in Computer Information/ General Information/ Selected Electronic Mailing List Archives/ Nih-image/* for the actual archived messages. The message archives which are available through gopher are also available via ftp to: The archive of email-retrievable files relevant to NIH Image available by request from the listprocessor; send the command index nih-image to get a list of the files, and a brief description of each one. NIH-IMAGE PROGRAM LOCATIONS =========================== The reference location for NIH-image is Programs, documentation, macro archive, and related information are stored there. More information about NIH Image is available on the NIH Image Web site at CONTACT/ADMINISTRATIVE INFORMATION ================================== Questions about the listprocessor system and the NIH-Image discussion list may be sent to owner-listproc@soils.umn.edu or owner-nih-image@soils.umn.edu Your humble List maintainer, John Ladwig owner-nih-image@soils.umn.edu From nih-image-request@io.ece.drexel.edu Sun Jun 28 15:59 EDT 1998 X-UIDL: cdc8d34e887c89b6a87d7576c7faedd2 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA17155; Sun, 28 Jun 1998 15:59:23 -0400 (EDT) Resent-Date: Sun, 28 Jun 1998 15:59:23 -0400 (EDT) Date: Sun, 28 Jun 1998 14:58:08 -0500 (CDT) Message-Id: <35969F4E.115A79A7@soils.umn.edu> Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu From: Ed Nater To: Multiple recipients of list Subject: IMPORTANT: The NIH-Image mailing list is moving X-Listprocessor-Version: 6.0c -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List Content-Transfer-Encoding: 7bit MIME-Version: 1.0 X-Mailer: Mozilla 4.05 (Macintosh; U; PPC) Resent-Message-ID: <"I_PmI2.0.l94.O1gbr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/15 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 2703 Status: RO !! IMPORTANT ANNOUNCEMENT !! The email mailing list, nih-image, has moved to a new location. The old list will cease operation on the 29th of June, 1998, but will continue to forward messages from the new list until 6 July, 1998. YOU HAVE ** 8 ** DAYS IN WHICH TO MAKE THE CHANGE To continue as a list member, you will have to subscribe to the new list. To do so, you need to do one of the following, depending on whether you wish to receive regular postings (each posting is sent individually) or a digested version (where you receive one composite posting per day). Please note that the commands are somewhat different from the old list.: To SUBSCRIBE to the REGULAR LIST, send E-mail to: nih-image request@biomed.drexel.edu The Subject of the message should contain "Subscribe" As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe To SUBSCRIBE to A DIGESTED VERSION of the list, send E-mail to: nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe IF YOU HAVE TROUBLE subscribing to the new list, please send an email message explaining the problem to nih-image-owner@biomed.drexel.edu. IN ADDITION, please unsubscribe from the old list. It will help us keep track of the changeover and it will prevent you from receiving additional messages like this one. To unsubscribe, send an email message to: listproc@soils.umn.edu with the message body: unsubscribe nih-image If you have difficulties in unsubscribing, please notify the list-owner at: owner-nih-image@soils.umn.edu and provide a copy of the message returned by the list processor following the unsuccessful attempt and your full name and, if possible, the exact email address by which you originally subscribed to nih-image. Thank you all for the patience, kindness, and respect you have shown us (John Ladwig, Ty Wilson, and Ed Nater) in the past. It has been an honor hosting this list and, although we take justifiable pride in the quality and usefulness of this list, it is you, the members, who have made it the high quality resource it has become. Please afford Jonathan Nissanov and Vaughn Adams the same degree of respect you have shown us and you will ensure its continued success. Thanks, Ed -- Edward A. Nater phone: 612-625-1725 Professor and fax: 612-624-4223 Director of Graduate Studies email: ed.nater@soils.umn.edu Department of Soil, Water, and Climate, 439 Borlaug Hall University of Minnesota, St. Paul, MN 55108-6028 USA "Science advances one funeral at a time." - Niels Bohr From nih-image-request@io.ece.drexel.edu Sun Jun 28 16:42 EDT 1998 X-UIDL: 469a03390dd126e5e43d82493bd674cd Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA20956; Sun, 28 Jun 1998 16:42:20 -0400 (EDT) Resent-Date: Sun, 28 Jun 1998 16:42:20 -0400 (EDT) Date: Sun, 28 Jun 1998 15:41:21 -0500 (CDT) Message-Id: <199806282018.QAA00076@scionserver.scioncorp.com> Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu From: Jeff Reidler To: Multiple recipients of list Subject: Scion Image Beta 3 X-Listprocessor-Version: 6.0c -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List Mime-Version: 1.0 Resent-Message-ID: <"23Wy.0.S55.sfgbr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/16 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 197 Status: RO Dear Imagers, Scion Corporation has released BETA 3 of Scion Image for Windows 95 and NT, available at http://www.scioncorp.com in 'Downloads'. Thank you for your patience and support. Jeff From nih-image-request@io.ece.drexel.edu Mon Jun 29 15:02 EDT 1998 X-UIDL: 80834e9595e48b1b63f71673b4b9bbaf Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA24436; Mon, 29 Jun 1998 15:00:08 -0400 (EDT) Resent-Date: Mon, 29 Jun 1998 15:00:08 -0400 (EDT) Date: Mon, 29 Jun 1998 13:49:58 -0500 (CDT) Message-Id: Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu From: Ty Wilson To: Multiple recipients of list Subject: CHANGEOVER IMMINENT! X-Listprocessor-Version: 6.0c -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List MIME-Version: 1.0 Resent-Message-ID: <"YuPTa1.0.pr5.PC-br"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/17 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2813 Status: RO ====== Dear List Members; Please take note: The changeover in the home for the NIH-Image mailing list will occur *today *at 3:00 pm CST. At the posting of this message, it is approximately 1:45 pm CST. Once the changeover has occurred, all messages posted to the NIH-Image mailing list *must* be posted to the new list. The old list will no longer accept postings. In order to post messages, you must be signed up to the new list. We will continue forwarding messages from the new list to the old list for one week, until 6 July, 1998, at which time we will terminate all message forwarding. If you have not subscribed to the new list, I urge you to do so soon. Thank you for your patience. Ed Instructions for subscription/unsubscription follow: ======= To continue as a list member, you will have to subscribe to the new list. To do so, you need to do one of the following, depending on whether you wish to receive regular postings (each posting is sent individually) or a digested version (where you receive one composite posting per day). Please note that the commands are somewhat different from the old list.: To SUBSCRIBE to the REGULAR LIST, send E-mail to: nih-image request@biomed.drexel.edu The Subject of the message should contain "Subscribe" As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe To SUBSCRIBE to A DIGESTED VERSION of the list, send E-mail to: nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe IF YOU HAVE TROUBLE subscribing to the new list, please send an email message explaining the problem to nih-image-owner@biomed.drexel.edu. IN ADDITION, please unsubscribe from the old list. It will help us keep track of the changeover and it will prevent you from receiving additional messages like this one. To unsubscribe, send an email message to: listproc@soils.umn.edu with the message body: unsubscribe nih-image If you have difficulties in unsubscribing, please notify the list-owner at: owner-nih-image@soils.umn.edu and provide a copy of the message returned by the list processor following the unsuccessful attempt and your full name and, if possible, the exact email address by which you originally subscribed to nih-image. Thank you all for the patience, kindness, and respect you have shown us (John Ladwig, Ty Wilson, and Ed Nater) in the past. It has been an honor hosting this list and, although we take justifiable pride in the quality and usefulness of this list, it is you, the members, who have made it the high quality resource it has become. Please afford Jonathan Nissanov and Vaughn Adams the same degree of respect you have shown us and you will ensure its continued success. From nih-image-request@io.ece.drexel.edu Mon Jun 29 15:25 EDT 1998 X-UIDL: 039911f2167fd463fc88f1d8e1d76dbb Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA26625; Mon, 29 Jun 1998 15:21:48 -0400 (EDT) Resent-Date: Mon, 29 Jun 1998 15:21:48 -0400 (EDT) Date: Mon, 29 Jun 1998 14:17:48 -0500 (CDT) Message-Id: Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu From: Brenda Leach To: Multiple recipients of list Subject: Image capturing crashes/digitizer problems X-Listprocessor-Version: 6.0c -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List Mime-Version: 1.0 Resent-Message-ID: <"etygC3.0.OP6.gX-br"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/18 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 663 Status: RO I am trying to capture live video using Image 1.61 on a Performa 5200 CD with an Adobe Photoshop Plug-in Digitizer. The problem I've always encountered on this computer (with different Image versions) is that when I try to use the "start capturing" command, it freezes. Instead, I have to use "Aquire - Plug-in Digitizer" to get a live image. But this has also stopped working for me. I just get a black field. I've used both of these commands on other computers to get images from video tapes, but never directly from the video camera. Is there some conflict I'm unaware of or a different digitizer I should be using? Thanks for any suggestions, Brenda Leach From nih-image-request@io.ece.drexel.edu Mon Jun 29 17:08 EDT 1998 X-UIDL: 9d5c26e9a13c848b9cc0d99459c1f15d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA06868; Mon, 29 Jun 1998 17:06:39 -0400 (EDT) Resent-Date: Mon, 29 Jun 1998 17:06:39 -0400 (EDT) From: Vaughn Adams Message-Id: <199806292103.RAA17168@cbis.ece.drexel.edu> Subject: Test - Ignore this X-ELM-OSV: (Our standard violations) no-mime=1; no-hdr-encoding=1 To: nih-image-d@io.ece.drexel.edu Date: Mon, 29 Jun 1998 17:03:47 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL31 (25)] Resent-Message-ID: <"o8iQP1.0.Yb1.y40cr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/19 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 303 Status: RO Please ignore. -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu From nih-image-request@io.ece.drexel.edu Mon Jun 29 17:16 EDT 1998 X-UIDL: 91fbb84bcaa5f1097b7b1c4007f0d574 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA07973; Mon, 29 Jun 1998 17:15:20 -0400 (EDT) Resent-Date: Mon, 29 Jun 1998 17:09:38 -0400 (EDT) From: Vaughn Adams Message-Id: <199806292106.RAA17549@cbis.ece.drexel.edu> Subject: Archive Test - please ignore X-ELM-OSV: (Our standard violations) no-mime=1; no-hdr-encoding=1 To: nih-image-d@io.ece.drexel.edu Date: Mon, 29 Jun 1998 17:06:47 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL31 (25)] Resent-Message-ID: <"AQUSQ1.0.Ai1.o70cr"@io> Resent-From: nih-image-d@io.ece.drexel.edu X-Mailing-List: archive/latest/1 X-Loop: nih-image-d@biomed.drexel.edu X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 300 Status: RO delete this -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu From nih-image-request@io.ece.drexel.edu Tue Jun 30 11:04 EDT 1998 X-UIDL: dcaeb5752186c01a01962b1e045a278b Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA25745; Tue, 30 Jun 1998 11:01:54 -0400 (EDT) Resent-Date: Tue, 30 Jun 1998 11:01:54 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Tue, 30 Jun 1998 09:51:21 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Welcome Resent-Message-ID: <"kTRxl.0.5-5.qjFcr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/20 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 3904 Status: RO Dear List Members; TimesWe at the Computer Vision Center for Vertebrate Brain Mapping (http://cbis.ece.drexel.edu/ICVC/) are pleased to serve as the new hosts of the NIH Image mail list. Ed Nater, John Ladwig and Ty Wilson have done a fantastic job in establishing and maintaining the list as an important forum for discussion on NIH Image issues and on image processing in general. It is a hard act to follow. Please bear with us while we make the transition. Listed below are important information for using the list. e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Help -------------------- To obtain a listing of help items, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-request@biomed.drexel.edu Subject: help Help on Digest -------------------- To obtain a listing of help items on digest version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* --------------------------------------------------------------------------- Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource --------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu http://cbis.ece.drexel.edu/ICVC/ --------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Wed Jul 1 14:08 EDT 1998 X-UIDL: e00de6af2720c0e745d2c227dcc1762d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA13706; Wed, 1 Jul 1998 14:07:11 -0400 (EDT) Resent-Date: Wed, 1 Jul 1998 14:07:11 -0400 (EDT) Message-ID: <359AC0A7.7C8C@pro.via-rs.com.br> Date: Wed, 01 Jul 1998 15:05:13 -0800 From: Luthero Martins Reply-To: luthero@pro.via-rs.com.br X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: question Content-Transfer-Encoding: 7bit Resent-Message-ID: <"U6XOd2.0.OA3.1bdcr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/21 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 459 Status: RO Group! I'm an ophthalmologist in Brazil. I have a power mac 7600, a frame grabber Miro motion DC-20. I take images from a Canon retinal camera non-mydriatic CR5-45NM and a Sony 3CCD video camera, with the Adobe Premiere software. I take color images. I'd like to capture this images directly from NIH, that will be Grayscale. What I'll need to do this? Somebody knows? Thanks Luthero Martins http://www.oftalmologia-digital.com From nih-image-request@io.ece.drexel.edu Wed Jul 1 19:22 EDT 1998 X-UIDL: 9a3b6447ed1389f76c00ded953f345dd Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id TAA13430; Wed, 1 Jul 1998 19:21:20 -0400 (EDT) Resent-Date: Wed, 1 Jul 1998 19:21:20 -0400 (EDT) Mime-Version: 1.0 X-Sender: scm@128.250.6.196 Message-Id: Date: Thu, 2 Jul 1998 09:14:49 +1000 To: nih-image@io.ece.drexel.edu From: Steve Martin Subject: New list reply-to setup Resent-Message-ID: <"IaRvF2.0.k73.xBicr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/22 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 537 Status: RO Hi to everyone who has jumped across... Messages from the new list host seem to have a 'reply-to' of the author of the posting, not the list. Is this an oversight, or a deliberate policy change? I only happened to notice because Eudora no longer filters my 'replyto: NIH-Image' mail. just wondering... regards, Steve ___________________________ Stephen Martin School of Physiotherapy The University of Melbourne 200 Berkeley St Parkville Victoria 3052 AUSTRALIA ph +61 3 9344 4171 fax +61 3 9344 4188 ___________________________ From nih-image-request@io.ece.drexel.edu Wed Jul 1 20:35 EDT 1998 X-UIDL: 01c3fb2865bc58b17f2966f48d11f3c4 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA20379; Wed, 1 Jul 1998 20:34:35 -0400 (EDT) Resent-Date: Wed, 1 Jul 1998 20:34:35 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Wed, 1 Jul 1998 19:30:46 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Re: New list reply-to setup Resent-Message-ID: <"QZiTn.0.0t4.2Jjcr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/23 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1328 Status: RO Not deliberate. We are working on it. Thanks. >Hi to everyone who has jumped across... > >Messages from the new list host seem to have a 'reply-to' of the author of >the posting, not the list. > >Is this an oversight, or a deliberate policy change? I only happened to >notice because Eudora no longer filters my 'replyto: NIH-Image' mail. > >just wondering... > >regards, > >Steve > >___________________________ >Stephen Martin >School of Physiotherapy >The University of Melbourne >200 Berkeley St >Parkville Victoria 3052 >AUSTRALIA >ph +61 3 9344 4171 >fax +61 3 9344 4188 >___________________________ --------------------------------------------------------------------------- Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource --------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu http://cbis.ece.drexel.edu/ICVC/ --------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Thu Jul 2 11:47 EDT 1998 X-UIDL: 169a7e48b7fcb3ce396e09962808113f Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA19692; Thu, 2 Jul 1998 11:45:39 -0400 (EDT) Resent-Date: Thu, 2 Jul 1998 11:45:39 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Thu, 2 Jul 1998 10:37:39 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Digest form Resent-Message-ID: <"eW3_G2.0.6b4.Dbwcr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/24 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1205 Status: RO Dear members. The digest form appears to vary greatly between different mail systems. Using Eudora, for example, each digest generates a new mailbox with each message stored individually. I very much like that mode myself. With some other systems we are getting less convenient formats. I would appreciate if those of you using the digest mode would let me know which system you are using and how the digest appears on that system. You can send your comments directly to me. Thanks. --------------------------------------------------------------------------- Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource --------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu http://cbis.ece.drexel.edu/ICVC/ --------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Thu Jul 2 11:47 EDT 1998 X-UIDL: 65ad81f388fed4e27c9b4e3e3bc885c2 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA19727; Thu, 2 Jul 1998 11:45:54 -0400 (EDT) Resent-Date: Thu, 2 Jul 1998 11:45:54 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Thu, 2 Jul 1998 10:39:35 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Reply to Resent-Message-ID: <"1MBRz1.0.be4.0dwcr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/25 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 881 Status: RO Dear members. We have now changed the reply to so it no longer automatically responds to the author of the posting but rather to the mail list. Regards, Yoni --------------------------------------------------------------------------- Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource --------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu http://cbis.ece.drexel.edu/ICVC/ --------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Fri Jul 3 06:33 EDT 1998 X-UIDL: 2aa3516d15007508a4970559aaa50df0 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA01376; Fri, 3 Jul 1998 06:31:24 -0400 (EDT) Resent-Date: Fri, 3 Jul 1998 06:31:24 -0400 (EDT) X-Sender: sdb@pop1.liv.ac.uk Message-Id: In-Reply-To: <199807031000.GAA27697@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Fri, 3 Jul 1998 11:22:18 +0100 To: nih-image@io.ece.drexel.edu From: Steve Barrett Subject: Re: Digest form Resent-Message-ID: <"w6D7T.0.z2.y2Bdr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/26 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 871 Status: RO Dear Jonathan, >Using Eudora, for example, each digest generates a new mailbox with each >message stored individually. I very much like that mode myself. With some >other systems we are getting less convenient formats. I would appreciate if >those of you using the digest mode would let me know which system you are >using and how the digest appears on that system. I use Eudora Light v3.1.3 and the digest appears as with the previous distribution system - a single email message containing all the day's postings. No problem. ___________________________________________________________________ Dr Steve Barrett Surface Science Research Centre University of Liverpool Liverpool L69 3BX United Kingdom Tel: 44-(0)151-794-3874 / 3894 / 3870 Fax: 44-(0)151-708-0662 Email: S.D.Barrett@liv.ac.uk ___________________________________________________________________ From nih-image-request@io.ece.drexel.edu Sun Jul 5 07:02 EDT 1998 X-UIDL: 3e02aed6c2f07e0a0718d1a4659f588b Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA03027; Sun, 5 Jul 1998 07:01:53 -0400 (EDT) Resent-Date: Sun, 5 Jul 1998 07:01:53 -0400 (EDT) X-Sender: a_team@pop.dds.nl Message-Id: Mime-Version: 1.0 Date: Sun, 5 Jul 1998 12:57:19 +0200 To: nih-image@io.ece.drexel.edu From: "Anneke M.Th. Harbers and Ard Jonker" Subject: long text files Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id GAA02512 Resent-Message-ID: <"T1Vk3.0.Xd.4mrdr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/27 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 743 Status: RO Hi, Currently, I need to output very long text results using NIH-Image. When over 32K, I understand, NIH can't handle text files. Having looked around but not being able to locate appropriate routines, I'm in the process of making my own routines, within the NIH-Image macro language. My personal needs are satisfied if I have fCreate (creates disk file with length known a priori) fPutC (puts a single character) fPutS (puts a string) fFlush (writes the file to disk) fClose (as is) fSeek (moves file pointer to a certain location) Should these routines be useful to anyone, please give some feed back. If useful, I could add some extra features (fGetC, fGetS, fOpen) before releasing the macro. Beta testers also welcome. Ard From nih-image-request@io.ece.drexel.edu Sun Jul 5 09:15 EDT 1998 X-UIDL: 5cb980260f0c04e55af75fdffe052744 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA12360; Sun, 5 Jul 1998 09:15:17 -0400 (EDT) Resent-Date: Sun, 5 Jul 1998 09:15:17 -0400 (EDT) Message-Id: <3.0.1.32.19980705090811.006ebe10@PO-Box.mcgill.ca> X-Sender: mliraj@PO-Box.mcgill.ca X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Sun, 05 Jul 1998 09:08:11 -0400 To: nih-image@io.ece.drexel.edu From: "Mario de A. Lira Junior" Subject: Re: long text files In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"qYbk53.0.Gu2.uhtdr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/28 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 424 Status: RO Hello, >Currently, I need to output very long text results using NIH-Image. When over 32K, I understand, NIH can't handle text >files. Having looked around but not being able to locate appropriate routines, I'm in the process of making my own I am quite a new user, so I may be very off-base, but I understand that the program can create the files, although it can't open or edit them... Best regards, Mario Lira Junior From nih-image-request@io.ece.drexel.edu Mon Jul 6 10:23 EDT 1998 X-UIDL: 532c51d4ecf70546c53cf4bab7e654f0 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA24770; Mon, 6 Jul 1998 10:22:39 -0400 (EDT) Resent-Date: Mon, 6 Jul 1998 10:22:39 -0400 (EDT) Subject: Re: long text files Date: Mon, 6 Jul 98 09:13:50 +0100 x-sender: mfroimow@cs.umass.edu x-mailer: Claris Emailer 2.0v2, June 6, 1997 From: "Michael P. Froimowitz" To: Mime-Version: 1.0 Message-ID: <1312406275-15087999@molpharm.mclean.org> Resent-Message-ID: <"dKB3x2.0.Ds5.0mDer"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/29 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 1106 Status: RO >Currently, I need to output very long text results using NIH-Image. When >over 32K, I understand, NIH can't handle text files. Having looked around >but not being able to locate appropriate routines, I'm in the process of >making my own routines, within the NIH-Image macro language. My personal >needs are satisfied if I have I'm actually in the process of working on something related. I'm attempting to modify the source code of NIH image so that the analyze particles function will also create a text file returning the cartesian coordinates of the centroids of all particles found. I would have preferred to write a macro, but it seemed to me that modifying the source code was the only way to go about doing this. I have actually been having a little difficulty figuring out how to go about creating and writing to a file from NIH Image procedures. If you have any suggestions on how to do this (and it sounds like your routines might do the trick), I'd love to hear them. Thanks. ------------------------- Michael Froimowitz frommy@mclean.harvard.edu ------------------------- From nih-image-request@io.ece.drexel.edu Mon Jul 6 11:06 EDT 1998 X-UIDL: b79cf459b0641c5492518e64d7ab1008 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA28303; Mon, 6 Jul 1998 11:05:47 -0400 (EDT) Resent-Date: Mon, 6 Jul 1998 11:05:47 -0400 (EDT) Message-ID: <35A0E537.D9919ACD@popmail.ucsd.edu> Date: Mon, 06 Jul 1998 07:54:47 -0700 From: Joshua McLaughlin Reply-To: josh@UCSD.Edu Organization: UCSD-Dept of Reproductive Medicine X-Mailer: Mozilla 4.04 [en] (Win95; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Cell Counting Content-Transfer-Encoding: 7bit Resent-Message-ID: <"ZW4xv.0.Lj6.rMEer"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/30 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 752 Status: RO I was wondering if anyone could give me some help in something I am trying to do: I have a SPOT camera and am doing image analysis on Scion's image program, currently I am doing some dark-field analysis of some in-situ hybridization slides, but now I want to do something new: We have some blood smears which are stained for immature Red Blood cells, which stain a dark purple, mature RBCs stain a light pink. I would like to simply be able to count both types of cells within an AOI. I have never done any color analysis with Image and would appreciate any help writing a Macro. Thank You, Josh McLaughlin -- Joshua McLaughlin UCSD Department of Reproductive Medicine 212 Dickinson St. 0802 San Diego, CA 92103-0802 (619)543-2678 josh@ucsd.edu From nih-image-request@io.ece.drexel.edu Tue Jul 7 10:21 EDT 1998 X-UIDL: a842e3c638fcfe71d993cdc4b6f70f8a Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA17182; Tue, 7 Jul 1998 10:20:59 -0400 (EDT) Resent-Date: Tue, 7 Jul 1998 10:20:59 -0400 (EDT) Date: Tue, 07 Jul 1998 09:11:05 -0600 (CST) Date-warning: Date header was inserted by uthscsa.edu From: David Morilak Subject: Re: Cell Counting In-reply-to: <199807071009.GAA22450@io.ECE.Drexel.EDU> X-Sender: morilak@arwen.uthscsa.edu To: nih-image@io.ece.drexel.edu Cc: jmclaughlin@popmail.ucsd.edu Message-id: MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"wxurm.0.Vy3.goYer"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/31 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1097 Status: RO Josh: Depending on how dark the purple is and how different the purple and pink are, the simplest solution for you might be to capture two different grayscale images with different filters to enhance or attenuate the two different stains. Using a pink or salmon filter might help you enhance the purple contrast and blend the pink into the background so that you can count only precursor cells. Selectively capturing pink relative to dark purple might be trickier, but I suppose you could count total cells and subtract the counts of the immature ones to get the mature erythrocyte count. I don't think using a blue filter would differentiate the pink from purple too well, but you might try it. The other possibility might be to capture your color image into photoshop and then use different color channels, but again I don't know how well pink and purple will be separated. Good luck! David Morilak David Morilak, Ph.D. Dept of Pharmacology Univ Texas Health Science Center 7703 Floyd Curl Drive San Antonio, TX 78284-7764 ph: 210-567-4174 FAX: 210-567-4303 E-mail: morilak@uthscsa.edu From nih-image-request@io.ece.drexel.edu Tue Jul 7 10:56 EDT 1998 X-UIDL: a75023fc7aada93e3fb0d42fcebe5aa9 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA21147; Tue, 7 Jul 1998 10:55:31 -0400 (EDT) Resent-Date: Tue, 7 Jul 1998 10:55:31 -0400 (EDT) X-Authentication-Warning: sunrise.ccs.yorku.ca: rethoret owned process doing -bs Date: Tue, 7 Jul 1998 10:46:40 -0400 (EDT) From: Karen Rethoret X-Sender: rethoret@sunrise.ccs.yorku.ca To: nih-image@io.ece.drexel.edu Subject: Perimeter and area measurement Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"ARJrV3.0.ju4.LJZer"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/32 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 564 Status: RO Hi, We are using NIH-Image for PC, and are currently doing freehand line drawing around cell structures in LM and would like to measure the perimeter in segments, the total perimeter and enclosed area all in one continuous operation. At the moment, we are using the Freehand/segmented line selection to make measurements of the segments and then redrawing the perimeter using the Freehand Region Tool to get the total perimeter and area measurements. Is it possible to avoid redrawing the area a second time? Thanks, Karen Rethoret York University, Toronto From nih-image-request@io.ece.drexel.edu Tue Jul 7 11:39 EDT 1998 X-UIDL: 44ca9d5610d162ca5798eca7e2ef0ac9 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA26276; Tue, 7 Jul 1998 11:38:35 -0400 (EDT) Resent-Date: Tue, 7 Jul 1998 11:38:35 -0400 (EDT) Message-Id: <3.0.1.32.19980707112824.0069a210@pop.service.ohio-state.edu> X-Sender: jianshi@pop.service.ohio-state.edu X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Tue, 07 Jul 1998 11:28:24 -0400 To: nih-image@io.ece.drexel.edu From: "j. s." Subject: CCD camera In-Reply-To: References: <199807071009.GAA22450@io.ECE.Drexel.EDU> Mime-Version: 1.0 Resent-Message-ID: <"Y3qDW2.0.o66.ovZer"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/33 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 535 Status: RO Is there anybody who knows area CCD (white/black) system? I only have a budget around $2000 or less. I need an area CCD (652X488, 12, 14, or 16 bits), and a card. Please email me the brand name, price, and tech info. Thanks much. **************************************** j. shi dept. of geological sciences the ohio state university columbus, ohio 43210 0000,0000,ffff(614)-292-0585/6193 (o) ffff,0000,ffff(614)-688-9686 (h) **************************************** From nih-image-request@io.ece.drexel.edu Tue Jul 7 15:38 EDT 1998 X-UIDL: 72a949693e6599e6f796b1e52f5009c8 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA19502; Tue, 7 Jul 1998 15:37:58 -0400 (EDT) Resent-Date: Tue, 7 Jul 1998 15:37:58 -0400 (EDT) Message-ID: <01BDAA30.C6D76940@Dialin1.jkmrc.uq.edu.au> From: Fernando To: "'nih-image@io.ece.drexel.edu'" Subject: Aanalyze particles self-consistancy? Date: Wed, 8 Jul 1998 05:25:09 +1000 MIME-Version: 1.0 Resent-Message-ID: <"ls3SG2.0.zT4.UQder"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/34 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/mixed; boundary="---- =_NextPart_000_01BDAA30.C6D76940" Content-Length: 6355 Status: RO ------ =_NextPart_000_01BDAA30.C6D76940 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear imagers: Firstly, greetings to all on the new list. Secondly, I would greatly appreciate if you can help me with this = bewildering problem: My binary image consists of a black background fully tessellated by a = two-pixel-wide white line, which constitutes the particles' boundaries. = Each of the black regions thus created is a "particle". When I AnalyzeParticles on one computer using the 'label ignore outline = reset' AnalyzeOptions (which are set by a macro), I obtain the expected = results. That is, a number of labelled, outlined, 128-greyed, areas = corresponding to each of the particles that are not touching the edges. = (The latter are also 128-greyed, but are not counted). However, when I analyze the same image, using the same macro (and = therefore the same Analyze Options) on the "headache" computer, all the = image frame, including the 2-pixel-wide particle boundaries are greyed = to 128gl. And no particle is counted. I've tried a number of different Analyze options (I played with all the = possible combinations of "ignore" and "include"), but can not reproduce = the results I obtain on my "healthy" computer. Moreover, the AnalyzeParticles command seems to realize that I am = bewildered, as it is adding a little of a quiz to the problem: I am able to get the "expected results" on my headache computer, with = the original AnalyzeOptions settings when I edit my image adding a very = wide (30 pixels) border all around the image. Please, notice that if the border is only 1, 2, 10 or even 15 pixels = wide, I obtain the headache results.=20 Is there anything that I am missing? Could it be because of the NIH-image version that I am using? Or, because of some little differences between different NIH versions? Are there any options that I am missing? I appreciate all your attention this far, and thank you in = advance. From nih-image-request@io.ece.drexel.edu Tue Jul 7 18:20 EDT 1998 X-UIDL: 8607deb6f7e44e515a5257cad7fe51b6 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA04947; Tue, 7 Jul 1998 18:19:33 -0400 (EDT) Resent-Date: Tue, 7 Jul 1998 18:19:33 -0400 (EDT) Message-Id: <3.0.5.32.19980707181646.007e1650@mohawk.net> X-Sender: microbill@mohawk.net X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Tue, 07 Jul 1998 18:16:46 -0400 To: nih-image@io.ece.drexel.edu From: Bill Miller Subject: Re: CCD camera In-Reply-To: <3.0.1.32.19980707112824.0069a210@pop.service.ohio-state.ed u> References: <199807071009.GAA22450@io.ECE.Drexel.EDU> Mime-Version: 1.0 Resent-Message-ID: <"oSzFp1.0.A11.gsfer"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/35 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 792 Status: RO See Electrim - http://www.electrim.com and DVC http://members.aol.com/dvcco/ Both are affordable and do at least what you want - probably more. Best Regards - Bill Miller At 11:28 AM 7/7/98 -0400, you wrote: >>>> Is there anybody who knows area CCD (white/black) system? I only have a budget around $2000 or less. I need an area CCD (652X488, 12, 14, or 16 bits), and a card. Please email me the brand name, price, and tech info. Thanks much. **************************************** j. shi dept. of geological sciences the ohio state university columbus, ohio 43210 0000,0000,ffff(614)-292-0585/6193 (o) ffff,0000,ffff(614)-688-9686 (h) **************************************** <<<<<<<< From nih-image-request@io.ece.drexel.edu Wed Jul 8 01:44 EDT 1998 X-UIDL: 7631f71b56036085c50088d8b1f740e5 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id BAA19795; Wed, 8 Jul 1998 01:41:51 -0400 (EDT) Resent-Date: Wed, 8 Jul 1998 01:41:51 -0400 (EDT) Mime-Version: 1.0 X-Sender: jfneron@rescol.fse.ulaval.ca Message-Id: In-Reply-To: <199807071000.GAA21486@io.ECE.Drexel.EDU> Date: Wed, 8 Jul 1998 13:20:39 +0800 To: nih-image@io.ece.drexel.edu From: Jean-Francois Neron Subject: How to unsuscribe Resent-Message-ID: <"2zh4f.0.Uh4.oMmer"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/36 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 425 Status: RO Can someone please post a message explaining how to unsuscribe from the NEW NIH-Image mailing list. Thanks! ----------------------------------------------------------------- Jean-Francois Neron, M.Sc. Department of Human Movement University of Western Australia Telephone 011-618-9386-3686 ICQ 4213717 mailto:jfneron@fse.ulaval.ca ----------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Wed Jul 8 10:17 EDT 1998 X-UIDL: 3c6d4734a042f7c206a1a6a69ab798c3 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA11538; Wed, 8 Jul 1998 10:16:33 -0400 (EDT) Resent-Date: Wed, 8 Jul 1998 10:16:33 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Wed, 8 Jul 1998 10:15:37 -0500 To: nih-image@io.ece.drexel.edu From: Laird Bloom Subject: Help with controlling Optronics camera from Image Resent-Message-ID: <"7ErOx2.0.1a2.Vqter"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/37 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 693 Status: RO Hi, We have an Optronics DEI-750 camera connected to a Macintosh G3 via a Scion CG-7 frame grabber, and we're obtaining images using Scion Image 1.62a. The Optronics camera controller has no way of saving settings put in through the camera controller keyboard, which is a nuisance when we're trying to go back and forth between different lighting conditions (e.g. brightfield and fluorescence microscopy of the same sample). We would like to be able to save the Optronics camera settings and use an Image macro (or some other Mac program) to send the saved settings back to the camera. Has anyone done something like this? Thanks Laird Bloom MIT Center for Cancer Research lbloom@mit.edu From nih-image-request@io.ece.drexel.edu Wed Jul 8 10:23 EDT 1998 X-UIDL: 89d28ae0c7e14788ba5384631fc79f65 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA12274; Wed, 8 Jul 1998 10:22:44 -0400 (EDT) Resent-Date: Wed, 8 Jul 1998 10:22:44 -0400 (EDT) From: JLinn24538@aol.com Message-ID: Date: Wed, 8 Jul 1998 10:14:30 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Perimeter and area measurement Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 85 Resent-Message-ID: <"z58Vj2.0.ym2.uxter"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/38 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 377 Status: RO Trace your outline with the freehand tool then use the 'Save As' an Outline option. With that done you can reproduce the outline in the target image (or a duplicate) as many times as you need to. If you have multiple discontinuous outlines then reproduce each as a binary in a new window after drawing it. Then to reproduce the outline you can use the wand tool. Jeff Linn From nih-image-request@io.ece.drexel.edu Wed Jul 8 10:49 EDT 1998 X-UIDL: a9358e3d25c72ac4b8e1abf0beb77323 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA15110; Wed, 8 Jul 1998 10:49:33 -0400 (EDT) Resent-Date: Wed, 8 Jul 1998 10:49:33 -0400 (EDT) Message-ID: <35A392C9.1C12@chuma.cas.usf.edu> Date: Wed, 08 Jul 1998 10:39:54 -0500 From: mkimble@chuma.cas.usf.edu Reply-To: mkimble@chuma.cas.usf.edu Organization: Dept. of Biology, USF X-Mailer: Mozilla 3.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: analysis of fluorescent images Content-Transfer-Encoding: 7bit Resent-Message-ID: <"1G6v_2.0.hQ3.KIuer"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/39 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1335 Status: RO To all, I have recently begun trying to use NIH-image to capture and analyze images from a Nikon inverted fluorescent microscope. I am using a low light level, SIT 66 camera from DAGE-mti, Inc., and capturing the images with NIH-Image on a PowerMac G3. Specs for the computer are 32 Meg RAM, 266MHz, and 512K. The frame grabber is an LG3 from Scion. The problem I am running into is that the images I'm getting are incredibly grainy. In fact, they look worse on the computer screen than they do when looking through the microscope. Is there any way to change the parameters (preferences) of the camera function? The other question I have is, is there a way to set the software to capture frames at timed intervals? I would like to be able to take short exposures at timed intervals. For example, take a 0.1 second exposure every 10 sec. Is there a way to do this? So far whenever I set the exposure time the software automatically changes the number of frames per second. For example, when I set the camera for a 0.1 second exposure, the software then automatically sets the computer to capture 10 frames per second. The problem with this is that I very rapidly reach the memory limit of the computer and thus cannot capture images over a long period of time (ie. several minutes). Any suggestions on this? Mary Kimble From nih-image-request@io.ece.drexel.edu Wed Jul 8 11:04 EDT 1998 X-UIDL: 4e1997fadfac5b5b63e5ce007216b23a Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA16753; Wed, 8 Jul 1998 11:03:52 -0400 (EDT) Resent-Date: Wed, 8 Jul 1998 11:03:52 -0400 (EDT) From: Vaughn Adams Message-Id: <199807081454.KAA07481@cbis.ece.drexel.edu> Subject: Re: How to unsuscribe In-Reply-To: from "Jean-Francois Neron" at "Jul 8, 98 01:20:39 pm" X-ELM-OSV: (Our standard violations) no-mime=1; no-hdr-encoding=1 To: nih-image@io.ece.drexel.edu Date: Wed, 8 Jul 1998 10:54:04 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL31 (25)] Resent-Message-ID: <"_OkME3.0.gp3.IWuer"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/40 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 968 Status: RO > Can someone please post a message explaining how to unsuscribe from the NEW > NIH-Image mailing list. Thanks! Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu From nih-image-request@io.ece.drexel.edu Thu Jul 9 08:01 EDT 1998 X-UIDL: efc37cf7dbb88969a6078789d0edeb7b Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA18202; Thu, 9 Jul 1998 08:01:08 -0400 (EDT) Resent-Date: Thu, 9 Jul 1998 08:01:08 -0400 (EDT) Message-Id: <9807091151.AA14183@gorca.gorca.com> Subject: Window position Date: Thu, 9 Jul 1998 07:52:41 -0400 X-Mailer: Claris Emailer 2.0v3, January 22, 1998 From: Brett Helbig To: "NIH Image List" Mime-Version: 1.0 Resent-Message-ID: <"giQ-P3.0.nC4.EyAfr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/41 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 328 Status: RO Is there a way to get the position of a window from within a macro? I would like to be able to get and store the location of a window, so I can position another window in the same locaiton (using the MoveWindow() command). Can this be done? Thanks. Brett Helbig Systems Engineer GORCA Technologies, Inc. bhelbig@gorca.com From nih-image-request@io.ece.drexel.edu Thu Jul 9 12:41 EDT 1998 X-UIDL: adf6186c85dccc0fc847b17b4dbb9130 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA13929; Thu, 9 Jul 1998 12:40:20 -0400 (EDT) Resent-Date: Thu, 9 Jul 1998 12:40:20 -0400 (EDT) X-Sender: goerke@128.218.95.21 Message-Id: Mime-Version: 1.0 Date: Thu, 9 Jul 1998 09:32:24 -0700 To: nih-image@io.ece.drexel.edu From: Jon Goerke Subject: Unwanted Mailboxes Resent-Message-ID: <"dF99w1.0.I63.I_Efr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/42 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 639 Status: RO With the changeover of the Image List host, I now get an unwanted permanent mailbox created in Eudora each time I receive the NIH Image Digest. Manually discarding these mailboxes each time is a drag. I'm using a Mac 9500, System 8.0 and Eudora 4.0 with an existing mailbox set to receive NIH Image transmissions. Any suggestions? _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Jon Goerke, MD EMail: goerke@itsa.ucsf.edu Prof. Physiology, Univ. Calif. Phone: 415-476-3252 3333 California St., Suite 150, San Francisco, CA 94118 _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From nih-image-request@io.ece.drexel.edu Thu Jul 9 15:34 EDT 1998 X-UIDL: a8e091665732d75354c8b9789a851d2c Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA01467; Thu, 9 Jul 1998 15:33:37 -0400 (EDT) Resent-Date: Thu, 9 Jul 1998 15:33:37 -0400 (EDT) Message-ID: <35A5276D.BE79A93C@u.washington.edu> Date: Thu, 09 Jul 1998 12:26:13 -0800 From: Glen MacDonald X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Perimeter and area measurement References: <199807080545.BAA20296@io.ECE.Drexel.EDU> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"BHc3v2.0.l5.-YHfr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/43 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1179 Status: RO Karen,Try 'Restore Selection' if working manually. In a macro, use 'RestoreROI' then make the second measurement. > Subject: Perimeter and area measurement > Date: Tue, 7 Jul 1998 10:46:40 -0400 (EDT) > From: Karen Rethoret > To: nih-image@io.ece.drexel.edu > > Hi, > > We are using NIH-Image for PC, and are currently doing freehand line > drawing around cell structures in LM and would like to measure the > perimeter in segments, the total perimeter and enclosed area all in one > continuous operation. > > At the moment, we are using the Freehand/segmented line selection to make > measurements of the segments and then redrawing the perimeter using the > Freehand Region Tool to get the total perimeter and area measurements. > > Is it possible to avoid redrawing the area a second time? > > Thanks, > > Karen Rethoret > York University, Toronto > > ------------------------------------- -- Glen MacDonald Virginia Merrill Bloedel Hearing Research Center Box 357923 University of Washington Seattle, WA 98195-7923 glenmac@u.washington.edu (206) 616-4156 (206) 616-1828 fax The box said "Requires Windows95 or better". So I bought a Macintosh. From nih-image-request@io.ece.drexel.edu Thu Jul 9 20:58 EDT 1998 X-UIDL: 64f7ccfe47dba09d047d7451becce640 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA05984; Thu, 9 Jul 1998 20:54:10 -0400 (EDT) Resent-Date: Thu, 9 Jul 1998 20:54:10 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: nih-image@io.ece.drexel.edu Date: Fri, 10 Jul 1998 10:47:27 GMT+1000 Subject: Re: Window position Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <26587491A09@rna.bio.mq.edu.au> Resent-Message-ID: <"S4v291.0.eC1.hGMfr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/44 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1495 Status: RO >Date: Thu, 9 Jul 1998 07:52:41 -0400 > >Is there a way to get the position of a window from within a macro? I >would like to be able to get and store the location of a window, so I can >position another window in the same locaiton (using the MoveWindow() >command). Can this be done? > >Thanks. > >Brett Helbig >Systems Engineer >GORCA Technologies, Inc. >bhelbig@gorca.com Brett, procedure allignWindows(w1,w2); {alligns window w1 with w2} {would return TLcorner coords via x0,y0} if x0,y0 declaration was made globably or in calling procedure. to test, create any two windows and position; then invoke either by pulldown Special menu or <0>. (It is not sensitive to mouse use :-) macro'/0test' uses picNumber but in practice pidNumber would be used. procedure allignWindows(w1,w2); {alligns window w1 with w2} {would return TLcorner coords via x0,y0} var x0,y0,x1,y1,x2,y2:integer;begin x0:=84;y0:=40; selectPic(w1); moveWindow(x0,y0); repeat begin choosePic(w1);getMouse(x1,y1); choosePic(w2);getMouse(x2,y2); showMessage(x0,y0,'\',x1,y1,'\',x2,y2,'\',x2-x1,y2-y1); selectPic(w1); x0:=x0-(x2-x1);y0:=y0-(y2-y1); moveWindow(x0,y0); end until (x1=x2) and (y1=y2); showMessage('corner at\',x0,y0); end macro'/0test';begin allignWindows(1,2);end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Tue Jul 14 12:13 EDT 1998 X-UIDL: be206e14b4025fa9461ffa6ce9628d65 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA10327; Tue, 14 Jul 1998 12:11:14 -0400 (EDT) Resent-Date: Tue, 14 Jul 1998 12:11:14 -0400 (EDT) Message-ID: <35AB8F21.7F51@wxs.nl> Date: Tue, 14 Jul 1998 18:02:27 +0100 From: Pieter Houpt Organization: BIOMET X-Mailer: Mozilla 3.01-C-WXS-Mac (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: silence Content-Transfer-Encoding: 7bit Resent-Message-ID: <"rgf343.0.ZG2.J3ugr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/45 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 324 Status: RO Dear listowners, For several days there a complete silence on the NIH-list.No discussions , no e-mails where recieved.Whats going on. I redescribed so that's not the reason I presume. best wishes of a NIH-list member -- BIOMET P.M.Houpt -123 Timorstraat. 2585 SE The Hague,The Netherlands. voice/fax.: 0031703504466 From nih-image-request@io.ece.drexel.edu Tue Jul 14 13:08 EDT 1998 X-UIDL: d121a7b71aa6d3c8d135158a34131a01 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA15438; Tue, 14 Jul 1998 13:07:18 -0400 (EDT) Resent-Date: Tue, 14 Jul 1998 13:07:18 -0400 (EDT) Message-ID: <35AB8E70.3D61@maroon.tc.umn.edu> Date: Tue, 14 Jul 1998 10:59:41 -0600 From: "Michael J. Herron" Reply-To: Michael J Herron Organization: U of MN X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: silence References: <35AB8F21.7F51@wxs.nl> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"7cnE53.0.iX3.Zvugr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/46 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 853 Status: RO I got your message...perhaps everyone is on vacation? How many folk were lost in the transistion to the new list? Pieter Houpt wrote: > > Dear listowners, > > For several days there a complete silence on the NIH-list.No discussions > , no e-mails where recieved.Whats going on. > I redescribed so that's not the reason I presume. > > best wishes of a NIH-list member > > -- > BIOMET > P.M.Houpt -123 Timorstraat. > 2585 SE The Hague,The Netherlands. > voice/fax.: 0031703504466 -- ________________________________________________________ / Michael J. Herron, U of MN, Dept. of Dermatology / / herro001@maroon.tc.umn.edu / / 612-625-8935 Box 98 UMHC, Mpls MN 55455 / / http://RASH.med.umn.edu/ / /_______________________________________________________/ From nih-image-request@io.ece.drexel.edu Tue Jul 14 13:42 EDT 1998 X-UIDL: 81b2c8d6cd3b2997a135d3d777883f97 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA25278; Tue, 14 Jul 1998 13:42:06 -0400 (EDT) Resent-Date: Tue, 14 Jul 1998 13:42:06 -0400 (EDT) Date: Tue, 14 Jul 1998 13:34:24 -0400 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: archive Resent-Message-ID: <"3cAnL1.0.0Q4.nQvgr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/47 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 20 Status: RO archive/latest/12 From nih-image-request@io.ece.drexel.edu Tue Jul 14 13:43 EDT 1998 X-UIDL: 9971b52b11d04edc0d5a9661ea8c555a Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA25394; Tue, 14 Jul 1998 13:42:59 -0400 (EDT) Resent-Date: Tue, 14 Jul 1998 13:42:59 -0400 (EDT) Date: Tue, 14 Jul 1998 13:35:50 -0400 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: archive Resent-Message-ID: <"yUXSR3.0.aH5.BSvgr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/48 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 12 Status: RO ls latest From nih-image-request@io.ece.drexel.edu Tue Jul 14 13:52 EDT 1998 X-UIDL: ca26e2ef477173533c1339e93e3a5d9f Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA26348; Tue, 14 Jul 1998 13:51:55 -0400 (EDT) Resent-Date: Tue, 14 Jul 1998 13:51:55 -0400 (EDT) X-Sender: mdparadi@po9.mit.edu Message-Id: Mime-Version: 1.0 Date: Tue, 14 Jul 1998 13:50:29 -0400 To: nih-image@io.ece.drexel.edu From: mdparadi@MIT.EDU (Marc d. Paradis) Subject: Irony Resent-Message-ID: <"THNzl2.0.dF6.0avgr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/49 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 524 Status: RO >How many folk were lost in the transistion to the new list? Isn't this a little like asking everyone not present to raise their hands? :-) Marc d. Paradis Dept of Brain & Cognitive Sciences M.I.T. BTW - this is in no way meant as a flame to Michael J. Herron, I am sure the list administrators have an exact number to his question, but it just struck me as a little humor which I thouhgt that I would share while the list is relatively devoid of active content. -MdP From nih-image-request@io.ece.drexel.edu Tue Jul 14 14:51 EDT 1998 X-UIDL: a014d45223d57e4da94d2b441d37aa05 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA01677; Tue, 14 Jul 1998 14:50:53 -0400 (EDT) Resent-Date: Tue, 14 Jul 1998 14:50:53 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Tue, 14 Jul 1998 14:49:56 -0500 From: "Alan Townsend" To: nih-image@io.ece.drexel.edu Subject: NuBus frame grabber wanted Resent-Message-ID: <"zagF22.0.HA.IPwgr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/50 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 512 Status: RO I am looking for a new or used frame grabber card for use in a Power Mac 7100/80. The Scion LG3 would be my preference, but the AG-5 is also an option. Other cards may also be considered. If you have a spec sheet or web URL that would help. Please reply (including price) to (e-mail preferred) : Alan J. Townsend, Ph.D., Biochemistry Department, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, N.C. 27157, Phone (336)-716-7658, FAX (336)-716-7671, E-Mail : atown@wfubmc.edu From nih-image-d-request@io.ece.drexel.edu Wed Jul 15 06:12 EDT 1998 X-UIDL: 2b9ccb7d48b4498c53c153d50188e468 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA18498; Wed, 15 Jul 1998 06:12:29 -0400 (EDT) Date: Wed, 15 Jul 1998 06:12:29 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807151012.GAA18498@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #10 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/10 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4606 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 10 Today's Topics: silence [ Pieter Houpt ] Re: silence [ "Michael J. Herron" To: nih-image@io.ece.drexel.edu Subject: silence Message-ID: <35AB8F21.7F51@wxs.nl> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear listowners, For several days there a complete silence on the NIH-list.No discussions , no e-mails where recieved.Whats going on. I redescribed so that's not the reason I presume. best wishes of a NIH-list member -- BIOMET P.M.Houpt -123 Timorstraat. 2585 SE The Hague,The Netherlands. voice/fax.: 0031703504466 ------------------------------ Date: Tue, 14 Jul 1998 10:59:41 -0600 From: "Michael J. Herron" To: nih-image@io.ece.drexel.edu Subject: Re: silence Message-ID: <35AB8E70.3D61@maroon.tc.umn.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I got your message...perhaps everyone is on vacation? How many folk were lost in the transistion to the new list? Pieter Houpt wrote: > > Dear listowners, > > For several days there a complete silence on the NIH-list.No discussions > , no e-mails where recieved.Whats going on. > I redescribed so that's not the reason I presume. > > best wishes of a NIH-list member > > -- > BIOMET > P.M.Houpt -123 Timorstraat. > 2585 SE The Hague,The Netherlands. > voice/fax.: 0031703504466 -- ________________________________________________________ / Michael J. Herron, U of MN, Dept. of Dermatology / / herro001@maroon.tc.umn.edu / / 612-625-8935 Box 98 UMHC, Mpls MN 55455 / / http://RASH.med.umn.edu/ / /_______________________________________________________/ ------------------------------ Date: Tue, 14 Jul 1998 13:34:24 -0400 From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) Subject: archive Message-Id: Content-Type: text/plain; charset="us-ascii" archive/latest/12 ------------------------------ Date: Tue, 14 Jul 1998 13:35:50 -0400 From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) Subject: archive Message-Id: Content-Type: text/plain; charset="us-ascii" ls latest ------------------------------ Date: Tue, 14 Jul 1998 13:50:29 -0400 From: mdparadi@MIT.EDU (Marc d. Paradis) To: nih-image@io.ece.drexel.edu Subject: Irony Message-Id: Content-Type: text/plain; charset="us-ascii" >How many folk were lost in the transistion to the new list? Isn't this a little like asking everyone not present to raise their hands? :-) Marc d. Paradis Dept of Brain & Cognitive Sciences M.I.T. BTW - this is in no way meant as a flame to Michael J. Herron, I am sure the list administrators have an exact number to his question, but it just struck me as a little humor which I thouhgt that I would share while the list is relatively devoid of active content. -MdP ------------------------------ Date: Tue, 14 Jul 1998 14:49:56 -0500 From: "Alan Townsend" To: nih-image@io.ece.drexel.edu Subject: NuBus frame grabber wanted Message-Id: I am looking for a new or used frame grabber card for use in a Power Mac 7100/80. The Scion LG3 would be my preference, but the AG-5 is also an option. Other cards may also be considered. If you have a spec sheet or web URL that would help. Please reply (including price) to (e-mail preferred) : Alan J. Townsend, Ph.D., Biochemistry Department, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, N.C. 27157, Phone (336)-716-7658, FAX (336)-716-7671, E-Mail : atown@wfubmc.edu -------------------------------- End of nih-image-d Digest V98 Issue #10 *************************************** From nih-image-request@io.ece.drexel.edu Wed Jul 15 07:21 EDT 1998 X-UIDL: ef780a329c2c21d9fc44d666bde4f9e3 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA24729; Wed, 15 Jul 1998 07:21:14 -0400 (EDT) Resent-Date: Wed, 15 Jul 1998 07:21:14 -0400 (EDT) Message-Id: <9807151124.AA00061@pp1.rheo.matse.fukui-u.ac.jp> Date: Wed, 15 Jul 1998 20:24:28 +0900 From: yokota@rheo.matse.fukui-u.ac.jp (=?ISO-2022-JP?B?GyRCMiNFRCEhT0I4dxsoSg==?= ) To: nih-image@io.ece.drexel.edu Subject: Question Mime-Version: 1.0 X-Mailer: AL-Mail 1.22 Resent-Message-ID: <"WA2hx.0.Ms5.Ey8hr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/51 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-2022-jp Content-Length: 260 Status: RO Hello, Can I use your NIH-image on Power Macintosh G3 series. $BJ!0fBg3X!!!!9)3XIt!!!!:`NA2=3X2J!!!!9bJ,;R2C9)3X9V:B(J $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!2#ED!!!!OB8w(J (Kazumitsu Yokota) E-mail yokota@rheo.matse.fukui-u.ac.jp From nih-image-request@io.ece.drexel.edu Wed Jul 15 07:54 EDT 1998 X-UIDL: 9f1353c7fbfaa9874a920c632e0f7ce6 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA27956; Wed, 15 Jul 1998 07:54:02 -0400 (EDT) Resent-Date: Wed, 15 Jul 1998 07:54:02 -0400 (EDT) X-Sender: cgustafs@ece.drexel.edu Message-Id: In-Reply-To: <9807151124.AA00061@pp1.rheo.matse.fukui-u.ac.jp> Mime-Version: 1.0 Date: Wed, 15 Jul 1998 07:48:23 -0400 To: nih-image@io.ece.drexel.edu From: Carl Gustafson Subject: Re: Question Resent-Message-ID: <"CNAbC1.0.ib6.TQ9hr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/52 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 603 Status: RO >Can I use your NIH-image on Power Macintosh G3 series. Yes. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== From nih-image-request@io.ece.drexel.edu Wed Jul 15 07:57 EDT 1998 X-UIDL: c93e2193f7e5de90b76b5908d25a5909 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA28339; Wed, 15 Jul 1998 07:57:11 -0400 (EDT) Resent-Date: Wed, 15 Jul 1998 07:57:11 -0400 (EDT) Message-ID: <01BDAFC4.E2FD8C00@STEVE-Z> From: Steve Zullo To: "nih-image@io.ece.drexel.edu" Subject: Please distribute: Call for POSTERS and/or ATTENDANCE Date: Wed, 15 Jul 1998 07:47:58 -0400 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id HAA27271 Resent-Message-ID: <"F5Pfv.0.Gg6.PS9hr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/53 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 3525 Status: RO An NIH Director's Wednesday Afternoon Lecture Series Event Sponsor: NIH Inter-Institute Mitochondria Interest Group (MIG) A Day-long Minisymposium Mitochondria: Genetics, Health, and Disease 2 December 1998 Featuring The Wednesday Afternoon Lecture by Dr. Eric A. Schon (Columbia) Molecular Genetics of Human Mitochondrial Disease Jack Masur Auditorium, Clinical Center, NIH For special accommodation needs call 301-594-5595 CME credit awarded MITOCHONDRIA: GENETICS, HEALTH, AND DISEASE MINISYMPOSIUM 2 DECEMBER 1998 Lectures Venue: Masur Auditorium, Clinical Center, NIH Poster/Exhibitor Venue: Visitor Information Center, Clinical Center, NIH * 0745 Registration, Poster Set-up, Continental Breakfast in Exhibit Area * 0830 Dr. David A. Clayton (HHMI): Mitochondrial DNA Control Features * 0905 Dr. William C. Copeland (NIEHS): Avoidance of Mitochondrial DNA Mutations by DNA Polymerase Gamma * 0940 Dr. Vilhelm A. Bohr (NIA): Oxidative DNA Damage Repair in Mammalian Mitochondria * 1015 Poster Session/Coffee Break in Product Exhibit Area * 1045 Dr. Tracey Rouault (NICHD): Abnormalities of Mitochondrial Iron Metabolism and Human Disease * 1120 Dr. Steven J. Zullo (NIMH): In situ Localization of the common Human 4977bp Mitochondrial DNA Deletion Mutation * 1200 Lunch Break * 1330 Dr. Mariana Gerschenson (NCI): Mitochondrial Genotoxic and Functional Consequences of Chemotherapeutic Drugs * 1400 Poster Session/Coffee Break in Product Exhibit Area * 1500 Wednesday Afternoon Lecture: Dr. Eric A. Schon (Columbia):Molecular Genetics of Human Mitochondrial Disease * 1600 Reception/Poster Session in Product Exhibit Area * 1700 Poster Session/Product Exhibition Closes Continental Breakfast, Coffee Breaks, Lunch Break, and Reception sponsored by the Technical Sales Association Attendance/Poster Registration Form Mitochondria: Genetics, Health, and Disease Wednesday Afternoon Lecture Series Minisymposium 2 December 1998 Masur Auditorium and Visitor Information Center Clinical Center (Building 10), NIH Bethesda, MD Note: There is no registration fee to attend this minisymposium! Name: Title: Affiliation: Address: State: Country: Postal Code: Telephone: Fax: E-mail: Web Page URL: I will attend and present a poster I will attend but not present a poster________ Poster Title: Abstract (Abstract Booklet available at the meeting): Do you need special accommodations while at NIH?______________ For a map of NIH and area, please check the following Web Site: http://www.nih.gov/welcome/maps.html WARNING: Parking is limited on campus, plan to use METRO! A block of rooms at a special meeting rate has been reserved at The Bethesda Ramada. Call 800-272-6232, or 301-654-2703, before 9 November 1998. Mention NIH Minisymposium, group # 6210. For other accommodations in the area, please check the following Web Site: http://www.patsys.com/ftd/city.cgi?pcityid=2521&pcity=Bethesda Submit advanced registration via Minisymposium web site at http://www-lecb.ncifcrf.gov/~zullo/migDB/symposium.html or via e-mail to: zullo@helix.nih.gov deadline by e-mail is 8 November 1998 or via regular mail to: Steven J. Zullo, PhD postmark deadline is 2 November 1998 Building 10, Room 2D54 NIH Bethesda, MD 20892 Steven J. Zullo, PhD Laboratory of Biochemical Genetics NIMH-NIH; Bldg. 10, Rm. 2D56; 9000 Rockville Pike Bethesda, MD 20892 301-435-3576; FAX 301-480-9862 zullo@helix.nih.gov Mitochondria Interest Group Web Page: http://www-lecb.ncifcrf.gov/~zullo/migDB/ From nih-image-request@io.ece.drexel.edu Wed Jul 15 10:39 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA11959; Wed, 15 Jul 1998 10:39:02 -0400 (EDT) Resent-Date: Wed, 15 Jul 1998 10:39:02 -0400 (EDT) Message-Id: <3.0.5.32.19980715102804.0079d890@codon.nih.gov> X-Sender: wayne@codon.nih.gov (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 15 Jul 1998 10:28:04 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Question In-Reply-To: <9807151124.AA00061@pp1.rheo.matse.fukui-u.ac.jp> Mime-Version: 1.0 Resent-Message-ID: <"K-C2L1.0.ud2.UlBhr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/54 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 552 Status: O At 08:24 PM 7/15/98 +0900, you wrote: >Hello, > >Can I use your NIH-image on Power Macintosh G3 series. You can but the "Start Capturing" command does not support the G3's built-in video digitizer. You can, however, use the Plugin Digitizer available at "ftp://codon.nih.gov/pub/nih-image/plug-ins/". I have attempted, without much success, to fix this problem. Also, NIH Image does not correctly support Scion frame grabbers on G3 Macs. You need to use Scion's version of the program. This problem will be fixed in the next NIH Image beta. -wayne From nih-image-request@io.ece.drexel.edu Wed Jul 15 15:14 EDT 1998 X-UIDL: 82ec681cf28709f0e1a7112f6b2f2eac From nih-image-request@io.ece.drexel.edu Wed Jul 15 15:14 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA02352; Wed, 15 Jul 1998 15:12:52 -0400 (EDT) Resent-Date: Wed, 15 Jul 1998 15:12:52 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Wed, 15 Jul 1998 14:59:25 -0400 From: "Mike Smith" To: nih-image@io.ece.drexel.edu Subject: Mac built-in frame grabber Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id PAA01331 Resent-Message-ID: <"ooxVA1.0._K.XoFhr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/55 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 687 Status: O Dear List Members, I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board? Mike Smith From nih-image-d-request@io.ece.drexel.edu Thu Jul 16 06:14 EDT 1998 X-UIDL: 2f3b1676bf26c7aff4b714fed30801bd Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA14581; Thu, 16 Jul 1998 06:14:27 -0400 (EDT) Date: Thu, 16 Jul 1998 06:14:27 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807161014.GAA14581@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #11 From nih-image-request@io.ece.drexel.edu Wed Jul 15 15:14 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA02352; Wed, 15 Jul 1998 15:12:52 -0400 (EDT) Resent-Date: Wed, 15 Jul 1998 15:12:52 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Wed, 15 Jul 1998 14:59:25 -0400 From: "Mike Smith" To: nih-image@io.ece.drexel.edu Subject: Mac built-in frame grabber Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id PAA01331 Resent-Message-ID: <"ooxVA1.0._K.XoFhr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/55 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 687 Status: O Dear List Members, I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board? Mike Smith From nih-image-d-request@io.ece.drexel.edu Thu Jul 16 06:14 EDT 1998 X-UIDL: 2f3b1676bf26c7aff4b714fed30801bd Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA14581; Thu, 16 Jul 1998 06:14:27 -0400 (EDT) Date: Thu, 16 Jul 1998 06:14:27 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807161014.GAA14581@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #11 From nih-image-request@io.ece.drexel.edu Wed Jul 15 15:14 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA02352; Wed, 15 Jul 1998 15:12:52 -0400 (EDT) Resent-Date: Wed, 15 Jul 1998 15:12:52 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Wed, 15 Jul 1998 14:59:25 -0400 From: "Mike Smith" To: nih-image@io.ece.drexel.edu Subject: Mac built-in frame grabber Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id PAA01331 Resent-Message-ID: <"ooxVA1.0._K.XoFhr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/55 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 278 Status: RO Dear List Members, I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board? Mike Smith From nih-image-d-request@io.ece.drexel.edu Thu Jul 16 06:14 EDT 1998 X-UIDL: 2f3b1676bf26c7aff4b714fed30801bd Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA14581; Thu, 16 Jul 1998 06:14:27 -0400 (EDT) Date: Thu, 16 Jul 1998 06:14:27 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807161014.GAA14581@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #11 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/11 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7399 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 11 Today's Topics: Question [ yokota@rheo.matse.fukui-u.ac.jp (=? ] Re: Question [ Carl Gustafson ] Re: Question [ Wayne Rasband ] Mac built-in frame grabber [ "Mike Smith" Content-Type: text/plain; charset=iso-2022-jp Hello, Can I use your NIH-image on Power Macintosh G3 series. $BJ!0fBg3X!!!!9)3XIt!!!!:`NA2=3X2J!!!!9bJ,;R2C9)3X9V:B(J $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!2#ED!!!!OB8w(J (Kazumitsu Yokota) E-mail yokota@rheo.matse.fukui-u.ac.jp ------------------------------ Date: Wed, 15 Jul 1998 07:48:23 -0400 From: Carl Gustafson To: nih-image@io.ece.drexel.edu Subject: Re: Question Message-Id: Content-Type: text/plain; charset="us-ascii" >Can I use your NIH-image on Power Macintosh G3 series. Yes. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== ------------------------------ Date: Wed, 15 Jul 1998 07:47:58 -0400 From: Steve Zullo To: "nih-image@io.ece.drexel.edu" Subject: Please distribute: Call for POSTERS and/or ATTENDANCE Message-ID: <01BDAFC4.E2FD8C00@STEVE-Z> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit An NIH Director's Wednesday Afternoon Lecture Series Event Sponsor: NIH Inter-Institute Mitochondria Interest Group (MIG) A Day-long Minisymposium Mitochondria: Genetics, Health, and Disease 2 December 1998 Featuring The Wednesday Afternoon Lecture by Dr. Eric A. Schon (Columbia) Molecular Genetics of Human Mitochondrial Disease Jack Masur Auditorium, Clinical Center, NIH For special accommodation needs call 301-594-5595 CME credit awarded MITOCHONDRIA: GENETICS, HEALTH, AND DISEASE MINISYMPOSIUM 2 DECEMBER 1998 Lectures Venue: Masur Auditorium, Clinical Center, NIH Poster/Exhibitor Venue: Visitor Information Center, Clinical Center, NIH * 0745 Registration, Poster Set-up, Continental Breakfast in Exhibit Area * 0830 Dr. David A. Clayton (HHMI): Mitochondrial DNA Control Features * 0905 Dr. William C. Copeland (NIEHS): Avoidance of Mitochondrial DNA Mutations by DNA Polymerase Gamma * 0940 Dr. Vilhelm A. Bohr (NIA): Oxidative DNA Damage Repair in Mammalian Mitochondria * 1015 Poster Session/Coffee Break in Product Exhibit Area * 1045 Dr. Tracey Rouault (NICHD): Abnormalities of Mitochondrial Iron Metabolism and Human Disease * 1120 Dr. Steven J. Zullo (NIMH): In situ Localization of the common Human 4977bp Mitochondrial DNA Deletion Mutation * 1200 Lunch Break * 1330 Dr. Mariana Gerschenson (NCI): Mitochondrial Genotoxic and Functional Consequences of Chemotherapeutic Drugs * 1400 Poster Session/Coffee Break in Product Exhibit Area * 1500 Wednesday Afternoon Lecture: Dr. Eric A. Schon (Columbia):Molecular Genetics of Human Mitochondrial Disease * 1600 Reception/Poster Session in Product Exhibit Area * 1700 Poster Session/Product Exhibition Closes Continental Breakfast, Coffee Breaks, Lunch Break, and Reception sponsored by the Technical Sales Association Attendance/Poster Registration Form Mitochondria: Genetics, Health, and Disease Wednesday Afternoon Lecture Series Minisymposium 2 December 1998 Masur Auditorium and Visitor Information Center Clinical Center (Building 10), NIH Bethesda, MD Note: There is no registration fee to attend this minisymposium! Name: Title: Affiliation: Address: State: Country: Postal Code: Telephone: Fax: E-mail: Web Page URL: I will attend and present a poster I will attend but not present a poster________ Poster Title: Abstract (Abstract Booklet available at the meeting): Do you need special accommodations while at NIH?______________ For a map of NIH and area, please check the following Web Site: http://www.nih.gov/welcome/maps.html WARNING: Parking is limited on campus, plan to use METRO! A block of rooms at a special meeting rate has been reserved at The Bethesda Ramada. Call 800-272-6232, or 301-654-2703, before 9 November 1998. Mention NIH Minisymposium, group # 6210. For other accommodations in the area, please check the following Web Site: http://www.patsys.com/ftd/city.cgi?pcityid=2521&pcity=Bethesda Submit advanced registration via Minisymposium web site at http://www-lecb.ncifcrf.gov/~zullo/migDB/symposium.html or via e-mail to: zullo@helix.nih.gov deadline by e-mail is 8 November 1998 or via regular mail to: Steven J. Zullo, PhD postmark deadline is 2 November 1998 Building 10, Room 2D54 NIH Bethesda, MD 20892 Steven J. Zullo, PhD Laboratory of Biochemical Genetics NIMH-NIH; Bldg. 10, Rm. 2D56; 9000 Rockville Pike Bethesda, MD 20892 301-435-3576; FAX 301-480-9862 zullo@helix.nih.gov Mitochondria Interest Group Web Page: http://www-lecb.ncifcrf.gov/~zullo/migDB/ ------------------------------ Date: Wed, 15 Jul 1998 10:28:04 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Question Message-Id: <3.0.5.32.19980715102804.0079d890@codon.nih.gov> Content-Type: text/plain; charset="us-ascii" At 08:24 PM 7/15/98 +0900, you wrote: >Hello, > >Can I use your NIH-image on Power Macintosh G3 series. You can but the "Start Capturing" command does not support the G3's built-in video digitizer. You can, however, use the Plugin Digitizer available at "ftp://codon.nih.gov/pub/nih-image/plug-ins/". I have attempted, without much success, to fix this problem. Also, NIH Image does not correctly support Scion frame grabbers on G3 Macs. You need to use Scion's version of the program. This problem will be fixed in the next NIH Image beta. -wayne ------------------------------ Date: Wed, 15 Jul 1998 14:59:25 -0400 From: "Mike Smith" To: nih-image@io.ece.drexel.edu Subject: Mac built-in frame grabber Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit Dear List Members, I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board? Mike Smith -------------------------------- End of nih-image-d Digest V98 Issue #11 *************************************** From nih-image-request@io.ece.drexel.edu Thu Jul 16 06:25 EDT 1998 X-UIDL: 2e55c24a37b6657d0272369d2bc4ff91 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA15683; Thu, 16 Jul 1998 06:25:12 -0400 (EDT) Resent-Date: Thu, 16 Jul 1998 06:25:12 -0400 (EDT) Message-ID: <35ADD486.E0B71177@elis.rug.ac.be> Date: Thu, 16 Jul 1998 12:23:03 +0200 From: Tom Vanzieleghem X-Mailer: Mozilla 4.02 [en] (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #11 References: <199807161000.GAA13196@io.ECE.Drexel.EDU> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"6HHFf2.0.Od3.UCThr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/56 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 82 Status: RO Hi, How can I cancel my subscription to this list ? thanks, Tom Vanzieleghem From nih-image-request@io.ece.drexel.edu Thu Jul 16 09:16 EDT 1998 X-UIDL: ba73c4117f2393931f72372d23f61b22 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA00292; Thu, 16 Jul 1998 09:15:51 -0400 (EDT) Resent-Date: Thu, 16 Jul 1998 09:15:51 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Thu, 16 Jul 1998 15:05:56 +0200 To: NIH-Image Mailing List From: Paul Human Subject: Apple and NIH or Leica and QWin? Resent-Message-ID: <"akpSk.0.HA7.ZhVhr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/57 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1931 Status: RO Dear Imager We run an exclusive Apple Mac network and use NIH-Image (and some of the spin-off programmes) regularly. Before we chanced upon NIH though, we purchased an Image Analyser (together with a Fluorescence microscope) from Leica. The PC unit (a 486 but, due to problems, upgraded with a Pentium processor only) with its frame grabber (Elvis, 16 bit) has given us more problems than we care to mention. It has been shipped to the UK twice and is now currently with the local agents in another city. To cut a long story short, the agents are offering us a new Pentium II 166 MX with Matrox framegrabber (32 bit) and latest QWin Pro software (includes QWin gallery) at a price tag of R20,000 (about $3,225). One of the biggest problems we had with the old system was to get it networked, with the local agent stating emphatically that we could not network. The Pentium on offer will apparantly network, but we would need to buy the ethernet card as an extra. My feeling is that we should rather buy a decent framegrabber for the Apple Mac (am I right in thinking that one could get a similar card to the Matrox card at around $3,000?). The camera we use (JVC colour) gives S-video and composite output . We could then use NIH-Image (which I think in many respects is better than QWin). Networking also would be problem free. I would appreciate any suggestions in this regard, but basically we seem to be spending an endless amount of money on a system which is more out of order than in order. Specifically, I would appreciate advice on which framegrabber card would be suitable for hires colour grabbing on the Mac. Thakns in advance. ____________________________________________________________________ PAUL A HUMAN, M.Sc. Deputy Director Cardiovascular Research Unit University of Cape Town Medical School OBSERVATORY 7925, Cape Town, South Africa Voice:+27-21-406 6418 Fax:+27-21-448 5935 Cell:+27-82-770 3612 From nih-image-request@io.ece.drexel.edu Thu Jul 16 10:01 EDT 1998 X-UIDL: d706125342e3f44d2f4714480e76208e Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA04268; Thu, 16 Jul 1998 10:01:43 -0400 (EDT) Resent-Date: Thu, 16 Jul 1998 10:01:43 -0400 (EDT) From: Vaughn Adams Message-Id: <199807161351.JAA28577@cbis.ece.drexel.edu> Subject: Re: nih-image-d Digest V98 #11 In-Reply-To: <35ADD486.E0B71177@elis.rug.ac.be> from "Tom Vanzieleghem" at "Jul 16, 98 12:23:03 pm" X-ELM-OSV: (Our standard violations) no-mime=1; no-hdr-encoding=1 To: nih-image@io.ece.drexel.edu Date: Thu, 16 Jul 1998 09:51:21 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL31 (25)] Resent-Message-ID: <"VGa0w.0.Oo.YLWhr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/58 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 444 Status: RO Tom: > How can I cancel my subscription to this list ? Sure. Just send a message to nih-image-request@biomed.drexel.edu with Unsubscribe in the Subject. -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu From nih-image-request@io.ece.drexel.edu Thu Jul 16 12:01 EDT 1998 X-UIDL: 72ff50bd97e0aea8f092acc81b25b564 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA13027; Thu, 16 Jul 1998 12:01:17 -0400 (EDT) Resent-Date: Thu, 16 Jul 1998 12:01:17 -0400 (EDT) From: SolamereTG@aol.com Message-ID: Date: Thu, 16 Jul 1998 11:53:11 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Apple and NIH or Leica and QWin? Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 16-bit for Windows sub 38 Resent-Message-ID: <"KoeLJ1.0.k03.J8Yhr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/59 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1070 Status: RO Dear Dr. Human: I can recommend the CG-7 board from Scion ($2195). This board has RGB inputs, or can be used for monochrome. It has a serial/digital I/O to control peripheral equipment, 2 DAC channels out, and both standard 640x480 capture and high res capture mode that interpolates the pixels to provide 1280 x 960 pixel image. The board can be used in any PCI platform and comes with the Scion version of NIH for both Mac OS and Windows 95. Another choice would be an ITI IC PCI board with AM DIG-16 for digital cameras $2300. QED writes software that can take a digital cameras input into ADOBE photoshop, or NIH image, and archiving software. I agree NIH image is more flexible than most commercial software available on the PC or Mac. A major problem is that most commercial vendors rarely mention it as your best option either because they aren't familiar with it or can't sell it. Please feel free to contact me if you have questions about the boards. Dr. George A. Peeters Solamere Technology Group Salt Lake City UT 84103 Solameretg@aol.com 801 322-2645 From nih-image-request@io.ece.drexel.edu Thu Jul 16 17:29 EDT 1998 X-UIDL: 9c3501869d55506b0a753e2050046ec4 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA04670; Thu, 16 Jul 1998 17:28:51 -0400 (EDT) Resent-Date: Thu, 16 Jul 1998 17:28:51 -0400 (EDT) Message-ID: <35AE6DAE.6B03@cornell.edu> Date: Thu, 16 Jul 1998 17:16:30 -0400 From: Pei-Chen Hsieh X-Mailer: Mozilla 3.04 (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Opton-click with text tool in PC? Content-Transfer-Encoding: 7bit Resent-Message-ID: <"JQeSO.0.8y.-tchr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/60 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 307 Status: RO I use ImagePC to analyze electrophoretic gel density. After I measure the areas with the wand tool.How can I use text tool to label measurement result on the peak? I use Macintosh computer befor, in Maci I can use opton button. But, how can I use it in PC systen? Thank you for your help. Pei-Chin Hsieh From nih-image-request@io.ece.drexel.edu Fri Jul 17 00:12 EDT 1998 X-UIDL: beb524f7c0271430b4ff658271f488d1 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id AAA09208; Fri, 17 Jul 1998 00:12:31 -0400 (EDT) Resent-Date: Fri, 17 Jul 1998 00:12:31 -0400 (EDT) Message-ID: <35AECE4F.3D6EF315@sisna.com> Date: Thu, 16 Jul 1998 22:08:47 -0600 From: "Christopher P. Tully" Reply-To: cptully@sisna.com X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Apple and NIH or Leica and QWin? References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"lz9vM.0.d32.1tihr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/61 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2562 Status: RO Even though I personally prefer PC's, since your network is exclusively Mac, and you are obviously more comfortable with Macs, I would recomend putting a decent frame grabber in a Mac and scrap the PC... Since your camera only outputs S-video and composite (NTSC I assume), you can probably get a good frame grabber for less than $1500 US, unless you are planning to upgrade to a RGB camera some time in the next few years. As George Peters mentioned, the Scion boards are a good choice for use with NIH-Image. Chris Tully Paul Human wrote: > > Dear Imager > > We run an exclusive Apple Mac network and use NIH-Image (and some of the > spin-off programmes) regularly. Before we chanced upon NIH though, we > purchased an Image Analyser (together with a Fluorescence microscope) from > Leica. The PC unit (a 486 but, due to problems, upgraded with a Pentium > processor only) with its frame grabber (Elvis, 16 bit) has given us more > problems than we care to mention. It has been shipped to the UK twice and > is now currently with the local agents in another city. > > To cut a long story short, the agents are offering us a new Pentium II 166 > MX with Matrox framegrabber (32 bit) and latest QWin Pro software (includes > QWin gallery) at a price tag of R20,000 (about $3,225). > > One of the biggest problems we had with the old system was to get it > networked, with the local agent stating emphatically that we could not > network. The Pentium on offer will apparantly network, but we would need > to buy the ethernet card as an extra. > > My feeling is that we should rather buy a decent framegrabber for the Apple > Mac (am I right in thinking that one could get a similar card to the Matrox > card at around $3,000?). The camera we use (JVC colour) gives S-video and > composite output . We could then use NIH-Image (which I think in many > respects is better than QWin). Networking also would be problem free. > > I would appreciate any suggestions in this regard, but basically we seem to > be spending an endless amount of money on a system which is more out of > order than in order. > > Specifically, I would appreciate advice on which framegrabber card would be > suitable for hires colour grabbing on the Mac. > > Thakns in advance. > > ____________________________________________________________________ > PAUL A HUMAN, M.Sc. > Deputy Director > Cardiovascular Research Unit > University of Cape Town Medical School > OBSERVATORY 7925, Cape Town, South Africa > Voice:+27-21-406 6418 Fax:+27-21-448 5935 Cell:+27-82-770 3612 From nih-image-d-request@io.ece.drexel.edu Fri Jul 17 00:15 EDT 1998 X-UIDL: 0c5aec1015f0337f82e23007be838da0 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id AAA09747; Fri, 17 Jul 1998 00:15:55 -0400 (EDT) Date: Fri, 17 Jul 1998 00:15:55 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807170415.AAA09747@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #12 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/12 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 8895 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 12 Today's Topics: Re: nih-image-d Digest V98 #11 [ Tom Vanzieleghem ] Re: Apple and NIH or Leica and QWin? [ "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #11 Message-ID: <35ADD486.E0B71177@elis.rug.ac.be> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, How can I cancel my subscription to this list ? thanks, Tom Vanzieleghem ------------------------------ Date: Thu, 16 Jul 1998 15:05:56 +0200 From: Paul Human To: NIH-Image Mailing List Subject: Apple and NIH or Leica and QWin? Message-Id: Content-Type: text/plain; charset="us-ascii" Dear Imager We run an exclusive Apple Mac network and use NIH-Image (and some of the spin-off programmes) regularly. Before we chanced upon NIH though, we purchased an Image Analyser (together with a Fluorescence microscope) from Leica. The PC unit (a 486 but, due to problems, upgraded with a Pentium processor only) with its frame grabber (Elvis, 16 bit) has given us more problems than we care to mention. It has been shipped to the UK twice and is now currently with the local agents in another city. To cut a long story short, the agents are offering us a new Pentium II 166 MX with Matrox framegrabber (32 bit) and latest QWin Pro software (includes QWin gallery) at a price tag of R20,000 (about $3,225). One of the biggest problems we had with the old system was to get it networked, with the local agent stating emphatically that we could not network. The Pentium on offer will apparantly network, but we would need to buy the ethernet card as an extra. My feeling is that we should rather buy a decent framegrabber for the Apple Mac (am I right in thinking that one could get a similar card to the Matrox card at around $3,000?). The camera we use (JVC colour) gives S-video and composite output . We could then use NIH-Image (which I think in many respects is better than QWin). Networking also would be problem free. I would appreciate any suggestions in this regard, but basically we seem to be spending an endless amount of money on a system which is more out of order than in order. Specifically, I would appreciate advice on which framegrabber card would be suitable for hires colour grabbing on the Mac. Thakns in advance. ____________________________________________________________________ PAUL A HUMAN, M.Sc. Deputy Director Cardiovascular Research Unit University of Cape Town Medical School OBSERVATORY 7925, Cape Town, South Africa Voice:+27-21-406 6418 Fax:+27-21-448 5935 Cell:+27-82-770 3612 ------------------------------ Date: Thu, 16 Jul 1998 09:51:21 -0400 (EDT) From: Vaughn Adams To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #11 Message-Id: <199807161351.JAA28577@cbis.ece.drexel.edu> Content-Type: text Tom: > How can I cancel my subscription to this list ? Sure. Just send a message to nih-image-request@biomed.drexel.edu with Unsubscribe in the Subject. -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu ------------------------------ Date: Thu, 16 Jul 1998 11:53:11 EDT From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Apple and NIH or Leica and QWin? Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Dear Dr. Human: I can recommend the CG-7 board from Scion ($2195). This board has RGB inputs, or can be used for monochrome. It has a serial/digital I/O to control peripheral equipment, 2 DAC channels out, and both standard 640x480 capture and high res capture mode that interpolates the pixels to provide 1280 x 960 pixel image. The board can be used in any PCI platform and comes with the Scion version of NIH for both Mac OS and Windows 95. Another choice would be an ITI IC PCI board with AM DIG-16 for digital cameras $2300. QED writes software that can take a digital cameras input into ADOBE photoshop, or NIH image, and archiving software. I agree NIH image is more flexible than most commercial software available on the PC or Mac. A major problem is that most commercial vendors rarely mention it as your best option either because they aren't familiar with it or can't sell it. Please feel free to contact me if you have questions about the boards. Dr. George A. Peeters Solamere Technology Group Salt Lake City UT 84103 Solameretg@aol.com 801 322-2645 ------------------------------ Date: Thu, 16 Jul 1998 17:16:30 -0400 From: Pei-Chen Hsieh To: nih-image@io.ece.drexel.edu Subject: Opton-click with text tool in PC? Message-ID: <35AE6DAE.6B03@cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I use ImagePC to analyze electrophoretic gel density. After I measure the areas with the wand tool.How can I use text tool to label measurement result on the peak? I use Macintosh computer befor, in Maci I can use opton button. But, how can I use it in PC systen? Thank you for your help. Pei-Chin Hsieh ------------------------------ Date: Thu, 16 Jul 1998 22:08:47 -0600 From: "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: Apple and NIH or Leica and QWin? Message-ID: <35AECE4F.3D6EF315@sisna.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Even though I personally prefer PC's, since your network is exclusively Mac, and you are obviously more comfortable with Macs, I would recomend putting a decent frame grabber in a Mac and scrap the PC... Since your camera only outputs S-video and composite (NTSC I assume), you can probably get a good frame grabber for less than $1500 US, unless you are planning to upgrade to a RGB camera some time in the next few years. As George Peters mentioned, the Scion boards are a good choice for use with NIH-Image. Chris Tully Paul Human wrote: > > Dear Imager > > We run an exclusive Apple Mac network and use NIH-Image (and some of the > spin-off programmes) regularly. Before we chanced upon NIH though, we > purchased an Image Analyser (together with a Fluorescence microscope) from > Leica. The PC unit (a 486 but, due to problems, upgraded with a Pentium > processor only) with its frame grabber (Elvis, 16 bit) has given us more > problems than we care to mention. It has been shipped to the UK twice and > is now currently with the local agents in another city. > > To cut a long story short, the agents are offering us a new Pentium II 166 > MX with Matrox framegrabber (32 bit) and latest QWin Pro software (includes > QWin gallery) at a price tag of R20,000 (about $3,225). > > One of the biggest problems we had with the old system was to get it > networked, with the local agent stating emphatically that we could not > network. The Pentium on offer will apparantly network, but we would need > to buy the ethernet card as an extra. > > My feeling is that we should rather buy a decent framegrabber for the Apple > Mac (am I right in thinking that one could get a similar card to the Matrox > card at around $3,000?). The camera we use (JVC colour) gives S-video and > composite output . We could then use NIH-Image (which I think in many > respects is better than QWin). Networking also would be problem free. > > I would appreciate any suggestions in this regard, but basically we seem to > be spending an endless amount of money on a system which is more out of > order than in order. > > Specifically, I would appreciate advice on which framegrabber card would be > suitable for hires colour grabbing on the Mac. > > Thakns in advance. > > ____________________________________________________________________ > PAUL A HUMAN, M.Sc. > Deputy Director > Cardiovascular Research Unit > University of Cape Town Medical School > OBSERVATORY 7925, Cape Town, South Africa > Voice:+27-21-406 6418 Fax:+27-21-448 5935 Cell:+27-82-770 3612 -------------------------------- End of nih-image-d Digest V98 Issue #12 *************************************** From nih-image-request@io.ece.drexel.edu Fri Jul 17 09:27 EDT 1998 X-UIDL: 349ecc972b2a3c1977353387a3b91f5d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA00306; Fri, 17 Jul 1998 09:26:49 -0400 (EDT) Resent-Date: Fri, 17 Jul 1998 09:26:49 -0400 (EDT) X-Sender: tmorton@10.0.0.1 Message-Id: In-Reply-To: <199807170407.AAA08672@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Fri, 17 Jul 1998 08:53:56 -0500 To: nih-image@io.ece.drexel.edu From: Tom Morton Subject: Re: nih-image-d Digest V98 #12 Resent-Message-ID: <"LuCEk.0.E37.Gtqhr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/62 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 919 Status: RO Hello, In Beta 3 of Scion Image you need to hold the Scroll Lock key while clicking with the Text Tool. Tom > >I use ImagePC to analyze electrophoretic gel density. After I measure >the areas with the wand tool.How can I use text tool to label >measurement result on the peak? I use Macintosh computer befor, in Maci >I can use opton button. But, how can I use it in PC systen? >Thank you for your help. > >Pei-Chin Hsieh ----------------------------------------------------------------------- Tom Morton support@scioncorp.com Technical Services http://www.scioncorp.com Scion Corporation ftp://scioncorp.com 82 Wormans Mill Rd., Suite H Phone: (301) 695-7870 Frederick, MD 21701 Fax: (301) 695-0035 ----------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Fri Jul 17 11:05 EDT 1998 X-UIDL: 9f30a3754aade6cc569318df63a982f0 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA17305; Fri, 17 Jul 1998 11:05:29 -0400 (EDT) Resent-Date: Fri, 17 Jul 1998 11:05:29 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Fri, 17 Jul 1998 07:47:32 -0700 To: nih-image@io.ece.drexel.edu, Jonathan Nissanov From: Glenn Hammonds Subject: Re: Digest form Resent-Message-ID: <"ZjG6K2.0.Ms1.uLshr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/63 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1188 Status: RO Johnathan et al, After trying it for a while, I'm sorry to report that the new digest format definitely is not working for me. I'm using Eudora Pro 3.1.1, and I use filtering to sort mail. With the new digests I get a new mailbox for every issue which shows up at the top of the mail heirarchy instead of in my intended location for NIH Image, and the naming conventions are somehow messed up such that the name of the mailbox is not the same as the name of the digest. The result is a confusing mess of nearly identical but incorrectly named misplaced mailboxes, plus packaging. Ouch! My "solution" to date has been to dump all the contents of each digest back into a single NIH Image mailbox, thus losing the digest character as well as the appropriate "reply-to" address, then delete all those mailboxes, attachments, original container messages, etc. In the short run this is (barely) OK, but in the long run, a single mailbox for individual messages from the NIH Image list is impractical, and I'm tired of dealing with the mess. I would much prefer to go back to the older plain vanilla style of digest. Could there be two styles of digest offered? Best, Glenn Hammonds From nih-image-request@io.ece.drexel.edu Fri Jul 17 11:34 EDT 1998 X-UIDL: 29937bc31ef0d5b69e1a7b282aada418 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA19498; Fri, 17 Jul 1998 11:34:27 -0400 (EDT) Resent-Date: Fri, 17 Jul 1998 11:34:27 -0400 (EDT) Message-ID: <35AF6E61.AA495F8C@nfinity.com> Date: Fri, 17 Jul 1998 10:31:46 -0500 From: "Jud Gurney, M.D." X-Mailer: Mozilla 4.5b1 (Macintosh; I; PPC) X-Accept-Language: English [en] MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Digest form References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"4gLkC1.0.CY4.hoshr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/64 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1443 Status: RO Same for me. Eudora does not handle this digest version without making a new mailbox each time. I had to unsubscribe and subscribe to the individual messages. Jud Gurney Univ of NE Glenn Hammonds wrote: > Johnathan et al, > > After trying it for a while, I'm sorry to report that the new digest format > definitely is not working for me. > > I'm using Eudora Pro 3.1.1, and I use filtering to sort mail. With the new > digests I get a new mailbox for every issue which shows up at the top of > the mail heirarchy instead of in my intended location for NIH Image, and > the naming conventions are somehow messed up such that the name of the > mailbox is not the same as the name of the digest. The result is a > confusing mess of nearly identical but incorrectly named misplaced > mailboxes, plus packaging. Ouch! > > My "solution" to date has been to dump all the contents of each digest back > into a single NIH Image mailbox, thus losing the digest character as well > as the appropriate "reply-to" address, then delete all those mailboxes, > attachments, original container messages, etc. In the short run this is > (barely) OK, but in the long run, a single mailbox for individual messages > from the NIH Image list is impractical, and I'm tired of dealing with the > mess. > > I would much prefer to go back to the older plain vanilla style of digest. > Could there be two styles of digest offered? > > Best, > > Glenn Hammonds > From nih-image-request@io.ece.drexel.edu Fri Jul 17 11:35 EDT 1998 X-UIDL: b7d6112ae26a43829b380685be88d8f8 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA19592; Fri, 17 Jul 1998 11:35:09 -0400 (EDT) Resent-Date: Fri, 17 Jul 1998 11:35:09 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Fri, 17 Jul 1998 11:24:21 -0400 From: "Mike Smith" To: nih-image@io.ece.drexel.edu Subject: Mac built-in frame grabber -Reply Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA18764 Resent-Message-ID: <"frTGk2.0.Jb4.iqshr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/65 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 626 Status: RO Dear list Members, I posted the enclosed question a few days ago. Though no one replied, I managed to find the answer myself. If anyone else has the same problem, the answer is to hold down the SHIFT key when opening IMAGE. Doing so selects the internal frame grabber. Mike Smith >>> "Mike Smith" 07/15 3:12 pm >>> Dear List Members, I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board? Mike Smith From nih-image-request@io.ece.drexel.edu Fri Jul 17 17:36 EDT 1998 X-UIDL: 3028d96c582fe45c918965057ff124c2 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA20854; Fri, 17 Jul 1998 17:36:25 -0400 (EDT) Resent-Date: Fri, 17 Jul 1998 17:36:25 -0400 (EDT) Date: Fri, 17 Jul 1998 16:02:38 -0500 From: scidi Subject: Re: NuBus frame grabber wanted To: nih-image@io.ece.drexel.edu Reply-to: scidi@mci2000.com Message-id: <0EW900MEECXDKX@PM06SM.PMM.MCI.NET> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1161 Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-Priority: 3 Resent-Message-ID: <"iKDOR.0.Go4.71yhr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/66 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 1148 Status: RO To all on the list: I have posted this before, but I will try again. I am in need of a Nubus VG-5 card or the combination of the LG-3 and TV-3 cards. I would be willing to either pay top dollar or to trade for a brand new VG-5 PCI card. This is needed ASAP!!!! Please respond soon!! Mark R. Molenda, Owner Scientific Digital Imaging 1407 S 59th St. Milwaukee, WI 53214 phone (414) 476-2694 fax (414) 645-8037 scidi@mci2000.com ---------- > From: Alan Townsend > To: nih-image@io.ece.drexel.edu > Subject: NuBus frame grabber wanted > Date: Tuesday, July 14, 1998 2:49 PM > > I am looking for a new or used frame grabber card for use in > a Power Mac 7100/80. The Scion LG3 would be my preference, > but the AG-5 is also an option. Other cards may also be > considered. If you have a spec sheet or web URL that would > help. Please reply (including price) to (e-mail preferred) > : > Alan J. Townsend, Ph.D., Biochemistry Department, Wake > Forest University School of Medicine, Medical Center Blvd., > Winston-Salem, N.C. 27157, Phone (336)-716-7658, FAX > (336)-716-7671, E-Mail : atown@wfubmc.edu From nih-image-d-request@io.ece.drexel.edu Sat Jul 18 06:06 EDT 1998 X-UIDL: ef1f33579e65a26ab4716ba2ac9318fe Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA11856; Sat, 18 Jul 1998 06:06:46 -0400 (EDT) Date: Sat, 18 Jul 1998 06:06:46 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807181006.GAA11856@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #13 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/13 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7519 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 13 Today's Topics: Re: nih-image-d Digest V98 #12 [ Tom Morton ] Re: Digest form [ Glenn Hammonds ] ------------------------------ Date: Fri, 17 Jul 1998 08:53:56 -0500 From: Tom Morton To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #12 Message-Id: Content-Type: text/plain; charset="us-ascii" Hello, In Beta 3 of Scion Image you need to hold the Scroll Lock key while clicking with the Text Tool. Tom > >I use ImagePC to analyze electrophoretic gel density. After I measure >the areas with the wand tool.How can I use text tool to label >measurement result on the peak? I use Macintosh computer befor, in Maci >I can use opton button. But, how can I use it in PC systen? >Thank you for your help. > >Pei-Chin Hsieh ----------------------------------------------------------------------- Tom Morton support@scioncorp.com Technical Services http://www.scioncorp.com Scion Corporation ftp://scioncorp.com 82 Wormans Mill Rd., Suite H Phone: (301) 695-7870 Frederick, MD 21701 Fax: (301) 695-0035 ----------------------------------------------------------------------- ------------------------------ Date: Fri, 17 Jul 1998 07:47:32 -0700 From: Glenn Hammonds To: nih-image@io.ece.drexel.edu, Jonathan Nissanov Subject: Re: Digest form Message-Id: Content-Type: text/plain; charset="us-ascii" Johnathan et al, After trying it for a while, I'm sorry to report that the new digest format definitely is not working for me. I'm using Eudora Pro 3.1.1, and I use filtering to sort mail. With the new digests I get a new mailbox for every issue which shows up at the top of the mail heirarchy instead of in my intended location for NIH Image, and the naming conventions are somehow messed up such that the name of the mailbox is not the same as the name of the digest. The result is a confusing mess of nearly identical but incorrectly named misplaced mailboxes, plus packaging. Ouch! My "solution" to date has been to dump all the contents of each digest back into a single NIH Image mailbox, thus losing the digest character as well as the appropriate "reply-to" address, then delete all those mailboxes, attachments, original container messages, etc. In the short run this is (barely) OK, but in the long run, a single mailbox for individual messages from the NIH Image list is impractical, and I'm tired of dealing with the mess. I would much prefer to go back to the older plain vanilla style of digest. Could there be two styles of digest offered? Best, Glenn Hammonds ------------------------------ Date: Fri, 17 Jul 1998 10:31:46 -0500 From: "Jud Gurney, M.D." To: nih-image@io.ece.drexel.edu Subject: Re: Digest form Message-ID: <35AF6E61.AA495F8C@nfinity.com> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Same for me. Eudora does not handle this digest version without making a new mailbox each time. I had to unsubscribe and subscribe to the individual messages. Jud Gurney Univ of NE Glenn Hammonds wrote: > Johnathan et al, > > After trying it for a while, I'm sorry to report that the new digest format > definitely is not working for me. > > I'm using Eudora Pro 3.1.1, and I use filtering to sort mail. With the new > digests I get a new mailbox for every issue which shows up at the top of > the mail heirarchy instead of in my intended location for NIH Image, and > the naming conventions are somehow messed up such that the name of the > mailbox is not the same as the name of the digest. The result is a > confusing mess of nearly identical but incorrectly named misplaced > mailboxes, plus packaging. Ouch! > > My "solution" to date has been to dump all the contents of each digest back > into a single NIH Image mailbox, thus losing the digest character as well > as the appropriate "reply-to" address, then delete all those mailboxes, > attachments, original container messages, etc. In the short run this is > (barely) OK, but in the long run, a single mailbox for individual messages > from the NIH Image list is impractical, and I'm tired of dealing with the > mess. > > I would much prefer to go back to the older plain vanilla style of digest. > Could there be two styles of digest offered? > > Best, > > Glenn Hammonds > ------------------------------ Date: Fri, 17 Jul 1998 11:24:21 -0400 From: "Mike Smith" To: nih-image@io.ece.drexel.edu Subject: Mac built-in frame grabber -Reply Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit Dear list Members, I posted the enclosed question a few days ago. Though no one replied, I managed to find the answer myself. If anyone else has the same problem, the answer is to hold down the SHIFT key when opening IMAGE. Doing so selects the internal frame grabber. Mike Smith >>> "Mike Smith" 07/15 3:12 pm >>> Dear List Members, I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board? Mike Smith ------------------------------ Date: Fri, 17 Jul 1998 16:02:38 -0500 From: scidi To: nih-image@io.ece.drexel.edu Subject: Re: NuBus frame grabber wanted Message-id: <0EW900MEECXDKX@PM06SM.PMM.MCI.NET> Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit To all on the list: I have posted this before, but I will try again. I am in need of a Nubus VG-5 card or the combination of the LG-3 and TV-3 cards. I would be willing to either pay top dollar or to trade for a brand new VG-5 PCI card. This is needed ASAP!!!! Please respond soon!! Mark R. Molenda, Owner Scientific Digital Imaging 1407 S 59th St. Milwaukee, WI 53214 phone (414) 476-2694 fax (414) 645-8037 scidi@mci2000.com ---------- > From: Alan Townsend > To: nih-image@io.ece.drexel.edu > Subject: NuBus frame grabber wanted > Date: Tuesday, July 14, 1998 2:49 PM > > I am looking for a new or used frame grabber card for use in > a Power Mac 7100/80. The Scion LG3 would be my preference, > but the AG-5 is also an option. Other cards may also be > considered. If you have a spec sheet or web URL that would > help. Please reply (including price) to (e-mail preferred) > : > Alan J. Townsend, Ph.D., Biochemistry Department, Wake > Forest University School of Medicine, Medical Center Blvd., > Winston-Salem, N.C. 27157, Phone (336)-716-7658, FAX > (336)-716-7671, E-Mail : atown@wfubmc.edu -------------------------------- End of nih-image-d Digest V98 Issue #13 *************************************** From nih-image-request@io.ece.drexel.edu Sat Jul 18 19:51 EDT 1998 X-UIDL: 53f438bf15ce2198d24aba9e13e6e509 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id TAA06708; Sat, 18 Jul 1998 19:49:19 -0400 (EDT) Resent-Date: Sat, 18 Jul 1998 19:49:19 -0400 (EDT) Date: Sat, 18 Jul 1998 16:28:30 -0700 (PDT) From: "T. Hickson" Reply-To: "T. Hickson" To: nih-image@io.ece.drexel.edu Subject: image lineations and angle measurement (fwd) Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"nzDBa2.0.v41.Y-Iir"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/67 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1604 Status: RO Hello, I got this address from the sci.image.processing and I'm hoping that you can help me out. I am a mac user. I'm familiar with NIH-Image and Photoshop. I have a series of images that I need to analyze for clusters of lineations. 1. Are there any plug-ins for Photoshop or macros for NIH-image that can look for lineations, measure their orientation and dump the data to a text file? 2. Is there any commercially available software that might handle this (such as Prism)? 3. Is there anyone out there that might like to take a crack at coding an NIH-Image macro that would do this? Basically, I think that I can segment my data and generate clusters of pixels (particles) that have a variety of long-axis orientations on the image. I would like to be able to measure the orientation, magnitude, and density per unit area of each particle within a selected area of the image, then generate a circular histogram (rose diagram) of the orientations. If you can help me on this, I'd much appreciate it. Cheers, Tom Hickson ************************************************************** Thomas A. Hickson Department of Geological and Environmental Sciences Stanford University Stanford, CA 94305-2115 Phone: (650)725-0043 E-mail: hickson@pangea.stanford.edu Web site: http://pangea.stanford.edu/~hickson/hickson.html New Home: Geo-Corner (Bldg. 320), Room 319 ************************************************************** To doubt everything or to believe everything are two equally convenient solutions; both dispense with the necessity of reflection. H. Poincare From nih-image-d-request@io.ece.drexel.edu Sun Jul 19 21:19 EDT 1998 X-UIDL: f31e7a92a34edfee9d297c3e67dce6e6 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA04766; Sun, 19 Jul 1998 21:19:03 -0400 (EDT) Date: Sun, 19 Jul 1998 21:19:03 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807200119.VAA04766@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #14 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/14 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4761 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 14 Today's Topics: image lineations and angle measureme [ "T. Hickson" To: nih-image@io.ece.drexel.edu Subject: image lineations and angle measurement (fwd) Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I got this address from the sci.image.processing and I'm hoping that you can help me out. I am a mac user. I'm familiar with NIH-Image and Photoshop. I have a series of images that I need to analyze for clusters of lineations. 1. Are there any plug-ins for Photoshop or macros for NIH-image that can look for lineations, measure their orientation and dump the data to a text file? 2. Is there any commercially available software that might handle this (such as Prism)? 3. Is there anyone out there that might like to take a crack at coding an NIH-Image macro that would do this? Basically, I think that I can segment my data and generate clusters of pixels (particles) that have a variety of long-axis orientations on the image. I would like to be able to measure the orientation, magnitude, and density per unit area of each particle within a selected area of the image, then generate a circular histogram (rose diagram) of the orientations. If you can help me on this, I'd much appreciate it. Cheers, Tom Hickson ************************************************************** Thomas A. Hickson Department of Geological and Environmental Sciences Stanford University Stanford, CA 94305-2115 Phone: (650)725-0043 E-mail: hickson@pangea.stanford.edu Web site: http://pangea.stanford.edu/~hickson/hickson.html New Home: Geo-Corner (Bldg. 320), Room 319 ************************************************************** To doubt everything or to believe everything are two equally convenient solutions; both dispense with the necessity of reflection. H. Poincare ------------------------------ Date: Sun, 19 Jul 1998 21:14:38 -0400 From: David Milstone To: nih-image@io.ece.drexel.edu Subject: Re: Digest form Message-Id: Content-Type: text/plain; charset="us-ascii" I am using Eudora Pro 3.1 and find the new digest format O.K but not great. I am able to filter a "table of contents" file into any desired mailbox. This file then links to the actual posts which are contained in a newly, and automatically, created mailbox in my Eudora attachments folder.When I trash the "table of contents" file the mailbox containing the corresponding posts is automatically moved to the trash. This works fine but seems needlessly comlex. Other than the need to empty the trash to actually delete the mailbox containing the posts this system works fine for me. Dave >Same for me. Eudora does not handle this digest version without making a new >mailbox each time. I had to unsubscribe and subscribe to the individual >messages. > >Jud Gurney >Univ of NE > >Glenn Hammonds wrote: > >> Johnathan et al, >> >> After trying it for a while, I'm sorry to report that the new digest format >> definitely is not working for me. >> >> I'm using Eudora Pro 3.1.1, and I use filtering to sort mail. With the new >> digests I get a new mailbox for every issue which shows up at the top of >> the mail heirarchy instead of in my intended location for NIH Image, and >> the naming conventions are somehow messed up such that the name of the >> mailbox is not the same as the name of the digest. The result is a >> confusing mess of nearly identical but incorrectly named misplaced >> mailboxes, plus packaging. Ouch! >> >> My "solution" to date has been to dump all the contents of each digest back >> into a single NIH Image mailbox, thus losing the digest character as well >> as the appropriate "reply-to" address, then delete all those mailboxes, >> attachments, original container messages, etc. In the short run this is >> (barely) OK, but in the long run, a single mailbox for individual messages >> from the NIH Image list is impractical, and I'm tired of dealing with the >> mess. >> >> I would much prefer to go back to the older plain vanilla style of digest. >> Could there be two styles of digest offered? >> >> Best, >> >> Glenn Hammonds -------------------------------- End of nih-image-d Digest V98 Issue #14 *************************************** From nih-image-request@io.ece.drexel.edu Sun Jul 19 21:22 EDT 1998 X-UIDL: 1a7504afc336831794e8ec5515f8dd60 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA05144; Sun, 19 Jul 1998 21:21:47 -0400 (EDT) Resent-Date: Sun, 19 Jul 1998 21:21:47 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Sun, 19 Jul 1998 21:14:38 -0400 To: nih-image@io.ece.drexel.edu From: David Milstone Subject: Re: Digest form Resent-Message-ID: <"3aF6H.0.mt.iafir"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/68 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2159 Status: RO I am using Eudora Pro 3.1 and find the new digest format O.K but not great. I am able to filter a "table of contents" file into any desired mailbox. This file then links to the actual posts which are contained in a newly, and automatically, created mailbox in my Eudora attachments folder.When I trash the "table of contents" file the mailbox containing the corresponding posts is automatically moved to the trash. This works fine but seems needlessly comlex. Other than the need to empty the trash to actually delete the mailbox containing the posts this system works fine for me. Dave >Same for me. Eudora does not handle this digest version without making a new >mailbox each time. I had to unsubscribe and subscribe to the individual >messages. > >Jud Gurney >Univ of NE > >Glenn Hammonds wrote: > >> Johnathan et al, >> >> After trying it for a while, I'm sorry to report that the new digest format >> definitely is not working for me. >> >> I'm using Eudora Pro 3.1.1, and I use filtering to sort mail. With the new >> digests I get a new mailbox for every issue which shows up at the top of >> the mail heirarchy instead of in my intended location for NIH Image, and >> the naming conventions are somehow messed up such that the name of the >> mailbox is not the same as the name of the digest. The result is a >> confusing mess of nearly identical but incorrectly named misplaced >> mailboxes, plus packaging. Ouch! >> >> My "solution" to date has been to dump all the contents of each digest back >> into a single NIH Image mailbox, thus losing the digest character as well >> as the appropriate "reply-to" address, then delete all those mailboxes, >> attachments, original container messages, etc. In the short run this is >> (barely) OK, but in the long run, a single mailbox for individual messages >> from the NIH Image list is impractical, and I'm tired of dealing with the >> mess. >> >> I would much prefer to go back to the older plain vanilla style of digest. >> Could there be two styles of digest offered? >> >> Best, >> >> Glenn Hammonds From nih-image-request@io.ece.drexel.edu Sun Jul 19 23:12 EDT 1998 X-UIDL: 7cff5fcd60764aef251274bca0c6412d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id XAA15804; Sun, 19 Jul 1998 23:11:55 -0400 (EDT) Resent-Date: Sun, 19 Jul 1998 23:11:55 -0400 (EDT) Message-ID: From: "Goldsmith, Noel" To: "'Image Mailing List'" Subject: LUDL MAC2000 (and 2002) controller Date: Mon, 20 Jul 1998 13:02:12 +1000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"Ne5343.0.5c3.xChir"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/69 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 213 Status: RO Hi, Does or has anyone got the code for the RS232C driving of a LUDL 2000 XYZ stage from NIH-IMAGE? And if so would they like to share it with me? Otherwise I will have to do it myself. Thank you. Noel Goldsmith From nih-image-request@io.ece.drexel.edu Mon Jul 20 03:03 EDT 1998 X-UIDL: 4b76e67f049f4e9e7ee49847f60d8bcc Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id DAA07971; Mon, 20 Jul 1998 03:03:33 -0400 (EDT) Resent-Date: Mon, 20 Jul 1998 03:03:33 -0400 (EDT) Message-Id: In-Reply-To: <199807200114.VAA04202@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Sun, 19 Jul 1998 23:52:44 -0700 To: nih-image@io.ece.drexel.edu From: Glenn Hammonds Subject: Re: Digest Form Resent-Message-ID: <"AelFx.0.7d1.7Zkir"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/70 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 369 Status: RO I earlier posted that Eudora Pro 3.1.1 was returning a Eudora mailbox for each issue of the digest. Thanks to suggestions from Ard Jonker I found a setting that turns off this "feature". Deselect the check box Special:Settings:"Receive MIME digests as attachments", and the digest appears as text. No further trouble here, and thanks Ard! Glenn From nih-image-request@io.ece.drexel.edu Mon Jul 20 08:06 EDT 1998 X-UIDL: a74034f6b841bc3cfd818815ba892308 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA06945; Mon, 20 Jul 1998 08:05:48 -0400 (EDT) Resent-Date: Mon, 20 Jul 1998 08:05:48 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 20 Jul 1998 13:48:13 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Re: LUDL MAC2000 (and 2002) controller Resent-Message-ID: <"e0Dzc.0.2G1.3woir"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/71 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3916 Status: RO >Does or has anyone got the code for the RS232C driving of a LUDL 2000 >XYZ stage from NIH-IMAGE? >And if so would they like to share it with me? >Otherwise I will have to do it myself. >Thank you. >Noel Goldsmith I have written such code and posted an example macro to the list in April 1997. Below is the macro I sent. As you see, it is pretty straightforward to run this stage using serial commands. I also have some Pascal code with a custom dialog. Contact me off-list if you are interested in this as well. (I am going on vacation for two weeks from tomorrow morning and will not reply to email until I am back.) >To: nih-image@soils.umn.edu >From: steinr@kjemi.unit.no (Stein Roervik) >Subject: Ludl Macro > >Below is a general macro to run the Ludl focus controller. >It only includes a few basic example functions: >Do autofocus, read position and move to position. >All other functions follow the same syntax, so this >macro should be easy to modify. Read the manual. >The macro requires NIH image 1.60 or higher. > >First press [F1] to verify that the communication is working. >The reply should read ":A ". Then press [F4] to initialize the unit, >[f] to do focus or [m] to move to a given position. > macro 'test serial [F1]'; var CommandString, ReplyChar, ReplyString: string; begin OpenSerial('9600 baud, no parity, eight data, two stop'); CommandString:= 'window +'; PutSerial(CommandString,chr(13)); wait(0.1); ReplyString := ''; repeat ReplyChar:= GetSerial; ReplyString := concat(ReplyString, ReplyChar); until ReplyChar = ''; ShowMessage('Command: "',CommandString,'"\', 'Reply: "',ReplyString,'"'); end; macro 'reset serial [F2]'; begin OpenSerial('9600 baud, no parity, eight data, two stop'); PutSerial(chr(255),chr(82)); {reset Ludl device} wait(10); { it takes approx. 9.6 seconds until Ludl device is reset } beep; end; macro 'flush serial input buffer [F3]'; var i: integer; ch, str: string; begin str:= ''; i:= 0; repeat i:= i+1; ch:= GetSerial; str:= concat(str,ch); until ch=''; ShowMessage('Buffer: "',str,'"'); end; function GetLudlValue(CommandString: string): real; var ReplyChar, ReplyString: string; begin PutSerial(CommandString,chr(13)); wait(0.1); ReplyString := ''; repeat ReplyChar:= GetSerial; ReplyString := concat(ReplyString, ReplyChar); until ReplyChar = ''; ShowMessage('Ludl request "',CommandString,'"\', 'Ludl response "',ReplyString,'"'); GetLudlValue:= StringToNum(ReplyString)/100; {100 steps in a micron} end; procedure SendLudlCommand(CommandString: string); var ReplyChar, ReplyString: string; begin PutSerial(CommandString,chr(13)); wait(0.1); ReplyString := ''; repeat ReplyChar:= GetSerial; ReplyString := concat(ReplyString, ReplyChar); until ReplyChar = ''; ShowMessage('Ludl command "',CommandString,'"\', 'Ludl response "',ReplyString,'"'); end; macro 'init focus driver [F4]'; begin OpenSerial('9600 baud, no parity, eight data, two stop'); SendLudlCommand('window +'); SendLudlCommand('speed F=5000'); SendLudlCommand('here F=0'); end; macro 'do AutoFocus [f]'; begin SendLudlCommand('focus'); end; macro 'do MovePosition [m]'; var Position: real; begin Position:= GetNumber('Move to new position:',GetLudlValue('where F')); SendLudlCommand(concat('move F =',round(Position*100))); end; +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Mon Jul 20 08:49 EDT 1998 X-UIDL: 1d15431fa978b3707acf1b7b60ecfb23 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA11311; Mon, 20 Jul 1998 08:49:18 -0400 (EDT) Resent-Date: Mon, 20 Jul 1998 08:49:18 -0400 (EDT) From: "Samu Ruuhonen" Organization: HUT/GALA To: nih-image@io.ece.drexel.edu Date: Mon, 20 Jul 1998 15:21:42 +0000 MIME-Version: 1.0 Content-transfer-encoding: 7BIT Subject: AutoThreshold -algorithm? Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <1E2C698500A@nippi.hut.fi> Resent-Message-ID: <"fkOA03.0.nI2.JYpir"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/72 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 319 Status: RO I am using ImagePC for thresholding graylevel images taken from a paper surface. Does anybody know what is the algorithm that "AutoThreshold" -macro command uses to calculate the correct threshold value? Thank you, Samu Ruuhonen Research assist in Helsinki University of Technology Laboratory of Media Technology From nih-image-request@io.ece.drexel.edu Mon Jul 20 09:54 EDT 1998 X-UIDL: 3f3bed6b2bee5eb168c65a4e4b3a1361 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA17585; Mon, 20 Jul 1998 09:53:48 -0400 (EDT) Resent-Date: Mon, 20 Jul 1998 09:53:48 -0400 (EDT) X-Sender: tmorton@10.0.0.1 Message-Id: In-Reply-To: <199807181001.GAA11140@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Mon, 20 Jul 1998 09:05:35 -0500 To: nih-image@io.ece.drexel.edu From: Tom Morton Subject: Re: nih-image-d Digest V98 #13 Resent-Message-ID: <"mUcr1.0.Eh3.qNqir"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/73 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1312 Status: RO Hello, Try holding down the Shift key while invoking Scion Image. This should bypass the detection of the Scion frame grabbers and then alow detection of the AV board. Tom > >Dear list Members, > >I posted the enclosed question a few days ago. Though no one replied, I >managed to find the answer myself. If anyone else has the same problem, >the answer is to hold down the SHIFT key when opening IMAGE. Doing so >selects the internal frame grabber. > >Mike Smith > >>>> "Mike Smith" 07/15 3:12 pm >>> >Dear List Members, > >I have a PowerMac with a built-in frame grabber (low quality). Recently, I >installed a Scion frame grabber. Now I cannot seem to access the built-in >frame grabber from NIH-Image. Is there a way to do this, or must I >ununstall the Scion board? > >Mike Smith ----------------------------------------------------------------------- Tom Morton support@scioncorp.com Technical Services http://www.scioncorp.com Scion Corporation ftp://scioncorp.com 82 Wormans Mill Rd., Suite H Phone: (301) 695-7870 Frederick, MD 21701 Fax: (301) 695-0035 ----------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Mon Jul 20 12:11 EDT 1998 X-UIDL: 7be9474d420a45db9f7348f0e5628906 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA28871; Mon, 20 Jul 1998 12:11:23 -0400 (EDT) Resent-Date: Mon, 20 Jul 1998 12:11:23 -0400 (EDT) Mime-Version: 1.0 X-Sender: goerke@128.218.95.21 Message-Id: Date: Mon, 20 Jul 1998 09:00:46 -0700 To: nih-image@io.ece.drexel.edu From: Jon Goerke Subject: Re: Digest Form Resent-Message-ID: <"MmINn.0.dl6.LZsir"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/74 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1690 Status: RO Four posts to the list have been somewhat critical of the new Digest Form and its interactions with Eudora. The basic problem is that it automatically inserts new Image Digest mailboxes in the Eudora Menu. Since my own complaint was posted, however, I've developed a workaround that seems fairly painless -- and it no longer requires a trip to Menu/Window/Mailboxes to implement. I filter each digest into a mailbox as previously ( "from" contains "NIH-Image" into the mailbox). Clicking on the new message line appearing in the NIH-Image mailbox window opens a new-appearing Digest Window containing an Icon indicating an attached file. Clicking on this Icon opens the Digest headed by the ????? index entry. I click on the topics I want to see, and then use Menu/Delete to trash what I don't want to save for future reference, all the way back through the Digest itself. A singular advantage to the new scheme is that I can save individual posts directly and easily. The old Digest system required selecting, copying, opening Simple Text or Word, pasting, and saving. What appeared to be residual new mailboxes in Menu/Mailbox, even after Menu/Special/Empty Trash, had disappeared when the Mac System was next booted. I'm using Eudora 4.0, but I doubt that the described behavior is specific to this version. Put me down for maintaining the current Digest form please. Jon _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Jon Goerke, MD EMail: goerke@itsa.ucsf.edu Prof. Physiology, Univ. Calif. Phone: 415-476-3252 3333 California St., Suite 150, San Francisco, CA 94118 _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From nih-image-request@io.ece.drexel.edu Mon Jul 20 13:44 EDT 1998 X-UIDL: c7ca563e299d3750ddcd267a28d04642 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA05980; Mon, 20 Jul 1998 13:44:26 -0400 (EDT) Resent-Date: Mon, 20 Jul 1998 13:44:26 -0400 (EDT) Date: Mon, 20 Jul 1998 12:33:50 -0500 (EST) X-Sender: tsteffen@topaz.iupui.edu Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Tim Steffens Subject: Test just delete Resent-Message-ID: <"5yr501.0.4F1.2-tir"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/75 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 101 Status: RO just delete this message. Tim Steffens, CRA Indiana University Medical Center tsteffen@iupui.edu From nih-image-d-request@io.ece.drexel.edu Mon Jul 20 17:47 EDT 1998 X-UIDL: 333d23f421ac6fbff798ae8b4cd43da2 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA24376; Mon, 20 Jul 1998 17:47:52 -0400 (EDT) Date: Mon, 20 Jul 1998 17:47:52 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807202147.RAA24376@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #15 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/15 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 11387 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 15 Today's Topics: LUDL MAC2000 (and 2002) controller [ "Goldsmith, Noel" ] Re: nih-image-d Digest V98 #13 [ Tom Morton ] Re: Digest Form [ Jon Goerke ] Test just delete [ Tim Steffens ] NIH Image for the MAC [ "Michael A. Richardson, M.D." To: "'Image Mailing List'" Subject: LUDL MAC2000 (and 2002) controller Message-ID: Content-Type: text/plain Hi, Does or has anyone got the code for the RS232C driving of a LUDL 2000 XYZ stage from NIH-IMAGE? And if so would they like to share it with me? Otherwise I will have to do it myself. Thank you. Noel Goldsmith ------------------------------ Date: Sun, 19 Jul 1998 23:52:44 -0700 From: Glenn Hammonds To: nih-image@io.ece.drexel.edu Subject: Re: Digest Form Message-Id: Content-Type: text/plain; charset="us-ascii" I earlier posted that Eudora Pro 3.1.1 was returning a Eudora mailbox for each issue of the digest. Thanks to suggestions from Ard Jonker I found a setting that turns off this "feature". Deselect the check box Special:Settings:"Receive MIME digests as attachments", and the digest appears as text. No further trouble here, and thanks Ard! Glenn ------------------------------ Date: Mon, 20 Jul 1998 13:48:13 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: LUDL MAC2000 (and 2002) controller Message-Id: Content-Type: text/plain; charset="us-ascii" >Does or has anyone got the code for the RS232C driving of a LUDL 2000 >XYZ stage from NIH-IMAGE? >And if so would they like to share it with me? >Otherwise I will have to do it myself. >Thank you. >Noel Goldsmith I have written such code and posted an example macro to the list in April 1997. Below is the macro I sent. As you see, it is pretty straightforward to run this stage using serial commands. I also have some Pascal code with a custom dialog. Contact me off-list if you are interested in this as well. (I am going on vacation for two weeks from tomorrow morning and will not reply to email until I am back.) >To: nih-image@soils.umn.edu >From: steinr@kjemi.unit.no (Stein Roervik) >Subject: Ludl Macro > >Below is a general macro to run the Ludl focus controller. >It only includes a few basic example functions: >Do autofocus, read position and move to position. >All other functions follow the same syntax, so this >macro should be easy to modify. Read the manual. >The macro requires NIH image 1.60 or higher. > >First press [F1] to verify that the communication is working. >The reply should read ":A ". Then press [F4] to initialize the unit, >[f] to do focus or [m] to move to a given position. > macro 'test serial [F1]'; var CommandString, ReplyChar, ReplyString: string; begin OpenSerial('9600 baud, no parity, eight data, two stop'); CommandString:= 'window +'; PutSerial(CommandString,chr(13)); wait(0.1); ReplyString := ''; repeat ReplyChar:= GetSerial; ReplyString := concat(ReplyString, ReplyChar); until ReplyChar = ''; ShowMessage('Command: "',CommandString,'"\', 'Reply: "',ReplyString,'"'); end; macro 'reset serial [F2]'; begin OpenSerial('9600 baud, no parity, eight data, two stop'); PutSerial(chr(255),chr(82)); {reset Ludl device} wait(10); { it takes approx. 9.6 seconds until Ludl device is reset } beep; end; macro 'flush serial input buffer [F3]'; var i: integer; ch, str: string; begin str:= ''; i:= 0; repeat i:= i+1; ch:= GetSerial; str:= concat(str,ch); until ch=''; ShowMessage('Buffer: "',str,'"'); end; function GetLudlValue(CommandString: string): real; var ReplyChar, ReplyString: string; begin PutSerial(CommandString,chr(13)); wait(0.1); ReplyString := ''; repeat ReplyChar:= GetSerial; ReplyString := concat(ReplyString, ReplyChar); until ReplyChar = ''; ShowMessage('Ludl request "',CommandString,'"\', 'Ludl response "',ReplyString,'"'); GetLudlValue:= StringToNum(ReplyString)/100; {100 steps in a micron} end; procedure SendLudlCommand(CommandString: string); var ReplyChar, ReplyString: string; begin PutSerial(CommandString,chr(13)); wait(0.1); ReplyString := ''; repeat ReplyChar:= GetSerial; ReplyString := concat(ReplyString, ReplyChar); until ReplyChar = ''; ShowMessage('Ludl command "',CommandString,'"\', 'Ludl response "',ReplyString,'"'); end; macro 'init focus driver [F4]'; begin OpenSerial('9600 baud, no parity, eight data, two stop'); SendLudlCommand('window +'); SendLudlCommand('speed F=5000'); SendLudlCommand('here F=0'); end; macro 'do AutoFocus [f]'; begin SendLudlCommand('focus'); end; macro 'do MovePosition [m]'; var Position: real; begin Position:= GetNumber('Move to new position:',GetLudlValue('where F')); SendLudlCommand(concat('move F =',round(Position*100))); end; +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Mon, 20 Jul 1998 15:21:42 +0000 From: "Samu Ruuhonen" To: nih-image@io.ece.drexel.edu Subject: AutoThreshold -algorithm? Message-ID: <1E2C698500A@nippi.hut.fi> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT I am using ImagePC for thresholding graylevel images taken from a paper surface. Does anybody know what is the algorithm that "AutoThreshold" -macro command uses to calculate the correct threshold value? Thank you, Samu Ruuhonen Research assist in Helsinki University of Technology Laboratory of Media Technology ------------------------------ Date: Mon, 20 Jul 1998 09:05:35 -0500 From: Tom Morton To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #13 Message-Id: Content-Type: text/plain; charset="us-ascii" Hello, Try holding down the Shift key while invoking Scion Image. This should bypass the detection of the Scion frame grabbers and then alow detection of the AV board. Tom > >Dear list Members, > >I posted the enclosed question a few days ago. Though no one replied, I >managed to find the answer myself. If anyone else has the same problem, >the answer is to hold down the SHIFT key when opening IMAGE. Doing so >selects the internal frame grabber. > >Mike Smith > >>>> "Mike Smith" 07/15 3:12 pm >>> >Dear List Members, > >I have a PowerMac with a built-in frame grabber (low quality). Recently, I >installed a Scion frame grabber. Now I cannot seem to access the built-in >frame grabber from NIH-Image. Is there a way to do this, or must I >ununstall the Scion board? > >Mike Smith ----------------------------------------------------------------------- Tom Morton support@scioncorp.com Technical Services http://www.scioncorp.com Scion Corporation ftp://scioncorp.com 82 Wormans Mill Rd., Suite H Phone: (301) 695-7870 Frederick, MD 21701 Fax: (301) 695-0035 ----------------------------------------------------------------------- ------------------------------ Date: Mon, 20 Jul 1998 09:00:46 -0700 From: Jon Goerke To: nih-image@io.ece.drexel.edu Subject: Re: Digest Form Message-Id: Content-Type: text/plain; charset="us-ascii" Four posts to the list have been somewhat critical of the new Digest Form and its interactions with Eudora. The basic problem is that it automatically inserts new Image Digest mailboxes in the Eudora Menu. Since my own complaint was posted, however, I've developed a workaround that seems fairly painless -- and it no longer requires a trip to Menu/Window/Mailboxes to implement. I filter each digest into a mailbox as previously ( "from" contains "NIH-Image" into the mailbox). Clicking on the new message line appearing in the NIH-Image mailbox window opens a new-appearing Digest Window containing an Icon indicating an attached file. Clicking on this Icon opens the Digest headed by the ????? index entry. I click on the topics I want to see, and then use Menu/Delete to trash what I don't want to save for future reference, all the way back through the Digest itself. A singular advantage to the new scheme is that I can save individual posts directly and easily. The old Digest system required selecting, copying, opening Simple Text or Word, pasting, and saving. What appeared to be residual new mailboxes in Menu/Mailbox, even after Menu/Special/Empty Trash, had disappeared when the Mac System was next booted. I'm using Eudora 4.0, but I doubt that the described behavior is specific to this version. Put me down for maintaining the current Digest form please. Jon _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Jon Goerke, MD EMail: goerke@itsa.ucsf.edu Prof. Physiology, Univ. Calif. Phone: 415-476-3252 3333 California St., Suite 150, San Francisco, CA 94118 _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ ------------------------------ Date: Mon, 20 Jul 1998 12:33:50 -0500 (EST) From: Tim Steffens To: nih-image@io.ece.drexel.edu Subject: Test just delete Message-Id: Content-Type: text/plain; charset="us-ascii" just delete this message. Tim Steffens, CRA Indiana University Medical Center tsteffen@iupui.edu ------------------------------ Date: Mon, 20 Jul 1998 14:38:59 -0700 From: "Michael A. Richardson, M.D." To: nih-image@io.ece.drexel.edu Subject: NIH Image for the MAC Message-Id: Content-Type: text/plain; charset="us-ascii" Ladies and Gentlemen: Where can I obtain a copy of NIH image for the MAC (PPC, system 8.1)? Michael A. Richardson, M.D. FCAP Department of Laboratory Medicine Saint Francis Medical Center 601 East Micheltorena Street Santa Barbara, California 93103 (805) 568-5743 (805) 568-5742 drtoad@silcom.com -------------------------------- End of nih-image-d Digest V98 Issue #15 *************************************** From nih-image-request@io.ece.drexel.edu Mon Jul 20 17:49 EDT 1998 X-UIDL: 31b1d01801e9cbc8a6dc1720b9148ebd Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA24408; Mon, 20 Jul 1998 17:48:03 -0400 (EDT) Resent-Date: Mon, 20 Jul 1998 17:48:03 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Mon, 20 Jul 1998 14:38:59 -0700 To: nih-image@io.ece.drexel.edu From: "Michael A. Richardson, M.D." Subject: NIH Image for the MAC Resent-Message-ID: <"_vp9l3.0.Ig5.8Zxir"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/76 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 303 Status: RO Ladies and Gentlemen: Where can I obtain a copy of NIH image for the MAC (PPC, system 8.1)? Michael A. Richardson, M.D. FCAP Department of Laboratory Medicine Saint Francis Medical Center 601 East Micheltorena Street Santa Barbara, California 93103 (805) 568-5743 (805) 568-5742 drtoad@silcom.com From nih-image-request@io.ece.drexel.edu Mon Jul 20 18:05 EDT 1998 X-UIDL: fbfb7683c646855935ea90644c51a656 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA26146; Mon, 20 Jul 1998 18:04:57 -0400 (EDT) Resent-Date: Mon, 20 Jul 1998 18:04:57 -0400 (EDT) X-Authentication-Warning: rac6.wam.umd.edu: jgthomas owned process doing -bs Date: Mon, 20 Jul 1998 17:53:27 -0400 (EDT) From: Jim G Thomas Reply-To: Jim G Thomas To: nih-image@io.ece.drexel.edu Subject: movie help Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"fqspj3.0.m76.Tnxir"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/77 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 570 Status: RO Hi. I have a power mac 7600 with 32meg ram. I am running NIH image 1.61 with around 19meg allocated towards it. My problem is that I can make standard movies just fine when I have the picture size at 1/4 (in Video Control). If I increase the picture size to 1/2 or full-size I can still see what is being captured, though it is quite slow. But when I try to make a movie, all I get is a black window and hence a black movie. Any ideas? Is this just a memory problem? Or I am not properly configured. I do not have scion, if that makes a difference. jim thomas From nih-image-request@io.ece.drexel.edu Tue Jul 21 06:16 EDT 1998 X-UIDL: 1069b4ac27d06819a8b42f0fe81345f4 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA01865; Tue, 21 Jul 1998 06:16:14 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 06:16:14 -0400 (EDT) X-Sender: cesc@cucafera Message-Id: Mime-Version: 1.0 Date: Tue, 21 Jul 1998 11:59:30 +0200 To: support@scioncorp.com, nih-image@io.ece.drexel.edu From: Francesc Peters Subject: help with LG-3 Resent-Message-ID: <"8OVXH2.0.D8.oT6jr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/78 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1178 Status: RO Hi, We just bought an LG-3 and installed it in a new PowerMac G3 (desktop) running MacOS 8.0. We installed the ScionImage1.62a provided. The computer seems to recognize the board fine since we have connected a video to the board and can capture images without problems. But we can not get to the settings under File: Acquire to change the grab size and all the other feature we were used to with the built in boards from apple on other computers. It keeps saying that there is no quicktime compatible video and that we need the correct vdig file. I do hold down the shift key to get to the settings. Do we need to upgrade soft? Put a special plug-in digitizer from Scion? Take out the other plug-in digitizer or upgrade it (currently using 1.2.4)? Upgrade to MacOS8.1? Thanks for your help. ****************************************************************** PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!! Francesc Peters FAX: 34-93-221-7340 Institut de Ciencies del Mar (CSIC) Phone: 34-93-221-6416 (Ext. 255) Passeig Joan de Borbo s/n cesc@icm.csic.es E-08039 Barcelona, Catalunya Spain From nih-image-request@io.ece.drexel.edu Tue Jul 21 06:51 EDT 1998 X-UIDL: fc45933225280d8606e67e2dd60d7d60 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA05401; Tue, 21 Jul 1998 06:51:49 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 06:51:49 -0400 (EDT) Message-Id: <3.0.1.32.19980721063939.00772da0@med.wayne.edu> X-Sender: baberko@med.wayne.edu X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Tue, 21 Jul 1998 06:39:39 -0400 To: nih-image@io.ece.drexel.edu From: Bruce Berkowitz Subject: median stack Mime-Version: 1.0 Resent-Message-ID: <"Yye0e.0.H61.f37jr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/79 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 600 Status: RO Hi, Is there a macro around that will calculate and display the pixel by pixel median of a stack of images? My data are not normally distributed so displaying the average is not really right and doesn't reflect the statitisics I have to do. Thanks! Bruce Berkowitz |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu From nih-image-request@io.ece.drexel.edu Tue Jul 21 07:36 EDT 1998 X-UIDL: 0a387327c761d44878866ed2ebead4a1 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA09785; Tue, 21 Jul 1998 07:36:17 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 07:36:17 -0400 (EDT) X-Sender: cgustafs@ece.drexel.edu Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Tue, 21 Jul 1998 07:27:07 -0400 To: nih-image@io.ece.drexel.edu From: Carl Gustafson Subject: Re: NIH Image for the MAC Resent-Message-ID: <"4RtbW3.0.T42.Jg7jr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/80 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 654 Status: RO >Where can I obtain a copy of NIH image for the MAC (PPC, system 8.1)? ftp://zippy.nimh.nih.gov/pub/nih-image/ Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== From nih-image-request@io.ece.drexel.edu Tue Jul 21 07:38 EDT 1998 X-UIDL: b5c57ad2f684fb8b603aa67437e798ad Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA10047; Tue, 21 Jul 1998 07:38:01 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 07:38:01 -0400 (EDT) X-Sender: cgustafs@ece.drexel.edu Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Tue, 21 Jul 1998 07:30:04 -0400 To: nih-image@io.ece.drexel.edu From: Carl Gustafson Subject: Re: help with LG-3 Resent-Message-ID: <"0ITsD.0.a92.4j7jr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/81 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1394 Status: RO >board and can capture images without problems. But we can not get to the >settings under File: Acquire to change the grab size and all the other >feature we were used to with the built in boards from apple on other >computers. It keeps saying that there is no quicktime compatible video and >that we need the correct vdig file. I do hold down the shift key to get to >the settings. Do we need to upgrade soft? Put a special plug-in digitizer >from Scion? Take out the other plug-in digitizer or upgrade it (currently >using 1.2.4)? Upgrade to MacOS8.1? Unless I am sadly mistaken (could happen), the LG-3 doesn't support this kind of thing, as there is no built-in vdig for it (and there is no low-level support on the board, as I recall). I suppose some intrepid programmer (other than me) could write a vdig, but I doubt it's for the casual coder. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== From nih-image-request@io.ece.drexel.edu Tue Jul 21 08:50 EDT 1998 X-UIDL: 5d0422e6ba64c77386768dae2d70753a Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA16897; Tue, 21 Jul 1998 08:50:41 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 08:50:41 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Tue, 21 Jul 1998 08:44:58 -0400 To: nih-image@io.ece.drexel.edu From: David Milstone Subject: Re: Digest Form Resent-Message-ID: <"5k0OA.0.zt3.pn8jr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/82 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1806 Status: RO I use the same system with Eudora Pro 3.1 and agree that it is an improvement. >Four posts to the list have been somewhat critical of the new Digest Form >and its interactions with Eudora. The basic problem is that it >automatically inserts new Image Digest mailboxes in the Eudora Menu. Since >my own complaint was posted, however, I've developed a workaround that >seems fairly painless -- and it no longer requires a trip to >Menu/Window/Mailboxes to implement. > >I filter each digest into a mailbox as previously ( "from" contains >"NIH-Image" into the mailbox). Clicking on the new message line appearing >in the NIH-Image mailbox window opens a new-appearing Digest Window >containing an Icon indicating an attached file. Clicking on this Icon >opens the Digest headed by the ????? index entry. I click on the topics I >want to see, and then use Menu/Delete to trash what I don't want to save >for future reference, all the way back through the Digest itself. > >A singular advantage to the new scheme is that I can save individual posts >directly and easily. The old Digest system required selecting, copying, >opening Simple Text or Word, pasting, and saving. > >What appeared to be residual new mailboxes in Menu/Mailbox, even after >Menu/Special/Empty Trash, had disappeared when the Mac System was next >booted. > >I'm using Eudora 4.0, but I doubt that the described behavior is specific >to this version. > >Put me down for maintaining the current Digest form please. > >Jon >_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ >Jon Goerke, MD EMail: goerke@itsa.ucsf.edu >Prof. Physiology, Univ. Calif. Phone: 415-476-3252 >3333 California St., Suite 150, San Francisco, CA 94118 >_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From nih-image-request@io.ece.drexel.edu Tue Jul 21 10:59 EDT 1998 X-UIDL: bb3087c9301ea87aa281cc73f82fcdbc Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA28361; Tue, 21 Jul 1998 10:59:24 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 10:59:24 -0400 (EDT) Date: Tue, 21 Jul 1998 07:48:41 -0700 (PDT) From: "R. Hard" To: nih-image@io.ece.drexel.edu Subject: Course Announcement Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"r_QLL3.0.Xc6.JfAjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/83 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2607 Status: RO Course Announcement Title: Optical Microscopy and Imaging in the Biomedical Sciences When: October 7 - October 15, 1998 Where: Marine Biology Laboratory, Woods Hole, MA, USA Tuition: $2050 (Includes room and board) Application Deadline: August 4, 1998 Admission application and information: Carol Harnel, Admissions Coordinator Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543-1015 (508) 289-7401 Internet: admissions@mbl.edu WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat) Course Director: Colin S. Izzard, State University of New York @ Albany Phone: [518] 442 - 4367 EMail: csizzard@csc.albany.edu Course Description: For Whom: Designed primarily for research scientists, physicians, postdoctoral trainees and advanced graduate students in animal, plant, medical and material sciences. Non-biologists seeking a comprehensive introduction to microscopy and video-imaging will benefit greatly from this course as well. There are no specific prerequisites, but an understanding of the basic principles of optics is desirable. Limited to 24 students. The eight day course consists of lectures, laboratory demonstrations, exercises and discussions that will enable the participant to obtain and interpret microscope images of high quality, to perform quantitative optical measurements, and to produce photographic and video records for documentation and analysis. Topics to be covered include: principles of microscope design and image formation bright field, dark field, phase contrast, differential interference contrast, interference reflection, and fluorescence microscopy confocal scanning microscopy and image deconvolution digital image restoration and 3-D reconstruction video imaging, recording, enhancement, and intensification analog and digital image processing and analysis fluorescent probes and ratio-imaging laser tweezers and laser scissors Applications to live cells will be emphasized; other specimens will be covered as well. Students will have direct hands-on experience with state-of-the-art microscopes, video cameras, recorders and image processing equipment provided by major optical and electronics companies. Instruction will be provided by experienced staff from universities and industry. Students are encouraged to bring their own biological (primary cultures, cell lines, etc.) and material specimens and to discuss individual research problems with the faculty. From nih-image-d-request@io.ece.drexel.edu Tue Jul 21 11:05 EDT 1998 X-UIDL: a23ebc6aeffa6dde6992a459c1243d16 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA28869; Tue, 21 Jul 1998 11:05:16 -0400 (EDT) Date: Tue, 21 Jul 1998 11:05:16 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807211505.LAA28869@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #16 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/16 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 11623 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 16 Today's Topics: movie help [ Jim G Thomas ] help with LG-3 [ Francesc Peters ] ------------------------------ Date: Mon, 20 Jul 1998 17:53:27 -0400 (EDT) From: Jim G Thomas To: nih-image@io.ece.drexel.edu Subject: movie help Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi. I have a power mac 7600 with 32meg ram. I am running NIH image 1.61 with around 19meg allocated towards it. My problem is that I can make standard movies just fine when I have the picture size at 1/4 (in Video Control). If I increase the picture size to 1/2 or full-size I can still see what is being captured, though it is quite slow. But when I try to make a movie, all I get is a black window and hence a black movie. Any ideas? Is this just a memory problem? Or I am not properly configured. I do not have scion, if that makes a difference. jim thomas ------------------------------ Date: Tue, 21 Jul 1998 11:59:30 +0200 From: Francesc Peters To: support@scioncorp.com, nih-image@io.ece.drexel.edu Subject: help with LG-3 Message-Id: Content-Type: text/plain; charset="us-ascii" Hi, We just bought an LG-3 and installed it in a new PowerMac G3 (desktop) running MacOS 8.0. We installed the ScionImage1.62a provided. The computer seems to recognize the board fine since we have connected a video to the board and can capture images without problems. But we can not get to the settings under File: Acquire to change the grab size and all the other feature we were used to with the built in boards from apple on other computers. It keeps saying that there is no quicktime compatible video and that we need the correct vdig file. I do hold down the shift key to get to the settings. Do we need to upgrade soft? Put a special plug-in digitizer from Scion? Take out the other plug-in digitizer or upgrade it (currently using 1.2.4)? Upgrade to MacOS8.1? Thanks for your help. ****************************************************************** PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!! Francesc Peters FAX: 34-93-221-7340 Institut de Ciencies del Mar (CSIC) Phone: 34-93-221-6416 (Ext. 255) Passeig Joan de Borbo s/n cesc@icm.csic.es E-08039 Barcelona, Catalunya Spain ------------------------------ Date: Tue, 21 Jul 1998 06:39:39 -0400 From: Bruce Berkowitz To: nih-image@io.ece.drexel.edu Subject: median stack Message-Id: <3.0.1.32.19980721063939.00772da0@med.wayne.edu> Content-Type: text/plain; charset="us-ascii" Hi, Is there a macro around that will calculate and display the pixel by pixel median of a stack of images? My data are not normally distributed so displaying the average is not really right and doesn't reflect the statitisics I have to do. Thanks! Bruce Berkowitz |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu ------------------------------ Date: Tue, 21 Jul 1998 07:27:07 -0400 From: Carl Gustafson To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image for the MAC Message-Id: Content-Type: text/plain; charset="us-ascii" >Where can I obtain a copy of NIH image for the MAC (PPC, system 8.1)? ftp://zippy.nimh.nih.gov/pub/nih-image/ Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== ------------------------------ Date: Tue, 21 Jul 1998 07:30:04 -0400 From: Carl Gustafson To: nih-image@io.ece.drexel.edu Subject: Re: help with LG-3 Message-Id: Content-Type: text/plain; charset="us-ascii" >board and can capture images without problems. But we can not get to the >settings under File: Acquire to change the grab size and all the other >feature we were used to with the built in boards from apple on other >computers. It keeps saying that there is no quicktime compatible video and >that we need the correct vdig file. I do hold down the shift key to get to >the settings. Do we need to upgrade soft? Put a special plug-in digitizer >from Scion? Take out the other plug-in digitizer or upgrade it (currently >using 1.2.4)? Upgrade to MacOS8.1? Unless I am sadly mistaken (could happen), the LG-3 doesn't support this kind of thing, as there is no built-in vdig for it (and there is no low-level support on the board, as I recall). I suppose some intrepid programmer (other than me) could write a vdig, but I doubt it's for the casual coder. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== ------------------------------ Date: Tue, 21 Jul 1998 08:44:58 -0400 From: David Milstone To: nih-image@io.ece.drexel.edu Subject: Re: Digest Form Message-Id: Content-Type: text/plain; charset="us-ascii" I use the same system with Eudora Pro 3.1 and agree that it is an improvement. >Four posts to the list have been somewhat critical of the new Digest Form >and its interactions with Eudora. The basic problem is that it >automatically inserts new Image Digest mailboxes in the Eudora Menu. Since >my own complaint was posted, however, I've developed a workaround that >seems fairly painless -- and it no longer requires a trip to >Menu/Window/Mailboxes to implement. > >I filter each digest into a mailbox as previously ( "from" contains >"NIH-Image" into the mailbox). Clicking on the new message line appearing >in the NIH-Image mailbox window opens a new-appearing Digest Window >containing an Icon indicating an attached file. Clicking on this Icon >opens the Digest headed by the ????? index entry. I click on the topics I >want to see, and then use Menu/Delete to trash what I don't want to save >for future reference, all the way back through the Digest itself. > >A singular advantage to the new scheme is that I can save individual posts >directly and easily. The old Digest system required selecting, copying, >opening Simple Text or Word, pasting, and saving. > >What appeared to be residual new mailboxes in Menu/Mailbox, even after >Menu/Special/Empty Trash, had disappeared when the Mac System was next >booted. > >I'm using Eudora 4.0, but I doubt that the described behavior is specific >to this version. > >Put me down for maintaining the current Digest form please. > >Jon >_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ >Jon Goerke, MD EMail: goerke@itsa.ucsf.edu >Prof. Physiology, Univ. Calif. Phone: 415-476-3252 >3333 California St., Suite 150, San Francisco, CA 94118 >_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ ------------------------------ Date: Tue, 21 Jul 1998 07:48:41 -0700 (PDT) From: "R. Hard" To: nih-image@io.ece.drexel.edu Subject: Course Announcement Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Course Announcement Title: Optical Microscopy and Imaging in the Biomedical Sciences When: October 7 - October 15, 1998 Where: Marine Biology Laboratory, Woods Hole, MA, USA Tuition: $2050 (Includes room and board) Application Deadline: August 4, 1998 Admission application and information: Carol Harnel, Admissions Coordinator Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543-1015 (508) 289-7401 Internet: admissions@mbl.edu WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat) Course Director: Colin S. Izzard, State University of New York @ Albany Phone: [518] 442 - 4367 EMail: csizzard@csc.albany.edu Course Description: For Whom: Designed primarily for research scientists, physicians, postdoctoral trainees and advanced graduate students in animal, plant, medical and material sciences. Non-biologists seeking a comprehensive introduction to microscopy and video-imaging will benefit greatly from this course as well. There are no specific prerequisites, but an understanding of the basic principles of optics is desirable. Limited to 24 students. The eight day course consists of lectures, laboratory demonstrations, exercises and discussions that will enable the participant to obtain and interpret microscope images of high quality, to perform quantitative optical measurements, and to produce photographic and video records for documentation and analysis. Topics to be covered include: principles of microscope design and image formation bright field, dark field, phase contrast, differential interference contrast, interference reflection, and fluorescence microscopy confocal scanning microscopy and image deconvolution digital image restoration and 3-D reconstruction video imaging, recording, enhancement, and intensification analog and digital image processing and analysis fluorescent probes and ratio-imaging laser tweezers and laser scissors Applications to live cells will be emphasized; other specimens will be covered as well. Students will have direct hands-on experience with state-of-the-art microscopes, video cameras, recorders and image processing equipment provided by major optical and electronics companies. Instruction will be provided by experienced staff from universities and industry. Students are encouraged to bring their own biological (primary cultures, cell lines, etc.) and material specimens and to discuss individual research problems with the faculty. -------------------------------- End of nih-image-d Digest V98 Issue #16 *************************************** From nih-image-request@io.ece.drexel.edu Tue Jul 21 11:17 EDT 1998 X-UIDL: c8ea1d9360d367b1e561ee212ba2893b Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA00065; Tue, 21 Jul 1998 11:16:34 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 11:16:34 -0400 (EDT) Mime-Version: 1.0 X-Sender: rwadkins@wwwctrc.fs.saci.org Message-Id: In-Reply-To: <199807211449.KAA27112@io.ECE.Drexel.EDU> Date: Tue, 21 Jul 1998 10:12:13 -0700 To: nih-image@io.ece.drexel.edu From: "Randy M. Wadkins" Subject: Re: Eudora users Resent-Message-ID: <"BOTU81.0.r37.CvAjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/84 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1442 Status: RO As someone else pointed out, if you want the mailbox of individual files, check the box in the Settings->Attachments box that says "receive MIME digests as attachments". If you want the old, single message digest, uncheck this box. --Randy > >------------------------------ >Date: Tue, 21 Jul 1998 08:44:58 -0400 >From: David Milstone >To: nih-image@io.ece.drexel.edu >Subject: Re: Digest Form >Message-Id: >Content-Type: text/plain; charset="us-ascii" > >I use the same system with Eudora Pro 3.1 and agree that it is an improvement. > >>Four posts to the list have been somewhat critical of the new Digest Form >>and its interactions with Eudora. The basic problem is that it >>automatically inserts new Image Digest mailboxes in the Eudora Menu. Since >>my own complaint was posted, however, I've developed a workaround that >>seems fairly painless -- and it no longer requires a trip to >>Menu/Window/Mailboxes to implement. ****************************************************************** "To be or not to...beeeeeeeeeeeeeee" --Hamlet vs. Godzilla Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** From nih-image-request@io.ece.drexel.edu Tue Jul 21 12:23 EDT 1998 X-UIDL: 97261e513ce8e026dc02f90e9e002ce2 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA05137; Tue, 21 Jul 1998 12:23:17 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 12:23:17 -0400 (EDT) From: "Evdokia Achilleos" Message-Id: <9807211156.ZM7001@chavi> Date: Tue, 21 Jul 1998 11:56:24 -0400 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: nih-image@io.ece.drexel.edu Subject: Plug-in,Unsharp,and set origin Mime-Version: 1.0 Resent-Message-ID: <"yJk6e1.0.S01.lsBjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/85 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 517 Status: RO I have downloaded nih 1.62 beta Version and have a couple of questions 1. I can not ge the plug ins to work - even if i place plug ins in the nih.Image folder , I get ``no plug ins '' when I go to the aquire submenu Is there something ``extra'' I need to do? 2. Is there a plug-in available for the photoshop unsharp mask filter (or an equivalent way of doing it) in NIH 3. Can I change my origin from the lower left corner to some known x,y? Thanks in advance Evie Achilleos -- Evdokia Achilleos From nih-image-request@io.ece.drexel.edu Tue Jul 21 14:13 EDT 1998 X-UIDL: b961840df53f57de469428786cf5660c Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA12983; Tue, 21 Jul 1998 14:12:40 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 14:12:40 -0400 (EDT) Message-ID: <35B4D6EA.D176103D@biomail.ucsd.edu> Date: Tue, 21 Jul 1998 10:59:06 -0700 From: Jamie Eisenhart Organization: University of California, San Diego X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: median stack References: <3.0.1.32.19980721063939.00772da0@med.wayne.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"T9a3S.0.gu2.mRDjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/86 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1038 Status: RO Hi Bruce, It sounds like you want to run a median filter on each slice of the stack. That will calculate the median of each pixel within a 3x3 window. You could try: macro '2D Median Filter'; var i, n: integer; begin n := nSlices; for i := 1 to n do begin chooseSlice(i); filter('median'); end; end Jamie Eisenhart UCSD Neuroscience Bruce Berkowitz wrote: > > Hi, > > Is there a macro around that will calculate and display the pixel by pixel > median of a stack of images? My data are not normally distributed so > displaying the average is not really right and doesn't reflect the > statitisics I have to do. > > Thanks! > > Bruce Berkowitz > |-------------------------------------------| > |Berkowitz Lab Home Page: http://146.9.7.69 | > |-------------------------------------------| > > Bruce Berkowitz, Ph.D. > Department of Anatomy and Cell Biology > Wayne State Univeristy > 540 E. Canfield > Detroit, MI 48201 > > Phone: (313) 577-9035 > FAX: (313) 577-3125 > E-mail: baberko@med.wayne.edu From nih-image-request@io.ece.drexel.edu Tue Jul 21 14:31 EDT 1998 X-UIDL: cc9870e7d8803675ff5c7ce33ca50d1c Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA14578; Tue, 21 Jul 1998 14:31:02 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 14:31:02 -0400 (EDT) Message-Id: <3.0.1.32.19980721141257.0077ba6c@med.wayne.edu> X-Sender: baberko@med.wayne.edu X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Tue, 21 Jul 1998 14:12:57 -0400 To: nih-image@io.ece.drexel.edu From: Bruce Berkowitz Subject: Re: median stack In-Reply-To: <35B4D6EA.D176103D@biomail.ucsd.edu> References: <3.0.1.32.19980721063939.00772da0@med.wayne.edu> Mime-Version: 1.0 Resent-Message-ID: <"WbbF43.0.9H3.eiDjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/87 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1717 Status: RO Hi, Thank you for your response but I don't think that was what I was looking for. Because my data are not normally distributed I would like to calculate a median image from a stack of 10 images INSTEAD of calculating one average image of that stack. Bruce At 10:59 AM 7/21/98 -0700, you wrote: >Hi Bruce, > >It sounds like you want to run a median filter on each slice of the stack. That >will calculate the median of each pixel within a 3x3 window. You could try: > >macro '2D Median Filter'; >var > i, n: integer; >begin > n := nSlices; > for i := 1 to n do begin > chooseSlice(i); > filter('median'); > end; >end > >Jamie Eisenhart >UCSD Neuroscience > >Bruce Berkowitz wrote: >> >> Hi, >> >> Is there a macro around that will calculate and display the pixel by pixel >> median of a stack of images? My data are not normally distributed so >> displaying the average is not really right and doesn't reflect the >> statitisics I have to do. >> >> Thanks! >> >> Bruce Berkowitz >> |-------------------------------------------| >> |Berkowitz Lab Home Page: http://146.9.7.69 | >> |-------------------------------------------| >> >> Bruce Berkowitz, Ph.D. >> Department of Anatomy and Cell Biology >> Wayne State Univeristy >> 540 E. Canfield >> Detroit, MI 48201 >> >> Phone: (313) 577-9035 >> FAX: (313) 577-3125 >> E-mail: baberko@med.wayne.edu > > |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu From nih-image-request@io.ece.drexel.edu Tue Jul 21 14:59 EDT 1998 X-UIDL: 699ca17e54aef428543d0730e84d2598 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA16626; Tue, 21 Jul 1998 14:58:58 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 14:58:58 -0400 (EDT) Date: Tue, 21 Jul 1998 14:50:07 -0400 (EDT) From: Kanu P Singh To: nih-image@io.ece.drexel.edu Subject: VOID SIZE MEASUREMENT IN POLYMERS Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"8vXi32.0.ru3.ZBEjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/88 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 802 Status: RO Hi! I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem that I am facing is that the boundaries of my voids are clear in the micrographs, but the inside of the voids is the same as the rest of the image. When I threshold the Images the boundaries appear as white while all the rest of the image appears black. I have no idea of how to get the void fraction or the sizes of these voids. One option that I have is to outline each void by hand and measure the major and minor axes of the closest ellipses (the voids are all nearly spherical). This is a very time consuming process since I have a lot of micrographs to analyze. I would apreciate any ideas that anyone might have to help me out. -Kanu From nih-image-request@io.ece.drexel.edu Tue Jul 21 15:21 EDT 1998 X-UIDL: f4a8e913a5ae0dd4c9f5b48d5b717a4a Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA18260; Tue, 21 Jul 1998 15:20:31 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 15:20:31 -0400 (EDT) Message-ID: <35B4E776.A54349A8@biomail.ucsd.edu> Date: Tue, 21 Jul 1998 12:09:42 -0700 From: Jamie Eisenhart Organization: University of California, San Diego X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: median stack References: <3.0.1.32.19980721063939.00772da0@med.wayne.edu> <3.0.1.32.19980721141257.0077ba6c@med.wayne.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"7oy53.0._F4.-TEjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/89 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2035 Status: RO Ah, that is different and would be hard to do efficiently in Image. I do have a Matlab macro that would do what you want, if that would help. Jamie Bruce Berkowitz wrote: > > Hi, > > Thank you for your response but I don't think that was what I was looking > for. Because my data are not normally distributed I would like to calculate > a median image from a stack of 10 images INSTEAD of calculating one average > image of that stack. > > Bruce > > At 10:59 AM 7/21/98 -0700, you wrote: > >Hi Bruce, > > > >It sounds like you want to run a median filter on each slice of the stack. > That > >will calculate the median of each pixel within a 3x3 window. You could try: > > > >macro '2D Median Filter'; > >var > > i, n: integer; > >begin > > n := nSlices; > > for i := 1 to n do begin > > chooseSlice(i); > > filter('median'); > > end; > >end > > > >Jamie Eisenhart > >UCSD Neuroscience > > > >Bruce Berkowitz wrote: > >> > >> Hi, > >> > >> Is there a macro around that will calculate and display the pixel by pixel > >> median of a stack of images? My data are not normally distributed so > >> displaying the average is not really right and doesn't reflect the > >> statitisics I have to do. > >> > >> Thanks! > >> > >> Bruce Berkowitz > >> |-------------------------------------------| > >> |Berkowitz Lab Home Page: http://146.9.7.69 | > >> |-------------------------------------------| > >> > >> Bruce Berkowitz, Ph.D. > >> Department of Anatomy and Cell Biology > >> Wayne State Univeristy > >> 540 E. Canfield > >> Detroit, MI 48201 > >> > >> Phone: (313) 577-9035 > >> FAX: (313) 577-3125 > >> E-mail: baberko@med.wayne.edu > > > > > |-------------------------------------------| > |Berkowitz Lab Home Page: http://146.9.7.69 | > |-------------------------------------------| > > Bruce Berkowitz, Ph.D. > Department of Anatomy and Cell Biology > Wayne State Univeristy > 540 E. Canfield > Detroit, MI 48201 > > Phone: (313) 577-9035 > FAX: (313) 577-3125 > E-mail: baberko@med.wayne.edu From nih-image-request@io.ece.drexel.edu Tue Jul 21 15:26 EDT 1998 X-UIDL: 68062a1c8e0c1897da94d055fc62fc9d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA18648; Tue, 21 Jul 1998 15:25:57 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 15:25:57 -0400 (EDT) X-Sender: cgustafs@ece.drexel.edu Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Tue, 21 Jul 1998 15:14:34 -0400 To: nih-image@io.ece.drexel.edu From: Carl Gustafson Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS Resent-Message-ID: <"CMtac3.0.hJ4.ZWEjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/90 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1141 Status: RO >I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of >hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem >that I am facing is that the boundaries of my voids are clear in the >micrographs, but the inside of the voids is the same as the rest of the >image. When I threshold the Images the boundaries appear as white while >all the rest of the image appears black. I have no idea of how to get the >void fraction or the sizes of these voids. Can you invert the image, and do an Analyse Particles on the image, which should now be light, with dark rings? Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== From nih-image-request@io.ece.drexel.edu Tue Jul 21 15:45 EDT 1998 X-UIDL: 53180b9bf11a44b03819c77853c725ee Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA19752; Tue, 21 Jul 1998 15:45:07 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 15:45:07 -0400 (EDT) Message-Id: <3.0.1.32.19980721153149.00774140@med.wayne.edu> X-Sender: baberko@med.wayne.edu X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Tue, 21 Jul 1998 15:31:49 -0400 To: nih-image@io.ece.drexel.edu From: Bruce Berkowitz Subject: Re: median stack In-Reply-To: <35B4E776.A54349A8@biomail.ucsd.edu> References: <3.0.1.32.19980721063939.00772da0@med.wayne.edu> <3.0.1.32.19980721141257.0077ba6c@med.wayne.edu> Mime-Version: 1.0 Resent-Message-ID: <"9tNqL1.0.0h4.fsEjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/91 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2661 Status: RO You imply that it could be done. I don't mind if its not efficient. Any suggestions? Yes, please send the Matlab macro along if you don't mind. Thank you again for your time. At 12:09 PM 7/21/98 -0700, you wrote: >Ah, that is different and would be hard to do efficiently in Image. I do have a >Matlab macro that would do what you want, if that would help. > >Jamie > >Bruce Berkowitz wrote: >> >> Hi, >> >> Thank you for your response but I don't think that was what I was looking >> for. Because my data are not normally distributed I would like to calculate >> a median image from a stack of 10 images INSTEAD of calculating one average >> image of that stack. >> >> Bruce >> >> At 10:59 AM 7/21/98 -0700, you wrote: >> >Hi Bruce, >> > >> >It sounds like you want to run a median filter on each slice of the stack. >> That >> >will calculate the median of each pixel within a 3x3 window. You could try: >> > >> >macro '2D Median Filter'; >> >var >> > i, n: integer; >> >begin >> > n := nSlices; >> > for i := 1 to n do begin >> > chooseSlice(i); >> > filter('median'); >> > end; >> >end >> > >> >Jamie Eisenhart >> >UCSD Neuroscience >> > >> >Bruce Berkowitz wrote: >> >> >> >> Hi, >> >> >> >> Is there a macro around that will calculate and display the pixel by pixel >> >> median of a stack of images? My data are not normally distributed so >> >> displaying the average is not really right and doesn't reflect the >> >> statitisics I have to do. >> >> >> >> Thanks! >> >> >> >> Bruce Berkowitz >> >> |-------------------------------------------| >> >> |Berkowitz Lab Home Page: http://146.9.7.69 | >> >> |-------------------------------------------| >> >> >> >> Bruce Berkowitz, Ph.D. >> >> Department of Anatomy and Cell Biology >> >> Wayne State Univeristy >> >> 540 E. Canfield >> >> Detroit, MI 48201 >> >> >> >> Phone: (313) 577-9035 >> >> FAX: (313) 577-3125 >> >> E-mail: baberko@med.wayne.edu >> > >> > >> |-------------------------------------------| >> |Berkowitz Lab Home Page: http://146.9.7.69 | >> |-------------------------------------------| >> >> Bruce Berkowitz, Ph.D. >> Department of Anatomy and Cell Biology >> Wayne State Univeristy >> 540 E. Canfield >> Detroit, MI 48201 >> >> Phone: (313) 577-9035 >> FAX: (313) 577-3125 >> E-mail: baberko@med.wayne.edu > > |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu From nih-image-request@io.ece.drexel.edu Tue Jul 21 16:08 EDT 1998 X-UIDL: 0e4c993433b2fff293d98772201ed4fd Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA21353; Tue, 21 Jul 1998 16:08:33 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 16:08:33 -0400 (EDT) From: Alex_Courtade@huntsman.com Mime-Version: 1.0 Date: Tue, 21 Jul 1998 14:48:35 -0500 Message-ID: <0000665B.CE21466@huntsman.com> Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS To: nih-image@io.ece.drexel.edu Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Resent-Message-ID: <"WLMea1.0.w_4.MAFjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/92 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1475 Status: RO If your image is clean, perhaps you could threshold the image as normal, and instead of highlighting the individual voids with the wand, you could highlight the "black" area of the photo (the area of the whole photo, minus the void area.) Then you could take the area of the entire image and subtract the "black" area, leaving you with the area of your voids. Again, I don't have a detailed description of your images, so I don't know whether this will work, but it's worth a shot. ----- Alex Courtade ____________________Reply Separator____________________ Subject: VOID SIZE MEASUREMENT IN POLYMERS Author: Kanu P Singh Date: 7/21/98 2:50 PM Hi! I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem that I am facing is that the boundaries of my voids are clear in the micrographs, but the inside of the voids is the same as the rest of the image. When I threshold the Images the boundaries appear as white while all the rest of the image appears black. I have no idea of how to get the void fraction or the sizes of these voids. One option that I have is to outline each void by hand and measure the major and minor axes of the closest ellipses (the voids are all nearly spherical). This is a very time consuming process since I have a lot of micrographs to analyze. I would apreciate any ideas that anyone might have to help me out. -Kanu From nih-image-request@io.ece.drexel.edu Tue Jul 21 16:29 EDT 1998 X-UIDL: 065741b4d0a54960e63eed09bb37ecfe Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA22971; Tue, 21 Jul 1998 16:29:11 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 16:29:11 -0400 (EDT) From: DrJohnRuss@aol.com Message-ID: <6f909b7b.35b4f741@aol.com> Date: Tue, 21 Jul 1998 16:17:04 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Re: median stack Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"Br-R03.0.-M5.gTFjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/93 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 824 Status: RO In a message dated 7/21/98 6:33:18 PM, you wrote: >Thank you for your response but I don't think that was what I was looking >for. Because my data are not normally distributed I would like to calculate >a median image from a stack of 10 images INSTEAD of calculating one average >image of that stack. I think you need to define what you want, and the answer may then be obvious. for instance do you want to take the pixel values at each x,y location from all 10 images and find the median value, and repeat this for all pixels? That doesn't sound like a median image to me, but if that is what you want then it is easy (but slow) to do. You will have to use a sort procedure in your macro to get the median (and then since you have an even number of images will have to probably average the 5th and 6th ranked values). From nih-image-request@io.ece.drexel.edu Tue Jul 21 16:33 EDT 1998 X-UIDL: 424f9e38db634aff4488d39f2c98061c Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA23350; Tue, 21 Jul 1998 16:32:55 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 16:32:55 -0400 (EDT) From: "Grace,John" To: Subject: Sum of Values in particle analysis Message-Id: <0055600001401889000002L092*@MHS> Date: Tue, 21 Jul 1998 15:24:36 -0500 Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id QAA22403 Resent-Message-ID: <"WZiKW1.0.GU5.LZFjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/94 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-1 Content-Length: 394 Status: RO Dear imagers, I am trying to find the amount of ink in spots printed on a card, I also want the degree of variation/uniformity of the coating of these spots. I have been thresholding the spot then using the analyze particles command I am getting the mean intensity, SD and area of the spot. Is there a way to get the sum of pixel values in the spot? Thanks, John P. Grace Abbott Laboratories From nih-image-request@io.ece.drexel.edu Tue Jul 21 17:58 EDT 1998 X-UIDL: 8fdc7506bc79c4bce30dd6d3f1326a63 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA28720; Tue, 21 Jul 1998 17:58:06 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 17:58:06 -0400 (EDT) Date: Tue, 21 Jul 1998 17:48:15 -0400 From: Xudong Cao X-Sender: xudong@chem-eng To: nih-image@io.ece.drexel.edu Subject: Image density?? Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"mSC-T3.0.4r6.noGjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/95 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 894 Status: RO Hi there, I am trying to evaluate the concentration of my fluorescin labeled protein in gels by determining the optic density of the fluorescence under the microscope by NIH image analysis software. My question is whether the pixels that are represented by the 8-bit integers are in a linear relationship, say value 1 represents as twice intensity as that of value 2? and how about value 0 (the white color)? I would highly appreciate any help from you in this regard. thanks. Sincerely, _______________________________ Xudong CAO Center for Biomaterials University of Toronto Phone: (416) 978 0343 Fax: (416) 978 1462 In science one tries to tell people, in such a way as to be understood by everyone, something that no one ever knew before. But in poetry, it's the exact opposite. - Paul Dirac From nih-image-request@io.ece.drexel.edu Tue Jul 21 18:41 EDT 1998 X-UIDL: e4c6347c8ef636bdd8f123c15c1057bc Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA01722; Tue, 21 Jul 1998 18:41:23 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 18:41:23 -0400 (EDT) Message-ID: <002101bdb4f8$312c0720$ccc07182@MyHost.McMaster.CA> From: "Todd Prior" To: Subject: Re: Sum of Values in particle analysis Date: Tue, 21 Jul 1998 18:37:47 -0400 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Resent-Message-ID: <"ZqBr72.0.DE.USHjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/96 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 780 Status: RO Unless I am mistaken the total that you want is simply the mean X the area (which should be the number of pixels if you have not calibrated anything) -----Original Message----- From: Grace,John To: nih-image@io.ece.drexel.edu Date: Tuesday, July 21, 1998 4:22 PM Subject: Sum of Values in particle analysis >Dear imagers, >I am trying to find the amount of ink in spots printed on a card, I also want >the degree of variation/uniformity of the coating of these spots. I have been >thresholding the spot then using the analyze particles command I am getting >the mean intensity, SD and area of the spot. Is there a way to get the sum >of pixel values in the spot? >Thanks, >John P. Grace >Abbott Laboratories > > From nih-image-request@io.ece.drexel.edu Tue Jul 21 19:51 EDT 1998 X-UIDL: a9c92d9accdde71062f4f45452a65a77 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id TAA06477; Tue, 21 Jul 1998 19:51:16 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 19:51:16 -0400 (EDT) Message-ID: <35B5277A.544C55B6@biomail.ucsd.edu> Date: Tue, 21 Jul 1998 16:42:50 -0700 From: Jamie Eisenhart Organization: University of California, San Diego X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: median stack References: <3.0.1.32.19980721063939.00772da0@med.wayne.edu> <3.0.1.32.19980721141257.0077ba6c@med.wayne.edu> <3.0.1.32.19980721153149.00774140@med.wayne.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"P3-Am1.0.TP1.1UIjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/97 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 653 Status: RO I think that the only way to do it in Image would be to do the median calculation directly in the macro and iterate over each x-y pixel location. This could take hours. I'll send you my Matlab median routine separately. Good luck, Jamie Bruce Berkowitz wrote: > > You imply that it could be done. I don't mind if its not efficient. Any > suggestions? Yes, please send the Matlab macro along if you don't mind. > Thank you again for your time. > > At 12:09 PM 7/21/98 -0700, you wrote: > >Ah, that is different and would be hard to do efficiently in Image. I do > have a > >Matlab macro that would do what you want, if that would help. > > > >Jamie From nih-image-request@io.ece.drexel.edu Tue Jul 21 21:12 EDT 1998 X-UIDL: 88f211e6438f0f6a15cb17c5eb6536a2 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA12760; Tue, 21 Jul 1998 21:12:45 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 21:12:45 -0400 (EDT) Message-ID: <35B53B39.50D0@cmgm.stanford.edu> Date: Tue, 21 Jul 1998 18:07:05 -0700 From: "R. Aaron (Boy) Warnock" X-Mailer: Mozilla 3.04 (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Dage SIT cameras Content-Transfer-Encoding: 7bit Resent-Message-ID: <"DJdtt2.0.5y2.dhJjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/98 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 974 Status: RO Howdy, We're thinking of replacing our very old COHU SIT and therefore have been considering the Dage-MTI and Hamamatsu cameras. We were considering the Dage VE 1000 SIT system, but then heard that Dage-MTI was getting out of the "Scientific imaging" and/or perhaps the "SIT camera" market(s); and have been advised to avoid them. Any truth to this? Furthermore, we've been told the Hamamatsu 2400-8 system comes with no choice of tube grade (but most likely a grade 2). Is this also true? Any additional thoughts about these cameras, and/or the Argus-20 DSP versus the Dage-MTI DSP-2000 would be appreciated. Thanks in advace, Aaron -- R. Aaron Warnock "Nothing more is needed to destroy a man than the conviction that his life's work is useless." -Antonin Artaud Lab Address: Dept. of Pathology L-235 awarnock@cmgm.stanford.edu Stanford, CA 94305 Tel. (650) 493-5000 x63167 Home Address: 777 Arguello Blvd. #304 Tel. (415) 831-3425 San Francisco, CA 94118 From nih-image-request@io.ece.drexel.edu Tue Jul 21 21:21 EDT 1998 X-UIDL: 67c9c6008b32b109a2f586eed2083164 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA13654; Tue, 21 Jul 1998 21:21:29 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 21:21:29 -0400 (EDT) Message-ID: <35B53D77.D9B6FDCB@sisna.com> Date: Tue, 21 Jul 1998 19:16:39 -0600 From: "Christopher P. Tully" Reply-To: cptully@sisna.com X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: Kanu P Singh CC: NIH-Image Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"QJOl71.0.q93.apJjr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/99 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1659 Status: RO Well, I see too solutions to your problem: 1) The physical solution: Before photographing your samples, rub them with a white paste or wax to fill the voids, then photograph. This should produce white spots where the voids are on a black background. The only possible problem with this approach is if the samples are too delicate to be handled in this fashion. 2) The computational approcah: Choose 'Anaylze Particles' from the Analyze menu, and select 'Include interior holes.' This should treat the black center of your voids as a hole in a white particle, and give you the measurements you want. The only problem here would be if the boundry is thin enough that it has breaks in it, preventing the program from identifying the border as an object. Chris Tully Image Processing Consultant Kanu P Singh wrote: > > Hi! > > I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of > hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem > that I am facing is that the boundaries of my voids are clear in the > micrographs, but the inside of the voids is the same as the rest of the > image. When I threshold the Images the boundaries appear as white while > all the rest of the image appears black. I have no idea of how to get the > void fraction or the sizes of these voids. > > One option that I have is to outline each void by hand and measure the > major and minor axes of the closest ellipses (the voids are all nearly > spherical). This is a very time consuming process since I have a lot of > micrographs to analyze. > > I would apreciate any ideas that anyone might have to help me out. > > -Kanu From nih-image-request@io.ece.drexel.edu Tue Jul 21 22:58 EDT 1998 X-UIDL: 2d677c4f6529582e411f68881fe36d45 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id WAA21288; Tue, 21 Jul 1998 22:58:33 -0400 (EDT) Resent-Date: Tue, 21 Jul 1998 22:58:33 -0400 (EDT) Message-ID: <001c01bdb51c$3e596680$b3c07182@MyHost.McMaster.CA> From: "Todd Prior" To: Subject: Re: Image density?? Date: Tue, 21 Jul 1998 22:55:50 -0400 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Resent-Message-ID: <"L0mmO3.0.K15.eELjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/100 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1235 Status: RO No they are not . Your gels must be calibrated ie OD vs grey scale. See the tutorial at NIH Image home page for a detailed explanation. I believe you will find it under the "More Documentation" link. -----Original Message----- From: Xudong Cao To: nih-image@io.ece.drexel.edu Date: Tuesday, July 21, 1998 5:49 PM Subject: Image density?? > >Hi there, >I am trying to evaluate the concentration of my fluorescin labeled >protein in gels by determining the optic density of the fluorescence >under the microscope by NIH image analysis software. My question is >whether the pixels that are represented by the 8-bit integers are in a >linear relationship, say value 1 represents as twice intensity as that >of value 2? and how about value 0 (the white color)? > >I would highly appreciate any help from you in this regard. > >thanks. > >Sincerely, >_______________________________ >Xudong CAO >Center for Biomaterials >University of Toronto >Phone: (416) 978 0343 >Fax: (416) 978 1462 > >In science one tries to tell people, in such a way as to be >understood by everyone, something that no one ever knew >before. But in poetry, it's the exact opposite. >- Paul Dirac > > > > From nih-image-request@io.ece.drexel.edu Wed Jul 22 05:21 EDT 1998 X-UIDL: f18779d0383fa18388fdf218357e9337 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA20893; Wed, 22 Jul 1998 05:21:34 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 05:21:34 -0400 (EDT) Message-ID: <01BDB59C.EE03E440.sleigh@risnet.rist.re.kr> From: SangHa Leigh Reply-To: "sleigh@risnet.rist.re.kr" To: "'nih-image@biomed.drexel.edu'" Subject: unsubscribe Date: Wed, 22 Jul 1998 18:17:02 +0900 Organization: RIST X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"2Rv9b3.0.5r4.VoQjr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/101 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 531 Status: RO ========================================================= SangHa Leigh, Ph.D. Materials Research Division Research Institute of Industrial Science and Technology (RIST) P.O. Box 135 Pohang 790-600, Korea Tel: +82-(0)562-279-6498 Fax: +82-(0)562-279-6199 (Office) +82-(0)562-46-0643 (Home) Cellular: +82-(0)17-342-0643 Personal homepage - http://dol1.eng.sunysb.edu/students/sangha.html RIST homepage - http://www.rist.re.kr POSCO homepage - http://www.posco.co.kr =================================================== From nih-image-d-request@io.ece.drexel.edu Wed Jul 22 05:23 EDT 1998 X-UIDL: 184b85b609d6c6d0f2a841b519b94085 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA21196; Wed, 22 Jul 1998 05:23:45 -0400 (EDT) Date: Wed, 22 Jul 1998 05:23:45 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807220923.FAA21196@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #17 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/17 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 27926 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 17 Today's Topics: Re: Eudora users [ "Randy M. Wadkins" ] Re: median stack [ Jamie Eisenhart ] Re: median stack [ Jamie Eisenhart ] unsubscribe [ SangHa Leigh ] ------------------------------ Date: Tue, 21 Jul 1998 10:12:13 -0700 From: "Randy M. Wadkins" To: nih-image@io.ece.drexel.edu Subject: Re: Eudora users Message-Id: Content-Type: text/plain; charset="us-ascii" As someone else pointed out, if you want the mailbox of individual files, check the box in the Settings->Attachments box that says "receive MIME digests as attachments". If you want the old, single message digest, uncheck this box. --Randy > >------------------------------ >Date: Tue, 21 Jul 1998 08:44:58 -0400 >From: David Milstone >To: nih-image@io.ece.drexel.edu >Subject: Re: Digest Form >Message-Id: >Content-Type: text/plain; charset="us-ascii" > >I use the same system with Eudora Pro 3.1 and agree that it is an improvement. > >>Four posts to the list have been somewhat critical of the new Digest Form >>and its interactions with Eudora. The basic problem is that it >>automatically inserts new Image Digest mailboxes in the Eudora Menu. Since >>my own complaint was posted, however, I've developed a workaround that >>seems fairly painless -- and it no longer requires a trip to >>Menu/Window/Mailboxes to implement. ****************************************************************** "To be or not to...beeeeeeeeeeeeeee" --Hamlet vs. Godzilla Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** ------------------------------ Date: Tue, 21 Jul 1998 11:56:24 -0400 From: "Evdokia Achilleos" To: nih-image@io.ece.drexel.edu Subject: Plug-in,Unsharp,and set origin Message-Id: <9807211156.ZM7001@chavi> Content-Type: text/plain; charset=us-ascii I have downloaded nih 1.62 beta Version and have a couple of questions 1. I can not ge the plug ins to work - even if i place plug ins in the nih.Image folder , I get ``no plug ins '' when I go to the aquire submenu Is there something ``extra'' I need to do? 2. Is there a plug-in available for the photoshop unsharp mask filter (or an equivalent way of doing it) in NIH 3. Can I change my origin from the lower left corner to some known x,y? Thanks in advance Evie Achilleos -- Evdokia Achilleos ------------------------------ Date: Tue, 21 Jul 1998 10:59:06 -0700 From: Jamie Eisenhart To: nih-image@io.ece.drexel.edu Subject: Re: median stack Message-ID: <35B4D6EA.D176103D@biomail.ucsd.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Bruce, It sounds like you want to run a median filter on each slice of the stack. That will calculate the median of each pixel within a 3x3 window. You could try: macro '2D Median Filter'; var i, n: integer; begin n := nSlices; for i := 1 to n do begin chooseSlice(i); filter('median'); end; end Jamie Eisenhart UCSD Neuroscience Bruce Berkowitz wrote: > > Hi, > > Is there a macro around that will calculate and display the pixel by pixel > median of a stack of images? My data are not normally distributed so > displaying the average is not really right and doesn't reflect the > statitisics I have to do. > > Thanks! > > Bruce Berkowitz > |-------------------------------------------| > |Berkowitz Lab Home Page: http://146.9.7.69 | > |-------------------------------------------| > > Bruce Berkowitz, Ph.D. > Department of Anatomy and Cell Biology > Wayne State Univeristy > 540 E. Canfield > Detroit, MI 48201 > > Phone: (313) 577-9035 > FAX: (313) 577-3125 > E-mail: baberko@med.wayne.edu ------------------------------ Date: Tue, 21 Jul 1998 14:12:57 -0400 From: Bruce Berkowitz To: nih-image@io.ece.drexel.edu Subject: Re: median stack Message-Id: <3.0.1.32.19980721141257.0077ba6c@med.wayne.edu> Content-Type: text/plain; charset="us-ascii" Hi, Thank you for your response but I don't think that was what I was looking for. Because my data are not normally distributed I would like to calculate a median image from a stack of 10 images INSTEAD of calculating one average image of that stack. Bruce At 10:59 AM 7/21/98 -0700, you wrote: >Hi Bruce, > >It sounds like you want to run a median filter on each slice of the stack. That >will calculate the median of each pixel within a 3x3 window. You could try: > >macro '2D Median Filter'; >var > i, n: integer; >begin > n := nSlices; > for i := 1 to n do begin > chooseSlice(i); > filter('median'); > end; >end > >Jamie Eisenhart >UCSD Neuroscience > >Bruce Berkowitz wrote: >> >> Hi, >> >> Is there a macro around that will calculate and display the pixel by pixel >> median of a stack of images? My data are not normally distributed so >> displaying the average is not really right and doesn't reflect the >> statitisics I have to do. >> >> Thanks! >> >> Bruce Berkowitz >> |-------------------------------------------| >> |Berkowitz Lab Home Page: http://146.9.7.69 | >> |-------------------------------------------| >> >> Bruce Berkowitz, Ph.D. >> Department of Anatomy and Cell Biology >> Wayne State Univeristy >> 540 E. Canfield >> Detroit, MI 48201 >> >> Phone: (313) 577-9035 >> FAX: (313) 577-3125 >> E-mail: baberko@med.wayne.edu > > |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu ------------------------------ Date: Tue, 21 Jul 1998 14:50:07 -0400 (EDT) From: Kanu P Singh To: nih-image@io.ece.drexel.edu Subject: VOID SIZE MEASUREMENT IN POLYMERS Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem that I am facing is that the boundaries of my voids are clear in the micrographs, but the inside of the voids is the same as the rest of the image. When I threshold the Images the boundaries appear as white while all the rest of the image appears black. I have no idea of how to get the void fraction or the sizes of these voids. One option that I have is to outline each void by hand and measure the major and minor axes of the closest ellipses (the voids are all nearly spherical). This is a very time consuming process since I have a lot of micrographs to analyze. I would apreciate any ideas that anyone might have to help me out. -Kanu ------------------------------ Date: Tue, 21 Jul 1998 12:09:42 -0700 From: Jamie Eisenhart To: nih-image@io.ece.drexel.edu Subject: Re: median stack Message-ID: <35B4E776.A54349A8@biomail.ucsd.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Ah, that is different and would be hard to do efficiently in Image. I do have a Matlab macro that would do what you want, if that would help. Jamie Bruce Berkowitz wrote: > > Hi, > > Thank you for your response but I don't think that was what I was looking > for. Because my data are not normally distributed I would like to calculate > a median image from a stack of 10 images INSTEAD of calculating one average > image of that stack. > > Bruce > > At 10:59 AM 7/21/98 -0700, you wrote: > >Hi Bruce, > > > >It sounds like you want to run a median filter on each slice of the stack. > That > >will calculate the median of each pixel within a 3x3 window. You could try: > > > >macro '2D Median Filter'; > >var > > i, n: integer; > >begin > > n := nSlices; > > for i := 1 to n do begin > > chooseSlice(i); > > filter('median'); > > end; > >end > > > >Jamie Eisenhart > >UCSD Neuroscience > > > >Bruce Berkowitz wrote: > >> > >> Hi, > >> > >> Is there a macro around that will calculate and display the pixel by pixel > >> median of a stack of images? My data are not normally distributed so > >> displaying the average is not really right and doesn't reflect the > >> statitisics I have to do. > >> > >> Thanks! > >> > >> Bruce Berkowitz > >> |-------------------------------------------| > >> |Berkowitz Lab Home Page: http://146.9.7.69 | > >> |-------------------------------------------| > >> > >> Bruce Berkowitz, Ph.D. > >> Department of Anatomy and Cell Biology > >> Wayne State Univeristy > >> 540 E. Canfield > >> Detroit, MI 48201 > >> > >> Phone: (313) 577-9035 > >> FAX: (313) 577-3125 > >> E-mail: baberko@med.wayne.edu > > > > > |-------------------------------------------| > |Berkowitz Lab Home Page: http://146.9.7.69 | > |-------------------------------------------| > > Bruce Berkowitz, Ph.D. > Department of Anatomy and Cell Biology > Wayne State Univeristy > 540 E. Canfield > Detroit, MI 48201 > > Phone: (313) 577-9035 > FAX: (313) 577-3125 > E-mail: baberko@med.wayne.edu ------------------------------ Date: Tue, 21 Jul 1998 15:14:34 -0400 From: Carl Gustafson To: nih-image@io.ece.drexel.edu Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS Message-Id: Content-Type: text/plain; charset="us-ascii" >I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of >hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem >that I am facing is that the boundaries of my voids are clear in the >micrographs, but the inside of the voids is the same as the rest of the >image. When I threshold the Images the boundaries appear as white while >all the rest of the image appears black. I have no idea of how to get the >void fraction or the sizes of these voids. Can you invert the image, and do an Analyse Particles on the image, which should now be light, with dark rings? Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== ------------------------------ Date: Tue, 21 Jul 1998 15:31:49 -0400 From: Bruce Berkowitz To: nih-image@io.ece.drexel.edu Subject: Re: median stack Message-Id: <3.0.1.32.19980721153149.00774140@med.wayne.edu> Content-Type: text/plain; charset="us-ascii" You imply that it could be done. I don't mind if its not efficient. Any suggestions? Yes, please send the Matlab macro along if you don't mind. Thank you again for your time. At 12:09 PM 7/21/98 -0700, you wrote: >Ah, that is different and would be hard to do efficiently in Image. I do have a >Matlab macro that would do what you want, if that would help. > >Jamie > >Bruce Berkowitz wrote: >> >> Hi, >> >> Thank you for your response but I don't think that was what I was looking >> for. Because my data are not normally distributed I would like to calculate >> a median image from a stack of 10 images INSTEAD of calculating one average >> image of that stack. >> >> Bruce >> >> At 10:59 AM 7/21/98 -0700, you wrote: >> >Hi Bruce, >> > >> >It sounds like you want to run a median filter on each slice of the stack. >> That >> >will calculate the median of each pixel within a 3x3 window. You could try: >> > >> >macro '2D Median Filter'; >> >var >> > i, n: integer; >> >begin >> > n := nSlices; >> > for i := 1 to n do begin >> > chooseSlice(i); >> > filter('median'); >> > end; >> >end >> > >> >Jamie Eisenhart >> >UCSD Neuroscience >> > >> >Bruce Berkowitz wrote: >> >> >> >> Hi, >> >> >> >> Is there a macro around that will calculate and display the pixel by pixel >> >> median of a stack of images? My data are not normally distributed so >> >> displaying the average is not really right and doesn't reflect the >> >> statitisics I have to do. >> >> >> >> Thanks! >> >> >> >> Bruce Berkowitz >> >> |-------------------------------------------| >> >> |Berkowitz Lab Home Page: http://146.9.7.69 | >> >> |-------------------------------------------| >> >> >> >> Bruce Berkowitz, Ph.D. >> >> Department of Anatomy and Cell Biology >> >> Wayne State Univeristy >> >> 540 E. Canfield >> >> Detroit, MI 48201 >> >> >> >> Phone: (313) 577-9035 >> >> FAX: (313) 577-3125 >> >> E-mail: baberko@med.wayne.edu >> > >> > >> |-------------------------------------------| >> |Berkowitz Lab Home Page: http://146.9.7.69 | >> |-------------------------------------------| >> >> Bruce Berkowitz, Ph.D. >> Department of Anatomy and Cell Biology >> Wayne State Univeristy >> 540 E. Canfield >> Detroit, MI 48201 >> >> Phone: (313) 577-9035 >> FAX: (313) 577-3125 >> E-mail: baberko@med.wayne.edu > > |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu ------------------------------ Date: Tue, 21 Jul 1998 14:48:35 -0500 From: Alex_Courtade@huntsman.com To: nih-image@io.ece.drexel.edu Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS Message-ID: <0000665B.CE21466@huntsman.com> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part If your image is clean, perhaps you could threshold the image as normal, and instead of highlighting the individual voids with the wand, you could highlight the "black" area of the photo (the area of the whole photo, minus the void area.) Then you could take the area of the entire image and subtract the "black" area, leaving you with the area of your voids. Again, I don't have a detailed description of your images, so I don't know whether this will work, but it's worth a shot. ----- Alex Courtade ____________________Reply Separator____________________ Subject: VOID SIZE MEASUREMENT IN POLYMERS Author: Kanu P Singh Date: 7/21/98 2:50 PM Hi! I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem that I am facing is that the boundaries of my voids are clear in the micrographs, but the inside of the voids is the same as the rest of the image. When I threshold the Images the boundaries appear as white while all the rest of the image appears black. I have no idea of how to get the void fraction or the sizes of these voids. One option that I have is to outline each void by hand and measure the major and minor axes of the closest ellipses (the voids are all nearly spherical). This is a very time consuming process since I have a lot of micrographs to analyze. I would apreciate any ideas that anyone might have to help me out. -Kanu ------------------------------ Date: Tue, 21 Jul 1998 16:17:04 EDT From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Re: median stack Message-ID: <6f909b7b.35b4f741@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 7/21/98 6:33:18 PM, you wrote: >Thank you for your response but I don't think that was what I was looking >for. Because my data are not normally distributed I would like to calculate >a median image from a stack of 10 images INSTEAD of calculating one average >image of that stack. I think you need to define what you want, and the answer may then be obvious. for instance do you want to take the pixel values at each x,y location from all 10 images and find the median value, and repeat this for all pixels? That doesn't sound like a median image to me, but if that is what you want then it is easy (but slow) to do. You will have to use a sort procedure in your macro to get the median (and then since you have an even number of images will have to probably average the 5th and 6th ranked values). ------------------------------ Date: Tue, 21 Jul 1998 15:24:36 -0500 From: "Grace,John" To: Subject: Sum of Values in particle analysis Message-Id: <0055600001401889000002L092*@MHS> Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit Dear imagers, I am trying to find the amount of ink in spots printed on a card, I also want the degree of variation/uniformity of the coating of these spots. I have been thresholding the spot then using the analyze particles command I am getting the mean intensity, SD and area of the spot. Is there a way to get the sum of pixel values in the spot? Thanks, John P. Grace Abbott Laboratories ------------------------------ Date: Tue, 21 Jul 1998 17:48:15 -0400 From: Xudong Cao To: nih-image@io.ece.drexel.edu Subject: Image density?? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi there, I am trying to evaluate the concentration of my fluorescin labeled protein in gels by determining the optic density of the fluorescence under the microscope by NIH image analysis software. My question is whether the pixels that are represented by the 8-bit integers are in a linear relationship, say value 1 represents as twice intensity as that of value 2? and how about value 0 (the white color)? I would highly appreciate any help from you in this regard. thanks. Sincerely, _______________________________ Xudong CAO Center for Biomaterials University of Toronto Phone: (416) 978 0343 Fax: (416) 978 1462 In science one tries to tell people, in such a way as to be understood by everyone, something that no one ever knew before. But in poetry, it's the exact opposite. - Paul Dirac ------------------------------ Date: Tue, 21 Jul 1998 18:37:47 -0400 From: "Todd Prior" To: Subject: Re: Sum of Values in particle analysis Message-ID: <002101bdb4f8$312c0720$ccc07182@MyHost.McMaster.CA> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Unless I am mistaken the total that you want is simply the mean X the area (which should be the number of pixels if you have not calibrated anything) -----Original Message----- From: Grace,John To: nih-image@io.ece.drexel.edu Date: Tuesday, July 21, 1998 4:22 PM Subject: Sum of Values in particle analysis >Dear imagers, >I am trying to find the amount of ink in spots printed on a card, I also want >the degree of variation/uniformity of the coating of these spots. I have been >thresholding the spot then using the analyze particles command I am getting >the mean intensity, SD and area of the spot. Is there a way to get the sum >of pixel values in the spot? >Thanks, >John P. Grace >Abbott Laboratories > > ------------------------------ Date: Tue, 21 Jul 1998 16:42:50 -0700 From: Jamie Eisenhart To: nih-image@io.ece.drexel.edu Subject: Re: median stack Message-ID: <35B5277A.544C55B6@biomail.ucsd.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I think that the only way to do it in Image would be to do the median calculation directly in the macro and iterate over each x-y pixel location. This could take hours. I'll send you my Matlab median routine separately. Good luck, Jamie Bruce Berkowitz wrote: > > You imply that it could be done. I don't mind if its not efficient. Any > suggestions? Yes, please send the Matlab macro along if you don't mind. > Thank you again for your time. > > At 12:09 PM 7/21/98 -0700, you wrote: > >Ah, that is different and would be hard to do efficiently in Image. I do > have a > >Matlab macro that would do what you want, if that would help. > > > >Jamie ------------------------------ Date: Tue, 21 Jul 1998 18:07:05 -0700 From: "R. Aaron (Boy) Warnock" To: nih-image@io.ece.drexel.edu Subject: Dage SIT cameras Message-ID: <35B53B39.50D0@cmgm.stanford.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Howdy, We're thinking of replacing our very old COHU SIT and therefore have been considering the Dage-MTI and Hamamatsu cameras. We were considering the Dage VE 1000 SIT system, but then heard that Dage-MTI was getting out of the "Scientific imaging" and/or perhaps the "SIT camera" market(s); and have been advised to avoid them. Any truth to this? Furthermore, we've been told the Hamamatsu 2400-8 system comes with no choice of tube grade (but most likely a grade 2). Is this also true? Any additional thoughts about these cameras, and/or the Argus-20 DSP versus the Dage-MTI DSP-2000 would be appreciated. Thanks in advace, Aaron -- R. Aaron Warnock "Nothing more is needed to destroy a man than the conviction that his life's work is useless." -Antonin Artaud Lab Address: Dept. of Pathology L-235 awarnock@cmgm.stanford.edu Stanford, CA 94305 Tel. (650) 493-5000 x63167 Home Address: 777 Arguello Blvd. #304 Tel. (415) 831-3425 San Francisco, CA 94118 ------------------------------ Date: Tue, 21 Jul 1998 19:16:39 -0600 From: "Christopher P. Tully" To: Kanu P Singh CC: NIH-Image Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS Message-ID: <35B53D77.D9B6FDCB@sisna.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Well, I see too solutions to your problem: 1) The physical solution: Before photographing your samples, rub them with a white paste or wax to fill the voids, then photograph. This should produce white spots where the voids are on a black background. The only possible problem with this approach is if the samples are too delicate to be handled in this fashion. 2) The computational approcah: Choose 'Anaylze Particles' from the Analyze menu, and select 'Include interior holes.' This should treat the black center of your voids as a hole in a white particle, and give you the measurements you want. The only problem here would be if the boundry is thin enough that it has breaks in it, preventing the program from identifying the border as an object. Chris Tully Image Processing Consultant Kanu P Singh wrote: > > Hi! > > I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of > hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem > that I am facing is that the boundaries of my voids are clear in the > micrographs, but the inside of the voids is the same as the rest of the > image. When I threshold the Images the boundaries appear as white while > all the rest of the image appears black. I have no idea of how to get the > void fraction or the sizes of these voids. > > One option that I have is to outline each void by hand and measure the > major and minor axes of the closest ellipses (the voids are all nearly > spherical). This is a very time consuming process since I have a lot of > micrographs to analyze. > > I would apreciate any ideas that anyone might have to help me out. > > -Kanu ------------------------------ Date: Tue, 21 Jul 1998 22:55:50 -0400 From: "Todd Prior" To: Subject: Re: Image density?? Message-ID: <001c01bdb51c$3e596680$b3c07182@MyHost.McMaster.CA> Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit No they are not . Your gels must be calibrated ie OD vs grey scale. See the tutorial at NIH Image home page for a detailed explanation. I believe you will find it under the "More Documentation" link. -----Original Message----- From: Xudong Cao To: nih-image@io.ece.drexel.edu Date: Tuesday, July 21, 1998 5:49 PM Subject: Image density?? > >Hi there, >I am trying to evaluate the concentration of my fluorescin labeled >protein in gels by determining the optic density of the fluorescence >under the microscope by NIH image analysis software. My question is >whether the pixels that are represented by the 8-bit integers are in a >linear relationship, say value 1 represents as twice intensity as that >of value 2? and how about value 0 (the white color)? > >I would highly appreciate any help from you in this regard. > >thanks. > >Sincerely, >_______________________________ >Xudong CAO >Center for Biomaterials >University of Toronto >Phone: (416) 978 0343 >Fax: (416) 978 1462 > >In science one tries to tell people, in such a way as to be >understood by everyone, something that no one ever knew >before. But in poetry, it's the exact opposite. >- Paul Dirac > > > > ------------------------------ Date: Wed, 22 Jul 1998 18:17:02 +0900 From: SangHa Leigh To: "'nih-image@biomed.drexel.edu'" Subject: unsubscribe Message-ID: <01BDB59C.EE03E440.sleigh@risnet.rist.re.kr> Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit ========================================================= SangHa Leigh, Ph.D. Materials Research Division Research Institute of Industrial Science and Technology (RIST) P.O. Box 135 Pohang 790-600, Korea Tel: +82-(0)562-279-6498 Fax: +82-(0)562-279-6199 (Office) +82-(0)562-46-0643 (Home) Cellular: +82-(0)17-342-0643 Personal homepage - http://dol1.eng.sunysb.edu/students/sangha.html RIST homepage - http://www.rist.re.kr POSCO homepage - http://www.posco.co.kr =================================================== -------------------------------- End of nih-image-d Digest V98 Issue #17 *************************************** From nih-image-request@io.ece.drexel.edu Wed Jul 22 06:40 EDT 1998 X-UIDL: 656cf3fff1fe6fffa47125022d295549 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA27283; Wed, 22 Jul 1998 06:40:28 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 06:40:28 -0400 (EDT) Message-Id: <3.0.1.32.19980722062320.01affe7c@med.wayne.edu> X-Sender: baberko@med.wayne.edu X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Wed, 22 Jul 1998 06:23:20 -0400 To: nih-image@io.ece.drexel.edu From: Bruce Berkowitz Subject: Re: Re: median stack In-Reply-To: <6f909b7b.35b4f741@aol.com> Mime-Version: 1.0 Resent-Message-ID: <"90jMH.0.3O6.VwRjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/102 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1436 Status: RO yes, I want to create a new image using the median value at a particular x,y location from those 10 images, repeated over all pixels. Do you have an example of a sort routine that will do this? Thank you for your time! Bruce At 04:17 PM 7/21/98 EDT, you wrote: > >In a message dated 7/21/98 6:33:18 PM, you wrote: > >>Thank you for your response but I don't think that was what I was looking >>for. Because my data are not normally distributed I would like to calculate >>a median image from a stack of 10 images INSTEAD of calculating one average >>image of that stack. > >I think you need to define what you want, and the answer may then be obvious. >for instance do you want to take the pixel values at each x,y location from >all 10 images and find the median value, and repeat this for all pixels? That >doesn't sound like a median image to me, but if that is what you want then it >is easy (but slow) to do. You will have to use a sort procedure in your macro >to get the median (and then since you have an even number of images will have >to probably average the 5th and 6th ranked values). > > |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu From nih-image-request@io.ece.drexel.edu Wed Jul 22 07:44 EDT 1998 X-UIDL: 401a8b2f11531fec2906e2d0eccc36d4 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA02410; Wed, 22 Jul 1998 07:44:24 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 07:44:24 -0400 (EDT) From: DrJohnRuss@aol.com Message-ID: <1090f786.35b5ce58@aol.com> Date: Wed, 22 Jul 1998 07:34:47 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Re: Re: median stack Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"6Bs2r.0.DO.EwSjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/103 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 422 Status: RO In a message dated 7/22/98 10:33:31 AM, you wrote: >yes, I want to create a new image using the median value at a particular >x,y location from those 10 images, repeated over all pixels. Do you have an >example of a sort routine that will do this? For a small number of values, a shell sort is probably the most efficient and easy to program. Details and code examples available in any standard numerical recipes book From nih-image-request@io.ece.drexel.edu Wed Jul 22 08:23 EDT 1998 X-UIDL: 14ee0f0c1555bd20c647a611d92b5f23 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA05635; Wed, 22 Jul 1998 08:23:27 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 08:23:27 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Wed, 22 Jul 1998 08:16:27 -0500 To: nih-image@io.ece.drexel.edu From: Mark A Vivino Subject: Re: Image density?? Resent-Message-ID: <"qfSfq.0.0B1.1VTjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/104 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 802 Status: RO >Hi there, >I am trying to evaluate the concentration of my fluorescin labeled >protein in gels by determining the optic density of the fluorescence >under the microscope by NIH image analysis software. My question is >whether the pixels that are represented by the 8-bit integers are in a >linear relationship, say value 1 represents as twice intensity as that >of value 2? and how about value 0 (the white color)? You can see in: http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometr y As often stated on the list, never make the mistake in assuming a linear relationship of pixels and concentrations. 100 is not twice 50 and for good reasons. If pixels represented linear relationships to concentration we would have pretty ugly looking (poor contrast) images. Mark From nih-image-request@io.ece.drexel.edu Wed Jul 22 08:58 EDT 1998 X-UIDL: dee4679b84191baab423a09e38b21641 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA08577; Wed, 22 Jul 1998 08:58:03 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 08:58:03 -0400 (EDT) X-SMTP-Posting-Origin: 198.168.189.48 (C-08.DAS.McGill.CA [198.168.189.48]) Message-ID: <35B5DE9C.B66@po-box.mcgill.ca> Date: Wed, 22 Jul 1998 08:44:12 -0400 From: Jeri Miller Reply-To: jmille@po-box.mcgill.ca Organization: McGill University X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: pixel range Content-Transfer-Encoding: 7bit Resent-Message-ID: <"AUAMi2.0.9t1.4-Tjr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/105 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 552 Status: RO Hello to all. I am a new user to NIH Image. I am looking for any assistance in how to determine the percentage of pixels of a specificed color range contained within an image. This would be used in histological slide analyses. I have used 'Sort by LUT' and individual macros such as 'count BluePixels'. Is there a way to specify specific pixel color ranges, then count or derive percentages of this range within a ROI? Your help is appreciated. J. Miller, Ph. D. Candidate Ultrasound Research Imaging Lab McGill University/RVH Montreal, Quebec From nih-image-request@io.ece.drexel.edu Wed Jul 22 09:13 EDT 1998 X-UIDL: b70a587af929270f4a98ca0e79d24934 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA10012; Wed, 22 Jul 1998 09:12:56 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 09:12:56 -0400 (EDT) Message-Id: <3.0.3.32.19980722090218.006c3e40@pop.cwru.edu> X-Sender: sdh6@pop.cwru.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Wed, 22 Jul 1998 09:02:18 -0400 To: nih-image@io.ece.drexel.edu From: Steven Hudson Subject: Macro for circularly averaging an FFT Mime-Version: 1.0 Resent-Message-ID: <"Kankl1.0.CC2.iBUjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/106 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 399 Status: RO Dear discussion group, Is there a macro available for circularly averaging a 2D FFT and then outputing the 1D result (i.e. the power spectrum as a function of spatial frequency)? Thanking you in advance, Steve Hudson Steve Hudson Assist. Professor of Macromolecular Science Case Western Reserve University 10900 Euclid Av. Cleveland, OH 44106-7202 216-368-6373 216-368-4202 Fax sdh6@po.cwru.edu From nih-image-request@io.ece.drexel.edu Wed Jul 22 09:37 EDT 1998 X-UIDL: f40915cb39cc42099ad4bc8dddf99fc1 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA12042; Wed, 22 Jul 1998 09:37:20 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 09:37:20 -0400 (EDT) Message-Id: In-Reply-To: <3.0.3.32.19980722090218.006c3e40@pop.cwru.edu> Mime-Version: 1.0 Date: Wed, 22 Jul 1998 09:28:51 -0500 To: nih-image@io.ece.drexel.edu From: Mark A Vivino Subject: Re: Macro for circularly averaging an FFT Resent-Message-ID: <"zg-kZ.0.yj2.uYUjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/107 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1937 Status: RO >Dear discussion group, > >Is there a macro available for circularly averaging a 2D FFT and then >outputing the 1D result (i.e. the power spectrum as a function of spatial >frequency)? Don't know if this slow old macro I wrote for someone does all of what you want, but you can try. Macro 'circle avg [C]'; var OrigPid, WorkPid:Integer; i,ignore,ignore2:integer; imgleft,imgtop,imgwidth,imgheight, tempwidth,tempheight:integer; left,top,width,height,ovalwidth,ovalheight:integer; Total:real; begin SetOptions('Mean, User1'); SetUser1Label('Normalized Mean'); OrigPid := PidNumber; Duplicate('Working'); WorkPid := PidNumber; SelectAll; Clear; KillROI; SelectPic(OrigPid); ResetCounter; SelectAll; GetROI(imgleft,imgtop,imgwidth,imgheight); KillROI; ChoosePic(origPid); MakeOvalROI(imgwidth/2,imgheight/2,2,2); GetROI(ignore,ignore2,Ovalwidth,Ovalheight); Copy; SelectPic(WorkPid); Paste; SetThreshold(1); Measure; Clear; SelectPic(OrigPid); Ovalwidth := Ovalwidth +2; Ovalheight := Ovalheight +2; for i := 1 to (imgwidth/2-6) do begin MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,Ovalwidth,O valHeight); copy; ChoosePic(WorkPid); MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,Ovalwidth,O valHeight); Paste; MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,OvalWidth-1, OvalHeight-1); Ovalwidth := Ovalwidth +2; Ovalheight := Ovalheight +2; Clear; KillROI; SetThreshold(1); Measure; SetThreshold(-1); SelectAll; Clear; KillROI; ChoosePic(OrigPid); KillROI; end; Total := 0.00; for i := 1 to rCount do begin Total := Total + rMean[i]; end; for i := 1 to rCount do begin rUser1[i] := rMean[i]/Total; end; ShowResults; end; From nih-image-request@io.ece.drexel.edu Wed Jul 22 09:51 EDT 1998 X-UIDL: d14b120d0e7db6f92750fe4cc1cc11f3 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA13339; Wed, 22 Jul 1998 09:51:17 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 09:51:17 -0400 (EDT) Message-Id: In-Reply-To: <35B5DE9C.B66@po-box.mcgill.ca> Mime-Version: 1.0 Date: Wed, 22 Jul 1998 09:40:58 -0500 To: nih-image@io.ece.drexel.edu From: Mark A Vivino Subject: Re: pixel range Resent-Message-ID: <"YK05v.0.P_2.FkUjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/108 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1327 Status: RO >Hello to all. >I am a new user to NIH Image. I am looking for any assistance in how to >determine the percentage of pixels of a specificed color range contained >within an image. This would be used in histological slide analyses. I >have used 'Sort by LUT' and individual macros such as 'count >BluePixels'. Is there a way to specify specific pixel color ranges, then >count or derive percentages of this range within a ROI? Your help is >appreciated. Just to start off on a tangent, I often have seen this or a related idea asked. Fundamentally what a scientist really needs is to know is: which pixels, or how many pixels, or what percent, have a dominant wavelength between 400 and 500 nm wavelength (or whatever range). It would be easier if pixels were not RGB or HSV, or anything else unrelated. Instead they should be wavelength(s) and density. Unfortunately, this is not the case but is sort or roughly like that with RGB and then the density is incorportated and things are sort of lumped all up and its a mess. I once wrote a macro which looked at the LUT to find which pixels have more of R than G or B. I then sought and counted those pixels in the image. This is sort of roughly what you request. Don't know if I can find it because it was years ago, but thats how I would still implement what you ask. Mark From nih-image-request@io.ece.drexel.edu Wed Jul 22 10:19 EDT 1998 X-UIDL: 5fa4004182f16a6d4eca6291bc516d7e Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA15529; Wed, 22 Jul 1998 10:19:14 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 10:19:14 -0400 (EDT) From: Jon Vaughan Message-Id: <199807221406.KAA11385@hamilton.edu> Subject: Digest form in elm on unix machine To: nih-image@io.ece.drexel.edu Date: Wed, 22 Jul 1998 10:06:20 -0400 (EDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"rH10C1.0.CX3.X6Vjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/109 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 577 Status: RO I read the digest using the 'elm' mail program on a unix machine (ELM 2.4 PL25, using 'more' to page through messages. Because the digest comes through as a multi-part MIME message, until now I have had to read through all the messages of the digest format of the list, but I have discovered how to skip the messages I don't want to read: at the --Press any key to go on.-- prompt, press the control-c (^C) key combination, and the remainder of the message(s) will be skipped. -- Jonathan Vaughan Psychology, Hamilton College jvaughan@hamilton.edu From nih-image-request@io.ece.drexel.edu Wed Jul 22 10:39 EDT 1998 X-UIDL: 44ec1b1b6098a33e3c4a64ac0f7b51f2 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA17272; Wed, 22 Jul 1998 10:38:59 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 10:38:59 -0400 (EDT) From: paul stoodley Sender: P.Stoodley@exeter.ac.uk To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: Image density?? In-Reply-To: Message-ID: Date: Wed, 22 Jul 1998 15:29:57 +0100 (GMT Daylight Time) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1.2 Build (32) X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"ykag93.0.J_3.-SVjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/110 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 2346 Status: RO We calibrated the relative fluorescence intensity [FI] of different concentrations of fluorescein measured by confocal microscopy. We found a peak FI value at 2mM fluorescien. However we had to overcome a couple of problems to "standardize" the technique. 1) We used neutral density filters and low magnification to mimimize photobleaching effects. We checked this by plotting the FI against time of exposure to UV light. 2) Because of light extinction with depth we first did a saggital scan to find the brightest point. We then frame averaged at that point and used the average FI of the field for our value. 3) Because the FI varies with light intensity and contrast settings etc. we calibrated just before taking the measurements. Other things to be careful with - fluorescien FI is strongly influenced by pH. We found FI decreased with alginate concentration this could be due to reduced pH or possible changes in density. This work is reported in: deBeer, D., Stoodley, P., and Lewandowski, Z. 1997. "Measurement of local diffusion coefficients in biofilms by micro-injection and confocal microscopy." Biotech. and Bioeng. 53(2):151-158. We were only interested in relating the relative changes of FI to relative changes in fluorescien concentration - not making absolute measurements. Confocal laser microscopy is also much more controlled than conventional fluorescence. However, if you are very careful with your calibration steps and run the right controls you might be able to get something. Good luck, Paul. On Wed, 22 Jul 1998 08:16:27 -0500 Mark A Vivino wrote: > >Hi there, > >I am trying to evaluate the concentration of my fluorescin labeled > >protein in gels by determining the optic density of the fluorescence > >under the microscope by NIH image analysis software. My question is > >whether the pixels that are represented by the 8-bit integers are in a > >linear relationship, say value 1 represents as twice intensity as that > >of value 2? and how about value 0 (the white color)? ---------------------- Paul Stoodley Environmental Tel: 01392 264348 Microbiology Fax: 01392 263700 Research email: p.stoodley@exeter.ac.uk Group Exeter University Biological Sciences Hatherly Laboratories Prince of Wales Road Exeter EX4 4PS. UK. From nih-image-request@io.ece.drexel.edu Wed Jul 22 15:17 EDT 1998 X-UIDL: 06bfef61519513589a0a7328646fe054 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA05577; Wed, 22 Jul 1998 15:14:32 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 15:14:32 -0400 (EDT) X-Sender: a_team@pop.dds.nl Message-Id: In-Reply-To: <199807211453.KAA27514@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Wed, 22 Jul 1998 20:24:46 +0200 To: nih-image@io.ece.drexel.edu From: "Anneke M.Th. Harbers and Ard Jonker" Subject: zero prefix Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id OAA02049 Resent-Message-ID: <"JBlay2.0.CW.azYjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/111 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 440 Status: RO Hi List, I'm looking for an elegant solution to have a prefix on a string, so as to obtain ' 00001' or ' 00012' ie. constant length. I also like to find an elegant way to get a part of a string without character by character moving to another string and then deleting that character from the input string, ie. string1:=concat(string2:3);delete(string2,0,3), which does not seem to work for me. Please reply by e-mail to a_team@dds.nl Ard From nih-image-request@io.ece.drexel.edu Wed Jul 22 15:42 EDT 1998 X-UIDL: 26609eac61c45d9a7f717906bd09fb6c Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA08035; Wed, 22 Jul 1998 15:40:19 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 15:40:19 -0400 (EDT) Message-Id: <3.0.1.32.19980722152048.0077e110@med.wayne.edu> X-Sender: baberko@med.wayne.edu X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Wed, 22 Jul 1998 15:20:48 -0400 To: nih-image@io.ece.drexel.edu From: Bruce Berkowitz Subject: unsubscribe In-Reply-To: References: <199807211453.KAA27514@io.ECE.Drexel.EDU> Mime-Version: 1.0 Resent-Message-ID: <"RYESX3.0.9a1.HoZjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/112 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 344 Status: RO unsubscribe |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu From nih-image-request@io.ece.drexel.edu Wed Jul 22 15:55 EDT 1998 X-UIDL: c25c2073eafc1417758565a577afdf80 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA09313; Wed, 22 Jul 1998 15:54:33 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 15:54:33 -0400 (EDT) Date: Wed, 22 Jul 1998 12:34:01 -0700 (PDT) From: David Ehrhardt To: nih-image@io.ece.drexel.edu Subject: Re: pixel range In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"lQgY21.0.Cx1.L_Zjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/113 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1893 Status: RO On Wed, 22 Jul 1998, Mark A Vivino wrote: > >Hello to all. > >I am a new user to NIH Image. I am looking for any assistance in how to > >determine the percentage of pixels of a specificed color range contained > >within an image. This would be used in histological slide analyses. I > >have used 'Sort by LUT' and individual macros such as 'count > >BluePixels'. Is there a way to specify specific pixel color ranges, then > >count or derive percentages of this range within a ROI? Your help is > >appreciated. > > Just to start off on a tangent, I often have seen this or a related idea > asked. Fundamentally what a scientist really needs is to know is: which > pixels, or how many pixels, or what percent, have a dominant wavelength > between 400 and 500 nm wavelength (or whatever range). It would be easier > if pixels were not RGB or HSV, or anything else unrelated. Instead they > should be wavelength(s) and density. Unfortunately, this is not the case > but is sort or roughly like that with RGB and then the density is > incorportated and things are sort of lumped all up and its a mess. > > I once wrote a macro which looked at the LUT to find which pixels have more > of R than G or B. I then sought and counted those pixels in the image. This > is sort of roughly what you request. Don't know if I can find it because it > was years ago, but thats how I would still implement what you ask. > > Mark This may be hopelessly naive, but Photoshop allows selection of a color range. You can do a pretty good job isolating parts of a color image with these selection tools. How does Photoshop define a color range and sort pixels by that definition? Could this be incorporated into a macro for Image? -David David Ehrhardt Carnegie Institution of Washington Department of Plant Biology Phone (650) 325-1521 x261 260 Panama St., Stanford, CA 94305 FAX (650) 325-6857 From nih-image-request@io.ece.drexel.edu Wed Jul 22 17:07 EDT 1998 X-UIDL: ff273c9e5f3fdd7e6163a66e66a924be Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA15240; Wed, 22 Jul 1998 17:07:14 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 17:07:14 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Wed, 22 Jul 1998 15:07:27 -0500 From: "STEPHEN MOORMAN" To: nih-image@io.ece.drexel.edu Subject: G3 Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id QAA10510 Resent-Message-ID: <"VdHVt1.0.Ra2.5Tajr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/114 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 116 Status: RO Is there a fix yet for the digitizer error when trying to capture images from the built-in video card in the G3's? From nih-image-request@io.ece.drexel.edu Wed Jul 22 18:16 EDT 1998 X-UIDL: d168da1272cefe7984f33679c971b8e1 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA20598; Wed, 22 Jul 1998 18:16:38 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 18:16:38 -0400 (EDT) Date: Wed, 22 Jul 1998 17:04:39 -0500 Message-Id: In-Reply-To: References: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Arnout Ruifrok Subject: Re: pixel range Resent-Message-ID: <"BzhQq2.0.Om4.W8cjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/115 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2437 Status: RO >On Wed, 22 Jul 1998, Mark A Vivino wrote: > >> >Hello to all. >> >I am a new user to NIH Image. I am looking for any assistance in how to >> >determine the percentage of pixels of a specificed color range contained >> >within an image. This would be used in histological slide analyses. I >> >have used 'Sort by LUT' and individual macros such as 'count >> >BluePixels'. Is there a way to specify specific pixel color ranges, then >> >count or derive percentages of this range within a ROI? Your help is >> >appreciated. >> >> Just to start off on a tangent, I often have seen this or a related idea >> asked. Fundamentally what a scientist really needs is to know is: which >> pixels, or how many pixels, or what percent, have a dominant wavelength >> between 400 and 500 nm wavelength (or whatever range). It would be easier >> if pixels were not RGB or HSV, or anything else unrelated. Instead they >> should be wavelength(s) and density. Unfortunately, this is not the case >> but is sort or roughly like that with RGB and then the density is >> incorportated and things are sort of lumped all up and its a mess. >> >> I once wrote a macro which looked at the LUT to find which pixels have more >> of R than G or B. I then sought and counted those pixels in the image. This >> is sort of roughly what you request. Don't know if I can find it because it >> was years ago, but thats how I would still implement what you ask. >> >> Mark > >This may be hopelessly naive, but Photoshop allows selection of a color >range. You can do a pretty good job isolating parts of a color image with >these selection tools. How does Photoshop define a color range and sort >pixels by that definition? Could this be incorporated into a macro for >Image? > >-David > >David Ehrhardt >Carnegie Institution of Washington >Department of Plant Biology Phone (650) 325-1521 x261 >260 Panama St., Stanford, CA 94305 FAX (650) 325-6857 If I am not mistaken (I never carefully tested this), photoshop determines the R,G and B values in the selected points and adds a range to each value according to the 'fuzziness' setting (don't ask me how exactly the range is determined), and then thresholds the whole image according to these values, resulting in the selection of a 'box'(rectangular prism) (or multiple boxes) with sides parallel with the RGB axes. This is doable in image by density slicing in R, G, and B, and 'and'-ing the three color planes. From nih-image-request@io.ece.drexel.edu Wed Jul 22 18:48 EDT 1998 X-UIDL: 106af3124670f68bfe5b8886f1f66865 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA23112; Wed, 22 Jul 1998 18:48:03 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 18:48:03 -0400 (EDT) Message-Id: <3.0.5.32.19980722184144.00803920@mohawk.net> X-Sender: microbill@mohawk.net X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Wed, 22 Jul 1998 18:41:44 -0400 To: nih-image@io.ece.drexel.edu, c.cathcart@sympatico.ca From: Bill Miller Subject: Re: Dage SIT cameras In-Reply-To: <35B53B39.50D0@cmgm.stanford.edu> Mime-Version: 1.0 Resent-Message-ID: <"Uc2VX2.0.3R5.1ecjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/116 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1126 Status: RO Chris - maybe you should have someone from Princeton contact him.. Bill At 06:07 PM 7/21/98 -0700, you wrote: >Howdy, > > We're thinking of replacing our very old COHU SIT >and therefore have been considering the Dage-MTI and Hamamatsu >cameras. We were considering the Dage VE 1000 SIT system, but >then heard that Dage-MTI was getting out of the "Scientific >imaging" and/or perhaps the "SIT camera" market(s); and have >been advised to avoid them. Any truth to this? > >Furthermore, we've been told the Hamamatsu 2400-8 system comes >with no choice of tube grade (but most likely a grade 2). Is >this also true? > >Any additional thoughts about these cameras, and/or the Argus-20 >DSP versus the Dage-MTI DSP-2000 would be appreciated. > >Thanks in advace, > >Aaron > > >-- >R. Aaron Warnock >"Nothing more is needed to destroy a man than the conviction >that his life's work is useless." -Antonin Artaud > >Lab Address: >Dept. of Pathology L-235 awarnock@cmgm.stanford.edu >Stanford, CA 94305 Tel. (650) 493-5000 x63167 > >Home Address: >777 Arguello Blvd. #304 Tel. (415) 831-3425 >San Francisco, CA 94118 > > > From nih-image-request@io.ece.drexel.edu Wed Jul 22 20:08 EDT 1998 X-UIDL: 5193116ec56e27e12d63726280d42b3f Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA29480; Wed, 22 Jul 1998 20:08:41 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 20:08:41 -0400 (EDT) Mime-Version: 1.0 X-Sender: scm@128.250.6.196 Message-Id: In-Reply-To: References: Date: Thu, 23 Jul 1998 09:58:58 +1000 To: nih-image@io.ece.drexel.edu From: Steve Martin Subject: Re: pixel range Resent-Message-ID: <"Wiqzj1.0.rz6.Bpdjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/117 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1684 Status: RO Dear list, On Wed, 22 Jul 1998, amongst other things, Mark A Vivino wrote: > >It would be easier >if pixels were not RGB or HSV, or anything else unrelated. Instead they >should be wavelength(s) and density. Unfortunately, this is not the case Mark, I found these comments very thought-provoking. excuse my probable ignorance or niaivity, isn't hue angle related in some way to wavelength in many cases? I realise the pixels on our screens are mixtures of rgb, but they usually do not represent mixtures of rgb brought in from the real world. Unless we are using spectrophotometers, electronically we most often represent wavelengths in the real world in rgb because it is convenient to sample it and then display it that way. If I digitally photograph or frame grab a sodium yellow flame, isn't the hue of the resulting image some sort of representation of the original wavelength(s)? So if I had a table which converted hue angle to wavelength, perhaps I could create a real-values image in which pixel values represented the centres of wavelength ranges. Once I had made the table, I could code it into Image for all to use (:-) ? Maybe all you need is hue angle, but wavelength ranges may not be related in a very linear way to hue, I haven't tried to figure that out. I am sure there can be lots of dangers in this approach (mixed light sources etc.) and I am sure the list will hear about them 5 minutes after this is posted! This could still help out all those people who post to the list asking how to separate their coloured stains / leaf colours / etc. I hope this promotes some discussion even if it is only that I have just re-invented a wheel called hue! Steve From nih-image-request@io.ece.drexel.edu Wed Jul 22 22:48 EDT 1998 X-UIDL: e172c4ed296bdb0b88d5b9b1c530d13d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id WAA12866; Wed, 22 Jul 1998 22:47:27 -0400 (EDT) Resent-Date: Wed, 22 Jul 1998 22:47:27 -0400 (EDT) Date: Wed, 22 Jul 1998 21:30:35 -0500 From: scidi Subject: Integration on the LG-3 NuBus Card To: nih-image@io.ece.drexel.edu Reply-to: scidi@mci2000.com Message-id: <0EWJ00NUI0NM4Y@PM02SM.PMM.MCI.NET> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1161 Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-Priority: 3 Resent-Message-ID: <"bYGd42.0.Qv2.r8gjr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/118 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 603 Status: RO To NIH Users: I have recently installed NuBus LG-3 and TV-3 cards in my Power Mac 7100. I have had relatively few problems, except that when I go to Integrate on Chip, I get a printout on the Mitsubishi thermal printer that came with the system instead of the on chip integration. I can't figure it out. The only time I get any type of integration is when I select a small area within the image. I do have the Scion integration cable and I am using a Cohu 4910 CCD camera. Any help would be greatly appreciated. Thanks. Mark R. Molenda phone (414) 476-2694 fax (414) 645-8037 scidi@mci2000.com From nih-image-d-request@io.ece.drexel.edu Wed Jul 22 22:51 EDT 1998 X-UIDL: cc5d60eceb115dcb23adfc6262dafd45 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id WAA13272; Wed, 22 Jul 1998 22:51:04 -0400 (EDT) Date: Wed, 22 Jul 1998 22:51:04 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807230251.WAA13272@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #18 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/18 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 25352 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 18 Today's Topics: Re: Re: median stack [ Bruce Berkowitz ] Re: Macro for circularly averaging a [ Mark A Vivino ] Re: Image density?? [ paul stoodley ] Re: pixel range [ Steve Martin ] ------------------------------ Date: Wed, 22 Jul 1998 06:23:20 -0400 From: Bruce Berkowitz To: nih-image@io.ece.drexel.edu Subject: Re: Re: median stack Message-Id: <3.0.1.32.19980722062320.01affe7c@med.wayne.edu> Content-Type: text/plain; charset="us-ascii" yes, I want to create a new image using the median value at a particular x,y location from those 10 images, repeated over all pixels. Do you have an example of a sort routine that will do this? Thank you for your time! Bruce At 04:17 PM 7/21/98 EDT, you wrote: > >In a message dated 7/21/98 6:33:18 PM, you wrote: > >>Thank you for your response but I don't think that was what I was looking >>for. Because my data are not normally distributed I would like to calculate >>a median image from a stack of 10 images INSTEAD of calculating one average >>image of that stack. > >I think you need to define what you want, and the answer may then be obvious. >for instance do you want to take the pixel values at each x,y location from >all 10 images and find the median value, and repeat this for all pixels? That >doesn't sound like a median image to me, but if that is what you want then it >is easy (but slow) to do. You will have to use a sort procedure in your macro >to get the median (and then since you have an even number of images will have >to probably average the 5th and 6th ranked values). > > |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu ------------------------------ Date: Wed, 22 Jul 1998 07:34:47 EDT From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Re: Re: median stack Message-ID: <1090f786.35b5ce58@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 7/22/98 10:33:31 AM, you wrote: >yes, I want to create a new image using the median value at a particular >x,y location from those 10 images, repeated over all pixels. Do you have an >example of a sort routine that will do this? For a small number of values, a shell sort is probably the most efficient and easy to program. Details and code examples available in any standard numerical recipes book ------------------------------ Date: Wed, 22 Jul 1998 08:16:27 -0500 From: Mark A Vivino To: nih-image@io.ece.drexel.edu Subject: Re: Image density?? Message-Id: Content-Type: text/plain; charset="us-ascii" >Hi there, >I am trying to evaluate the concentration of my fluorescin labeled >protein in gels by determining the optic density of the fluorescence >under the microscope by NIH image analysis software. My question is >whether the pixels that are represented by the 8-bit integers are in a >linear relationship, say value 1 represents as twice intensity as that >of value 2? and how about value 0 (the white color)? You can see in: http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometr y As often stated on the list, never make the mistake in assuming a linear relationship of pixels and concentrations. 100 is not twice 50 and for good reasons. If pixels represented linear relationships to concentration we would have pretty ugly looking (poor contrast) images. Mark ------------------------------ Date: Wed, 22 Jul 1998 08:44:12 -0400 From: Jeri Miller To: nih-image@io.ece.drexel.edu Subject: pixel range Message-ID: <35B5DE9C.B66@po-box.mcgill.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello to all. I am a new user to NIH Image. I am looking for any assistance in how to determine the percentage of pixels of a specificed color range contained within an image. This would be used in histological slide analyses. I have used 'Sort by LUT' and individual macros such as 'count BluePixels'. Is there a way to specify specific pixel color ranges, then count or derive percentages of this range within a ROI? Your help is appreciated. J. Miller, Ph. D. Candidate Ultrasound Research Imaging Lab McGill University/RVH Montreal, Quebec ------------------------------ Date: Wed, 22 Jul 1998 09:02:18 -0400 From: Steven Hudson To: nih-image@io.ece.drexel.edu Subject: Macro for circularly averaging an FFT Message-Id: <3.0.3.32.19980722090218.006c3e40@pop.cwru.edu> Content-Type: text/plain; charset="us-ascii" Dear discussion group, Is there a macro available for circularly averaging a 2D FFT and then outputing the 1D result (i.e. the power spectrum as a function of spatial frequency)? Thanking you in advance, Steve Hudson Steve Hudson Assist. Professor of Macromolecular Science Case Western Reserve University 10900 Euclid Av. Cleveland, OH 44106-7202 216-368-6373 216-368-4202 Fax sdh6@po.cwru.edu ------------------------------ Date: Wed, 22 Jul 1998 09:28:51 -0500 From: Mark A Vivino To: nih-image@io.ece.drexel.edu Subject: Re: Macro for circularly averaging an FFT Message-Id: Content-Type: text/plain; charset="us-ascii" >Dear discussion group, > >Is there a macro available for circularly averaging a 2D FFT and then >outputing the 1D result (i.e. the power spectrum as a function of spatial >frequency)? Don't know if this slow old macro I wrote for someone does all of what you want, but you can try. Macro 'circle avg [C]'; var OrigPid, WorkPid:Integer; i,ignore,ignore2:integer; imgleft,imgtop,imgwidth,imgheight, tempwidth,tempheight:integer; left,top,width,height,ovalwidth,ovalheight:integer; Total:real; begin SetOptions('Mean, User1'); SetUser1Label('Normalized Mean'); OrigPid := PidNumber; Duplicate('Working'); WorkPid := PidNumber; SelectAll; Clear; KillROI; SelectPic(OrigPid); ResetCounter; SelectAll; GetROI(imgleft,imgtop,imgwidth,imgheight); KillROI; ChoosePic(origPid); MakeOvalROI(imgwidth/2,imgheight/2,2,2); GetROI(ignore,ignore2,Ovalwidth,Ovalheight); Copy; SelectPic(WorkPid); Paste; SetThreshold(1); Measure; Clear; SelectPic(OrigPid); Ovalwidth := Ovalwidth +2; Ovalheight := Ovalheight +2; for i := 1 to (imgwidth/2-6) do begin MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,Ovalwidth,O valHeight); copy; ChoosePic(WorkPid); MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,Ovalwidth,O valHeight); Paste; MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,OvalWidth-1, OvalHeight-1); Ovalwidth := Ovalwidth +2; Ovalheight := Ovalheight +2; Clear; KillROI; SetThreshold(1); Measure; SetThreshold(-1); SelectAll; Clear; KillROI; ChoosePic(OrigPid); KillROI; end; Total := 0.00; for i := 1 to rCount do begin Total := Total + rMean[i]; end; for i := 1 to rCount do begin rUser1[i] := rMean[i]/Total; end; ShowResults; end; ------------------------------ Date: Wed, 22 Jul 1998 09:40:58 -0500 From: Mark A Vivino To: nih-image@io.ece.drexel.edu Subject: Re: pixel range Message-Id: Content-Type: text/plain; charset="us-ascii" >Hello to all. >I am a new user to NIH Image. I am looking for any assistance in how to >determine the percentage of pixels of a specificed color range contained >within an image. This would be used in histological slide analyses. I >have used 'Sort by LUT' and individual macros such as 'count >BluePixels'. Is there a way to specify specific pixel color ranges, then >count or derive percentages of this range within a ROI? Your help is >appreciated. Just to start off on a tangent, I often have seen this or a related idea asked. Fundamentally what a scientist really needs is to know is: which pixels, or how many pixels, or what percent, have a dominant wavelength between 400 and 500 nm wavelength (or whatever range). It would be easier if pixels were not RGB or HSV, or anything else unrelated. Instead they should be wavelength(s) and density. Unfortunately, this is not the case but is sort or roughly like that with RGB and then the density is incorportated and things are sort of lumped all up and its a mess. I once wrote a macro which looked at the LUT to find which pixels have more of R than G or B. I then sought and counted those pixels in the image. This is sort of roughly what you request. Don't know if I can find it because it was years ago, but thats how I would still implement what you ask. Mark ------------------------------ Date: Wed, 22 Jul 1998 10:06:20 -0400 (EDT) From: Jon Vaughan To: nih-image@io.ece.drexel.edu Subject: Digest form in elm on unix machine Message-Id: <199807221406.KAA11385@hamilton.edu> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I read the digest using the 'elm' mail program on a unix machine (ELM 2.4 PL25, using 'more' to page through messages. Because the digest comes through as a multi-part MIME message, until now I have had to read through all the messages of the digest format of the list, but I have discovered how to skip the messages I don't want to read: at the --Press any key to go on.-- prompt, press the control-c (^C) key combination, and the remainder of the message(s) will be skipped. -- Jonathan Vaughan Psychology, Hamilton College jvaughan@hamilton.edu ------------------------------ Date: Wed, 22 Jul 1998 15:29:57 +0100 (GMT Daylight Time) From: paul stoodley To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: Image density?? Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII We calibrated the relative fluorescence intensity [FI] of different concentrations of fluorescein measured by confocal microscopy. We found a peak FI value at 2mM fluorescien. However we had to overcome a couple of problems to "standardize" the technique. 1) We used neutral density filters and low magnification to mimimize photobleaching effects. We checked this by plotting the FI against time of exposure to UV light. 2) Because of light extinction with depth we first did a saggital scan to find the brightest point. We then frame averaged at that point and used the average FI of the field for our value. 3) Because the FI varies with light intensity and contrast settings etc. we calibrated just before taking the measurements. Other things to be careful with - fluorescien FI is strongly influenced by pH. We found FI decreased with alginate concentration this could be due to reduced pH or possible changes in density. This work is reported in: deBeer, D., Stoodley, P., and Lewandowski, Z. 1997. "Measurement of local diffusion coefficients in biofilms by micro-injection and confocal microscopy." Biotech. and Bioeng. 53(2):151-158. We were only interested in relating the relative changes of FI to relative changes in fluorescien concentration - not making absolute measurements. Confocal laser microscopy is also much more controlled than conventional fluorescence. However, if you are very careful with your calibration steps and run the right controls you might be able to get something. Good luck, Paul. On Wed, 22 Jul 1998 08:16:27 -0500 Mark A Vivino wrote: > >Hi there, > >I am trying to evaluate the concentration of my fluorescin labeled > >protein in gels by determining the optic density of the fluorescence > >under the microscope by NIH image analysis software. My question is > >whether the pixels that are represented by the 8-bit integers are in a > >linear relationship, say value 1 represents as twice intensity as that > >of value 2? and how about value 0 (the white color)? ---------------------- Paul Stoodley Environmental Tel: 01392 264348 Microbiology Fax: 01392 263700 Research email: p.stoodley@exeter.ac.uk Group Exeter University Biological Sciences Hatherly Laboratories Prince of Wales Road Exeter EX4 4PS. UK. ------------------------------ Date: Wed, 22 Jul 1998 20:24:46 +0200 From: "Anneke M.Th. Harbers and Ard Jonker" To: nih-image@io.ece.drexel.edu Subject: zero prefix Message-Id: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit Hi List, I'm looking for an elegant solution to have a prefix on a string, so as to obtain ' 00001' or ' 00012' ie. constant length. I also like to find an elegant way to get a part of a string without character by character moving to another string and then deleting that character from the input string, ie. string1:=concat(string2:3);delete(string2,0,3), which does not seem to work for me. Please reply by e-mail to a_team@dds.nl Ard ------------------------------ Date: Wed, 22 Jul 1998 15:20:48 -0400 From: Bruce Berkowitz To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <3.0.1.32.19980722152048.0077e110@med.wayne.edu> Content-Type: text/plain; charset="us-ascii" unsubscribe |-------------------------------------------| |Berkowitz Lab Home Page: http://146.9.7.69 | |-------------------------------------------| Bruce Berkowitz, Ph.D. Department of Anatomy and Cell Biology Wayne State Univeristy 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-9035 FAX: (313) 577-3125 E-mail: baberko@med.wayne.edu ------------------------------ Date: Wed, 22 Jul 1998 12:34:01 -0700 (PDT) From: David Ehrhardt To: nih-image@io.ece.drexel.edu Subject: Re: pixel range Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 22 Jul 1998, Mark A Vivino wrote: > >Hello to all. > >I am a new user to NIH Image. I am looking for any assistance in how to > >determine the percentage of pixels of a specificed color range contained > >within an image. This would be used in histological slide analyses. I > >have used 'Sort by LUT' and individual macros such as 'count > >BluePixels'. Is there a way to specify specific pixel color ranges, then > >count or derive percentages of this range within a ROI? Your help is > >appreciated. > > Just to start off on a tangent, I often have seen this or a related idea > asked. Fundamentally what a scientist really needs is to know is: which > pixels, or how many pixels, or what percent, have a dominant wavelength > between 400 and 500 nm wavelength (or whatever range). It would be easier > if pixels were not RGB or HSV, or anything else unrelated. Instead they > should be wavelength(s) and density. Unfortunately, this is not the case > but is sort or roughly like that with RGB and then the density is > incorportated and things are sort of lumped all up and its a mess. > > I once wrote a macro which looked at the LUT to find which pixels have more > of R than G or B. I then sought and counted those pixels in the image. This > is sort of roughly what you request. Don't know if I can find it because it > was years ago, but thats how I would still implement what you ask. > > Mark This may be hopelessly naive, but Photoshop allows selection of a color range. You can do a pretty good job isolating parts of a color image with these selection tools. How does Photoshop define a color range and sort pixels by that definition? Could this be incorporated into a macro for Image? -David David Ehrhardt Carnegie Institution of Washington Department of Plant Biology Phone (650) 325-1521 x261 260 Panama St., Stanford, CA 94305 FAX (650) 325-6857 ------------------------------ Date: Wed, 22 Jul 1998 15:07:27 -0500 From: "STEPHEN MOORMAN" To: nih-image@io.ece.drexel.edu Subject: G3 Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit Is there a fix yet for the digitizer error when trying to capture images from the built-in video card in the G3's? ------------------------------ Date: Thu, 23 Jul 1998 09:10:19 +1200 From: Glenn Kearney To: nih-image-d@io.ece.drexel.edu Subject: Unsubscribe Message-Id: Content-Type: text/plain; charset="us-ascii" unsubscribe ------------------------------ Date: Wed, 22 Jul 1998 17:04:39 -0500 From: Arnout Ruifrok To: nih-image@io.ece.drexel.edu Subject: Re: pixel range Message-Id: Content-Type: text/plain; charset="us-ascii" >On Wed, 22 Jul 1998, Mark A Vivino wrote: > >> >Hello to all. >> >I am a new user to NIH Image. I am looking for any assistance in how to >> >determine the percentage of pixels of a specificed color range contained >> >within an image. This would be used in histological slide analyses. I >> >have used 'Sort by LUT' and individual macros such as 'count >> >BluePixels'. Is there a way to specify specific pixel color ranges, then >> >count or derive percentages of this range within a ROI? Your help is >> >appreciated. >> >> Just to start off on a tangent, I often have seen this or a related idea >> asked. Fundamentally what a scientist really needs is to know is: which >> pixels, or how many pixels, or what percent, have a dominant wavelength >> between 400 and 500 nm wavelength (or whatever range). It would be easier >> if pixels were not RGB or HSV, or anything else unrelated. Instead they >> should be wavelength(s) and density. Unfortunately, this is not the case >> but is sort or roughly like that with RGB and then the density is >> incorportated and things are sort of lumped all up and its a mess. >> >> I once wrote a macro which looked at the LUT to find which pixels have more >> of R than G or B. I then sought and counted those pixels in the image. This >> is sort of roughly what you request. Don't know if I can find it because it >> was years ago, but thats how I would still implement what you ask. >> >> Mark > >This may be hopelessly naive, but Photoshop allows selection of a color >range. You can do a pretty good job isolating parts of a color image with >these selection tools. How does Photoshop define a color range and sort >pixels by that definition? Could this be incorporated into a macro for >Image? > >-David > >David Ehrhardt >Carnegie Institution of Washington >Department of Plant Biology Phone (650) 325-1521 x261 >260 Panama St., Stanford, CA 94305 FAX (650) 325-6857 If I am not mistaken (I never carefully tested this), photoshop determines the R,G and B values in the selected points and adds a range to each value according to the 'fuzziness' setting (don't ask me how exactly the range is determined), and then thresholds the whole image according to these values, resulting in the selection of a 'box'(rectangular prism) (or multiple boxes) with sides parallel with the RGB axes. This is doable in image by density slicing in R, G, and B, and 'and'-ing the three color planes. ------------------------------ Date: Wed, 22 Jul 1998 18:41:44 -0400 From: Bill Miller To: nih-image@io.ece.drexel.edu, c.cathcart@sympatico.ca Subject: Re: Dage SIT cameras Message-Id: <3.0.5.32.19980722184144.00803920@mohawk.net> Content-Type: text/plain; charset="us-ascii" Chris - maybe you should have someone from Princeton contact him.. Bill At 06:07 PM 7/21/98 -0700, you wrote: >Howdy, > > We're thinking of replacing our very old COHU SIT >and therefore have been considering the Dage-MTI and Hamamatsu >cameras. We were considering the Dage VE 1000 SIT system, but >then heard that Dage-MTI was getting out of the "Scientific >imaging" and/or perhaps the "SIT camera" market(s); and have >been advised to avoid them. Any truth to this? > >Furthermore, we've been told the Hamamatsu 2400-8 system comes >with no choice of tube grade (but most likely a grade 2). Is >this also true? > >Any additional thoughts about these cameras, and/or the Argus-20 >DSP versus the Dage-MTI DSP-2000 would be appreciated. > >Thanks in advace, > >Aaron > > >-- >R. Aaron Warnock >"Nothing more is needed to destroy a man than the conviction >that his life's work is useless." -Antonin Artaud > >Lab Address: >Dept. of Pathology L-235 awarnock@cmgm.stanford.edu >Stanford, CA 94305 Tel. (650) 493-5000 x63167 > >Home Address: >777 Arguello Blvd. #304 Tel. (415) 831-3425 >San Francisco, CA 94118 > > > ------------------------------ Date: Thu, 23 Jul 1998 09:58:58 +1000 From: Steve Martin To: nih-image@io.ece.drexel.edu Subject: Re: pixel range Message-Id: Content-Type: text/plain; charset="us-ascii" Dear list, On Wed, 22 Jul 1998, amongst other things, Mark A Vivino wrote: > >It would be easier >if pixels were not RGB or HSV, or anything else unrelated. Instead they >should be wavelength(s) and density. Unfortunately, this is not the case Mark, I found these comments very thought-provoking. excuse my probable ignorance or niaivity, isn't hue angle related in some way to wavelength in many cases? I realise the pixels on our screens are mixtures of rgb, but they usually do not represent mixtures of rgb brought in from the real world. Unless we are using spectrophotometers, electronically we most often represent wavelengths in the real world in rgb because it is convenient to sample it and then display it that way. If I digitally photograph or frame grab a sodium yellow flame, isn't the hue of the resulting image some sort of representation of the original wavelength(s)? So if I had a table which converted hue angle to wavelength, perhaps I could create a real-values image in which pixel values represented the centres of wavelength ranges. Once I had made the table, I could code it into Image for all to use (:-) ? Maybe all you need is hue angle, but wavelength ranges may not be related in a very linear way to hue, I haven't tried to figure that out. I am sure there can be lots of dangers in this approach (mixed light sources etc.) and I am sure the list will hear about them 5 minutes after this is posted! This could still help out all those people who post to the list asking how to separate their coloured stains / leaf colours / etc. I hope this promotes some discussion even if it is only that I have just re-invented a wheel called hue! Steve ------------------------------ Date: Wed, 22 Jul 1998 21:30:35 -0500 From: scidi To: nih-image@io.ece.drexel.edu Subject: Integration on the LG-3 NuBus Card Message-id: <0EWJ00NUI0NM4Y@PM02SM.PMM.MCI.NET> Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit To NIH Users: I have recently installed NuBus LG-3 and TV-3 cards in my Power Mac 7100. I have had relatively few problems, except that when I go to Integrate on Chip, I get a printout on the Mitsubishi thermal printer that came with the system instead of the on chip integration. I can't figure it out. The only time I get any type of integration is when I select a small area within the image. I do have the Scion integration cable and I am using a Cohu 4910 CCD camera. Any help would be greatly appreciated. Thanks. Mark R. Molenda phone (414) 476-2694 fax (414) 645-8037 scidi@mci2000.com -------------------------------- End of nih-image-d Digest V98 Issue #18 *************************************** From nih-image-request@io.ece.drexel.edu Thu Jul 23 01:03 EDT 1998 X-UIDL: e5c2ff11d62cb68f6caee38752dc54d0 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id BAA25145; Thu, 23 Jul 1998 01:03:31 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 01:03:31 -0400 (EDT) Message-ID: <35B6C23B.F9AF6BCF@sisna.com> Date: Wed, 22 Jul 1998 22:55:23 -0600 From: "Christopher P. Tully" Reply-To: cptully@sisna.com X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: jmille@po-box.mcgill.ca CC: NIH-Image Subject: Re: pixel range References: <35B5DE9C.B66@po-box.mcgill.ca> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"vi-9p2.0.ps5.V6ijr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/119 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 884 Status: RO Maybe I'm missing the point here, but couldn't you just take a histogram of your image, and get the numbers from that? EVen if you are working in color, taking the histogram for each of the three color slices in the three slice RGB stack should get the information you want. Chris Tully Jeri Miller wrote: > > Hello to all. > I am a new user to NIH Image. I am looking for any assistance in how to > determine the percentage of pixels of a specificed color range contained > within an image. This would be used in histological slide analyses. I > have used 'Sort by LUT' and individual macros such as 'count > BluePixels'. Is there a way to specify specific pixel color ranges, then > count or derive percentages of this range within a ROI? Your help is > appreciated. > > J. Miller, Ph. D. Candidate > Ultrasound Research Imaging Lab > McGill University/RVH > Montreal, Quebec From nih-image-request@io.ece.drexel.edu Thu Jul 23 08:43 EDT 1998 X-UIDL: bc43d6d1f8df3a34334b177023cbfeb3 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA05796; Thu, 23 Jul 1998 08:43:14 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 08:43:14 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Thu, 23 Jul 1998 08:31:54 -0400 To: nih-image@io.ece.drexel.edu From: Laird Bloom Subject: montage macro Resent-Message-ID: <"eYWWu3.0.k21.doojr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/120 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 681 Status: RO NIH Image Users: Does anyone have a macro that makes a montage of RGB TIFF images? There was some discussion of ways to do this last summer; has anyone written the code? Ideally, I'd like to be able to make a "contact sheet" (e.g. about 24-35 small images on a page) as a way of keeping track of images I've recorded. My computer can't open more than about 10 TIFF images at a time, but I'd like to be able to make a montage without having to open each file up individually. Is there a way to open files in a folder one at a time without having to give them sequential numbers? I'd appreciate help on this. Thanks very much. Laird Bloom MIT Center for Cancer Research From nih-image-request@io.ece.drexel.edu Thu Jul 23 09:50 EDT 1998 X-UIDL: 290bb5183b31f751f1b5594d0134023a Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA12068; Thu, 23 Jul 1998 09:49:44 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 09:49:44 -0400 (EDT) Message-Id: In-Reply-To: <35B6C23B.F9AF6BCF@sisna.com> References: <35B5DE9C.B66@po-box.mcgill.ca> Mime-Version: 1.0 Date: Thu, 23 Jul 1998 09:37:04 -0500 To: nih-image@io.ece.drexel.edu From: Mark A Vivino Subject: Re: pixel range Resent-Message-ID: <"dJUNL2.0.xa2.mmpjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/121 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 890 Status: RO Chris Tully asks: >Maybe I'm missing the point here, but couldn't you just take a histogram >of your >image, and get the numbers from that? EVen if you are working in color, >taking >the histogram for each of the three color slices in the three slice RGB stack >should get the information you want. Well I'll have to think about it a little more. Roughly the answer seems to be yes. Specifically I think the answer is not very well. It would be truer for example if R was a wavelength value from 0 to 255 (or 0 to 100, or 600 to 700 nm) which represented the redness or red wavelengths of of a point, same for G and B, and you had seperately an intensity plane to take care of density. Roughly though I think what you say gives as good a simple answer as can be gotten without forming new image standards and and using a spectrophotometer, etc. I think using hue might do better. Mark From nih-image-request@io.ece.drexel.edu Thu Jul 23 10:45 EDT 1998 X-UIDL: ef94e1c7985673372209e938b4456642 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA16956; Thu, 23 Jul 1998 10:45:24 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 10:45:24 -0400 (EDT) X-SMTP-Posting-Origin: grains.mcgill.ca ([132.206.29.33]) Message-Id: <3.0.5.32.19980723103438.007a6950@po-box.mcgill.ca> X-Sender: mayoub@po-box.mcgill.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Thu, 23 Jul 1998 10:34:38 -0400 To: nih-image@io.ece.drexel.edu From: Micheline Ayoub Subject: Fourier Descriptors Mime-Version: 1.0 Resent-Message-ID: <"q55l-3.0.4v3.Teqjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/122 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 527 Status: RO Hi there, I am looking for a software that can apply Fourier descriptors in ima0ge analysis. I have binary images of barley seeds and I am interested in calculating the area, perimeter, width and length each seed. If any one knows about such a software and where to get it, please e-mail me the info or post it in this forum. Thank you Micheline Ayoub Plant Science Department Macdonald Campus of Mcgill University 21111 Lakeshore Rd. Ste-Anne-de-bellevue, QC, H9X 3V9 Tel: 514-398-7851 ext 8733 Fax: 514-398-7897 From nih-image-request@io.ece.drexel.edu Thu Jul 23 11:38 EDT 1998 X-UIDL: 6ee04a749490da4346f8637573332bb1 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA21600; Thu, 23 Jul 1998 11:36:39 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 11:36:39 -0400 (EDT) Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9ED6@cheetah.uits.iupui.edu> From: "Kirk, Todd Jason" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: zero prefix Date: Thu, 23 Jul 1998 10:22:47 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"BJgoX1.0.2z4.8Lrjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/123 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 862 Status: RO Can you do something like? '0000'+your_num check the size or your_num to see how many characters or value it has to see how many zeros to put if your_num>9 then '000'+your_num else '0000'+your_num Todd > -----Original Message----- > From: Anneke M.Th. Harbers and Ard Jonker [SMTP:a_team@dds.nl] > Sent: Wednesday, July 22, 1998 1:25 PM > To: nih-image@io.ece.drexel.edu > Subject: zero prefix > > Hi List, > I'm looking for an elegant solution to have a prefix on a string, so > as to obtain ' 00001' or ' 00012' ie. constant length. I also like to > find an elegant way to get a part of a string without character by > character moving to another string and then deleting that character > from the input string, ie. > string1:=concat(string2:3);delete(string2,0,3), which does not seem to > work for me. > Please reply by e-mail to a_team@dds.nl > Ard > From nih-image-request@io.ece.drexel.edu Thu Jul 23 12:26 EDT 1998 X-UIDL: 17893ccc7835303ac1e30efe391c0685 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA25911; Thu, 23 Jul 1998 12:26:12 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 12:26:12 -0400 (EDT) Sender: oscar Message-ID: <35B7629F.4AF9351C@umh.es> Date: Thu, 23 Jul 1998 18:19:43 +0200 From: oscar X-Mailer: Mozilla 4.04 [en] (X11; I; Linux 2.0.30 i586) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Content-Transfer-Encoding: 7bit Resent-Message-ID: <"HIlF21.0.xu5.K-rjr"@io> Resent-From: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/124 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 13 Status: RO unsubscribe From nih-image-request@io.ece.drexel.edu Thu Jul 23 14:27 EDT 1998 X-UIDL: a639d5a7b88488532be401dc9ad477f0 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA06490; Thu, 23 Jul 1998 14:27:21 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 14:27:21 -0400 (EDT) Date: Thu, 23 Jul 1998 13:13:18 -0500 Message-Id: In-Reply-To: References: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Arnout Ruifrok Subject: Re: pixel range Resent-Message-ID: <"Yj3JF.0.0I1.Xrtjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/125 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2674 Status: RO >Dear list, > >On Wed, 22 Jul 1998, amongst other things, Mark A Vivino wrote: >> >>It would be easier >>if pixels were not RGB or HSV, or anything else unrelated. Instead they >>should be wavelength(s) and density. Unfortunately, this is not the case > >Mark, I found these comments very thought-provoking. > >excuse my probable ignorance or niaivity, isn't hue angle related in some >way to wavelength in many cases? > >I realise the pixels on our screens are mixtures of rgb, but they usually >do not represent mixtures of rgb brought in from the real world. Unless we >are using spectrophotometers, electronically we most often represent >wavelengths in the real world in rgb because it is convenient to sample it >and then display it that way. > >If I digitally photograph or frame grab a sodium yellow flame, isn't the >hue of the resulting image some sort of representation of the original >wavelength(s)? > >So if I had a table which converted hue angle to wavelength, perhaps I >could create a real-values image in which pixel values represented the >centres of wavelength ranges. Once I had made the table, I could code it >into Image for all to use (:-) ? Maybe all you need is hue angle, but >wavelength ranges may not be related in a very linear way to hue, I haven't >tried to figure that out. > >I am sure there can be lots of dangers in this approach (mixed light >sources etc.) and I am sure the list will hear about them 5 minutes after >this is posted! This could still help out all those people who post to the >list asking how to separate their coloured stains / leaf colours / etc. > >I hope this promotes some discussion >even if it is only that I have just re-invented a wheel called hue! > >Steve In imaging addition of red and green gives yellow. How do you know if the original color was red plus green or true yellow from an RGB picture? That is not possible. To really select only yellow, you would have to have a narrow band-pass filter for only yellow (the exact wavelength). The problem is that yellow light excites green as well as red cones in the eye (and the -broad band- elemnts in a RGB camera) and the brain interprets this as yellow. But the brain also interprets a mix of true (narrow band) red and true green as yellow. So, in contrast to the ear, the eye (and camera) does not register the wavelenth of the light, only the relative excitation of the three types of color-sensitive cones. No way to convert the RGB information back to wavelength. The problem remains the same irrespective the color representation (RGB, HSI, etc), all color representations contain basically the same information, and are interchangable. Arnout From nih-image-request@io.ece.drexel.edu Thu Jul 23 14:42 EDT 1998 X-UIDL: 66564c3908ddf0b35ecf6fbd66d04ca1 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA07966; Thu, 23 Jul 1998 14:41:43 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 14:41:43 -0400 (EDT) Date: Thu, 23 Jul 1998 11:23:53 -0700 (PDT) From: David Ehrhardt Reply-To: David Ehrhardt To: nih-image@io.ece.drexel.edu Subject: Re: pixel range In-Reply-To: <35B6C23B.F9AF6BCF@sisna.com> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Y05IM3.0.Yd1.c3ujr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/126 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1707 Status: RO The histogram appraoch does not really answer the question here. Jeri needs to know which pixels contain a particular relative amount of each color component. A pixel with a particular value of blue might be part of say a purple or a blue pixel. I guess what is needed is something like what Arnout suggested; you classify each pixel as falling within a certain range of R AND G AND B values. Possibly more sophisticated selections could be made by working with relative pixel values to select a hue across darkness and lightness gradients. -David On Wed, 22 Jul 1998, Christopher P. Tully wrote: > Maybe I'm missing the point here, but couldn't you just take a histogram of your > image, and get the numbers from that? EVen if you are working in color, taking > the histogram for each of the three color slices in the three slice RGB stack > should get the information you want. > > Chris Tully > > Jeri Miller wrote: > > > > Hello to all. > > I am a new user to NIH Image. I am looking for any assistance in how to > > determine the percentage of pixels of a specificed color range contained > > within an image. This would be used in histological slide analyses. I > > have used 'Sort by LUT' and individual macros such as 'count > > BluePixels'. Is there a way to specify specific pixel color ranges, then > > count or derive percentages of this range within a ROI? Your help is > > appreciated. > > > > J. Miller, Ph. D. Candidate > > Ultrasound Research Imaging Lab > > McGill University/RVH > > Montreal, Quebec > > David Ehrhardt Carnegie Institution of Washington Department of Plant Biology Phone (650) 325-1521 x261 260 Panama St., Stanford, CA 94305 FAX (650) 325-6857 From nih-image-request@io.ece.drexel.edu Thu Jul 23 14:44 EDT 1998 X-UIDL: ad1326b2f59543c8bca480def6e0bf49 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA08264; Thu, 23 Jul 1998 14:44:11 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 14:44:11 -0400 (EDT) Message-Id: <199807231828.PAA02162@ceiun01.elogica.com.br> From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: Fourier Descriptors Date: Thu, 23 Jul 1998 15:33:45 -0300 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"BRXfj1.0.wh1.T6ujr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/127 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 975 Status: RO Dear Micheline, I receive a message with a adress that I think have what you need SPM Image Analysis http://www.dfm.dtu.dk/spip/ Good luck Rejane Galindo Universidade Federal Rural de Pernamnuco Plant Morphology and Anatomy ---------- > From: Micheline Ayoub > To: nih-image@io.ece.drexel.edu > Subject: Fourier Descriptors > Date: Quinta-feira, 23 Julho, 1998 11:34 > > Hi there, > > I am looking for a software that can apply Fourier descriptors in ima0ge > analysis. I have binary images of barley seeds and I am interested in > calculating the area, perimeter, width and length each seed. > > If any one knows about such a software and where to get it, please e-mail > me the info or post it in this forum. > > Thank you > > > > > > Micheline Ayoub > > Plant Science Department > Macdonald Campus of Mcgill University > 21111 Lakeshore Rd. > Ste-Anne-de-bellevue, QC, H9X 3V9 > > Tel: 514-398-7851 ext 8733 > Fax: 514-398-7897 > From nih-image-request@io.ece.drexel.edu Thu Jul 23 14:55 EDT 1998 X-UIDL: 563e3e6c308ea5eb989bfe45974fac0f Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA09188; Thu, 23 Jul 1998 14:55:10 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 14:55:10 -0400 (EDT) Message-Id: In-Reply-To: References: Mime-Version: 1.0 Date: Thu, 23 Jul 1998 14:44:34 -0500 To: nih-image@io.ece.drexel.edu From: Mark A Vivino Subject: Re: pixel range Resent-Message-ID: <"gwIpi.0.N-1.sGujr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/128 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1388 Status: RO >In imaging addition of red and green gives yellow. How do you know if the >original color was red plus green or true yellow from an RGB picture? That >is not possible. To really select only yellow, you would have to have a >narrow band-pass filter for only yellow (the exact wavelength). The problem >is that yellow light excites green as well as red cones in the eye (and the >-broad band- elemnts in a RGB camera) and the brain interprets this as >yellow. But the brain also interprets a mix of true (narrow band) red and >true green as yellow. So, in contrast to the ear, the eye (and camera) does >not register the wavelenth of the light, only the relative excitation of >the three types of color-sensitive cones. No way to convert the RGB >information back to wavelength. The problem remains the same irrespective >the color representation (RGB, HSI, etc), all color representations contain >basically the same information, and are interchangable. Good point! Just read this myself in "Seeing the Light, Optics in Nature, Photography, Color, Vision and Holography" by David Falk. Wiley books. Nice easy to read, unlike most IP books. He shows on page 242 how a 590nm and a mix of 550 and 690 look the same to the eye. Oh well, I guess we need a 3D volume to represent a 2D plane. Have width, height and 300 planes of wavelength for each image. Anything less is a guess. Mark From nih-image-request@io.ece.drexel.edu Thu Jul 23 15:44 EDT 1998 X-UIDL: b643d708036c1b26881692759e74ee2e Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA12910; Thu, 23 Jul 1998 15:44:10 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 15:44:10 -0400 (EDT) Message-Id: <199807231925.QAA14158@ceiun01.elogica.com.br> From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: Fourier Descriptors Date: Thu, 23 Jul 1998 16:18:14 -0300 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"AHMKG.0._q2.Wxujr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/129 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 976 Status: RO Dear Micheline, I receive a message with a adress that I think have what you need SPM Image Analysis http://www.dfm.dtu.dk/spip/ Good luck Rejane Galindo Universidade Federal Rural de Pernambuco Plant Morphology and Anatomy ---------- > From: Micheline Ayoub > To: nih-image@io.ece.drexel.edu > Subject: Fourier Descriptors > Date: Quinta-feira, 23 Julho, 1998 11:34 > > Hi there, > > I am looking for a software that can apply Fourier descriptors in ima0ge > analysis. I have binary images of barley seeds and I am interested in > calculating the area, perimeter, width and length each seed. > > If any one knows about such a software and where to get it, please e-mail > me the info or post it in this forum. > > Thank you > > > > > > Micheline Ayoub > > Plant Science Department > Macdonald Campus of Mcgill University > 21111 Lakeshore Rd. > Ste-Anne-de-bellevue, QC, H9X 3V9 > > Tel: 514-398-7851 ext 8733 > Fax: 514-398-7897 > From nih-image-request@io.ece.drexel.edu Thu Jul 23 20:39 EDT 1998 X-UIDL: 3179772c16ac3039dab14acfe00bbf85 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA03048; Thu, 23 Jul 1998 20:39:23 -0400 (EDT) Resent-Date: Thu, 23 Jul 1998 20:39:23 -0400 (EDT) Message-ID: From: "Goldsmith, Noel" To: "'Image Mailing List'" Subject: Display of Changing Numbers. Date: Fri, 24 Jul 1998 10:29:57 +1000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"9ZEnp1.0.jV.PMzjr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/130 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1307 Status: RO Hi, Thanks to Stein Roervik I am now communicating happily with the Ludl stage. And it is all fairly painless so far. When I get it all working well I will share it. Now I can get the position of the stage by asking it where x y z , and it returns the appropriate numbers in a string which I can sort out and scale etc. The user can push a button on the joystick and this is noted by the controller and the postion at that point can be recorded. What I want to do is display a window or a panel in a window which shows the three numbers with appropriate labels (X Y and Z for instance) and updates these numbers until I tell it to stop. So that as the stage is moved with the joystick the numbers roll and follow the position. The frequency of update might be limited as the stage controller communicates at 9600 baud. But I guess if I get an update every 0.1 second or so it will be ok. Now my question. What is the best method to use in Image. A text window with big writing. How to delete the old numbers. An Image window with some hard written labels and the new numbers overwritten. How to remove the old ones. The Info window works well but it is in a small font. So if anyone has tried this sort of thing and is willing to share their experience I would be grateful. Best Regards Noel Goldsmith. From nih-image-d-request@io.ece.drexel.edu Thu Jul 23 20:39 EDT 1998 X-UIDL: 20d19228e25d3f118981dacb9ac4b214 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA03116; Thu, 23 Jul 1998 20:39:47 -0400 (EDT) Date: Thu, 23 Jul 1998 20:39:47 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807240039.UAA03116@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #19 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/19 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 17698 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 19 Today's Topics: Re: pixel range [ "Christopher P. Tully" ] Re: pixel range [ Mark A Vivino ] Re: pixel range [ Arnout Ruifrok To: jmille@po-box.mcgill.ca CC: NIH-Image Subject: Re: pixel range Message-ID: <35B6C23B.F9AF6BCF@sisna.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Maybe I'm missing the point here, but couldn't you just take a histogram of your image, and get the numbers from that? EVen if you are working in color, taking the histogram for each of the three color slices in the three slice RGB stack should get the information you want. Chris Tully Jeri Miller wrote: > > Hello to all. > I am a new user to NIH Image. I am looking for any assistance in how to > determine the percentage of pixels of a specificed color range contained > within an image. This would be used in histological slide analyses. I > have used 'Sort by LUT' and individual macros such as 'count > BluePixels'. Is there a way to specify specific pixel color ranges, then > count or derive percentages of this range within a ROI? Your help is > appreciated. > > J. Miller, Ph. D. Candidate > Ultrasound Research Imaging Lab > McGill University/RVH > Montreal, Quebec ------------------------------ Date: Thu, 23 Jul 1998 08:31:54 -0400 From: Laird Bloom To: nih-image@io.ece.drexel.edu Subject: montage macro Message-Id: Content-Type: text/plain; charset="us-ascii" NIH Image Users: Does anyone have a macro that makes a montage of RGB TIFF images? There was some discussion of ways to do this last summer; has anyone written the code? Ideally, I'd like to be able to make a "contact sheet" (e.g. about 24-35 small images on a page) as a way of keeping track of images I've recorded. My computer can't open more than about 10 TIFF images at a time, but I'd like to be able to make a montage without having to open each file up individually. Is there a way to open files in a folder one at a time without having to give them sequential numbers? I'd appreciate help on this. Thanks very much. Laird Bloom MIT Center for Cancer Research ------------------------------ Date: Thu, 23 Jul 1998 09:37:04 -0500 From: Mark A Vivino To: nih-image@io.ece.drexel.edu Subject: Re: pixel range Message-Id: Content-Type: text/plain; charset="us-ascii" Chris Tully asks: >Maybe I'm missing the point here, but couldn't you just take a histogram >of your >image, and get the numbers from that? EVen if you are working in color, >taking >the histogram for each of the three color slices in the three slice RGB stack >should get the information you want. Well I'll have to think about it a little more. Roughly the answer seems to be yes. Specifically I think the answer is not very well. It would be truer for example if R was a wavelength value from 0 to 255 (or 0 to 100, or 600 to 700 nm) which represented the redness or red wavelengths of of a point, same for G and B, and you had seperately an intensity plane to take care of density. Roughly though I think what you say gives as good a simple answer as can be gotten without forming new image standards and and using a spectrophotometer, etc. I think using hue might do better. Mark ------------------------------ Date: Thu, 23 Jul 1998 10:34:38 -0400 From: Micheline Ayoub To: nih-image@io.ece.drexel.edu Subject: Fourier Descriptors Message-Id: <3.0.5.32.19980723103438.007a6950@po-box.mcgill.ca> Content-Type: text/plain; charset="us-ascii" Hi there, I am looking for a software that can apply Fourier descriptors in ima0ge analysis. I have binary images of barley seeds and I am interested in calculating the area, perimeter, width and length each seed. If any one knows about such a software and where to get it, please e-mail me the info or post it in this forum. Thank you Micheline Ayoub Plant Science Department Macdonald Campus of Mcgill University 21111 Lakeshore Rd. Ste-Anne-de-bellevue, QC, H9X 3V9 Tel: 514-398-7851 ext 8733 Fax: 514-398-7897 ------------------------------ Date: Thu, 23 Jul 1998 10:22:47 -0500 From: "Kirk, Todd Jason" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: zero prefix Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9ED6@cheetah.uits.iupui.edu> Content-Type: text/plain Can you do something like? '0000'+your_num check the size or your_num to see how many characters or value it has to see how many zeros to put if your_num>9 then '000'+your_num else '0000'+your_num Todd > -----Original Message----- > From: Anneke M.Th. Harbers and Ard Jonker [SMTP:a_team@dds.nl] > Sent: Wednesday, July 22, 1998 1:25 PM > To: nih-image@io.ece.drexel.edu > Subject: zero prefix > > Hi List, > I'm looking for an elegant solution to have a prefix on a string, so > as to obtain ' 00001' or ' 00012' ie. constant length. I also like to > find an elegant way to get a part of a string without character by > character moving to another string and then deleting that character > from the input string, ie. > string1:=concat(string2:3);delete(string2,0,3), which does not seem to > work for me. > Please reply by e-mail to a_team@dds.nl > Ard > ------------------------------ Date: Thu, 23 Jul 1998 18:19:43 +0200 From: oscar To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-ID: <35B7629F.4AF9351C@umh.es> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit unsubscribe ------------------------------ Date: Thu, 23 Jul 1998 13:13:18 -0500 From: Arnout Ruifrok To: nih-image@io.ece.drexel.edu Subject: Re: pixel range Message-Id: Content-Type: text/plain; charset="us-ascii" >Dear list, > >On Wed, 22 Jul 1998, amongst other things, Mark A Vivino wrote: >> >>It would be easier >>if pixels were not RGB or HSV, or anything else unrelated. Instead they >>should be wavelength(s) and density. Unfortunately, this is not the case > >Mark, I found these comments very thought-provoking. > >excuse my probable ignorance or niaivity, isn't hue angle related in some >way to wavelength in many cases? > >I realise the pixels on our screens are mixtures of rgb, but they usually >do not represent mixtures of rgb brought in from the real world. Unless we >are using spectrophotometers, electronically we most often represent >wavelengths in the real world in rgb because it is convenient to sample it >and then display it that way. > >If I digitally photograph or frame grab a sodium yellow flame, isn't the >hue of the resulting image some sort of representation of the original >wavelength(s)? > >So if I had a table which converted hue angle to wavelength, perhaps I >could create a real-values image in which pixel values represented the >centres of wavelength ranges. Once I had made the table, I could code it >into Image for all to use (:-) ? Maybe all you need is hue angle, but >wavelength ranges may not be related in a very linear way to hue, I haven't >tried to figure that out. > >I am sure there can be lots of dangers in this approach (mixed light >sources etc.) and I am sure the list will hear about them 5 minutes after >this is posted! This could still help out all those people who post to the >list asking how to separate their coloured stains / leaf colours / etc. > >I hope this promotes some discussion >even if it is only that I have just re-invented a wheel called hue! > >Steve In imaging addition of red and green gives yellow. How do you know if the original color was red plus green or true yellow from an RGB picture? That is not possible. To really select only yellow, you would have to have a narrow band-pass filter for only yellow (the exact wavelength). The problem is that yellow light excites green as well as red cones in the eye (and the -broad band- elemnts in a RGB camera) and the brain interprets this as yellow. But the brain also interprets a mix of true (narrow band) red and true green as yellow. So, in contrast to the ear, the eye (and camera) does not register the wavelenth of the light, only the relative excitation of the three types of color-sensitive cones. No way to convert the RGB information back to wavelength. The problem remains the same irrespective the color representation (RGB, HSI, etc), all color representations contain basically the same information, and are interchangable. Arnout ------------------------------ Date: Thu, 23 Jul 1998 11:23:53 -0700 (PDT) From: David Ehrhardt To: nih-image@io.ece.drexel.edu Subject: Re: pixel range Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII The histogram appraoch does not really answer the question here. Jeri needs to know which pixels contain a particular relative amount of each color component. A pixel with a particular value of blue might be part of say a purple or a blue pixel. I guess what is needed is something like what Arnout suggested; you classify each pixel as falling within a certain range of R AND G AND B values. Possibly more sophisticated selections could be made by working with relative pixel values to select a hue across darkness and lightness gradients. -David On Wed, 22 Jul 1998, Christopher P. Tully wrote: > Maybe I'm missing the point here, but couldn't you just take a histogram of your > image, and get the numbers from that? EVen if you are working in color, taking > the histogram for each of the three color slices in the three slice RGB stack > should get the information you want. > > Chris Tully > > Jeri Miller wrote: > > > > Hello to all. > > I am a new user to NIH Image. I am looking for any assistance in how to > > determine the percentage of pixels of a specificed color range contained > > within an image. This would be used in histological slide analyses. I > > have used 'Sort by LUT' and individual macros such as 'count > > BluePixels'. Is there a way to specify specific pixel color ranges, then > > count or derive percentages of this range within a ROI? Your help is > > appreciated. > > > > J. Miller, Ph. D. Candidate > > Ultrasound Research Imaging Lab > > McGill University/RVH > > Montreal, Quebec > > David Ehrhardt Carnegie Institution of Washington Department of Plant Biology Phone (650) 325-1521 x261 260 Panama St., Stanford, CA 94305 FAX (650) 325-6857 ------------------------------ Date: Thu, 23 Jul 1998 15:33:45 -0300 From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: Fourier Descriptors Message-Id: <199807231828.PAA02162@ceiun01.elogica.com.br> Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Micheline, I receive a message with a adress that I think have what you need SPM Image Analysis http://www.dfm.dtu.dk/spip/ Good luck Rejane Galindo Universidade Federal Rural de Pernamnuco Plant Morphology and Anatomy ---------- > From: Micheline Ayoub > To: nih-image@io.ece.drexel.edu > Subject: Fourier Descriptors > Date: Quinta-feira, 23 Julho, 1998 11:34 > > Hi there, > > I am looking for a software that can apply Fourier descriptors in ima0ge > analysis. I have binary images of barley seeds and I am interested in > calculating the area, perimeter, width and length each seed. > > If any one knows about such a software and where to get it, please e-mail > me the info or post it in this forum. > > Thank you > > > > > > Micheline Ayoub > > Plant Science Department > Macdonald Campus of Mcgill University > 21111 Lakeshore Rd. > Ste-Anne-de-bellevue, QC, H9X 3V9 > > Tel: 514-398-7851 ext 8733 > Fax: 514-398-7897 > ------------------------------ Date: Thu, 23 Jul 1998 14:44:34 -0500 From: Mark A Vivino To: nih-image@io.ece.drexel.edu Subject: Re: pixel range Message-Id: Content-Type: text/plain; charset="us-ascii" >In imaging addition of red and green gives yellow. How do you know if the >original color was red plus green or true yellow from an RGB picture? That >is not possible. To really select only yellow, you would have to have a >narrow band-pass filter for only yellow (the exact wavelength). The problem >is that yellow light excites green as well as red cones in the eye (and the >-broad band- elemnts in a RGB camera) and the brain interprets this as >yellow. But the brain also interprets a mix of true (narrow band) red and >true green as yellow. So, in contrast to the ear, the eye (and camera) does >not register the wavelenth of the light, only the relative excitation of >the three types of color-sensitive cones. No way to convert the RGB >information back to wavelength. The problem remains the same irrespective >the color representation (RGB, HSI, etc), all color representations contain >basically the same information, and are interchangable. Good point! Just read this myself in "Seeing the Light, Optics in Nature, Photography, Color, Vision and Holography" by David Falk. Wiley books. Nice easy to read, unlike most IP books. He shows on page 242 how a 590nm and a mix of 550 and 690 look the same to the eye. Oh well, I guess we need a 3D volume to represent a 2D plane. Have width, height and 300 planes of wavelength for each image. Anything less is a guess. Mark ------------------------------ Date: Thu, 23 Jul 1998 16:18:14 -0300 From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: Fourier Descriptors Message-Id: <199807231925.QAA14158@ceiun01.elogica.com.br> Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Micheline, I receive a message with a adress that I think have what you need SPM Image Analysis http://www.dfm.dtu.dk/spip/ Good luck Rejane Galindo Universidade Federal Rural de Pernambuco Plant Morphology and Anatomy ---------- > From: Micheline Ayoub > To: nih-image@io.ece.drexel.edu > Subject: Fourier Descriptors > Date: Quinta-feira, 23 Julho, 1998 11:34 > > Hi there, > > I am looking for a software that can apply Fourier descriptors in ima0ge > analysis. I have binary images of barley seeds and I am interested in > calculating the area, perimeter, width and length each seed. > > If any one knows about such a software and where to get it, please e-mail > me the info or post it in this forum. > > Thank you > > > > > > Micheline Ayoub > > Plant Science Department > Macdonald Campus of Mcgill University > 21111 Lakeshore Rd. > Ste-Anne-de-bellevue, QC, H9X 3V9 > > Tel: 514-398-7851 ext 8733 > Fax: 514-398-7897 > ------------------------------ Date: Fri, 24 Jul 1998 10:29:57 +1000 From: "Goldsmith, Noel" To: "'Image Mailing List'" Subject: Display of Changing Numbers. Message-ID: Content-Type: text/plain Hi, Thanks to Stein Roervik I am now communicating happily with the Ludl stage. And it is all fairly painless so far. When I get it all working well I will share it. Now I can get the position of the stage by asking it where x y z , and it returns the appropriate numbers in a string which I can sort out and scale etc. The user can push a button on the joystick and this is noted by the controller and the postion at that point can be recorded. What I want to do is display a window or a panel in a window which shows the three numbers with appropriate labels (X Y and Z for instance) and updates these numbers until I tell it to stop. So that as the stage is moved with the joystick the numbers roll and follow the position. The frequency of update might be limited as the stage controller communicates at 9600 baud. But I guess if I get an update every 0.1 second or so it will be ok. Now my question. What is the best method to use in Image. A text window with big writing. How to delete the old numbers. An Image window with some hard written labels and the new numbers overwritten. How to remove the old ones. The Info window works well but it is in a small font. So if anyone has tried this sort of thing and is willing to share their experience I would be grateful. Best Regards Noel Goldsmith. -------------------------------- End of nih-image-d Digest V98 Issue #19 *************************************** From nih-image-request@io.ece.drexel.edu Fri Jul 24 09:50 EDT 1998 X-UIDL: e3f5088bde99af1cc7f1cb3c8f275c61 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA09492; Fri, 24 Jul 1998 09:50:04 -0400 (EDT) Resent-Date: Fri, 24 Jul 1998 09:50:04 -0400 (EDT) Message-ID: <19980724133612.22265.rocketmail@send1a.yahoomail.com> Date: Fri, 24 Jul 1998 06:36:12 -0700 (PDT) From: first last Subject: brightness values over time To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"Z3GLV.0.m22.cu8kr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/131 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 662 Status: RO Dear users of NIH image: I have stacks of gray scale images, representing a time lapse, and I would like to measure the values for the brightness of single pixels or for the average brightness of a small ROI, respectively, for each frame in the image stack. The results of these measurements should be written in a column to a text window for later saving to an ASCII file. I could not find a macro for doing this and I would highly appreciate any suggestions of how to write such a macro. Thank you very much in advance. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Fri Jul 24 10:08 EDT 1998 X-UIDL: 93a9b8df38c71c887a8ac5ea5a75ff60 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA11164; Fri, 24 Jul 1998 10:08:43 -0400 (EDT) Resent-Date: Fri, 24 Jul 1998 10:08:43 -0400 (EDT) Date: Fri, 24 Jul 1998 09:57:38 -0400 From: "J.P. Simmons" Message-Id: <9807241357.AA17033@cindy.ml.wpafb.af.mil> To: nih-image@io.ece.drexel.edu Subject: montage macro Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Md5: ojMfNMmjy49Q8MoSy5LZSA== Resent-Message-ID: <"5jlTT3.0.dU2.sB9kr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/132 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 967 Status: RO I don't know how to do that with NIH Image, but if you're running on a Mac, there's a software package by the name of GraphicConverter (shareware) that will do exactly this. You may also want to look at the commercial software Extensis Fetch. Jeff Simmons UES, Inc. >NIH Image Users: > > Does anyone have a macro that makes a montage of RGB TIFF images? >There was some discussion of ways to do this last summer; has anyone >written the code? > > Ideally, I'd like to be able to make a "contact sheet" (e.g. about >24-35 small images on a page) as a way of keeping track of images I've >recorded. My computer can't open more than about 10 TIFF images at a time, >but I'd like to be able to make a montage without having to open each file >up individually. Is there a way to open files in a folder one at a time >without having to give them sequential numbers? > > I'd appreciate help on this. > >Thanks very much. > >Laird Bloom >MIT Center for Cancer Research From nih-image-request@io.ece.drexel.edu Fri Jul 24 11:20 EDT 1998 X-UIDL: 81723c43c152f7e829110aaf9d812986 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA17538; Fri, 24 Jul 1998 11:20:43 -0400 (EDT) Resent-Date: Fri, 24 Jul 1998 11:20:43 -0400 (EDT) Date: Fri, 24 Jul 1998 08:10:16 -0700 (PDT) From: "R. Hard" To: nih-image@io.ece.drexel.edu Subject: 2nd Announcement-Optical Microscopy Course Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"n974p.0.q_3.XFAkr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/133 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2607 Status: RO Course Announcement Title: Optical Microscopy and Imaging in the Biomedical Sciences When: October 7 - October 15, 1998 Where: Marine Biology Laboratory, Woods Hole, MA, USA Tuition: $2050 (Includes room and board) Application Deadline: August 4, 1998 Admission application and information: Carol Harnel, Admissions Coordinator Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543-1015 (508) 289-7401 Internet: admissions@mbl.edu WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat) Course Director: Colin S. Izzard, State University of New York @ Albany Phone: [518] 442 - 4367 EMail: csizzard@csc.albany.edu Course Description: For Whom: Designed primarily for research scientists, physicians, postdoctoral trainees and advanced graduate students in animal, plant, medical and material sciences. Non-biologists seeking a comprehensive introduction to microscopy and video-imaging will benefit greatly from this course as well. There are no specific prerequisites, but an understanding of the basic principles of optics is desirable. Limited to 24 students. The eight day course consists of lectures, laboratory demonstrations, exercises and discussions that will enable the participant to obtain and interpret microscope images of high quality, to perform quantitative optical measurements, and to produce photographic and video records for documentation and analysis. Topics to be covered include: principles of microscope design and image formation bright field, dark field, phase contrast, differential interference contrast, interference reflection, and fluorescence microscopy confocal scanning microscopy and image deconvolution digital image restoration and 3-D reconstruction video imaging, recording, enhancement, and intensification analog and digital image processing and analysis fluorescent probes and ratio-imaging laser tweezers and laser scissors Applications to live cells will be emphasized; other specimens will be covered as well. Students will have direct hands-on experience with state-of-the-art microscopes, video cameras, recorders and image processing equipment provided by major optical and electronics companies. Instruction will be provided by experienced staff from universities and industry. Students are encouraged to bring their own biological (primary cultures, cell lines, etc.) and material specimens and to discuss individual research problems with the faculty. From nih-image-request@io.ece.drexel.edu Fri Jul 24 11:51 EDT 1998 X-UIDL: 305bc6b32814ae43fce4586b4951418a Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA20113; Fri, 24 Jul 1998 11:51:09 -0400 (EDT) Resent-Date: Fri, 24 Jul 1998 11:51:09 -0400 (EDT) X-Sender: sdb@pop1.liv.ac.uk Message-Id: In-Reply-To: <199807240031.UAA02203@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Fri, 24 Jul 1998 16:42:56 +0100 To: nih-image@io.ece.drexel.edu From: Steve Barrett Subject: Re: montage macro Cc: Laird Bloom Resent-Message-ID: <"LrBlA2.0.8i4.ciAkr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/134 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1032 Status: RO > Does anyone have a macro that makes a montage of RGB TIFF images? >There was some discussion of ways to do this last summer; has anyone >written the code? 'Image SXM' is a version of NIH Image that has been extended for use with scanning microscope images such as those from SEMs or SPMs. It also has a number of general features which users may find useful. One is the ability to browse through the images in a folder, creating 'contact sheets' that can be double-clicked to load the original image, or printed out automatically. Information about Image SXM can be found at http://reg.ssci.liv.ac.uk. A copy of the Image SXM installer is in the spin-offs folder of the NIH Image server. ___________________________________________________________________ Dr Steve Barrett Surface Science Research Centre University of Liverpool Liverpool L69 3BX United Kingdom Tel: 44-(0)151-794-3874 / 3894 / 3870 Fax: 44-(0)151-708-0662 Email: S.D.Barrett@liv.ac.uk ___________________________________________________________________ From nih-image-request@io.ece.drexel.edu Fri Jul 24 15:55 EDT 1998 X-UIDL: 0a6ca8ca37120954e8f988928c112cfa Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA07460; Fri, 24 Jul 1998 15:54:48 -0400 (EDT) Resent-Date: Fri, 24 Jul 1998 15:54:48 -0400 (EDT) X-Authentication-Warning: pagan.vims.edu: cutter owned process doing -bs Date: Fri, 24 Jul 1998 15:07:10 -0400 (EDT) From: Randy Cutter To: nih-image@io.ece.drexel.edu Subject: real result and thresholding In-Reply-To: <199807240039.UAA03132@io.ECE.Drexel.EDU> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"GACMu.0.Ie1.bHEkr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/135 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 504 Status: RO Is there a way in Image to threshold the real result of image subtraction such that negative values are all converted to zero? Since the real result is mapped to values from 0-255 for display, the LUT has those values. Should I work with a macro to examine each pixel value? Thanks, Randy. --------------------- Randy Cutter Virginia Institute of Marine Science Route 1208 Gloucester Point, VA 23062 USA phone 804 684-7365 fax 804 684-7399 or 7045 email: cutter@vims.edu --------------------- From nih-image-request@io.ece.drexel.edu Fri Jul 24 16:56 EDT 1998 X-UIDL: 5b247436d4237d3bdea29ddb4b7afd73 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA11240; Fri, 24 Jul 1998 16:56:31 -0400 (EDT) Resent-Date: Fri, 24 Jul 1998 16:56:31 -0400 (EDT) Message-ID: From: "Mariann Roetzheim" To: Subject: Question! Date: Fri, 24 Jul 1998 13:54:03 -0700 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"Pv99L2.0.fb2.wCFkr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/136 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 543 Status: RO Hello, My name is Elizabeth and I am a new user of Scion Image analysis beta version three. I have run into what I consider a bug, where I have outlined area of interest using the oval, polygonal, or freehand selection tool and the area measures 0.00sq inches no matter how much I select of the image. The only tool that will give me a measurement is the rectangle. Has anyone else run into this problem? I am also looking for the mean gray value. Any answers or input would be helpful. Thank you Elizabeth Roetzheim roetzheimm@marotz.com From nih-image-request@io.ece.drexel.edu Fri Jul 24 21:50 EDT 1998 X-UIDL: d77f71ea7fcc4dbc6553e9b26dfaac31 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA00614; Fri, 24 Jul 1998 21:50:09 -0400 (EDT) Resent-Date: Fri, 24 Jul 1998 21:50:09 -0400 (EDT) X-Sender: pmerm@pmerm.pobox.stanford.edu Message-Id: Mime-Version: 1.0 Date: Fri, 24 Jul 1998 18:44:02 -0800 To: nih-image@io.ece.drexel.edu From: Paul G Mermelstein Subject: subscribe Resent-Message-ID: <"4yXGb.0.yJ7.HXJkr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/137 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 228 Status: RO Paul G. Mermelstein Ph.D. Department of Molecular and Cellular Physiology Stanford University School of Medicine Beckman Center Room B101 Stanford, CA 94305 phone: (650) 725-7564 fax: (650) 498-5663 email: pmerm@stanford.edu From nih-image-d-request@io.ece.drexel.edu Sat Jul 25 06:11 EDT 1998 X-UIDL: cdd2b20a093889bd5f3e5d3957686b42 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA06640; Sat, 25 Jul 1998 06:11:38 -0400 (EDT) Date: Sat, 25 Jul 1998 06:11:38 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807251011.GAA06640@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #20 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/20 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 9453 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 20 Today's Topics: brightness values over time [ first last ] montage macro [ "J.P. Simmons" ] Re: montage macro [ Steve Barrett ] Question! [ "Mariann Roetzheim" To: nih-image@io.ece.drexel.edu Subject: brightness values over time Message-ID: <19980724133612.22265.rocketmail@send1a.yahoomail.com> Content-Type: text/plain; charset=us-ascii Dear users of NIH image: I have stacks of gray scale images, representing a time lapse, and I would like to measure the values for the brightness of single pixels or for the average brightness of a small ROI, respectively, for each frame in the image stack. The results of these measurements should be written in a column to a text window for later saving to an ASCII file. I could not find a macro for doing this and I would highly appreciate any suggestions of how to write such a macro. Thank you very much in advance. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Fri, 24 Jul 1998 09:57:38 -0400 From: "J.P. Simmons" To: nih-image@io.ece.drexel.edu Subject: montage macro Message-Id: <9807241357.AA17033@cindy.ml.wpafb.af.mil> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Md5: ojMfNMmjy49Q8MoSy5LZSA== I don't know how to do that with NIH Image, but if you're running on a Mac, there's a software package by the name of GraphicConverter (shareware) that will do exactly this. You may also want to look at the commercial software Extensis Fetch. Jeff Simmons UES, Inc. >NIH Image Users: > > Does anyone have a macro that makes a montage of RGB TIFF images? >There was some discussion of ways to do this last summer; has anyone >written the code? > > Ideally, I'd like to be able to make a "contact sheet" (e.g. about >24-35 small images on a page) as a way of keeping track of images I've >recorded. My computer can't open more than about 10 TIFF images at a time, >but I'd like to be able to make a montage without having to open each file >up individually. Is there a way to open files in a folder one at a time >without having to give them sequential numbers? > > I'd appreciate help on this. > >Thanks very much. > >Laird Bloom >MIT Center for Cancer Research ------------------------------ Date: Fri, 24 Jul 1998 08:10:16 -0700 (PDT) From: "R. Hard" To: nih-image@io.ece.drexel.edu Subject: 2nd Announcement-Optical Microscopy Course Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Course Announcement Title: Optical Microscopy and Imaging in the Biomedical Sciences When: October 7 - October 15, 1998 Where: Marine Biology Laboratory, Woods Hole, MA, USA Tuition: $2050 (Includes room and board) Application Deadline: August 4, 1998 Admission application and information: Carol Harnel, Admissions Coordinator Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543-1015 (508) 289-7401 Internet: admissions@mbl.edu WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat) Course Director: Colin S. Izzard, State University of New York @ Albany Phone: [518] 442 - 4367 EMail: csizzard@csc.albany.edu Course Description: For Whom: Designed primarily for research scientists, physicians, postdoctoral trainees and advanced graduate students in animal, plant, medical and material sciences. Non-biologists seeking a comprehensive introduction to microscopy and video-imaging will benefit greatly from this course as well. There are no specific prerequisites, but an understanding of the basic principles of optics is desirable. Limited to 24 students. The eight day course consists of lectures, laboratory demonstrations, exercises and discussions that will enable the participant to obtain and interpret microscope images of high quality, to perform quantitative optical measurements, and to produce photographic and video records for documentation and analysis. Topics to be covered include: principles of microscope design and image formation bright field, dark field, phase contrast, differential interference contrast, interference reflection, and fluorescence microscopy confocal scanning microscopy and image deconvolution digital image restoration and 3-D reconstruction video imaging, recording, enhancement, and intensification analog and digital image processing and analysis fluorescent probes and ratio-imaging laser tweezers and laser scissors Applications to live cells will be emphasized; other specimens will be covered as well. Students will have direct hands-on experience with state-of-the-art microscopes, video cameras, recorders and image processing equipment provided by major optical and electronics companies. Instruction will be provided by experienced staff from universities and industry. Students are encouraged to bring their own biological (primary cultures, cell lines, etc.) and material specimens and to discuss individual research problems with the faculty. ------------------------------ Date: Fri, 24 Jul 1998 16:42:56 +0100 From: Steve Barrett To: nih-image@io.ece.drexel.edu Cc: Laird Bloom Subject: Re: montage macro Message-Id: Content-Type: text/plain; charset="us-ascii" > Does anyone have a macro that makes a montage of RGB TIFF images? >There was some discussion of ways to do this last summer; has anyone >written the code? 'Image SXM' is a version of NIH Image that has been extended for use with scanning microscope images such as those from SEMs or SPMs. It also has a number of general features which users may find useful. One is the ability to browse through the images in a folder, creating 'contact sheets' that can be double-clicked to load the original image, or printed out automatically. Information about Image SXM can be found at http://reg.ssci.liv.ac.uk. A copy of the Image SXM installer is in the spin-offs folder of the NIH Image server. ___________________________________________________________________ Dr Steve Barrett Surface Science Research Centre University of Liverpool Liverpool L69 3BX United Kingdom Tel: 44-(0)151-794-3874 / 3894 / 3870 Fax: 44-(0)151-708-0662 Email: S.D.Barrett@liv.ac.uk ___________________________________________________________________ ------------------------------ Date: Fri, 24 Jul 1998 15:07:10 -0400 (EDT) From: Randy Cutter To: nih-image@io.ece.drexel.edu Subject: real result and thresholding Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Is there a way in Image to threshold the real result of image subtraction such that negative values are all converted to zero? Since the real result is mapped to values from 0-255 for display, the LUT has those values. Should I work with a macro to examine each pixel value? Thanks, Randy. --------------------- Randy Cutter Virginia Institute of Marine Science Route 1208 Gloucester Point, VA 23062 USA phone 804 684-7365 fax 804 684-7399 or 7045 email: cutter@vims.edu --------------------- ------------------------------ Date: Fri, 24 Jul 1998 13:54:03 -0700 From: "Mariann Roetzheim" To: Subject: Question! Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello, My name is Elizabeth and I am a new user of Scion Image analysis beta version three. I have run into what I consider a bug, where I have outlined area of interest using the oval, polygonal, or freehand selection tool and the area measures 0.00sq inches no matter how much I select of the image. The only tool that will give me a measurement is the rectangle. Has anyone else run into this problem? I am also looking for the mean gray value. Any answers or input would be helpful. Thank you Elizabeth Roetzheim roetzheimm@marotz.com ------------------------------ Date: Fri, 24 Jul 1998 18:44:02 -0800 From: Paul G Mermelstein To: nih-image@io.ece.drexel.edu Subject: subscribe Message-Id: Content-Type: text/plain; charset="us-ascii" Paul G. Mermelstein Ph.D. Department of Molecular and Cellular Physiology Stanford University School of Medicine Beckman Center Room B101 Stanford, CA 94305 phone: (650) 725-7564 fax: (650) 498-5663 email: pmerm@stanford.edu -------------------------------- End of nih-image-d Digest V98 Issue #20 *************************************** From nih-image-request@io.ece.drexel.edu Sat Jul 25 11:04 EDT 1998 X-UIDL: 76bb0454515a59393c50182633a9b62a Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA28082; Sat, 25 Jul 1998 11:04:44 -0400 (EDT) Resent-Date: Sat, 25 Jul 1998 11:04:44 -0400 (EDT) Mime-Version: 1.0 X-Sender: stwang@mail.clemson.edu Message-Id: In-Reply-To: <9807241357.AA17033@cindy.ml.wpafb.af.mil> Date: Sat, 25 Jul 1998 10:17:23 -0400 To: nih-image@io.ece.drexel.edu From: Sam Wang Subject: Re: montage macro Resent-Message-ID: <"eIMpT3.0.ec6.85Vkr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/138 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 952 Status: RO >> Does anyone have a macro that makes a montage of RGB TIFF images? >>There was some discussion of ways to do this last summer; has anyone >>written the code? >> >> Ideally, I'd like to be able to make a "contact sheet" (e.g. about >>24-35 small images on a page) as a way of keeping track of images I've >>recorded. My computer can't open more than about 10 TIFF images at a time, >>but I'd like to be able to make a montage without having to open each file >>up individually. Is there a way to open files in a folder one at a time >>without having to give them sequential numbers? >> >> I'd appreciate help on this. >> >>Thanks very much. >> >>Laird Bloom >>MIT Center for Cancer Research On the Mac, there is a great $25 graphics shareware called iView that does everything you mentioned plus. It's up on the usual Archive sites. -- Sam Wang Clemson University Art Department - Lee Hall Clemson, SC 29634-0509 864/656-3924 FAX 864/656-7523 From nih-image-d-request@io.ece.drexel.edu Sun Jul 26 06:15 EDT 1998 X-UIDL: 9ab8fe36284f0e5a293e51a5eaf15e0f Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA28165; Sun, 26 Jul 1998 06:15:10 -0400 (EDT) Date: Sun, 26 Jul 1998 06:15:10 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807261015.GAA28165@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #21 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/21 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1522 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 21 Today's Topics: Re: montage macro [ Sam Wang ] ------------------------------ Date: Sat, 25 Jul 1998 10:17:23 -0400 From: Sam Wang To: nih-image@io.ece.drexel.edu Subject: Re: montage macro Message-Id: Content-Type: text/plain; charset="us-ascii" >> Does anyone have a macro that makes a montage of RGB TIFF images? >>There was some discussion of ways to do this last summer; has anyone >>written the code? >> >> Ideally, I'd like to be able to make a "contact sheet" (e.g. about >>24-35 small images on a page) as a way of keeping track of images I've >>recorded. My computer can't open more than about 10 TIFF images at a time, >>but I'd like to be able to make a montage without having to open each file >>up individually. Is there a way to open files in a folder one at a time >>without having to give them sequential numbers? >> >> I'd appreciate help on this. >> >>Thanks very much. >> >>Laird Bloom >>MIT Center for Cancer Research On the Mac, there is a great $25 graphics shareware called iView that does everything you mentioned plus. It's up on the usual Archive sites. -- Sam Wang Clemson University Art Department - Lee Hall Clemson, SC 29634-0509 864/656-3924 FAX 864/656-7523 -------------------------------- End of nih-image-d Digest V98 Issue #21 *************************************** From nih-image-request@io.ece.drexel.edu Sun Jul 26 10:43 EDT 1998 X-UIDL: 88b145e330baf149ee7b3ec1bec70a8c Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA21822; Sun, 26 Jul 1998 10:43:28 -0400 (EDT) Resent-Date: Sun, 26 Jul 1998 10:43:28 -0400 (EDT) Sender: I.Reviakine@chem.rug.nl Message-ID: <35BB3E9B.CB6C0951@chem.rug.nl> Date: Sun, 26 Jul 1998 16:35:07 +0200 From: Ilya Reviakine X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: PRINTING THE FILE NAME ON THE IMAGE Content-Transfer-Encoding: 7bit Resent-Message-ID: <"oo8n33.0.h65.Vwpkr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/139 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 733 Status: RO Hi everyone - How does one print the file name with the image or text? This question has been posted previously, but I could not fine the answer to it among the archives. Thank you in advance, Ilya Reviakine. -- I.Reviakine@chem.rug.nl Ilya Reviakine, BSc (Biochemistry), Computer Science Minor Dept. of Biophysical Chemistry University of Groningen Nijenborgh, 4 9747 AG Groningen, the Netherlands. Phone: 31 (050)363-4220; 363-4213 Fax: 31 (050)363-4800 http://rugbe2.chem.rug.nl/~reviakin From nih-image-d-request@io.ece.drexel.edu Mon Jul 27 06:15 EDT 1998 X-UIDL: f7872032b642d8221f534a9530bc225e Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA06489; Mon, 27 Jul 1998 06:15:12 -0400 (EDT) Date: Mon, 27 Jul 1998 06:15:12 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807271015.GAA06489@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #22 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/22 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1359 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 22 Today's Topics: PRINTING THE FILE NAME ON THE IMAGE [ Ilya Reviakine To: nih-image@io.ece.drexel.edu Subject: PRINTING THE FILE NAME ON THE IMAGE Message-ID: <35BB3E9B.CB6C0951@chem.rug.nl> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone - How does one print the file name with the image or text? This question has been posted previously, but I could not fine the answer to it among the archives. Thank you in advance, Ilya Reviakine. -- I.Reviakine@chem.rug.nl Ilya Reviakine, BSc (Biochemistry), Computer Science Minor Dept. of Biophysical Chemistry University of Groningen Nijenborgh, 4 9747 AG Groningen, the Netherlands. Phone: 31 (050)363-4220; 363-4213 Fax: 31 (050)363-4800 http://rugbe2.chem.rug.nl/~reviakin -------------------------------- End of nih-image-d Digest V98 Issue #22 *************************************** From nih-image-request@io.ece.drexel.edu Mon Jul 27 12:35 EDT 1998 X-UIDL: 5c9d669caf3b8b6987af99d8109c89f7 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA11766; Mon, 27 Jul 1998 12:35:07 -0400 (EDT) Resent-Date: Mon, 27 Jul 1998 12:35:07 -0400 (EDT) From: Alex_Courtade@huntsman.com Mime-Version: 1.0 Date: Mon, 27 Jul 1998 10:54:32 -0500 Message-ID: <00009EF3.CE21466@huntsman.com> Subject: derivative processing and particle size histogram macros To: nih-image@io.ece.drexel.edu Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Resent-Message-ID: <"FfhYq1.0.qD2.dJAlr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/140 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 636 Status: RO I am analyzing rubber void images (taken using an SEM) with Scion beta 3. I threshold the image, and then do a particle size/ count. I was wondering if someone has any NIH Image/ Scion macros that can generate a histogram of particle size vs # of particles. Is this even within the program's capability? If not, does anyone have any other routines or programs that can do this? I was also wondering if anyone has any derivative processing (differential processing) macros that could be used. I know that derivative processing units are available for electron microscopes, but can it be performed by software? Thanks for any feedback. From nih-image-request@io.ece.drexel.edu Mon Jul 27 12:47 EDT 1998 X-UIDL: c3c5cdd49a87fb20a4c5e54ce3c8c726 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA12850; Mon, 27 Jul 1998 12:47:22 -0400 (EDT) Resent-Date: Mon, 27 Jul 1998 12:47:22 -0400 (EDT) Message-Id: <3.0.1.32.19980727122533.006b9a84@PO-Box.mcgill.ca> X-Sender: mliraj@PO-Box.mcgill.ca X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Mon, 27 Jul 1998 12:25:33 -0400 To: nih-image@io.ece.drexel.edu From: "Mario de A. Lira Junior" Subject: Re: derivative processing and particle size histogram macros In-Reply-To: <00009EF3.CE21466@huntsman.com> Mime-Version: 1.0 Resent-Message-ID: <"i2d98.0.Yp2.BlAlr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/141 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 448 Status: RO Alex, >someone has any NIH Image/ Scion macros that can generate a histogram of >particle size vs # of particles. Is this even within the program's capability? I'll be using the same kind of processing, but my idea is to simply save the measurements file, and then import into SAS or some other program, and proceed with the analysis from there. You probably would be able to do this even on a spreadsheet program, such as Excel or Quattro Pro. From nih-image-request@io.ece.drexel.edu Tue Jul 28 01:41 EDT 1998 X-UIDL: 96643022ca3ae4a31c8ec7e80ba1d8d0 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id BAA08259; Tue, 28 Jul 1998 01:41:49 -0400 (EDT) Resent-Date: Tue, 28 Jul 1998 01:41:49 -0400 (EDT) Message-ID: <35BD630C.7DECA269@sisna.com> Date: Mon, 27 Jul 1998 23:35:08 -0600 From: "Christopher P. Tully" Reply-To: cptully@sisna.com X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: PRINTING THE FILE NAME ON THE IMAGE References: <35BB3E9B.CB6C0951@chem.rug.nl> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"fltJh2.0.pp1.V9Mlr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/142 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1598 Status: RO To be blunt, read the documentation. Amoung the macros included with the distribution versions of Image for Macs is a file called 'Editing Macros.txt' which includes a macro titled 'Draw File Name in each Image,' which I think will do what you want. If not, it should be a good starting place for writing your own macro. I found this information by going to the NIH Image home page (http://rsb.info.nih.gov/nih-image/Default.html) and clicking on 'More Documentation' and then clicking on 'Macros Distributed with NIH Image' and scanning the list of included macros. There is also a reference to the 'File Paths Demo' macro in the 'Input/Output Macros' included with Image under the description of the GetFileInfo() macro command on the 'Macro Commands' page (http://rsb.info.nih.gov/nih-image/more-docs/commands.html). Chris Tully Ilya Reviakine wrote: > > Hi everyone - > > How does one print the file name with the image or text? > > This question has been posted previously, but I could not fine the > answer to it among the archives. > > Thank you in advance, > Ilya Reviakine. > > -- > > I.Reviakine@chem.rug.nl > Ilya Reviakine, BSc (Biochemistry), Computer Science Minor > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh, 4 > 9747 AG Groningen, the Netherlands. > > Phone: 31 (050)363-4220; 363-4213 > Fax: 31 (050)363-4800 > > http://rugbe2.chem.rug.nl/~reviakin From nih-image-d-request@io.ece.drexel.edu Tue Jul 28 06:12 EDT 1998 X-UIDL: 88e4a46c56b393d6d8e9deb9a38a3980 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA26893; Tue, 28 Jul 1998 06:12:02 -0400 (EDT) Date: Tue, 28 Jul 1998 06:12:02 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807281012.GAA26893@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #23 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/23 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4163 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 23 Today's Topics: derivative processing and particle s [ Alex_Courtade@huntsman.com ] Re: derivative processing and partic [ "Mario de A. Lira Junior" Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part I am analyzing rubber void images (taken using an SEM) with Scion beta 3. I threshold the image, and then do a particle size/ count. I was wondering if someone has any NIH Image/ Scion macros that can generate a histogram of particle size vs # of particles. Is this even within the program's capability? If not, does anyone have any other routines or programs that can do this? I was also wondering if anyone has any derivative processing (differential processing) macros that could be used. I know that derivative processing units are available for electron microscopes, but can it be performed by software? Thanks for any feedback. ------------------------------ Date: Mon, 27 Jul 1998 12:25:33 -0400 From: "Mario de A. Lira Junior" To: nih-image@io.ece.drexel.edu Subject: Re: derivative processing and particle size histogram macros Message-Id: <3.0.1.32.19980727122533.006b9a84@PO-Box.mcgill.ca> Content-Type: text/plain; charset="us-ascii" Alex, >someone has any NIH Image/ Scion macros that can generate a histogram of >particle size vs # of particles. Is this even within the program's capability? I'll be using the same kind of processing, but my idea is to simply save the measurements file, and then import into SAS or some other program, and proceed with the analysis from there. You probably would be able to do this even on a spreadsheet program, such as Excel or Quattro Pro. ------------------------------ Date: Mon, 27 Jul 1998 23:35:08 -0600 From: "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: PRINTING THE FILE NAME ON THE IMAGE Message-ID: <35BD630C.7DECA269@sisna.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To be blunt, read the documentation. Amoung the macros included with the distribution versions of Image for Macs is a file called 'Editing Macros.txt' which includes a macro titled 'Draw File Name in each Image,' which I think will do what you want. If not, it should be a good starting place for writing your own macro. I found this information by going to the NIH Image home page (http://rsb.info.nih.gov/nih-image/Default.html) and clicking on 'More Documentation' and then clicking on 'Macros Distributed with NIH Image' and scanning the list of included macros. There is also a reference to the 'File Paths Demo' macro in the 'Input/Output Macros' included with Image under the description of the GetFileInfo() macro command on the 'Macro Commands' page (http://rsb.info.nih.gov/nih-image/more-docs/commands.html). Chris Tully Ilya Reviakine wrote: > > Hi everyone - > > How does one print the file name with the image or text? > > This question has been posted previously, but I could not fine the > answer to it among the archives. > > Thank you in advance, > Ilya Reviakine. > > -- > > I.Reviakine@chem.rug.nl > Ilya Reviakine, BSc (Biochemistry), Computer Science Minor > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh, 4 > 9747 AG Groningen, the Netherlands. > > Phone: 31 (050)363-4220; 363-4213 > Fax: 31 (050)363-4800 > > http://rugbe2.chem.rug.nl/~reviakin -------------------------------- End of nih-image-d Digest V98 Issue #23 *************************************** From nih-image-request@io.ece.drexel.edu Tue Jul 28 10:42 EDT 1998 X-UIDL: 43aaf10ad9908cc4ebe0f88d81fa20eb Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA15485; Tue, 28 Jul 1998 10:42:40 -0400 (EDT) Resent-Date: Tue, 28 Jul 1998 10:42:40 -0400 (EDT) Date: Tue, 28 Jul 1998 10:27:30 -0400 (EDT) From: Kanu P Singh Reply-To: Kanu P Singh To: nih-image@io.ece.drexel.edu cc: Alex_Courtade@huntsman.com Subject: NIH image processing Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"qR6Cf3.0.yS3.L_Tlr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/143 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 525 Status: RO Hi Alex, I am working on the void distribution in hardened Phenolic resins. I would appreciate if you could let me know what kind of analysis you are doing for your study of rubber voids. I have some SEM pictures of my samples. I was wondering if you could tell me what kind of information can be obtained from them regarding the void sizes and volume fractions. I would also appreciate any information that you could give me regarding existing literature on void fraction studies through electron microscopy. Thanks, Kanu From nih-image-d-request@io.ece.drexel.edu Wed Jul 29 06:14 EDT 1998 X-UIDL: 05696e3b98ffaa20b84f73df2ecccbb7 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA14524; Wed, 29 Jul 1998 06:14:15 -0400 (EDT) Date: Wed, 29 Jul 1998 06:14:15 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807291014.GAA14524@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #24 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/24 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1149 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 24 Today's Topics: NIH image processing [ Kanu P Singh ] ------------------------------ Date: Tue, 28 Jul 1998 10:27:30 -0400 (EDT) From: Kanu P Singh To: nih-image@io.ece.drexel.edu cc: Alex_Courtade@huntsman.com Subject: NIH image processing Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Alex, I am working on the void distribution in hardened Phenolic resins. I would appreciate if you could let me know what kind of analysis you are doing for your study of rubber voids. I have some SEM pictures of my samples. I was wondering if you could tell me what kind of information can be obtained from them regarding the void sizes and volume fractions. I would also appreciate any information that you could give me regarding existing literature on void fraction studies through electron microscopy. Thanks, Kanu -------------------------------- End of nih-image-d Digest V98 Issue #24 *************************************** From nih-image-request@io.ece.drexel.edu Wed Jul 29 07:05 EDT 1998 X-UIDL: 75e9838bc0c0c20622f5f6fb6237971c Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA19172; Wed, 29 Jul 1998 07:05:49 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 07:05:49 -0400 (EDT) X-Sender: st004166@brandywine.otago.ac.nz Message-Id: Mime-Version: 1.0 Date: Wed, 29 Jul 1998 22:49:43 +1200 To: nih-image@io.ece.drexel.edu From: Glenn Kearney Subject: unsubscribe Resent-Message-ID: <"Yrsxl2.0.eM4.Jxllr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/144 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2 Status: RO From nih-image-request@io.ece.drexel.edu Wed Jul 29 07:57 EDT 1998 X-UIDL: 96698b679a4a87c892cd33c5a8207955 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA23695; Wed, 29 Jul 1998 07:57:09 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 07:57:09 -0400 (EDT) Date: Wed, 29 Jul 1998 13:44:24 +0200 (MDT) From: Rafael Carazo-Salas To: nih-image@io.ece.drexel.edu Subject: Re: unsubscribe In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"4D_qr1.0.2V5.Zimlr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/145 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 266 Status: RO ********************************************************************* Rafael Edgardo Carazo Salas EMBL Meyerhofstrasse 1 69117 Heidelberg Tel :: (00496221) 38 72 84 Fax :: (00496221) 38 75 12 ********************************************************************* From nih-image-request@io.ece.drexel.edu Wed Jul 29 08:09 EDT 1998 X-UIDL: 2ac24a8094a7d8a5538d8a8712647fa8 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA24960; Wed, 29 Jul 1998 08:09:26 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 08:09:26 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Wed, 29 Jul 1998 08:01:50 -0500 To: nih-image@io.ece.drexel.edu From: Mark A Vivino Subject: How to unsubscribe Resent-Message-ID: <"-gGBL.0.ps5.Axmlr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/146 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 638 Status: RO Whatever you do, do not send the request to: nih-image@io.ece.drexel.edu Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe From nih-image-request@io.ece.drexel.edu Wed Jul 29 09:28 EDT 1998 X-UIDL: 35f1855fcdcdca7e26cb436858dfeb43 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA02247; Wed, 29 Jul 1998 09:28:53 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 09:28:53 -0400 (EDT) Message-ID: <69B43248FE73D11197BB00A0C99AB06788CC@jvcserver.vanguardweb.org> From: "Mehmet Dondurur, Ph. D." To: "'NIH User Group'" Subject: Image comparison Date: Wed, 29 Jul 1998 09:10:00 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"tKzi.0.3D.U2olr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/147 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 516 Status: RO Hello, I have two B&W identical images: one is original and second one is interpolated. Both are same size and have same number of pixels as well. To my eyes, both looked same but I want to compare them pixel by pixel to how much they are different. Main goal is to see how much interpolated image is identical or close to the original one. Can I do that with NIH or other application?. Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of Michigan Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 From nih-image-request@io.ece.drexel.edu Wed Jul 29 09:29 EDT 1998 X-UIDL: 60a9538cfb5c61e12dea82083c4515ed Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA02362; Wed, 29 Jul 1998 09:29:30 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 09:29:30 -0400 (EDT) Message-ID: <69B43248FE73D11197BB00A0C99AB06788CD@jvcserver.vanguardweb.org> From: "Mehmet Dondurur, Ph. D." To: "'NIH User Group'" Subject: Image enhancment Date: Wed, 29 Jul 1998 09:11:49 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"tATvu2.0.FG.A4olr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/148 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 345 Status: RO Hello, Is there any way to enhance (sharpening edges) images in folder in one shot rather than enhancing one image a time using one of the filters?. I have B&W CAT scan images-100's of them. Any suggestion is appreciated. Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 From nih-image-request@io.ece.drexel.edu Wed Jul 29 10:36 EDT 1998 X-UIDL: 00081b812fb3f78b6184840587169202 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA08359; Wed, 29 Jul 1998 10:36:14 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 10:36:14 -0400 (EDT) From: Alex_Courtade@huntsman.com Mime-Version: 1.0 Date: Wed, 29 Jul 1998 09:13:09 -0700 Message-ID: <0000BC12.CE21466@huntsman.com> Subject: Re:NIH image processing To: Kanu P Singh , nih-image@io.ece.drexel.edu Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Resent-Message-ID: <"-unki2.0.1m1.21plr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/149 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1212 Status: RO I am chiefly looking at the voids in some polypropylene samples. It's essentially industrial analysis. The void size/ distribution apparently can have some important effects on the physical properties of the sample. I am only a summer intern, and unfortunately I don't know what specific information can be obtained from the void size/ volume. As far as existing literature of void fraction studies in electron microscopy, I'm pretty much in the dark as well. Perhaps someone else out there is aware of some of these studies? ____________________Reply Separator____________________ Subject: NIH image processing Author: Kanu P Singh Date: 7/28/98 10:27 AM Hi Alex, I am working on the void distribution in hardened Phenolic resins. I would appreciate if you could let me know what kind of analysis you are doing for your study of rubber voids. I have some SEM pictures of my samples. I was wondering if you could tell me what kind of information can be obtained from them regarding the void sizes and volume fractions. I would also appreciate any information that you could give me regarding existing literature on void fraction studies through electron microscopy. Thanks, Kanu From nih-image-request@io.ece.drexel.edu Wed Jul 29 14:03 EDT 1998 X-UIDL: 441bcc3ef0a320395dfc98f0d2ce9c7b Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA22420; Wed, 29 Jul 1998 14:02:35 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 14:02:35 -0400 (EDT) Date: Wed, 29 Jul 1998 18:55:18 -127532 From: "Swidbert R OTT" To: nih-image@io.ece.drexel.edu Subject: Re: Image comparison Message-ID: <437379.3110727318@neuron06.zoo.cam.ac.uk> X-Mailer: Mulberry [1.1.0, s/n #10001] X-Authenticated: sro21 by imap.hermes.cam.ac.uk X-Licensed-To: University of Cambridge MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"zVd2A2.0.jB5.H2slr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/150 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 309 Status: RO You may subtract one from the other in NIH Image, using some offset, e.g. 127 (to push those difference pixels that are negative back into range). Swidi -------------------------------------------------- Swidbert R OTT Department of Zoology University of Cambridge Downing Street Cambridge CB2 3EJ ENGLAND From nih-image-request@io.ece.drexel.edu Wed Jul 29 14:42 EDT 1998 X-UIDL: a7f007f8c0cfc63483e050c70136772f Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA25055; Wed, 29 Jul 1998 14:42:01 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 14:42:01 -0400 (EDT) Message-ID: <69B43248FE73D11197BB00A0C99AB06788CE@jvcserver.vanguardweb.org> From: "Mehmet Dondurur, Ph. D." To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Image comparison Date: Wed, 29 Jul 1998 14:21:52 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"G9JO-1.0.hv5.tcslr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/151 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 702 Status: RO I am sorry I could not understand exactly what you mean. Do you mean use: Image math then substarct image or what is the exact steps please? > ---------- > From: Swidbert R OTT[SMTP:sro21@hermes.cam.ac.uk] > Reply To: nih-image@io.ece.drexel.edu > Sent: Wednesday, July 29, 1998 2:55 PM > To: nih-image@io.ece.drexel.edu > Subject: Re: Image comparison > > You may subtract one from the other in NIH Image, using some offset, > e.g. > 127 (to push those difference pixels that are negative back into > range). > > Swidi > > -------------------------------------------------- > Swidbert R OTT > Department of Zoology > University of Cambridge > Downing Street > Cambridge CB2 3EJ > ENGLAND > From nih-image-request@io.ece.drexel.edu Wed Jul 29 16:46 EDT 1998 X-UIDL: 2e6fe68d7e3d1ff661c5a7c3e17eb12c Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA02903; Wed, 29 Jul 1998 16:46:20 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 16:46:20 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Wed, 29 Jul 1998 16:40:33 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: G3 Resent-Message-ID: <"Nmavh.0.oV.KUulr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/152 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 346 Status: RO >Is there a fix yet for the digitizer error when trying to capture images >from the built-in video card in the G3's? I tried to fix this problem by capturing to screen memory rather than offscreen memory but it only works when then monitor is set to 256 colors and only for single frames. I'm open to suggestions for what to try next. -wayne From nih-image-request@io.ece.drexel.edu Wed Jul 29 16:57 EDT 1998 X-UIDL: 8cdd2efb4a59692325e88acb9aa2896d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA03767; Wed, 29 Jul 1998 16:57:08 -0400 (EDT) Resent-Date: Wed, 29 Jul 1998 16:57:08 -0400 (EDT) Posted-Date: Wed, 29 Jul 1998 17:44:05 -0300 Message-Id: <199807292044.RAA16457@siso.fo.usp.br> Mime-Version: 1.0 Date: Wed, 29 Jul 1998 17:50:04 -0300 To: nih-image@io.ece.drexel.edu From: rgjaeger@fo.usp.br (Ruy Jaeger) Subject: Subscribe Resent-Message-ID: <"ufCFU3.0.8i.2eulr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/153 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 494 Status: RO ============================================================ Dr. Ruy G. Jaeger Phone 55-11-8187902 55-11-8187912 Patologia Bucal FAX 55-11-8187413 FOUSP E-mail rgjaeger@siso.fo.usp.br Av Prof. Lineu Prestes 2227 Cidade Universitaria Sao Paulo SP 05508-900 BRAZIL ============================================================ From nih-image-request@io.ece.drexel.edu Thu Jul 30 04:35 EDT 1998 X-UIDL: 723e46cd53c918ef8e8a5f2f73140d4c Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id EAA29902; Thu, 30 Jul 1998 04:34:36 -0400 (EDT) Resent-Date: Thu, 30 Jul 1998 04:34:36 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Thu, 30 Jul 1998 10:24:28 +0200 To: NIH-Image Mailing List From: Paul Human Subject: Avid Cinema and G3 drivers? Resent-Message-ID: <"7kfaI.0.My6.5t2mr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/154 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1362 Status: RO Dear Imagers Firstly, thank you to all the responses I received concerning the Mac and NIH or Leica and QWin issue. To my dismay, we have gone with the Leica system due to corporate political issues and I think already we are seeing the disadvantage of that decision. Nevertheless, we will be adding framegrabber cards to some of our existing Macs and the information this list has provided will certainly help in this area. Secondly, we have a Apple 6500/300 with an Avid Cinema card as well as a few G3's with their standard AV input/output. Although these are obviously not what one needs for individual framegrabs, they do nevertheless provide a suitable picture (in many ways better than we are getting with the Leica system with its Matrox Millenium card) which would be usable for simple morphometric analysis of LM specimens. My question is, are there drivers available which would allow direct capture from these cards into NIH? At present we have to use third party applications to grab an image and then save it on disk to get it into NIH. Thanks in advance. Paul ____________________________________________________________________ PAUL A HUMAN, M.Sc. Deputy Director Cardiovascular Research Unit University of Cape Town Medical School OBSERVATORY 7925, Cape Town, South Africa Voice:+27-21-406 6418 Fax:+27-21-448 5935 Cell:+27-82-770 3612 From nih-image-d-request@io.ece.drexel.edu Thu Jul 30 04:35 EDT 1998 X-UIDL: f5a1506fdbb26e0f548b49ed93c26a5d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id EAA00006; Thu, 30 Jul 1998 04:35:25 -0400 (EDT) Date: Thu, 30 Jul 1998 04:35:25 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807300835.EAA00006@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #25 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/25 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 10602 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 25 Today's Topics: unsubscribe [ Glenn Kearney ] Subscribe [ rgjaeger@fo.usp.br (Ruy Jaeger) ] Avid Cinema and G3 drivers? [ Paul Human To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: Content-Type: text/plain; charset="us-ascii" ------------------------------ Date: Wed, 29 Jul 1998 13:44:24 +0200 (MDT) From: Rafael Carazo-Salas To: nih-image@io.ece.drexel.edu Subject: Re: unsubscribe Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII ********************************************************************* Rafael Edgardo Carazo Salas EMBL Meyerhofstrasse 1 69117 Heidelberg Tel :: (00496221) 38 72 84 Fax :: (00496221) 38 75 12 ********************************************************************* ------------------------------ Date: Wed, 29 Jul 1998 08:01:50 -0500 From: Mark A Vivino To: nih-image@io.ece.drexel.edu Subject: How to unsubscribe Message-Id: Content-Type: text/plain; charset="us-ascii" Whatever you do, do not send the request to: nih-image@io.ece.drexel.edu Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe ------------------------------ Date: Wed, 29 Jul 1998 09:10:00 -0400 From: "Mehmet Dondurur, Ph. D." To: "'NIH User Group'" Subject: Image comparison Message-ID: <69B43248FE73D11197BB00A0C99AB06788CC@jvcserver.vanguardweb.org> Content-Type: text/plain Hello, I have two B&W identical images: one is original and second one is interpolated. Both are same size and have same number of pixels as well. To my eyes, both looked same but I want to compare them pixel by pixel to how much they are different. Main goal is to see how much interpolated image is identical or close to the original one. Can I do that with NIH or other application?. Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of Michigan Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 ------------------------------ Date: Wed, 29 Jul 1998 09:11:49 -0400 From: "Mehmet Dondurur, Ph. D." To: "'NIH User Group'" Subject: Image enhancment Message-ID: <69B43248FE73D11197BB00A0C99AB06788CD@jvcserver.vanguardweb.org> Content-Type: text/plain Hello, Is there any way to enhance (sharpening edges) images in folder in one shot rather than enhancing one image a time using one of the filters?. I have B&W CAT scan images-100's of them. Any suggestion is appreciated. Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 ------------------------------ Date: Wed, 29 Jul 1998 09:13:09 -0700 From: Alex_Courtade@huntsman.com To: Kanu P Singh , nih-image@io.ece.drexel.edu Subject: Re:NIH image processing Message-ID: <0000BC12.CE21466@huntsman.com> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part I am chiefly looking at the voids in some polypropylene samples. It's essentially industrial analysis. The void size/ distribution apparently can have some important effects on the physical properties of the sample. I am only a summer intern, and unfortunately I don't know what specific information can be obtained from the void size/ volume. As far as existing literature of void fraction studies in electron microscopy, I'm pretty much in the dark as well. Perhaps someone else out there is aware of some of these studies? ____________________Reply Separator____________________ Subject: NIH image processing Author: Kanu P Singh Date: 7/28/98 10:27 AM Hi Alex, I am working on the void distribution in hardened Phenolic resins. I would appreciate if you could let me know what kind of analysis you are doing for your study of rubber voids. I have some SEM pictures of my samples. I was wondering if you could tell me what kind of information can be obtained from them regarding the void sizes and volume fractions. I would also appreciate any information that you could give me regarding existing literature on void fraction studies through electron microscopy. Thanks, Kanu ------------------------------ Date: Wed, 29 Jul 1998 18:55:18 -127532 From: "Swidbert R OTT" To: nih-image@io.ece.drexel.edu Subject: Re: Image comparison Message-ID: <437379.3110727318@neuron06.zoo.cam.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit You may subtract one from the other in NIH Image, using some offset, e.g. 127 (to push those difference pixels that are negative back into range). Swidi -------------------------------------------------- Swidbert R OTT Department of Zoology University of Cambridge Downing Street Cambridge CB2 3EJ ENGLAND ------------------------------ Date: Wed, 29 Jul 1998 14:21:52 -0400 From: "Mehmet Dondurur, Ph. D." To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Image comparison Message-ID: <69B43248FE73D11197BB00A0C99AB06788CE@jvcserver.vanguardweb.org> Content-Type: text/plain I am sorry I could not understand exactly what you mean. Do you mean use: Image math then substarct image or what is the exact steps please? > ---------- > From: Swidbert R OTT[SMTP:sro21@hermes.cam.ac.uk] > Reply To: nih-image@io.ece.drexel.edu > Sent: Wednesday, July 29, 1998 2:55 PM > To: nih-image@io.ece.drexel.edu > Subject: Re: Image comparison > > You may subtract one from the other in NIH Image, using some offset, > e.g. > 127 (to push those difference pixels that are negative back into > range). > > Swidi > > -------------------------------------------------- > Swidbert R OTT > Department of Zoology > University of Cambridge > Downing Street > Cambridge CB2 3EJ > ENGLAND > ------------------------------ Date: Wed, 29 Jul 1998 16:40:33 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: G3 Message-Id: Content-Type: text/plain; charset="us-ascii" >Is there a fix yet for the digitizer error when trying to capture images >from the built-in video card in the G3's? I tried to fix this problem by capturing to screen memory rather than offscreen memory but it only works when then monitor is set to 256 colors and only for single frames. I'm open to suggestions for what to try next. -wayne ------------------------------ Date: Wed, 29 Jul 1998 17:50:04 -0300 From: rgjaeger@fo.usp.br (Ruy Jaeger) To: nih-image@io.ece.drexel.edu Subject: Subscribe Message-Id: <199807292044.RAA16457@siso.fo.usp.br> Content-Type: text/plain; charset="us-ascii" ============================================================ Dr. Ruy G. Jaeger Phone 55-11-8187902 55-11-8187912 Patologia Bucal FAX 55-11-8187413 FOUSP E-mail rgjaeger@siso.fo.usp.br Av Prof. Lineu Prestes 2227 Cidade Universitaria Sao Paulo SP 05508-900 BRAZIL ============================================================ ------------------------------ Date: Thu, 30 Jul 1998 10:24:28 +0200 From: Paul Human To: NIH-Image Mailing List Subject: Avid Cinema and G3 drivers? Message-Id: Content-Type: text/plain; charset="us-ascii" Dear Imagers Firstly, thank you to all the responses I received concerning the Mac and NIH or Leica and QWin issue. To my dismay, we have gone with the Leica system due to corporate political issues and I think already we are seeing the disadvantage of that decision. Nevertheless, we will be adding framegrabber cards to some of our existing Macs and the information this list has provided will certainly help in this area. Secondly, we have a Apple 6500/300 with an Avid Cinema card as well as a few G3's with their standard AV input/output. Although these are obviously not what one needs for individual framegrabs, they do nevertheless provide a suitable picture (in many ways better than we are getting with the Leica system with its Matrox Millenium card) which would be usable for simple morphometric analysis of LM specimens. My question is, are there drivers available which would allow direct capture from these cards into NIH? At present we have to use third party applications to grab an image and then save it on disk to get it into NIH. Thanks in advance. Paul ____________________________________________________________________ PAUL A HUMAN, M.Sc. Deputy Director Cardiovascular Research Unit University of Cape Town Medical School OBSERVATORY 7925, Cape Town, South Africa Voice:+27-21-406 6418 Fax:+27-21-448 5935 Cell:+27-82-770 3612 -------------------------------- End of nih-image-d Digest V98 Issue #25 *************************************** From nih-image-request@io.ece.drexel.edu Thu Jul 30 06:08 EDT 1998 X-UIDL: 20803253c67ea744145f0bde979b417f Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA08028; Thu, 30 Jul 1998 06:07:52 -0400 (EDT) Resent-Date: Thu, 30 Jul 1998 06:07:52 -0400 (EDT) Date: Thu, 30 Jul 1998 10:56:14 +0100 From: "Swidbert R OTT" To: nih-image@io.ece.drexel.edu Subject: RE: Image comparison Message-ID: <488223.3110784974@neuron05.zoo.cam.ac.uk> X-Mailer: Mulberry (MacOS) [1.3.2.2, s/n S-100001] X-Authenticated: sro21 by imap.hermes.cam.ac.uk X-Licensed-To: University of Cambridge MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"8kXSb3.0.9i1.qD4mr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/155 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1017 Status: RO --On Wed, Jul 29, 1998 2:21 pm -0400 "Mehmet Dondurur, Ph. D." wrote: > I am sorry I could not understand exactly what you mean. Do you mean > use: > Image math > then > substarct image > or what is the exact steps please? You go to menu "Process" item "Image math..." to bring up a dialog box. You specify your two windows containing the two images you want to compare by using the two popup-menues. You select "-" as the operator fom the pop-up menu of operators (next to the pop-up menue for the second image). You leave the offset (the number field next to the "+" in the dialog) as it is by default (128). You can crank up (scale, magnify) the differences by setting the number in the field next to the "X" to something bigger than 1. The whole operation is: C=((A-B)*k)+128 where A and B are your source images, C is the one containing the differences, and k is the multiplicative (scaling) factor. I hope this helps. Swidi From nih-image-request@io.ece.drexel.edu Thu Jul 30 06:24 EDT 1998 X-UIDL: 2bf5b448e15990af860fe8f75b2ac322 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA09868; Thu, 30 Jul 1998 06:24:34 -0400 (EDT) <69B43248FE73D11197BB00A0C99AB06788CC@jvcserver.vanguardweb.org> Resent-Date: Thu, 30 Jul 1998 06:24:34 -0400 (EDT) Message-Id: In-Reply-To: <69B43248FE73D11197BB00A0C99AB06788CC@jvcserver.vanguardweb.org> Mime-Version: 1.0 Date: Thu, 30 Jul 1998 11:15:28 +0100 To: nih-image@io.ece.drexel.edu From: Clive Washington Subject: Re: Image comparison Resent-Message-ID: <"CDiyt3.0.t52.RT4mr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/156 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1176 Status: RO >Hello, >I have two B&W identical images: one is original and second >one is interpolated. Both are same size and have same number >of pixels as well. To my eyes, both looked same but I want >to compare them pixel by pixel to how much they are >different. Main goal is to see how much interpolated image >is identical or close to the original one. Can I do that with >NIH or other application?. Just use the image maths function to subtract one image from the other. > >Thanks >Dr. Mehmet Dondurur >Research Scientist >Jobst Vascular Center-U of Michigan >Mehmet.Dondurur.ph.d@jvc.org >(419) 471-2087 ////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// Dr. Clive Washington, Tel. 0115 9515034 Senior Lecturer in Pharmaceutics, Fax 0115 9515102 Department of Pharmaceutical Sciences, University of Nottingham, University Park, Email pazcw@unix.ccc.nottingham.ac.uk Nottingham NG7 2RD. http://reliant.pharm.nottingham.ac.uk/clive.html "It's mail, Jim, but not as we know it." ////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// From nih-image-request@io.ece.drexel.edu Thu Jul 30 08:39 EDT 1998 X-UIDL: 3d820df1f3497ea2a1a73eeb2e0f81b3 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA21707; Thu, 30 Jul 1998 08:39:09 -0400 (EDT) Resent-Date: Thu, 30 Jul 1998 08:39:09 -0400 (EDT) Message-ID: <69B43248FE73D11197BB00A0C99AB06788D3@jvcserver.vanguardweb.org> From: "Mehmet Dondurur, Ph. D." To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Image comparison Date: Thu, 30 Jul 1998 08:17:58 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"FYJYT.0.My4.lN6mr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/157 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1384 Status: RO Yes sir, It is more than enough and appreciated for great help. Cheers Mehmet > ---------- > From: Swidbert R OTT[SMTP:sro21@hermes.cam.ac.uk] > Reply To: nih-image@io.ece.drexel.edu > Sent: Thursday, July 30, 1998 5:56 AM > To: nih-image@io.ece.drexel.edu > Subject: RE: Image comparison > > --On Wed, Jul 29, 1998 2:21 pm -0400 "Mehmet Dondurur, Ph. D." > wrote: > > > I am sorry I could not understand exactly what you mean. Do you mean > > use: > > Image math > > then > > substarct image > > or what is the exact steps please? > > You go to menu "Process" item "Image math..." to bring up a dialog > box. > You specify your two windows containing the two images you want to > compare > by using the two popup-menues. You select "-" as the operator fom the > pop-up menu of operators (next to the pop-up menue for the second > image). > You leave the offset (the number field next to the "+" in the dialog) > as > it is by default (128). You can crank up (scale, magnify) the > differences > by setting the number in the field next to the "X" to something bigger > than 1. > > The whole operation is: > > C=((A-B)*k)+128 where A and B are your source images, C is the > one containing the differences, and k is the > multiplicative (scaling) factor. > > I hope this helps. > > Swidi > From nih-image-request@io.ece.drexel.edu Thu Jul 30 09:59 EDT 1998 X-UIDL: 0d0b0b241b15041904c58f55f482c4b1 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA28629; Thu, 30 Jul 1998 09:58:49 -0400 (EDT) Resent-Date: Thu, 30 Jul 1998 09:58:49 -0400 (EDT) Message-Id: In-Reply-To: <199807292044.RAA16457@siso.fo.usp.br> Mime-Version: 1.0 Date: Thu, 30 Jul 1998 09:46:19 -0500 To: nih-image@io.ece.drexel.edu From: Mark A Vivino Subject: NIH'er seeking new employment Resent-Message-ID: <"y6yMY.0.Bi6.Wa7mr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/158 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1355 Status: RO Sorry for the use of bandwidth, but thought I would give this a shot. Biomedical Engineer, MSEE, seeking new employment opportunity. Trained and with experience in broad areas of electrical engineering, computing, biomedicine, imaging, data and signal acquisition. Ten years experience collaborating in clinical and basic science research, development of diagnostic tools and methodologies. Open to combining current skills with other kinds of work like networking or other. Much of my work over the years has been with the National Eye Institute, National Heart Lung and Blood Institute, National Institute of Neurological Disorders and Stroke and many other clinical and basic science labs on the NIH campus. I have extensive experience with the NIH Image package. Geographical and other preferences: Since my wife has an offer in Miami, FL this is now my first choice to relocate. However nothing is etched in concrete, and as her position is temporary, I am open to other possible locations. I am eligible to transfer as a federal employee as well. Note: I am on a vacation trip from Aug 1 until Aug 23. I will probably repost this again upon my return. But please feel free to drop me a line or a contact. How to contact: Mark Vivino Email: mvivino@rocketmail.com Or mvivino@helix.nih.gov Phone current w: 301-402-2633 Thanks in advance. From nih-image-request@io.ece.drexel.edu Thu Jul 30 13:51 EDT 1998 X-UIDL: 241ecc25887d4fe18140782a59b8b5b5 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA14992; Thu, 30 Jul 1998 13:51:39 -0400 (EDT) Resent-Date: Thu, 30 Jul 1998 13:51:39 -0400 (EDT) Message-ID: <35C0AF3C.13E8@genetronics.com> Date: Thu, 30 Jul 1998 10:37:00 -0700 From: "n.b.dev" Reply-To: nbdev@genetronics.com Organization: genetronics;inc X-Mailer: Mozilla 3.01 (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: NIH'er seeking new employment References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"OKVUL3.0.QO3.M-Amr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/159 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1557 Status: RO Mark A Vivino wrote: > > Sorry for the use of bandwidth, but thought I would give this a shot. > > Biomedical Engineer, MSEE, seeking new employment opportunity. Trained and > with experience in broad areas of electrical engineering, computing, > biomedicine, imaging, data and signal acquisition. Ten years experience > collaborating in clinical and basic science research, development of > diagnostic tools and methodologies. Open to combining current skills with > other kinds of work like networking or other. > > Much of my work over the years has been with the National Eye Institute, > National Heart Lung and Blood Institute, National Institute of Neurological > Disorders and Stroke and many other clinical and basic science labs on the > NIH campus. > > I have extensive experience with the NIH Image package. > > Geographical and other preferences: Since my wife has an offer in Miami, FL > this is now my first choice to relocate. However nothing is etched in > concrete, and as her position is temporary, I am open to other possible > locations. I am eligible to transfer as a federal employee as well. > > Note: I am on a vacation trip from Aug 1 until Aug 23. I will probably > repost this again upon my return. But please feel free to drop me a line or > a contact. > > How to contact: Mark Vivino > Email: mvivino@rocketmail.com > Or mvivino@helix.nih.gov > Phone current w: 301-402-2633 > > Thanks in advance. Mark: You have done a great job for the people over the years. Best wishes for future endeavor.--Dev, N.B; San Diego From nih-image-d-request@io.ece.drexel.edu Fri Jul 31 06:14 EDT 1998 X-UIDL: 09173036dc6f3107bcca65d38bb8e1bd Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA04849; Fri, 31 Jul 1998 06:14:17 -0400 (EDT) Date: Fri, 31 Jul 1998 06:14:17 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199807311014.GAA04849@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #26 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/26 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 8638 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 26 Today's Topics: RE: Image comparison [ "Swidbert R OTT" ] ------------------------------ Date: Thu, 30 Jul 1998 10:56:14 +0100 From: "Swidbert R OTT" To: nih-image@io.ece.drexel.edu Subject: RE: Image comparison Message-ID: <488223.3110784974@neuron05.zoo.cam.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --On Wed, Jul 29, 1998 2:21 pm -0400 "Mehmet Dondurur, Ph. D." wrote: > I am sorry I could not understand exactly what you mean. Do you mean > use: > Image math > then > substarct image > or what is the exact steps please? You go to menu "Process" item "Image math..." to bring up a dialog box. You specify your two windows containing the two images you want to compare by using the two popup-menues. You select "-" as the operator fom the pop-up menu of operators (next to the pop-up menue for the second image). You leave the offset (the number field next to the "+" in the dialog) as it is by default (128). You can crank up (scale, magnify) the differences by setting the number in the field next to the "X" to something bigger than 1. The whole operation is: C=((A-B)*k)+128 where A and B are your source images, C is the one containing the differences, and k is the multiplicative (scaling) factor. I hope this helps. Swidi ------------------------------ Date: Thu, 30 Jul 1998 11:15:28 +0100 From: Clive Washington To: nih-image@io.ece.drexel.edu Subject: Re: Image comparison Message-Id: Content-Type: text/plain; charset="us-ascii" >Hello, >I have two B&W identical images: one is original and second >one is interpolated. Both are same size and have same number >of pixels as well. To my eyes, both looked same but I want >to compare them pixel by pixel to how much they are >different. Main goal is to see how much interpolated image >is identical or close to the original one. Can I do that with >NIH or other application?. Just use the image maths function to subtract one image from the other. > >Thanks >Dr. Mehmet Dondurur >Research Scientist >Jobst Vascular Center-U of Michigan >Mehmet.Dondurur.ph.d@jvc.org >(419) 471-2087 ////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// Dr. Clive Washington, Tel. 0115 9515034 Senior Lecturer in Pharmaceutics, Fax 0115 9515102 Department of Pharmaceutical Sciences, University of Nottingham, University Park, Email pazcw@unix.ccc.nottingham.ac.uk Nottingham NG7 2RD. http://reliant.pharm.nottingham.ac.uk/clive.html "It's mail, Jim, but not as we know it." ////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// ------------------------------ Date: Thu, 30 Jul 1998 08:17:58 -0400 From: "Mehmet Dondurur, Ph. D." To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Image comparison Message-ID: <69B43248FE73D11197BB00A0C99AB06788D3@jvcserver.vanguardweb.org> Content-Type: text/plain Yes sir, It is more than enough and appreciated for great help. Cheers Mehmet > ---------- > From: Swidbert R OTT[SMTP:sro21@hermes.cam.ac.uk] > Reply To: nih-image@io.ece.drexel.edu > Sent: Thursday, July 30, 1998 5:56 AM > To: nih-image@io.ece.drexel.edu > Subject: RE: Image comparison > > --On Wed, Jul 29, 1998 2:21 pm -0400 "Mehmet Dondurur, Ph. D." > wrote: > > > I am sorry I could not understand exactly what you mean. Do you mean > > use: > > Image math > > then > > substarct image > > or what is the exact steps please? > > You go to menu "Process" item "Image math..." to bring up a dialog > box. > You specify your two windows containing the two images you want to > compare > by using the two popup-menues. You select "-" as the operator fom the > pop-up menu of operators (next to the pop-up menue for the second > image). > You leave the offset (the number field next to the "+" in the dialog) > as > it is by default (128). You can crank up (scale, magnify) the > differences > by setting the number in the field next to the "X" to something bigger > than 1. > > The whole operation is: > > C=((A-B)*k)+128 where A and B are your source images, C is the > one containing the differences, and k is the > multiplicative (scaling) factor. > > I hope this helps. > > Swidi > ------------------------------ Date: Thu, 30 Jul 1998 09:46:19 -0500 From: Mark A Vivino To: nih-image@io.ece.drexel.edu Subject: NIH'er seeking new employment Message-Id: Content-Type: text/plain; charset="us-ascii" Sorry for the use of bandwidth, but thought I would give this a shot. Biomedical Engineer, MSEE, seeking new employment opportunity. Trained and with experience in broad areas of electrical engineering, computing, biomedicine, imaging, data and signal acquisition. Ten years experience collaborating in clinical and basic science research, development of diagnostic tools and methodologies. Open to combining current skills with other kinds of work like networking or other. Much of my work over the years has been with the National Eye Institute, National Heart Lung and Blood Institute, National Institute of Neurological Disorders and Stroke and many other clinical and basic science labs on the NIH campus. I have extensive experience with the NIH Image package. Geographical and other preferences: Since my wife has an offer in Miami, FL this is now my first choice to relocate. However nothing is etched in concrete, and as her position is temporary, I am open to other possible locations. I am eligible to transfer as a federal employee as well. Note: I am on a vacation trip from Aug 1 until Aug 23. I will probably repost this again upon my return. But please feel free to drop me a line or a contact. How to contact: Mark Vivino Email: mvivino@rocketmail.com Or mvivino@helix.nih.gov Phone current w: 301-402-2633 Thanks in advance. ------------------------------ Date: Thu, 30 Jul 1998 10:37:00 -0700 From: "n.b.dev" To: nih-image@io.ece.drexel.edu Subject: Re: NIH'er seeking new employment Message-ID: <35C0AF3C.13E8@genetronics.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mark A Vivino wrote: > > Sorry for the use of bandwidth, but thought I would give this a shot. > > Biomedical Engineer, MSEE, seeking new employment opportunity. Trained and > with experience in broad areas of electrical engineering, computing, > biomedicine, imaging, data and signal acquisition. Ten years experience > collaborating in clinical and basic science research, development of > diagnostic tools and methodologies. Open to combining current skills with > other kinds of work like networking or other. > > Much of my work over the years has been with the National Eye Institute, > National Heart Lung and Blood Institute, National Institute of Neurological > Disorders and Stroke and many other clinical and basic science labs on the > NIH campus. > > I have extensive experience with the NIH Image package. > > Geographical and other preferences: Since my wife has an offer in Miami, FL > this is now my first choice to relocate. However nothing is etched in > concrete, and as her position is temporary, I am open to other possible > locations. I am eligible to transfer as a federal employee as well. > > Note: I am on a vacation trip from Aug 1 until Aug 23. I will probably > repost this again upon my return. But please feel free to drop me a line or > a contact. > > How to contact: Mark Vivino > Email: mvivino@rocketmail.com > Or mvivino@helix.nih.gov > Phone current w: 301-402-2633 > > Thanks in advance. Mark: You have done a great job for the people over the years. Best wishes for future endeavor.--Dev, N.B; San Diego -------------------------------- End of nih-image-d Digest V98 Issue #26 *************************************** From nih-image-d-request@io.ece.drexel.edu Sun Aug 2 06:10 EDT 1998 X-UIDL: bd41bf0c209cd8fc4d85763fb8d0e89b Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA12948; Sun, 2 Aug 1998 06:10:05 -0400 (EDT) Date: Sun, 2 Aug 1998 06:10:05 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808021010.GAA12948@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #27 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/27 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1108 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 27 Today's Topics: UNSUBSCRIBE [ Ilya Reviakine To: nih-image-d@io.ece.drexel.edu Subject: UNSUBSCRIBE Message-ID: <35C24C00.E277518A@chem.rug.nl> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit -- I.Reviakine@chem.rug.nl Ilya Reviakine, BSc (Biochemistry), Computer Science Minor Dept. of Biophysical Chemistry University of Groningen Nijenborgh, 4 9747 AG Groningen, the Netherlands. Phone: 31 (050)363-4220; 363-4213 Fax: 31 (050)363-4800 http://rugbe2.chem.rug.nl/~reviakin -------------------------------- End of nih-image-d Digest V98 Issue #27 *************************************** From nih-image-request@io.ece.drexel.edu Mon Aug 3 09:52 EDT 1998 X-UIDL: 246d93e86c622a07f01b952a7dfa3248 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA00707; Mon, 3 Aug 1998 09:51:43 -0400 (EDT) Resent-Date: Mon, 3 Aug 1998 09:51:43 -0400 (EDT) Message-ID: <35C5844D.57592B27@maine.rr.com> Date: Mon, 03 Aug 1998 09:35:10 +0000 From: Marcia Goldfarb X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: Nih-image Subject: G3 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"KeJw31.0.G97.roRnr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/160 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 599 Status: RO I have just upgraded my computer from a 7100 PowerMac to a G3. I believe I am using Nih-image 1.61 for powermac. Every so often I have a problem with printing results. That is after several times of printing, the computer says it can no longer find the printer. I have to quit, shut down, restart , select chooser and reselect the printer. Needless to say this is annoying. Would this have anything to do with a G3- Nih-image conflict? I am having no luck in tracking this problem down. Thanks for any help. Marcia Goldfarb Anatek-EP 17 Bishop St Portland, ME o4103 email: anatekep@maine.rr.com From nih-image-request@io.ece.drexel.edu Mon Aug 3 11:27 EDT 1998 X-UIDL: da2d3d103b80d25ccb193d4020aa86ce Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA07327; Mon, 3 Aug 1998 11:27:14 -0400 (EDT) Resent-Date: Mon, 3 Aug 1998 11:27:14 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Mon, 03 Aug 1998 10:13:17 -0500 From: "STEPHEN MOORMAN" To: nih-image@io.ece.drexel.edu Subject: G3 printing Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA06487 Resent-Message-ID: <"NyoiS2.0.eb1.1HTnr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/161 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 473 Status: RO As far as I can tell, the printing problem is specific to the G3 and has nothing to do with NIH Image. It usually manifests itself as a message saying it can't find the desktop print spooler. I have an 8600/300 running the same version of the OS with the same extensions loaded and I never have this problem. I suspect Apple will fix this with the next version of laserwriter 8. I still haven't found a good fix for acquiring images from the G3 built in video card. From nih-image-request@io.ece.drexel.edu Mon Aug 3 11:43 EDT 1998 X-UIDL: dd723d8b7d5744f8fee7ca70c34283bd Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA08595; Mon, 3 Aug 1998 11:42:51 -0400 (EDT) Resent-Date: Mon, 3 Aug 1998 11:42:51 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: Mime-Version: 1.0 Date: Mon, 3 Aug 1998 17:30:42 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Re: PCI to NuBus adapters Resent-Message-ID: <"X0lee2.0.ar1.oTTnr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/162 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1024 Status: RO >Imagers, >Does anyone know if a Scion LG-3 NuBus card will run at 30 fps in a PCI >machine with a PCI to NuBus adapter, or will it run at NuBus speed? > It will run at or slightly below NuBus speed. If your PCI machine is faster, that will counteract any overhead in the translation process, so you will get a higher capture speed on a fast PCI with an adapter than on a slow NuBus Mac. The only PCI to NuBus adapters I know of are from SecondWave and quite expensive ($900) so you would spend the money better on upgrading your LG-3 card. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Mon Aug 3 18:56 EDT 1998 X-UIDL: f431bbf0cf766d027b2c2e8c8acc26e1 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA06768; Mon, 3 Aug 1998 18:56:07 -0400 (EDT) Resent-Date: Mon, 3 Aug 1998 18:56:07 -0400 (EDT) Message-Id: <3.0.5.32.19980804084901.007a31a0@pop3.unsw.edu.au> X-Sender: s9500316@pop3.unsw.edu.au X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Tue, 04 Aug 1998 08:49:01 +1000 To: nih-image@io.ece.drexel.edu From: John Jamieson Subject: Re: G3 In-Reply-To: <35C5844D.57592B27@maine.rr.com> Mime-Version: 1.0 Resent-Message-ID: <"haVLt2.0._S1.OtZnr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/163 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1085 Status: RO I had a similar problem with a new G3 using the serial Localtalk printer connection. Here is what Apple Australia suggested: "Try trashing the LocalTalk PCI extension, restart the G3 and you should find that the problem is resolved." This fixed my problem immediately. At 09:35 03/08/98 +0000, you wrote: >I have just upgraded my computer from a 7100 PowerMac to a G3. I believe >I am using Nih-image 1.61 for powermac. Every so often I have a problem >with printing results. That is after several times of printing, the >computer says it can no longer find the printer. I have to quit, shut >down, restart , select chooser and reselect the printer. Needless to say >this is annoying. Would this have anything to do with a G3- Nih-image >conflict? I am having no luck in tracking this problem down. Thanks for >any help. > >Marcia Goldfarb >Anatek-EP >17 Bishop St >Portland, ME o4103 > >email: anatekep@maine.rr.com > > > John Jamieson Prince of Wales Medical Research Institute Randwick NSW AUSTRALIA tel: 61-2-9382-2696 fax: 61-2-9382-2723 email: j.jamieson@unsw.edu.au From nih-image-request@io.ece.drexel.edu Tue Aug 4 00:09 EDT 1998 X-UIDL: d414ed0dbc3a9ab45a5ddbe1bc3b796d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id AAA00492; Tue, 4 Aug 1998 00:09:04 -0400 (EDT) Resent-Date: Tue, 4 Aug 1998 00:09:04 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: mehmet.dondurur.ph.d@jvc.org, nih-image@io.ece.drexel.edu Date: Tue, 4 Aug 1998 14:00:46 GMT+1000 Subject: Batch Processing of Images Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <4C0E8FC1C9F@rna.bio.mq.edu.au> Resent-Message-ID: <"ZNMRg3.0.JB7.cRenr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/164 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1584 Status: RO >From: "Mehmet Dondurur, Ph. D." >To: "'NIH User Group'" >Subject: Image enhancment >Date: Wed, 29 Jul 1998 09:11:49 -0400 >........... >Is there any way to enhance (sharpening edges) images in >folder in one shot rather than enhancing one image a time >using one of the filters?. >I have B&W CAT scan images-100's of them. Any suggestion is >appreciated. > >Date: Thu, 23 Jul 1998 08:31:54 -0400 >To: nih-image@io.ece.drexel.edu >From: Laird Bloom >Subject: montage macro ...... My computer can't open more than about 10 TIFF images at a time, >but I'd like to be able to make a montage without having to open each file >up individually. Is there a way to open files in a folder one at a time >without having to give them sequential numbers? The above posts caused me to rethink some macro techniques I had used to do batch processing of images in NIH-Image and Object-Image. Using 'recent' extentions to macros, I have implemented a 'simple to use' macro suite which allows the user to make selections of files and directory contents. The selection process builds a 'tobeProcessed filelist' which can be listed and processed without the need for structured filenames. It will be emailed separately to Mehmet Dondurur as an attachment in anticipation of some feedback on its usefulness and the documentation. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Tue Aug 4 06:07 EDT 1998 X-UIDL: a6d52305dc7c609df736ec1e85c8a2fb Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA28604; Tue, 4 Aug 1998 06:07:33 -0400 (EDT) Date: Tue, 4 Aug 1998 06:07:33 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808041007.GAA28604@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #28 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/28 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6852 Status: RO ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 28 Today's Topics: G3 [ Marcia Goldfarb To: Nih-image Subject: G3 Message-ID: <35C5844D.57592B27@maine.rr.com> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit I have just upgraded my computer from a 7100 PowerMac to a G3. I believe I am using Nih-image 1.61 for powermac. Every so often I have a problem with printing results. That is after several times of printing, the computer says it can no longer find the printer. I have to quit, shut down, restart , select chooser and reselect the printer. Needless to say this is annoying. Would this have anything to do with a G3- Nih-image conflict? I am having no luck in tracking this problem down. Thanks for any help. Marcia Goldfarb Anatek-EP 17 Bishop St Portland, ME o4103 email: anatekep@maine.rr.com ------------------------------ Date: Mon, 03 Aug 1998 10:13:17 -0500 From: "STEPHEN MOORMAN" To: nih-image@io.ece.drexel.edu Subject: G3 printing Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit As far as I can tell, the printing problem is specific to the G3 and has nothing to do with NIH Image. It usually manifests itself as a message saying it can't find the desktop print spooler. I have an 8600/300 running the same version of the OS with the same extensions loaded and I never have this problem. I suspect Apple will fix this with the next version of laserwriter 8. I still haven't found a good fix for acquiring images from the G3 built in video card. ------------------------------ Date: Mon, 3 Aug 1998 17:30:42 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: PCI to NuBus adapters Message-Id: Content-Type: text/plain; charset="us-ascii" >Imagers, >Does anyone know if a Scion LG-3 NuBus card will run at 30 fps in a PCI >machine with a PCI to NuBus adapter, or will it run at NuBus speed? > It will run at or slightly below NuBus speed. If your PCI machine is faster, that will counteract any overhead in the translation process, so you will get a higher capture speed on a fast PCI with an adapter than on a slow NuBus Mac. The only PCI to NuBus adapters I know of are from SecondWave and quite expensive ($900) so you would spend the money better on upgrading your LG-3 card. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Tue, 04 Aug 1998 08:49:01 +1000 From: John Jamieson To: nih-image@io.ece.drexel.edu Subject: Re: G3 Message-Id: <3.0.5.32.19980804084901.007a31a0@pop3.unsw.edu.au> Content-Type: text/plain; charset="us-ascii" I had a similar problem with a new G3 using the serial Localtalk printer connection. Here is what Apple Australia suggested: "Try trashing the LocalTalk PCI extension, restart the G3 and you should find that the problem is resolved." This fixed my problem immediately. At 09:35 03/08/98 +0000, you wrote: >I have just upgraded my computer from a 7100 PowerMac to a G3. I believe >I am using Nih-image 1.61 for powermac. Every so often I have a problem >with printing results. That is after several times of printing, the >computer says it can no longer find the printer. I have to quit, shut >down, restart , select chooser and reselect the printer. Needless to say >this is annoying. Would this have anything to do with a G3- Nih-image >conflict? I am having no luck in tracking this problem down. Thanks for >any help. > >Marcia Goldfarb >Anatek-EP >17 Bishop St >Portland, ME o4103 > >email: anatekep@maine.rr.com > > > John Jamieson Prince of Wales Medical Research Institute Randwick NSW AUSTRALIA tel: 61-2-9382-2696 fax: 61-2-9382-2723 email: j.jamieson@unsw.edu.au ------------------------------ Date: Tue, 4 Aug 1998 14:00:46 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: mehmet.dondurur.ph.d@jvc.org, nih-image@io.ece.drexel.edu Subject: Batch Processing of Images Message-ID: <4C0E8FC1C9F@rna.bio.mq.edu.au> >From: "Mehmet Dondurur, Ph. D." >To: "'NIH User Group'" >Subject: Image enhancment >Date: Wed, 29 Jul 1998 09:11:49 -0400 >........... >Is there any way to enhance (sharpening edges) images in >folder in one shot rather than enhancing one image a time >using one of the filters?. >I have B&W CAT scan images-100's of them. Any suggestion is >appreciated. > >Date: Thu, 23 Jul 1998 08:31:54 -0400 >To: nih-image@io.ece.drexel.edu >From: Laird Bloom >Subject: montage macro ...... My computer can't open more than about 10 TIFF images at a time, >but I'd like to be able to make a montage without having to open each file >up individually. Is there a way to open files in a folder one at a time >without having to give them sequential numbers? The above posts caused me to rethink some macro techniques I had used to do batch processing of images in NIH-Image and Object-Image. Using 'recent' extentions to macros, I have implemented a 'simple to use' macro suite which allows the user to make selections of files and directory contents. The selection process builds a 'tobeProcessed filelist' which can be listed and processed without the need for structured filenames. It will be emailed separately to Mehmet Dondurur as an attachment in anticipation of some feedback on its usefulness and the documentation. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #28 *************************************** From nih-image-request@io.ece.drexel.edu Tue Aug 4 11:11 EDT 1998 X-UIDL: 026dc32629ff9e267f399e5444735ab0 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA24769; Tue, 4 Aug 1998 11:10:56 -0400 (EDT) Resent-Date: Tue, 4 Aug 1998 11:10:56 -0400 (EDT) Message-ID: <35C72EA5.5980097F@netmatters.co.uk> Date: Tue, 04 Aug 1998 15:53:58 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Point and click colour segmentation References: <4C0E8FC1C9F@rna.bio.mq.edu.au> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"OUosc2.0.Ce5.p2onr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/166 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 850 Status: RO In addition to Object Image and NIH Image I also use Image-Pro Plus for the Mac. The colour segmentation system used in the later was one of the few things that I feel gives this $3000 package an edge over Image. So I've implemented the point and click colour segmentation bit in Object Image. Click on one of the objects you want to segment in the index colour image and Object Image will segment the RGB image on the basis of independent density slices in each channel. Unlike Image-Pro Plus, you can easily discard any of the channels you don't want. You can also record your settings for use in batch processing. I still have to add a few features like the ability to segment several types of object in the same image, but if any one is interested I've sent it to Wayne for uploading to the NIH site. I welcome any feed back :-) Jeremy Brown From nih-image-request@io.ece.drexel.edu Tue Aug 4 11:11 EDT 1998 X-UIDL: a0f083ceb75760d63ef467ece74d2a62 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA24791; Tue, 4 Aug 1998 11:11:10 -0400 (EDT) Resent-Date: Tue, 4 Aug 1998 11:11:10 -0400 (EDT) Message-ID: <35C72780.B9F9B06E@netmatters.co.uk> Date: Tue, 04 Aug 1998 15:23:28 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Batch Processing of Images References: <4C0E8FC1C9F@rna.bio.mq.edu.au> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"iXwzW3.0.-c5.R2onr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/165 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1844 Status: RO Greg, This sounds good. It would be nice to batch process images by folder rather than by sequentially numbered file names. Could I get a copy? Jeremy Brown GJOSS@rna.bio.mq.edu.au wrote: > >From: "Mehmet Dondurur, Ph. D." > >To: "'NIH User Group'" > >Subject: Image enhancment > >Date: Wed, 29 Jul 1998 09:11:49 -0400 > >........... > >Is there any way to enhance (sharpening edges) images in > >folder in one shot rather than enhancing one image a time > >using one of the filters?. > >I have B&W CAT scan images-100's of them. Any suggestion is > >appreciated. > > > >Date: Thu, 23 Jul 1998 08:31:54 -0400 > >To: nih-image@io.ece.drexel.edu > >From: Laird Bloom > >Subject: montage macro > ...... > My computer can't open more than about 10 TIFF images at a time, > >but I'd like to be able to make a montage without having to open each file > >up individually. Is there a way to open files in a folder one at a time > >without having to give them sequential numbers? > > The above posts caused me to rethink some macro techniques I had used to do > batch processing of images in NIH-Image and Object-Image. > Using 'recent' extentions to macros, I have implemented a 'simple to use' macro > suite which allows the user to make selections of files and directory contents. > The selection process builds a 'tobeProcessed filelist' which can be listed > and processed without the need for structured filenames. > > It will be emailed separately to Mehmet Dondurur as an attachment in > anticipation of some feedback on its usefulness and the documentation. > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Tue Aug 4 11:49 EDT 1998 X-UIDL: 93616c71a0d446fb067d62bb4e094514 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA27806; Tue, 4 Aug 1998 11:48:31 -0400 (EDT) Resent-Date: Tue, 4 Aug 1998 11:48:31 -0400 (EDT) Date: Tue, 4 Aug 1998 17:27:44 +0200 (MET DST) Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: ablocker@pasteur.fr (Ariel Blocker) Subject: Re: Eudora users Resent-Message-ID: <"6VDns.0.KO6.zXonr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/167 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 594 Status: RO Dear List Managers and Users, Maybe I am stupid folks but when we swapped to the new list I, who was previously receiving only digests and not individual messages, started getting only individual messages (which is pretty troublesome when you go away on holidays for 2 weeks and return to find your mailbox clogged up with alomst exclusively list news). I subsbribed to nih-image@biomed.drexel.edu and use Eudora 1.5.3, is this like normal and if so what do I do to get back on a 1 digesty per day track? I would appreciate your advice before I drown in messages... Sincerely, Ariel Blocker. From nih-image-request@io.ece.drexel.edu Tue Aug 4 13:00 EDT 1998 X-UIDL: 0776b4929ef25ac58bd3804a857bf357 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA03276; Tue, 4 Aug 1998 12:58:35 -0400 (EDT) Resent-Date: Tue, 4 Aug 1998 12:58:35 -0400 (EDT) Date: Tue, 4 Aug 1998 11:19:19 -0500 (CDT) Message-Id: In-Reply-To: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: "Malinda E.C. Fitzgerald" Subject: Re: Eudora users Resent-Message-ID: <"nC9pf2.0.H3.CIpnr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/168 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 319 Status: RO I have always received individual messages and never received lists! I just thought that was the way it was! Malinda (I use Eudora 3.0) Malinda E.C. Fitzgerald, Ph.D. Associate Professor Department of Biology 650 E Parkway So. Christian Brothers University Memphis, TN 38104 901-321-3262 office 901-321-4433 fax From nih-image-request@io.ece.drexel.edu Tue Aug 4 13:23 EDT 1998 X-UIDL: 243fd5f1aeda6be050a76901475a108d Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA05359; Tue, 4 Aug 1998 13:23:05 -0400 (EDT) Resent-Date: Tue, 4 Aug 1998 13:23:05 -0400 (EDT) Message-ID: <69B43248FE73D11197BB00A0C99AB06788E0@jvcserver.vanguardweb.org> From: "Mehmet Dondurur, Ph. D." To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Eudora users Date: Tue, 4 Aug 1998 12:59:51 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"KXoxy1.0.cz.9-pnr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/169 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 831 Status: RO Hi, I am in same situation like your. What is the solution to get the list? Could you please let me know if you find out how to get the list? Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 > ---------- > From: Malinda E.C. Fitzgerald[SMTP:malinda@cbu.edu] > Reply To: nih-image@io.ece.drexel.edu > Sent: Tuesday, August 04, 1998 12:19 PM > To: nih-image@io.ece.drexel.edu > Subject: Re: Eudora users > > I have always received individual messages and never received lists! > I > just thought that was the way it was! Malinda (I use Eudora 3.0) > > Malinda E.C. Fitzgerald, Ph.D. > Associate Professor > Department of Biology > 650 E Parkway So. > Christian Brothers University > Memphis, TN 38104 > 901-321-3262 office > 901-321-4433 fax > > From nih-image-request@io.ece.drexel.edu Tue Aug 4 14:17 EDT 1998 X-UIDL: f7e04ca710e8802c6a49bb94e3aa917b Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA09571; Tue, 4 Aug 1998 14:17:27 -0400 (EDT) Resent-Date: Tue, 4 Aug 1998 14:17:27 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Tue, 4 Aug 1998 13:01:39 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: ADMINISTRATA Resent-Message-ID: <"BWw-1.0.X02.6oqnr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/170 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 3685 Status: RO TimesHi everyone. The following is a reminder to everyone regarding administrative issues on the list. Those who desire the digest form, should unsubscribe from the regular list and resubscribe to the digest list. e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Help -------------------- To obtain a listing of help items, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-request@biomed.drexel.edu Subject: help Help on Digest -------------------- To obtain a listing of help items on digest version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Tue Aug 4 15:13 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA13896; Tue, 4 Aug 1998 15:11:45 -0400 (EDT) Resent-Date: Tue, 4 Aug 1998 15:11:45 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Tue, 4 Aug 1998 13:35:27 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Digest Issue Resent-Message-ID: <"wy5P1.0.4g2.nHrnr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/171 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1844 Status: O Hi everyone. A Digestion of the Digest Issue. Digests are handled differently by depending on settings and email applications.Note that it is likely that you are able to control their appearance on your end by adjusting the preferences for MIME digests. Here is how they appear according to various users. Thank you everyone for your messages on the subject. Email software Elm v 2.4. Multi-part MIME. You can skip messages at the --Press any key to go on.-- prompt, press the control-c (^C) key combination, and the remainder of the message(s) will be skipped. Unix-Pine. Two modes. Single message with header at top or with each message a seperate attachment with one message consisting of table of content. Eudora Light v 3.1.3. Single message. Eudora Pro v 3.1.1. New mailbox with seperate messages (this can be filtered and made into a submailbox). Or, if you prefer a single message, under Special setting deselect "Receive MIME digests as attachments". Pegasus. New mailbox with seperate messages. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ From nih-image-request@io.ece.drexel.edu Tue Aug 4 15:22 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA14699; Tue, 4 Aug 1998 15:21:24 -0400 (EDT) Resent-Date: Tue, 4 Aug 1998 15:21:24 -0400 (EDT) From: Alex_Courtade@huntsman.com Mime-Version: 1.0 Date: Tue, 4 Aug 1998 13:51:27 -0500 Message-ID: <0000FFFF.CE21466@huntsman.com> Subject: Scion (beta 3) problems w/ major, minor axes To: nih-image@io.ece.drexel.edu Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Resent-Message-ID: <"HxRk_1.0.g53.abrnr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/172 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1082 Status: O This message is specifically directed at any of the PC Scion Image users out there, so most Mac NIH Image users can probably ignore this. I have been using (trying to, at least) Scion Beta 3 for particle analysis. The particles I am analyzing are somewhat oval shaped, fairly well defined, and usually a few hundred pixels in area (they don't appear small on the screen.) I have been trying to get Scion to give me the lengths of the major/ minor axes of the best fitting oval for the particle, but every time I attempt this I get error codes like "-1.#IO" instead of a measurement. Whether or not I have calibrated my scale to the proper units doesn't seem to have an effect. Has anyone else had this problem? Is there some way to get the major/ minor axes to work? I even drew perfect elipses on a blank image as a test, and it didn't even give me the measurements for that. __________________________________ Alex Courtade Huntsman Corporation 7114 N. Lamar Blvd Austin, TX 78752 Phone: (512) 483-0190 Email: alex_courtade@huntsman.com __________________________________ From nih-image-d-request@io.ece.drexel.edu Wed Aug 5 06:12 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA20069; Wed, 5 Aug 1998 06:12:06 -0400 (EDT) Date: Wed, 5 Aug 1998 06:12:06 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808051012.GAA20069@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #29 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/29 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 14367 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 29 Today's Topics: Re: Batch Processing of Images [ Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: Batch Processing of Images Message-ID: <35C72780.B9F9B06E@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Greg, This sounds good. It would be nice to batch process images by folder rather than by sequentially numbered file names. Could I get a copy? Jeremy Brown GJOSS@rna.bio.mq.edu.au wrote: > >From: "Mehmet Dondurur, Ph. D." > >To: "'NIH User Group'" > >Subject: Image enhancment > >Date: Wed, 29 Jul 1998 09:11:49 -0400 > >........... > >Is there any way to enhance (sharpening edges) images in > >folder in one shot rather than enhancing one image a time > >using one of the filters?. > >I have B&W CAT scan images-100's of them. Any suggestion is > >appreciated. > > > >Date: Thu, 23 Jul 1998 08:31:54 -0400 > >To: nih-image@io.ece.drexel.edu > >From: Laird Bloom > >Subject: montage macro > ...... > My computer can't open more than about 10 TIFF images at a time, > >but I'd like to be able to make a montage without having to open each file > >up individually. Is there a way to open files in a folder one at a time > >without having to give them sequential numbers? > > The above posts caused me to rethink some macro techniques I had used to do > batch processing of images in NIH-Image and Object-Image. > Using 'recent' extentions to macros, I have implemented a 'simple to use' macro > suite which allows the user to make selections of files and directory contents. > The selection process builds a 'tobeProcessed filelist' which can be listed > and processed without the need for structured filenames. > > It will be emailed separately to Mehmet Dondurur as an attachment in > anticipation of some feedback on its usefulness and the documentation. > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Tue, 04 Aug 1998 15:53:58 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Point and click colour segmentation Message-ID: <35C72EA5.5980097F@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In addition to Object Image and NIH Image I also use Image-Pro Plus for the Mac. The colour segmentation system used in the later was one of the few things that I feel gives this $3000 package an edge over Image. So I've implemented the point and click colour segmentation bit in Object Image. Click on one of the objects you want to segment in the index colour image and Object Image will segment the RGB image on the basis of independent density slices in each channel. Unlike Image-Pro Plus, you can easily discard any of the channels you don't want. You can also record your settings for use in batch processing. I still have to add a few features like the ability to segment several types of object in the same image, but if any one is interested I've sent it to Wayne for uploading to the NIH site. I welcome any feed back :-) Jeremy Brown ------------------------------ Date: Tue, 4 Aug 1998 17:27:44 +0200 (MET DST) From: ablocker@pasteur.fr (Ariel Blocker) To: nih-image@io.ece.drexel.edu Subject: Re: Eudora users Message-Id: Content-Type: text/plain; charset="us-ascii" Dear List Managers and Users, Maybe I am stupid folks but when we swapped to the new list I, who was previously receiving only digests and not individual messages, started getting only individual messages (which is pretty troublesome when you go away on holidays for 2 weeks and return to find your mailbox clogged up with alomst exclusively list news). I subsbribed to nih-image@biomed.drexel.edu and use Eudora 1.5.3, is this like normal and if so what do I do to get back on a 1 digesty per day track? I would appreciate your advice before I drown in messages... Sincerely, Ariel Blocker. ------------------------------ Date: Tue, 4 Aug 1998 11:19:19 -0500 (CDT) From: "Malinda E.C. Fitzgerald" To: nih-image@io.ece.drexel.edu Subject: Re: Eudora users Message-Id: Content-Type: text/plain; charset="us-ascii" I have always received individual messages and never received lists! I just thought that was the way it was! Malinda (I use Eudora 3.0) Malinda E.C. Fitzgerald, Ph.D. Associate Professor Department of Biology 650 E Parkway So. Christian Brothers University Memphis, TN 38104 901-321-3262 office 901-321-4433 fax ------------------------------ Date: Tue, 4 Aug 1998 12:59:51 -0400 From: "Mehmet Dondurur, Ph. D." To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Eudora users Message-ID: <69B43248FE73D11197BB00A0C99AB06788E0@jvcserver.vanguardweb.org> Content-Type: text/plain Hi, I am in same situation like your. What is the solution to get the list? Could you please let me know if you find out how to get the list? Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 > ---------- > From: Malinda E.C. Fitzgerald[SMTP:malinda@cbu.edu] > Reply To: nih-image@io.ece.drexel.edu > Sent: Tuesday, August 04, 1998 12:19 PM > To: nih-image@io.ece.drexel.edu > Subject: Re: Eudora users > > I have always received individual messages and never received lists! > I > just thought that was the way it was! Malinda (I use Eudora 3.0) > > Malinda E.C. Fitzgerald, Ph.D. > Associate Professor > Department of Biology > 650 E Parkway So. > Christian Brothers University > Memphis, TN 38104 > 901-321-3262 office > 901-321-4433 fax > > ------------------------------ Date: Tue, 4 Aug 1998 13:01:39 -0500 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: ADMINISTRATA Message-Id: Content-Type: text/enriched; charset="us-ascii" TimesHi everyone. The following is a reminder to everyone regarding administrative issues on the list. Those who desire the digest form, should unsubscribe from the regular list and resubscribe to the digest list. e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Help -------------------- To obtain a listing of help items, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-request@biomed.drexel.edu Subject: help Help on Digest -------------------- To obtain a listing of help items on digest version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- ------------------------------ Date: Tue, 4 Aug 1998 13:35:27 -0500 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Digest Issue Message-Id: Content-Type: text/plain; charset="us-ascii" Hi everyone. A Digestion of the Digest Issue. Digests are handled differently by depending on settings and email applications.Note that it is likely that you are able to control their appearance on your end by adjusting the preferences for MIME digests. Here is how they appear according to various users. Thank you everyone for your messages on the subject. Email software Elm v 2.4. Multi-part MIME. You can skip messages at the --Press any key to go on.-- prompt, press the control-c (^C) key combination, and the remainder of the message(s) will be skipped. Unix-Pine. Two modes. Single message with header at top or with each message a seperate attachment with one message consisting of table of content. Eudora Light v 3.1.3. Single message. Eudora Pro v 3.1.1. New mailbox with seperate messages (this can be filtered and made into a submailbox). Or, if you prefer a single message, under Special setting deselect "Receive MIME digests as attachments". Pegasus. New mailbox with seperate messages. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ ------------------------------ Date: Tue, 4 Aug 1998 13:51:27 -0500 From: Alex_Courtade@huntsman.com To: nih-image@io.ece.drexel.edu Subject: Scion (beta 3) problems w/ major, minor axes Message-ID: <0000FFFF.CE21466@huntsman.com> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part This message is specifically directed at any of the PC Scion Image users out there, so most Mac NIH Image users can probably ignore this. I have been using (trying to, at least) Scion Beta 3 for particle analysis. The particles I am analyzing are somewhat oval shaped, fairly well defined, and usually a few hundred pixels in area (they don't appear small on the screen.) I have been trying to get Scion to give me the lengths of the major/ minor axes of the best fitting oval for the particle, but every time I attempt this I get error codes like "-1.#IO" instead of a measurement. Whether or not I have calibrated my scale to the proper units doesn't seem to have an effect. Has anyone else had this problem? Is there some way to get the major/ minor axes to work? I even drew perfect elipses on a blank image as a test, and it didn't even give me the measurements for that. __________________________________ Alex Courtade Huntsman Corporation 7114 N. Lamar Blvd Austin, TX 78752 Phone: (512) 483-0190 Email: alex_courtade@huntsman.com __________________________________ -------------------------------- End of nih-image-d Digest V98 Issue #29 *************************************** From nih-image-request@io.ece.drexel.edu Wed Aug 5 11:41 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA17689; Wed, 5 Aug 1998 11:41:00 -0400 (EDT) Resent-Date: Wed, 5 Aug 1998 11:41:00 -0400 (EDT) Message-ID: <35C878D7.8A6A83F1@netreach.net> Date: Wed, 05 Aug 1998 11:23:03 -0400 From: Julie Mann X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Greg's batch processing macros Content-Transfer-Encoding: 7bit Resent-Message-ID: <"hgLLt2.0.E_3.1Z7or"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/173 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2114 Status: O Greg, I'd love to receive a copy, too, if that's possible! julie mann Subject: Re: Batch Processing of Images Date: Tue, 04 Aug 1998 15:23:28 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Greg, This sounds good. It would be nice to batch process images by folder rather than by sequentially numbered file names. Could I get a copy? Jeremy Brown GJOSS@rna.bio.mq.edu.au wrote: > >From: "Mehmet Dondurur, Ph. D." > >To: "'NIH User Group'" > >Subject: Image enhancment > >Date: Wed, 29 Jul 1998 09:11:49 -0400 > >........... > >Is there any way to enhance (sharpening edges) images in > >folder in one shot rather than enhancing one image a time > >using one of the filters?. > >I have B&W CAT scan images-100's of them. Any suggestion is > >appreciated. > > > >Date: Thu, 23 Jul 1998 08:31:54 -0400 > >To: nih-image@io.ece.drexel.edu > >From: Laird Bloom > >Subject: montage macro > ...... > My computer can't open more than about 10 TIFF images at a time, > >but I'd like to be able to make a montage without having to open each file > >up individually. Is there a way to open files in a folder one at a time > >without having to give them sequential numbers? > > The above posts caused me to rethink some macro techniques I had used to do > batch processing of images in NIH-Image and Object-Image. > Using 'recent' extentions to macros, I have implemented a 'simple to use' macro > suite which allows the user to make selections of files and directory contents. > The selection process builds a 'tobeProcessed filelist' which can be listed > and processed without the need for structured filenames. > > It will be emailed separately to Mehmet Dondurur as an attachment in > anticipation of some feedback on its usefulness and the documentation. > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Wed Aug 5 11:59 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA19104; Wed, 5 Aug 1998 11:59:50 -0400 (EDT) Resent-Date: Wed, 5 Aug 1998 11:59:50 -0400 (EDT) Date: Thu, 06 Aug 1998 01:49:58 +1000 From: "Kwang Y. Han" Subject: Measuring spot distances in electron diffraction patterns (EDP) To: nih-image@io.ece.drexel.edu Message-id: <000001bdc088$b2c54580$640ac282@ykhan1> MIME-version: 1.0 X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Content-transfer-encoding: 7bit Importance: Normal X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 X-Priority: 3 (Normal) Resent-Message-ID: <"4HXzr3.0.JQ4.Rv7or"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/174 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 669 Status: O I am hoping someone could point out to me a more accurate way of measuring spot distances in EDP for single-crystal materials. This is how i did: 1) manually threshold the inverted TIFF image to obtain all the desired spots 2) perform 'Analyze Particles...' 3) click 'Show Results' 4) import the results to Excel and calculate the distances The distance between 2 specific spots appears to depend very much on my threshold value. Should I be locating the centroid or geometrical centre of each spot? I am not sure if top-hat filter or Hough transform can help to reduce variability in measurements? If so, how should it be done? Thanks ahead for any suggestions.. From nih-image-request@io.ece.drexel.edu Wed Aug 5 16:54 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA09318; Wed, 5 Aug 1998 16:53:58 -0400 (EDT) Resent-Date: Wed, 5 Aug 1998 16:53:58 -0400 (EDT) From: "Toby Chai, M.D., 8-5544, S8D18" Organization: UMAB, Surgery To: nih-image@io.ece.drexel.edu Date: Wed, 5 Aug 1998 16:35:24 -0500 MIME-Version: 1.0 Content-transfer-encoding: 7BIT Subject: Video Capture with Futura II LX Card Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Message-ID: <74C71F31767@surgery1.umaryland.edu> Resent-Message-ID: <"dKTGM1.0.Tu1.t8Cor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/175 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 816 Status: O I am trying to get NIH Image to work on a Mac PowerPC 8100 with a Futura II LX Video Capture card and a video camera hooked up to a fluorescence microscope. The machine currently is running Oncor program which is working (it's capturing video feed fine). However, when I run NIH Image (1.61), I get the error message that I must use a frame grabber, etc. How do I "configure" the Mac so that NIH Image recognizes the already present video card/video signal? I looked briefly through Oncor's manuals, but it didn't really help me. I did "turn off" the Oncor init file and rebooting the computer, but still could not get NIH Imageto capture the video feed. So basically, I want to use NIH Image software instead of Oncor. Thanks in advance. T. Chai, M.D. Division of Urology University of Maryland From nih-image-request@io.ece.drexel.edu Wed Aug 5 16:55 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA09403; Wed, 5 Aug 1998 16:54:51 -0400 (EDT) Resent-Date: Wed, 5 Aug 1998 16:54:51 -0400 (EDT) Message-ID: <001d01bdc0b0$d248b7c0$0f0a13c0@oemcomputer> From: "Joan Main" To: , , Subject: Re: Batch Processing of Images Date: Tue, 4 Aug 1998 22:03:14 -0700 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Resent-Message-ID: <"_MdET.0.sz1.vCCor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/176 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 2377 Status: O HI, I have been using a program called hijaak pro which catalogs and labels each image I process. I am processing 100-200 ultrasound iimages for time intensity information. I set up a file for each study. The hijaak pro program catalogs, labels allows thumbnail viewing and printing for later analysis. This may help you. I am stacking 30 frames for analysis at a time . IMSI manufactures this program. Hope this is helpful jmain@acuson.com or joan.main@gte.net good luck -----Original Message----- From: GJOSS@rna.bio.mq.edu.au To: mehmet.dondurur.ph.d@jvc.org ; nih-image@io.ece.drexel.edu Date: Tuesday, August 04, 1998 7:00 AM Subject: Batch Processing of Images >>From: "Mehmet Dondurur, Ph. D." >>To: "'NIH User Group'" >>Subject: Image enhancment >>Date: Wed, 29 Jul 1998 09:11:49 -0400 >>........... >>Is there any way to enhance (sharpening edges) images in >>folder in one shot rather than enhancing one image a time >>using one of the filters?. >>I have B&W CAT scan images-100's of them. Any suggestion is >>appreciated. >> >>Date: Thu, 23 Jul 1998 08:31:54 -0400 >>To: nih-image@io.ece.drexel.edu >>From: Laird Bloom >>Subject: montage macro >...... > My computer can't open more than about 10 TIFF images at a time, >>but I'd like to be able to make a montage without having to open each file >>up individually. Is there a way to open files in a folder one at a time >>without having to give them sequential numbers? > >The above posts caused me to rethink some macro techniques I had used to do >batch processing of images in NIH-Image and Object-Image. >Using 'recent' extentions to macros, I have implemented a 'simple to use' macro >suite which allows the user to make selections of files and directory contents. >The selection process builds a 'tobeProcessed filelist' which can be listed >and processed without the need for structured filenames. > >It will be emailed separately to Mehmet Dondurur as an attachment in >anticipation of some feedback on its usefulness and the documentation. >Greg Joss, >School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 >Macquarie University, Email gjoss@rna.bio.mq.edu.au >North Ryde, (Sydney,) NSW 2109, Australia > From nih-image-request@io.ece.drexel.edu Thu Aug 6 05:49 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA14613; Thu, 6 Aug 1998 05:48:58 -0400 (EDT) Resent-Date: Thu, 6 Aug 1998 05:48:58 -0400 (EDT) X-Sender: btgi12@btr0x1.rz.uni-bayreuth.de Message-Id: Mime-Version: 1.0 Date: Thu, 6 Aug 1998 11:29:28 +0100 To: nih-image@io.ece.drexel.edu From: "Jed.Mosenfelder" Subject: dumb question about IP toolkit 2.5 Resent-Message-ID: <"lMa_g.0.B63.PYNor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/177 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1091 Status: O Has anyone tried threshholding greyscale images using the IPTK plugins in Adobe photoshop. It's driving me crazy because, contrary to the manual, the threshholded pixels do not appear highlighted in a color that you can easily distinguish (they appear in some shade of grey rather than red), so it's basically impossible to see what you're doing. I wonder if i'm missing something obvious. Anyway i'm using Photoshop 3.0 on a 90 MhZ mac. I'd really prefer to use NIH Image but the plugin filters in this toolkit that i want to use run unbelievably slow in Image, because it doesn't read the powerPC code (very disappointing!). Thanks much in advance for any help from the experts out there.... cheers, jed -X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X Jed Leigh Mosenfelder e-mail: Jed.Mosenfelder@uni-bayreuth.de Bayerisches Geoinstitut Tel: +49-921-553712 (office) Universitaet Bayreuth -553700 (dept. secretary) D-95440 Bayreuth -5160186 (home) Germany Fax:+49-921-553769 :-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-) From nih-image-d-request@io.ece.drexel.edu Thu Aug 6 05:55 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA15281; Thu, 6 Aug 1998 05:55:17 -0400 (EDT) Date: Thu, 6 Aug 1998 05:55:17 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808060955.FAA15281@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #30 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/30 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 9388 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 30 Today's Topics: Greg's batch processing macros [ Julie Mann ] Measuring spot distances in electron [ "Kwang Y. Han" ] dumb question about IP toolkit 2.5 [ "Jed.Mosenfelder" To: nih-image@io.ece.drexel.edu Subject: Greg's batch processing macros Message-ID: <35C878D7.8A6A83F1@netreach.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greg, I'd love to receive a copy, too, if that's possible! julie mann Subject: Re: Batch Processing of Images Date: Tue, 04 Aug 1998 15:23:28 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Greg, This sounds good. It would be nice to batch process images by folder rather than by sequentially numbered file names. Could I get a copy? Jeremy Brown GJOSS@rna.bio.mq.edu.au wrote: > >From: "Mehmet Dondurur, Ph. D." > >To: "'NIH User Group'" > >Subject: Image enhancment > >Date: Wed, 29 Jul 1998 09:11:49 -0400 > >........... > >Is there any way to enhance (sharpening edges) images in > >folder in one shot rather than enhancing one image a time > >using one of the filters?. > >I have B&W CAT scan images-100's of them. Any suggestion is > >appreciated. > > > >Date: Thu, 23 Jul 1998 08:31:54 -0400 > >To: nih-image@io.ece.drexel.edu > >From: Laird Bloom > >Subject: montage macro > ...... > My computer can't open more than about 10 TIFF images at a time, > >but I'd like to be able to make a montage without having to open each file > >up individually. Is there a way to open files in a folder one at a time > >without having to give them sequential numbers? > > The above posts caused me to rethink some macro techniques I had used to do > batch processing of images in NIH-Image and Object-Image. > Using 'recent' extentions to macros, I have implemented a 'simple to use' macro > suite which allows the user to make selections of files and directory contents. > The selection process builds a 'tobeProcessed filelist' which can be listed > and processed without the need for structured filenames. > > It will be emailed separately to Mehmet Dondurur as an attachment in > anticipation of some feedback on its usefulness and the documentation. > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 06 Aug 1998 01:49:58 +1000 From: "Kwang Y. Han" To: nih-image@io.ece.drexel.edu Subject: Measuring spot distances in electron diffraction patterns (EDP) Message-id: <000001bdc088$b2c54580$640ac282@ykhan1> Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit I am hoping someone could point out to me a more accurate way of measuring spot distances in EDP for single-crystal materials. This is how i did: 1) manually threshold the inverted TIFF image to obtain all the desired spots 2) perform 'Analyze Particles...' 3) click 'Show Results' 4) import the results to Excel and calculate the distances The distance between 2 specific spots appears to depend very much on my threshold value. Should I be locating the centroid or geometrical centre of each spot? I am not sure if top-hat filter or Hough transform can help to reduce variability in measurements? If so, how should it be done? Thanks ahead for any suggestions.. ------------------------------ Date: Wed, 5 Aug 1998 16:35:24 -0500 From: "Toby Chai, M.D., 8-5544, S8D18" To: nih-image@io.ece.drexel.edu Subject: Video Capture with Futura II LX Card Message-ID: <74C71F31767@surgery1.umaryland.edu> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT I am trying to get NIH Image to work on a Mac PowerPC 8100 with a Futura II LX Video Capture card and a video camera hooked up to a fluorescence microscope. The machine currently is running Oncor program which is working (it's capturing video feed fine). However, when I run NIH Image (1.61), I get the error message that I must use a frame grabber, etc. How do I "configure" the Mac so that NIH Image recognizes the already present video card/video signal? I looked briefly through Oncor's manuals, but it didn't really help me. I did "turn off" the Oncor init file and rebooting the computer, but still could not get NIH Imageto capture the video feed. So basically, I want to use NIH Image software instead of Oncor. Thanks in advance. T. Chai, M.D. Division of Urology University of Maryland ------------------------------ Date: Tue, 4 Aug 1998 22:03:14 -0700 From: "Joan Main" To: , , Subject: Re: Batch Processing of Images Message-ID: <001d01bdc0b0$d248b7c0$0f0a13c0@oemcomputer> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit HI, I have been using a program called hijaak pro which catalogs and labels each image I process. I am processing 100-200 ultrasound iimages for time intensity information. I set up a file for each study. The hijaak pro program catalogs, labels allows thumbnail viewing and printing for later analysis. This may help you. I am stacking 30 frames for analysis at a time . IMSI manufactures this program. Hope this is helpful jmain@acuson.com or joan.main@gte.net good luck -----Original Message----- From: GJOSS@rna.bio.mq.edu.au To: mehmet.dondurur.ph.d@jvc.org ; nih-image@io.ece.drexel.edu Date: Tuesday, August 04, 1998 7:00 AM Subject: Batch Processing of Images >>From: "Mehmet Dondurur, Ph. D." >>To: "'NIH User Group'" >>Subject: Image enhancment >>Date: Wed, 29 Jul 1998 09:11:49 -0400 >>........... >>Is there any way to enhance (sharpening edges) images in >>folder in one shot rather than enhancing one image a time >>using one of the filters?. >>I have B&W CAT scan images-100's of them. Any suggestion is >>appreciated. >> >>Date: Thu, 23 Jul 1998 08:31:54 -0400 >>To: nih-image@io.ece.drexel.edu >>From: Laird Bloom >>Subject: montage macro >...... > My computer can't open more than about 10 TIFF images at a time, >>but I'd like to be able to make a montage without having to open each file >>up individually. Is there a way to open files in a folder one at a time >>without having to give them sequential numbers? > >The above posts caused me to rethink some macro techniques I had used to do >batch processing of images in NIH-Image and Object-Image. >Using 'recent' extentions to macros, I have implemented a 'simple to use' macro >suite which allows the user to make selections of files and directory contents. >The selection process builds a 'tobeProcessed filelist' which can be listed >and processed without the need for structured filenames. > >It will be emailed separately to Mehmet Dondurur as an attachment in >anticipation of some feedback on its usefulness and the documentation. >Greg Joss, >School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 >Macquarie University, Email gjoss@rna.bio.mq.edu.au >North Ryde, (Sydney,) NSW 2109, Australia > ------------------------------ Date: Thu, 6 Aug 1998 11:29:28 +0100 From: "Jed.Mosenfelder" To: nih-image@io.ece.drexel.edu Subject: dumb question about IP toolkit 2.5 Message-Id: Content-Type: text/plain; charset="us-ascii" Has anyone tried threshholding greyscale images using the IPTK plugins in Adobe photoshop. It's driving me crazy because, contrary to the manual, the threshholded pixels do not appear highlighted in a color that you can easily distinguish (they appear in some shade of grey rather than red), so it's basically impossible to see what you're doing. I wonder if i'm missing something obvious. Anyway i'm using Photoshop 3.0 on a 90 MhZ mac. I'd really prefer to use NIH Image but the plugin filters in this toolkit that i want to use run unbelievably slow in Image, because it doesn't read the powerPC code (very disappointing!). Thanks much in advance for any help from the experts out there.... cheers, jed -X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X Jed Leigh Mosenfelder e-mail: Jed.Mosenfelder@uni-bayreuth.de Bayerisches Geoinstitut Tel: +49-921-553712 (office) Universitaet Bayreuth -553700 (dept. secretary) D-95440 Bayreuth -5160186 (home) Germany Fax:+49-921-553769 :-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-) -------------------------------- End of nih-image-d Digest V98 Issue #30 *************************************** From nih-image-request@io.ece.drexel.edu Thu Aug 6 08:26 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA29929; Thu, 6 Aug 1998 08:26:36 -0400 (EDT) Resent-Date: Thu, 6 Aug 1998 08:26:36 -0400 (EDT) From: DrJohnRuss@aol.com Message-ID: <4fc7f694.35c99c86@aol.com> Date: Thu, 6 Aug 1998 08:07:31 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: dumb question about IP toolkit 2.5 Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"BUqIF1.0.Lt6.hoPor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/178 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 639 Status: O In a message dated 8/6/98 9:40:10 AM, Jed.Mosenfelder@uni-bayreuth.de wrote: >Has anyone tried threshholding greyscale images using the IPTK plugins in >Adobe photoshop. It's driving me crazy because, contrary to the manual, the >threshholded pixels do not appear highlighted in a color that you can >easily distinguish (they appear in some shade of grey rather than red), so >it's basically impossible to see what you're doing. I wonder if i'm missing >something obvious. It sounds as though you have a 256 color display depth. With thousands or millions the preview of the thresholded region appears with a color overlay. John Russ From nih-image-request@io.ece.drexel.edu Thu Aug 6 17:35 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA15823; Thu, 6 Aug 1998 17:29:52 -0400 (EDT) Resent-Date: Thu, 6 Aug 1998 17:29:52 -0400 (EDT) X-Sender: tmorton@10.0.0.1 Message-Id: In-Reply-To: <199808051002.GAA18933@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Wed, 5 Aug 1998 08:46:48 -0500 To: nih-image@io.ece.drexel.edu From: Tom Morton Subject: Re: nih-image-d Digest V98 #29 Resent-Message-ID: <"Gz1xv3.0.8J3.QfXor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/179 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1753 Status: O Hello, Beta 3b fixes this problem. It was released on our website yesterday at http://www.scioncorp.com > >This message is specifically directed at any of the PC Scion Image users out >there, so most Mac NIH Image users can probably ignore this. > >I have been using (trying to, at least) Scion Beta 3 for particle >analysis. The >particles I am analyzing are somewhat oval shaped, fairly well defined, and >usually a few hundred pixels in area (they don't appear small on the >screen.) I >have been trying to get Scion to give me the lengths of the major/ minor >axes of >the best fitting oval for the particle, but every time I attempt this I get >error codes like "-1.#IO" instead of a measurement. Whether or not I have >calibrated my scale to the proper units doesn't seem to have an effect. > >Has anyone else had this problem? Is there some way to get the major/ >minor axes >to work? I even drew perfect elipses on a blank image as a test, and it didn't >even give me the measurements for that. > >__________________________________ > >Alex Courtade >Huntsman Corporation >7114 N. Lamar Blvd >Austin, TX 78752 > >Phone: (512) 483-0190 >Email: alex_courtade@huntsman.com > >__________________________________ > >-------------------------------- ----------------------------------------------------------------------- Tom Morton support@scioncorp.com Technical Services http://www.scioncorp.com Scion Corporation ftp://scioncorp.com 82 Wormans Mill Rd., Suite H Phone: (301) 695-7870 Frederick, MD 21701 Fax: (301) 695-0035 ----------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Thu Aug 6 17:48 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA16488; Thu, 6 Aug 1998 17:36:57 -0400 (EDT) Resent-Date: Thu, 6 Aug 1998 17:36:57 -0400 (EDT) Date: Thu, 6 Aug 1998 17:18:57 -0400 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: Skewed normal distribution Resent-Message-ID: <"MB2Dp3.0.4e3.EtXor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/180 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 890 Status: O This problem is mathematical, but started in NIH Image. I described the distribution of intensities in an ROI by the mean, standard deviation, and skewness of the distribution of pixel intensities. Now, I would like to generate the curve described by those 3 parameters. I've got the equation for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know how to put in the skewness term. Any advice as to the actual equation or where to look? Standard statistics books don't help. Maybe engineering, where similar parameters are called first, second and third moments. Thanks in advance, Harry. Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 From nih-image-request@io.ece.drexel.edu Thu Aug 6 19:51 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id TAA28144; Thu, 6 Aug 1998 19:50:52 -0400 (EDT) Resent-Date: Thu, 6 Aug 1998 19:50:52 -0400 (EDT) Message-ID: <35CA3EE5.4CE8@maroon.tc.umn.edu> Date: Thu, 06 Aug 1998 18:40:22 -0500 From: "Michael J. Herron" Reply-To: Michael J Herron Organization: U of MN X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: dumb question about IP toolkit 2.5 References: <4fc7f694.35c99c86@aol.com> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"1Gq8S1.0.Aa6.QvZor"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/181 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1158 Status: O Geez! That is something that has been bothering me for a long time. I thought it was a "feature". Glad to hear there is a way around it. DrJohnRuss@AOL.COM wrote: > > In a message dated 8/6/98 9:40:10 AM, Jed.Mosenfelder@uni-bayreuth.de wrote: > > >Has anyone tried threshholding greyscale images using the IPTK plugins in > >Adobe photoshop. It's driving me crazy because, contrary to the manual, the > >threshholded pixels do not appear highlighted in a color that you can > >easily distinguish (they appear in some shade of grey rather than red), so > >it's basically impossible to see what you're doing. I wonder if i'm missing > >something obvious. > > It sounds as though you have a 256 color display depth. With thousands or > millions the preview of the thresholded region appears with a color overlay. > > John Russ -- _____________________________________________________________ / Michael J. Herron University of MN, Dept. of Dermatology / / herro001@maroon.tc.umn.edu / /http://134.84.141.41/RASH.html / _____________________________________________________________ From nih-image-request@io.ece.drexel.edu Thu Aug 6 20:10 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA00132; Thu, 6 Aug 1998 20:10:03 -0400 (EDT) Resent-Date: Thu, 6 Aug 1998 20:10:03 -0400 (EDT) Message-ID: From: "Goldsmith, Noel" To: "'Kwang Y. Han'" , "'Image Mailing List'" Subject: RE: Measuring spot distances in electron diffraction patterns (ED P) Date: Fri, 7 Aug 1998 09:59:42 +1000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"Fn4763.0.057.2Eaor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/182 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1219 Status: O Kwang, Mail me an image and I will have a look. What you are doing looks fine, but maybe you have a centre to edge gradient which you must remove before thresholding. This would explain the shift in positions with a change in thresholding. Its a bit hard to tell what you need to be doing without the data. Noel. > ---------- > From: Kwang Y. Han > Sent: Thursday, 6 August 1998 1:49 AM > To: nih-image@io.ece.drexel.edu > Subject: Measuring spot distances in electron diffraction > patterns (EDP) > > I am hoping someone could point out to me a more accurate way of > measuring > spot distances in EDP for single-crystal materials. > > This is how i did: > 1) manually threshold the inverted TIFF image to obtain all the > desired > spots > 2) perform 'Analyze Particles...' > 3) click 'Show Results' > 4) import the results to Excel and calculate the distances > > The distance between 2 specific spots appears to depend very much on > my > threshold value. > > Should I be locating the centroid or geometrical centre of each spot? > I am not sure if top-hat filter or Hough transform can help to reduce > variability in measurements? If so, how should it be done? > > Thanks ahead for any suggestions.. > From nih-image-d-request@io.ece.drexel.edu Fri Aug 7 06:13 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA23680; Fri, 7 Aug 1998 06:13:24 -0400 (EDT) Date: Fri, 7 Aug 1998 06:13:24 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808071013.GAA23680@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #31 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/31 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7914 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 31 Today's Topics: Re: dumb question about IP toolkit 2 [ DrJohnRuss@aol.com ] Re: nih-image-d Digest V98 #29 [ Tom Morton ] Skewed normal distribution [ hmthomas@med.cornell.edu (Henry M. ] Re: dumb question about IP toolkit 2 [ "Michael J. Herron" Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 8/6/98 9:40:10 AM, Jed.Mosenfelder@uni-bayreuth.de wrote: >Has anyone tried threshholding greyscale images using the IPTK plugins in >Adobe photoshop. It's driving me crazy because, contrary to the manual, the >threshholded pixels do not appear highlighted in a color that you can >easily distinguish (they appear in some shade of grey rather than red), so >it's basically impossible to see what you're doing. I wonder if i'm missing >something obvious. It sounds as though you have a 256 color display depth. With thousands or millions the preview of the thresholded region appears with a color overlay. John Russ ------------------------------ Date: Wed, 5 Aug 1998 08:46:48 -0500 From: Tom Morton To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #29 Message-Id: Content-Type: text/plain; charset="us-ascii" Hello, Beta 3b fixes this problem. It was released on our website yesterday at http://www.scioncorp.com > >This message is specifically directed at any of the PC Scion Image users out >there, so most Mac NIH Image users can probably ignore this. > >I have been using (trying to, at least) Scion Beta 3 for particle >analysis. The >particles I am analyzing are somewhat oval shaped, fairly well defined, and >usually a few hundred pixels in area (they don't appear small on the >screen.) I >have been trying to get Scion to give me the lengths of the major/ minor >axes of >the best fitting oval for the particle, but every time I attempt this I get >error codes like "-1.#IO" instead of a measurement. Whether or not I have >calibrated my scale to the proper units doesn't seem to have an effect. > >Has anyone else had this problem? Is there some way to get the major/ >minor axes >to work? I even drew perfect elipses on a blank image as a test, and it didn't >even give me the measurements for that. > >__________________________________ > >Alex Courtade >Huntsman Corporation >7114 N. Lamar Blvd >Austin, TX 78752 > >Phone: (512) 483-0190 >Email: alex_courtade@huntsman.com > >__________________________________ > >-------------------------------- ----------------------------------------------------------------------- Tom Morton support@scioncorp.com Technical Services http://www.scioncorp.com Scion Corporation ftp://scioncorp.com 82 Wormans Mill Rd., Suite H Phone: (301) 695-7870 Frederick, MD 21701 Fax: (301) 695-0035 ----------------------------------------------------------------------- ------------------------------ Date: Thu, 6 Aug 1998 17:18:57 -0400 From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) Subject: Skewed normal distribution Message-Id: Content-Type: text/plain; charset="us-ascii" This problem is mathematical, but started in NIH Image. I described the distribution of intensities in an ROI by the mean, standard deviation, and skewness of the distribution of pixel intensities. Now, I would like to generate the curve described by those 3 parameters. I've got the equation for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know how to put in the skewness term. Any advice as to the actual equation or where to look? Standard statistics books don't help. Maybe engineering, where similar parameters are called first, second and third moments. Thanks in advance, Harry. Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 ------------------------------ Date: Thu, 06 Aug 1998 18:40:22 -0500 From: "Michael J. Herron" To: nih-image@io.ece.drexel.edu Subject: Re: dumb question about IP toolkit 2.5 Message-ID: <35CA3EE5.4CE8@maroon.tc.umn.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Geez! That is something that has been bothering me for a long time. I thought it was a "feature". Glad to hear there is a way around it. DrJohnRuss@AOL.COM wrote: > > In a message dated 8/6/98 9:40:10 AM, Jed.Mosenfelder@uni-bayreuth.de wrote: > > >Has anyone tried threshholding greyscale images using the IPTK plugins in > >Adobe photoshop. It's driving me crazy because, contrary to the manual, the > >threshholded pixels do not appear highlighted in a color that you can > >easily distinguish (they appear in some shade of grey rather than red), so > >it's basically impossible to see what you're doing. I wonder if i'm missing > >something obvious. > > It sounds as though you have a 256 color display depth. With thousands or > millions the preview of the thresholded region appears with a color overlay. > > John Russ -- _____________________________________________________________ / Michael J. Herron University of MN, Dept. of Dermatology / / herro001@maroon.tc.umn.edu / /http://134.84.141.41/RASH.html / _____________________________________________________________ ------------------------------ Date: Fri, 7 Aug 1998 09:59:42 +1000 From: "Goldsmith, Noel" To: "'Kwang Y. Han'" , "'Image Mailing List'" Subject: RE: Measuring spot distances in electron diffraction patterns (ED P) Message-ID: Content-Type: text/plain Kwang, Mail me an image and I will have a look. What you are doing looks fine, but maybe you have a centre to edge gradient which you must remove before thresholding. This would explain the shift in positions with a change in thresholding. Its a bit hard to tell what you need to be doing without the data. Noel. > ---------- > From: Kwang Y. Han > Sent: Thursday, 6 August 1998 1:49 AM > To: nih-image@io.ece.drexel.edu > Subject: Measuring spot distances in electron diffraction > patterns (EDP) > > I am hoping someone could point out to me a more accurate way of > measuring > spot distances in EDP for single-crystal materials. > > This is how i did: > 1) manually threshold the inverted TIFF image to obtain all the > desired > spots > 2) perform 'Analyze Particles...' > 3) click 'Show Results' > 4) import the results to Excel and calculate the distances > > The distance between 2 specific spots appears to depend very much on > my > threshold value. > > Should I be locating the centroid or geometrical centre of each spot? > I am not sure if top-hat filter or Hough transform can help to reduce > variability in measurements? If so, how should it be done? > > Thanks ahead for any suggestions.. > -------------------------------- End of nih-image-d Digest V98 Issue #31 *************************************** From nih-image-request@io.ece.drexel.edu Fri Aug 7 09:37 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA11073; Fri, 7 Aug 1998 09:36:54 -0400 (EDT) Resent-Date: Fri, 7 Aug 1998 09:36:54 -0400 (EDT) Message-ID: <35CAFD32.DEBB3212@ix.urz.uni-heidelberg.de> Date: Fri, 07 Aug 1998 15:12:18 +0200 From: Thomas Ehmer X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: NIH-image Mailinglist Subject: translate scanned b/w curves in xy (ascii) coordinates ? Content-Transfer-Encoding: 7bit Resent-Message-ID: <"xalWg2.0.oK2.lxlor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/183 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1083 Status: O What: A question about transfering paper plots in computer coordinates. Problem: translate b/w curves with marching line alg. automatically in xy coordinates Hello. In our lab, we often have plots from an analogue plotter (xy-plots, single trace) After having scanned the paper plots and having converted them into b/w pictures, it would be great to have a tool that transfers/translates the black pixel-trace into worksheet readable xy coordinates (ascii). I know about the capabilities from the SigmaScanPro program from Jandel Scientific, but unfortunately we do not have any funds to buy it. Has anyone already written a tool using kind of the marching line algorithm, so one only needs to click the trace and to give the start direction, and the software outputs a table of xy cooridnates? Thanks in advance, Thomas -- Thomas Ehmer, Dipl.-Phys. FON:+49 6221 544084 2nd Institute of Physiolgy FAX:+49 6221 544123 University of Heidelberg just have look at... INF 326 www.rzuser.uni-heidelberg.de/~jm0/fink D-69120 Heidelberg, Germany ---- From nih-image-request@io.ece.drexel.edu Fri Aug 7 10:18 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA14314; Fri, 7 Aug 1998 10:18:21 -0400 (EDT) Resent-Date: Fri, 7 Aug 1998 10:18:21 -0400 (EDT) Date: Fri, 7 Aug 1998 15:02:25 +0100 (BST) From: Jan Kreft X-Sender: sabjk@thor To: NIH-image Mailinglist Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ? In-Reply-To: <35CAFD32.DEBB3212@ix.urz.uni-heidelberg.de> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"dQXOL1.0.VD3.iamor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/184 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1627 Status: O Hi, there was a report on a freeware program called Tracer that is supposed to do exactly that in a computer mag (c't 12/98). I haven't tested it. It's Win95 only. Have a look at: http://www.ntu.edu.sg/home/akarol/data.htm Hope this helps, Jan. Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036 School of Pure and Applied Biology Fax +44 1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK On Fri, 7 Aug 1998, Thomas Ehmer wrote: > What: A question about transfering paper plots in computer coordinates. > Problem: translate b/w curves with marching line alg. automatically in > xy coordinates > > Hello. > > In our lab, we often have plots from an analogue plotter (xy-plots, > single trace) > After having scanned the paper plots and having converted them into b/w > pictures, it would be great to have a tool that transfers/translates the > black pixel-trace into worksheet readable xy coordinates (ascii). > I know about the capabilities from the SigmaScanPro program from Jandel > Scientific, but unfortunately we do not have any funds to buy it. > Has anyone already written a tool using kind of the marching line > algorithm, so one only needs to click the trace and to give the start > direction, and the software outputs a table of xy cooridnates? > > Thanks in advance, Thomas > > -- > Thomas Ehmer, Dipl.-Phys. FON:+49 6221 544084 > 2nd Institute of Physiolgy FAX:+49 6221 544123 > University of Heidelberg just have look at... > INF 326 www.rzuser.uni-heidelberg.de/~jm0/fink > D-69120 Heidelberg, Germany > ---- > > > From nih-image-request@io.ece.drexel.edu Fri Aug 7 11:23 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA18699; Fri, 7 Aug 1998 11:22:56 -0400 (EDT) Resent-Date: Fri, 7 Aug 1998 11:22:56 -0400 (EDT) X-Authentication-Warning: archa15.cc.uga.edu: mmiller owned process doing -bs Date: Fri, 7 Aug 1998 11:05:59 -0400 (EDT) From: "Michael G. Miller" X-Sender: mmiller@archa15.cc.uga.edu To: nih-image@io.ece.drexel.edu Subject: Reading DAT tapes on a Mac Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"ztf2-.0.jG4.4Xnor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/185 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 783 Status: O I'm trying to help a faculty member here who is using nih-image to work with mri image data from a local hospital. The image data is provided on 4mm DAT tapes. Currently we read those on a unix system (it's just raw data files, not tar) and transfer them to his Mac. He has acquired an 4mm DAT drive to do backups using the Retrospect software. I've taken a quick look around the web and could not find any software to read the mri image DAT tapes directly on the MAC (since it is not tar format the various Mac tar programs do not work). Does anyone know of software that will allow a mac to read raw data files off a DAT tape? Thanks in advance for any information, Michael Michael G. Miller UCNS Client Services University of Georgia mmiller@arches.uga.edu 706.542.5359 From nih-image-request@io.ece.drexel.edu Fri Aug 7 11:55 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA22186; Fri, 7 Aug 1998 11:55:10 -0400 (EDT) Resent-Date: Fri, 7 Aug 1998 11:55:10 -0400 (EDT) X-Sender: rh208@pop.cus.cam.ac.uk Message-Id: In-Reply-To: <35CAFD32.DEBB3212@ix.urz.uni-heidelberg.de> Mime-Version: 1.0 Date: Fri, 7 Aug 1998 16:43:19 +0100 To: nih-image@io.ece.drexel.edu From: Ray Hicks Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ? Resent-Message-ID: <"QBTHX2.0.IA5.72oor"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/186 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2771 Status: O Hi Thomas, there used to be a macro for this that ran with Image (as I remember the plot was ANDed with a grid of lines normal to the x axis, breaking the data line up into dots, co-ordinates for these could then be found using analyse particles). There is also a program that does this for you called dataThief, it allows you to calibrate the plot axes, and then either click where you want measurementsto be taken, or automatically trace a line, exporting the data as text. I haven't used it "in anger" but I remembered mention of it a few years ago on this list, and found it at: ftp://codon.nih.gov/pub/nih-image/programs/dataThief_2.0b.hqx I gave it a go and it seems to be just what you want. Good luck Ray ps have you tried digitising the voltage that goes into the chart recorder in the first place? It shouldn't be too expensive ($20-30? - at least for a pc),and would probably give better results than any plot/scan/trace methods where there are plenty of places for non-linearity and errors to creep in. >What: A question about transfering paper plots in computer coordinates. >Problem: translate b/w curves with marching line alg. automatically in >xy coordinates > >Hello. > >In our lab, we often have plots from an analogue plotter (xy-plots, >single trace) >After having scanned the paper plots and having converted them into b/w >pictures, it would be great to have a tool that transfers/translates the >black pixel-trace into worksheet readable xy coordinates (ascii). >I know about the capabilities from the SigmaScanPro program from Jandel >Scientific, but unfortunately we do not have any funds to buy it. >Has anyone already written a tool using kind of the marching line >algorithm, so one only needs to click the trace and to give the start >direction, and the software outputs a table of xy cooridnates? > >Thanks in advance, Thomas > >-- >Thomas Ehmer, Dipl.-Phys. FON:+49 6221 544084 >2nd Institute of Physiolgy FAX:+49 6221 544123 >University of Heidelberg just have look at... >INF 326 www.rzuser.uni-heidelberg.de/~jm0/fink >D-69120 Heidelberg, Germany >---- Ray Hicks ________________________________________________________________________ |University of Cambridge |Tel 01223 330149 | |Department of Medicine |Fax 01223 336846 | |Level 5, Addenbrookes Hospital |e-mail | |Hills Road Cambridge |Web http://facsmac.med.cam.ac.uk | |CB2 |ftp server ftp://131.111.80.78 | |UK | | |_________________________________|_____________________________________| From nih-image-request@io.ece.drexel.edu Fri Aug 7 15:51 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA08477; Fri, 7 Aug 1998 15:51:18 -0400 (EDT) Resent-Date: Fri, 7 Aug 1998 15:51:18 -0400 (EDT) Message-ID: <35CB5864.745C0ADE@usa.net> Date: Fri, 07 Aug 1998 13:41:24 -0600 From: "Christoopher P. Tully" Reply-To: cptully@usa.com X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ? References: <35CAFD32.DEBB3212@ix.urz.uni-heidelberg.de> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"M-S-02.0._r1.jUror"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/187 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1345 Status: O Thomas- Take look at a program called DataThief at this url: http://archives.math.utk.edu/software/mac/graphingAids/.directory.html I think it will do everything you need. Chris Tully Thomas Ehmer wrote: > > What: A question about transfering paper plots in computer coordinates. > Problem: translate b/w curves with marching line alg. automatically in > xy coordinates > > Hello. > > In our lab, we often have plots from an analogue plotter (xy-plots, > single trace) > After having scanned the paper plots and having converted them into b/w > pictures, it would be great to have a tool that transfers/translates the > black pixel-trace into worksheet readable xy coordinates (ascii). > I know about the capabilities from the SigmaScanPro program from Jandel > Scientific, but unfortunately we do not have any funds to buy it. > Has anyone already written a tool using kind of the marching line > algorithm, so one only needs to click the trace and to give the start > direction, and the software outputs a table of xy cooridnates? > > Thanks in advance, Thomas > > -- > Thomas Ehmer, Dipl.-Phys. FON:+49 6221 544084 > 2nd Institute of Physiolgy FAX:+49 6221 544123 > University of Heidelberg just have look at... > INF 326 www.rzuser.uni-heidelberg.de/~jm0/fink > D-69120 Heidelberg, Germany > ---- From nih-image-d-request@io.ece.drexel.edu Sat Aug 8 06:13 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA19980; Sat, 8 Aug 1998 06:13:18 -0400 (EDT) Date: Sat, 8 Aug 1998 06:13:18 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808081013.GAA19980@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #32 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/32 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 9906 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 32 Today's Topics: translate scanned b/w curves in xy ( [ Thomas Ehmer ] Reading DAT tapes on a Mac [ "Michael G. Miller" ] Re: translate scanned b/w curves in [ "Christoopher P. Tully" To: NIH-image Mailinglist Subject: translate scanned b/w curves in xy (ascii) coordinates ? Message-ID: <35CAFD32.DEBB3212@ix.urz.uni-heidelberg.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit What: A question about transfering paper plots in computer coordinates. Problem: translate b/w curves with marching line alg. automatically in xy coordinates Hello. In our lab, we often have plots from an analogue plotter (xy-plots, single trace) After having scanned the paper plots and having converted them into b/w pictures, it would be great to have a tool that transfers/translates the black pixel-trace into worksheet readable xy coordinates (ascii). I know about the capabilities from the SigmaScanPro program from Jandel Scientific, but unfortunately we do not have any funds to buy it. Has anyone already written a tool using kind of the marching line algorithm, so one only needs to click the trace and to give the start direction, and the software outputs a table of xy cooridnates? Thanks in advance, Thomas -- Thomas Ehmer, Dipl.-Phys. FON:+49 6221 544084 2nd Institute of Physiolgy FAX:+49 6221 544123 University of Heidelberg just have look at... INF 326 www.rzuser.uni-heidelberg.de/~jm0/fink D-69120 Heidelberg, Germany ---- ------------------------------ Date: Fri, 7 Aug 1998 15:02:25 +0100 (BST) From: Jan Kreft To: NIH-image Mailinglist Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, there was a report on a freeware program called Tracer that is supposed to do exactly that in a computer mag (c't 12/98). I haven't tested it. It's Win95 only. Have a look at: http://www.ntu.edu.sg/home/akarol/data.htm Hope this helps, Jan. Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036 School of Pure and Applied Biology Fax +44 1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK On Fri, 7 Aug 1998, Thomas Ehmer wrote: > What: A question about transfering paper plots in computer coordinates. > Problem: translate b/w curves with marching line alg. automatically in > xy coordinates > > Hello. > > In our lab, we often have plots from an analogue plotter (xy-plots, > single trace) > After having scanned the paper plots and having converted them into b/w > pictures, it would be great to have a tool that transfers/translates the > black pixel-trace into worksheet readable xy coordinates (ascii). > I know about the capabilities from the SigmaScanPro program from Jandel > Scientific, but unfortunately we do not have any funds to buy it. > Has anyone already written a tool using kind of the marching line > algorithm, so one only needs to click the trace and to give the start > direction, and the software outputs a table of xy cooridnates? > > Thanks in advance, Thomas > > -- > Thomas Ehmer, Dipl.-Phys. FON:+49 6221 544084 > 2nd Institute of Physiolgy FAX:+49 6221 544123 > University of Heidelberg just have look at... > INF 326 www.rzuser.uni-heidelberg.de/~jm0/fink > D-69120 Heidelberg, Germany > ---- > > > ------------------------------ Date: Fri, 7 Aug 1998 11:05:59 -0400 (EDT) From: "Michael G. Miller" To: nih-image@io.ece.drexel.edu Subject: Reading DAT tapes on a Mac Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I'm trying to help a faculty member here who is using nih-image to work with mri image data from a local hospital. The image data is provided on 4mm DAT tapes. Currently we read those on a unix system (it's just raw data files, not tar) and transfer them to his Mac. He has acquired an 4mm DAT drive to do backups using the Retrospect software. I've taken a quick look around the web and could not find any software to read the mri image DAT tapes directly on the MAC (since it is not tar format the various Mac tar programs do not work). Does anyone know of software that will allow a mac to read raw data files off a DAT tape? Thanks in advance for any information, Michael Michael G. Miller UCNS Client Services University of Georgia mmiller@arches.uga.edu 706.542.5359 ------------------------------ Date: Fri, 7 Aug 1998 16:43:19 +0100 From: Ray Hicks To: nih-image@io.ece.drexel.edu Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ? Message-Id: Content-Type: text/plain; charset="us-ascii" Hi Thomas, there used to be a macro for this that ran with Image (as I remember the plot was ANDed with a grid of lines normal to the x axis, breaking the data line up into dots, co-ordinates for these could then be found using analyse particles). There is also a program that does this for you called dataThief, it allows you to calibrate the plot axes, and then either click where you want measurementsto be taken, or automatically trace a line, exporting the data as text. I haven't used it "in anger" but I remembered mention of it a few years ago on this list, and found it at: ftp://codon.nih.gov/pub/nih-image/programs/dataThief_2.0b.hqx I gave it a go and it seems to be just what you want. Good luck Ray ps have you tried digitising the voltage that goes into the chart recorder in the first place? It shouldn't be too expensive ($20-30? - at least for a pc),and would probably give better results than any plot/scan/trace methods where there are plenty of places for non-linearity and errors to creep in. >What: A question about transfering paper plots in computer coordinates. >Problem: translate b/w curves with marching line alg. automatically in >xy coordinates > >Hello. > >In our lab, we often have plots from an analogue plotter (xy-plots, >single trace) >After having scanned the paper plots and having converted them into b/w >pictures, it would be great to have a tool that transfers/translates the >black pixel-trace into worksheet readable xy coordinates (ascii). >I know about the capabilities from the SigmaScanPro program from Jandel >Scientific, but unfortunately we do not have any funds to buy it. >Has anyone already written a tool using kind of the marching line >algorithm, so one only needs to click the trace and to give the start >direction, and the software outputs a table of xy cooridnates? > >Thanks in advance, Thomas > >-- >Thomas Ehmer, Dipl.-Phys. FON:+49 6221 544084 >2nd Institute of Physiolgy FAX:+49 6221 544123 >University of Heidelberg just have look at... >INF 326 www.rzuser.uni-heidelberg.de/~jm0/fink >D-69120 Heidelberg, Germany >---- Ray Hicks ________________________________________________________________________ |University of Cambridge |Tel 01223 330149 | |Department of Medicine |Fax 01223 336846 | |Level 5, Addenbrookes Hospital |e-mail | |Hills Road Cambridge |Web http://facsmac.med.cam.ac.uk | |CB2 |ftp server ftp://131.111.80.78 | |UK | | |_________________________________|_____________________________________| ------------------------------ Date: Fri, 07 Aug 1998 13:41:24 -0600 From: "Christoopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ? Message-ID: <35CB5864.745C0ADE@usa.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thomas- Take look at a program called DataThief at this url: http://archives.math.utk.edu/software/mac/graphingAids/.directory.html I think it will do everything you need. Chris Tully Thomas Ehmer wrote: > > What: A question about transfering paper plots in computer coordinates. > Problem: translate b/w curves with marching line alg. automatically in > xy coordinates > > Hello. > > In our lab, we often have plots from an analogue plotter (xy-plots, > single trace) > After having scanned the paper plots and having converted them into b/w > pictures, it would be great to have a tool that transfers/translates the > black pixel-trace into worksheet readable xy coordinates (ascii). > I know about the capabilities from the SigmaScanPro program from Jandel > Scientific, but unfortunately we do not have any funds to buy it. > Has anyone already written a tool using kind of the marching line > algorithm, so one only needs to click the trace and to give the start > direction, and the software outputs a table of xy cooridnates? > > Thanks in advance, Thomas > > -- > Thomas Ehmer, Dipl.-Phys. FON:+49 6221 544084 > 2nd Institute of Physiolgy FAX:+49 6221 544123 > University of Heidelberg just have look at... > INF 326 www.rzuser.uni-heidelberg.de/~jm0/fink > D-69120 Heidelberg, Germany > ---- -------------------------------- End of nih-image-d Digest V98 Issue #32 *************************************** From nih-image-request@io.ece.drexel.edu Mon Aug 10 06:50 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA02175; Mon, 10 Aug 1998 06:50:29 -0400 (EDT) Resent-Date: Mon, 10 Aug 1998 06:50:29 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 10 Aug 1998 11:35:53 +0100 To: nih-image@io.ece.drexel.edu From: Clive Washington Subject: Re: Skewed normal distribution Resent-Message-ID: <"amz0g2.0.F8.Eoipr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/188 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1976 Status: O >This problem is mathematical, but started in NIH Image. I described the >distribution of intensities in an ROI by the mean, standard deviation, and >skewness of the distribution of pixel intensities. Now, I would like to >generate the curve described by those 3 parameters. I've got the equation >for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know >how to put in the skewness term. I'm not sure about this but I think you'll find that you cannot reconstruct in this way. The normal distribution is unique so can be reconstructed knowing mean x and standard deviation. But there are an infinite number of different curves which can generate a particular skewedness. Admittedly they may not be smooth. For example if you take a normal and just pull up one channel a bit, the value of skewedness will increase. If you drop it down again and pull up another channel it will also increase similarly, and you won't be able to distinguish one from the other. So there is no unique solution. You might be better fitting a more explicit form to your data. The simplest skewed form is the lognormal, which has a tail to larger X. I haven't got the formula to hand but it's in the books. I expect there are others - consult the particle size literature, esp. Terry Allen's book 'particle size measurement' since particle people have to deal with this sort of data frequently. ////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// Dr. Clive Washington, Tel. 0115 9515034 Senior Lecturer in Pharmaceutics, Fax 0115 9515102 Department of Pharmaceutical Sciences, University of Nottingham, University Park, Email pazcw@unix.ccc.nottingham.ac.uk Nottingham NG7 2RD. http://reliant.pharm.nottingham.ac.uk/clive.html "It's mail, Jim, but not as we know it." ////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// From nih-image-request@io.ece.drexel.edu Mon Aug 10 07:12 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA04149; Mon, 10 Aug 1998 07:11:58 -0400 (EDT) Resent-Date: Mon, 10 Aug 1998 07:11:58 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: Mime-Version: 1.0 Date: Mon, 10 Aug 1998 13:00:01 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Clicking Zip disks Resent-Message-ID: <"RQ0m43.0.Sj.-9jpr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/189 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1077 Status: O Now it has finally happened, the dreaded thing I have heard happened to other users of Zip drives: The drive goes clicking when a Zip disk is inserted, and destroys all subsequent disks that are inserted. (Fortunately, I tested the drive with a blank disk after the clicking disk to avoid further data loss, as recommended on the Iomega web-pages). I have used 85+ disks without any problems since I bought my first Zip. I remember there was a thread about this last winter, but I am unable to locate it in the archives. So, is there any way to recover the data on the initial clicking disk ? +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Mon Aug 10 09:34 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA16340; Mon, 10 Aug 1998 09:34:46 -0400 (EDT) Resent-Date: Mon, 10 Aug 1998 09:34:46 -0400 (EDT) X-Sender: rhawkes@mailserv.mta.ca Message-Id: Mime-Version: 1.0 Date: Mon, 10 Aug 1998 10:19:13 -0300 To: nih-image@io.ece.drexel.edu From: rhawkes@mta.ca (Robert Hawkes) Subject: PowerBook, PCI Expansion and Frame Rate Resent-Message-ID: <"4M6Rl1.0.3f3.xDlpr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/190 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 430 Status: O I have recently acquired a PowerBook G3 / 233 MHz with a Magma PCI expansion system (3 slot, portable) which we are using with a SCION LG-3 video digitizer. Even though the G3 should be faster than the 9600/233 we use in the lab, I can only get 12 fps from NIH (or Scion) Image, even with virtual memory and extensions turned off. I am using system 8.1. I would very much appreciate any suggestions. Bob Hawkes rhawkes@mta.ca From nih-image-request@io.ece.drexel.edu Mon Aug 10 10:45 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA22654; Mon, 10 Aug 1998 10:45:27 -0400 (EDT) Resent-Date: Mon, 10 Aug 1998 10:45:27 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 10 Aug 1998 16:30:50 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Re: PowerBook, PCI Expansion and Frame Rate Resent-Message-ID: <"w0y7_.0.sA5.DFmpr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/191 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 995 Status: O >I have recently acquired a PowerBook G3 / 233 MHz with a Magma PCI >expansion system (3 slot, portable) which we are using with a SCION LG-3 >video digitizer. Even though the G3 should be faster than the 9600/233 we >use in the lab, I can only get 12 fps from NIH (or Scion) Image, even with >virtual memory and extensions turned off. I am using system 8.1. > >I would very much appreciate any suggestions. > >Bob Hawkes >rhawkes@mta.ca Try reducing the number of colors on the screen. Makes a big difference. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Mon Aug 10 12:53 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA02074; Mon, 10 Aug 1998 12:51:58 -0400 (EDT) Resent-Date: Mon, 10 Aug 1998 12:51:58 -0400 (EDT) Date: Mon, 10 Aug 1998 10:37:29 -0600 (CST) From: "Geoffrey D. Guttmann" To: nih-image@io.ece.drexel.edu Subject: Re: Clicking Zip disks In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"KMX5.0.vE.C7opr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/192 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1599 Status: O Hi folks The same problem happened to me. The drive was in warranty so Iomega replaced the Zip drive. The cost to recover the data was US$425 but they offered a 50% discount since the drive was under warranty. Maybe somebody can set up a cheaper Zip disk recovery service. Cheers, geoff >Now it has finally happened, the dreaded thing I have heard happened to >other users of Zip drives: The drive goes clicking when a Zip disk is >inserted, and destroys all subsequent disks that are inserted. >(Fortunately, I tested the drive with a blank disk after the clicking disk >to avoid further data loss, as recommended on the Iomega web-pages). I have >used 85+ disks without any problems since I bought my first Zip. > >I remember there was a thread about this last winter, but I am unable to >locate it in the archives. So, is there any way to recover the data on the >initial clicking disk ? ------------------------------------------------------------------------ Geoffrey D. Guttmann, Ph.D _/_/_/_/ _/_/ _/_/_/_/ _/ _/ Assistant Professor _/ _/ _/ _/ _/ _/ Dept. of Anatomy and Cell Biology _/ _/ _/ _/ _/ College of Medicine _/_/_/_/ _/_/_/_/ _/_/_/_/ _/_/ University of Saskatchewan _/ _/ _/ _/ _/ _/ A-315 Health Sciences Building _/ _/ _/ _/ _/ _/ 107 Wiggins Road _/_/_/_/ _/ _/ _/_/_/_/ _/ _/ _/ Saskatoon, SK S7N 5E5 CANADA Voice:(306)966-4079 Fax:(306)966-4298 E-mail:guttmann@duke.usask.ca ------------------------------------------------------------------------ From nih-image-request@io.ece.drexel.edu Mon Aug 10 13:41 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA06001; Mon, 10 Aug 1998 13:40:43 -0400 (EDT) Resent-Date: Mon, 10 Aug 1998 13:40:43 -0400 (EDT) Date: Mon, 10 Aug 1998 13:24:47 -0400 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: Re: Skewed normal distribution Resent-Message-ID: <"EFZn01.0.t71.gpopr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/193 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2837 Status: O >>This problem is mathematical, but started in NIH Image. I described the >>distribution of intensities in an ROI by the mean, standard deviation, and >>skewness of the distribution of pixel intensities. Now, I would like to >>generate the curve described by those 3 parameters. I've got the equation >>for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know >>how to put in the skewness term. > >I'm not sure about this but I think you'll find that you cannot reconstruct >in this way. The normal distribution is unique so can be reconstructed >knowing mean x and standard deviation. But there are an infinite number of >different curves which can generate a particular skewedness. Admittedly >they may not be smooth. For example if you take a normal and just pull up >one channel a bit, the value of skewedness will increase. If you drop it >down again and pull up another channel it will also increase similarly, and >you won't be able to distinguish one from the other. So there is no unique >solution. Thank you for your thought experiment with a normal curve. I believe that your logic applies to the SD of the the normal curve as well: there are an infinite number of actual distributions with the same mean and SD. What I'm looking for is a formula with 3 independent variables (mean, S.D. and skewness), which will generate a unique "standard" skewed normal (Gaussian) curve, the way mean and SD generate a standard normal curve. > >You might be better fitting a more explicit form to your data. The >simplest skewed form is the lognormal, which has a tail to larger X. I >haven't got the formula to hand but it's in the books. I expect there are >others - consult the particle size literature, esp. Terry Allen's book >'particle size measurement' since particle people have to deal with this >sort of data frequently. I'll try a log transformation, and also check the book. Thank you. Harry. > >////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// > >Dr. Clive Washington, Tel. 0115 9515034 >Senior Lecturer in Pharmaceutics, Fax 0115 9515102 >Department of Pharmaceutical Sciences, >University of Nottingham, >University Park, Email pazcw@unix.ccc.nottingham.ac.uk >Nottingham NG7 2RD. http://reliant.pharm.nottingham.ac.uk/clive.html > > "It's mail, Jim, but not as we know it." > >////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 From nih-image-request@io.ece.drexel.edu Mon Aug 10 13:42 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA06177; Mon, 10 Aug 1998 13:42:28 -0400 (EDT) Resent-Date: Mon, 10 Aug 1998 13:42:28 -0400 (EDT) Message-ID: <35CF2E67.A8656FE6@usa.net> Date: Mon, 10 Aug 1998 11:31:19 -0600 From: "Christopher P. Tully" Reply-To: cptully@usa.net X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Clicking Zip disks References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"_ocL7.0.JD1.lsopr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/194 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2564 Status: O My experieneces were with an internal IDE zip on a Wintel box, but they may be relavent: 1) when the drive started clicking, I was unable to read any disks on that drive, but had no problems reading them on other zip drives. 2) Taking the Zip drive out of the computer case and putting it back in cured the problem TEMPORARILY - I'd try gently knocking on the case of an external drive. However, the drive did eventually die and have to be replaced (in fact, the replacement was DOA, and had to be replaced as well...). 3) At this point, I think long and hard before buying any more Zip drives. First because at 100 - 200 MB of images per experiment Zips get used up fast, and second because CD-R disks are cheaper and less prone to being killed by a defective drive. Chris Tully Geoffrey D. Guttmann wrote: > > Hi folks > The same problem happened to me. The drive was in warranty so > Iomega replaced the Zip drive. The cost to recover the data was US$425 > but they offered a 50% discount since the drive was under warranty. Maybe > somebody can set up a cheaper Zip disk recovery service. > Cheers, geoff > > >Now it has finally happened, the dreaded thing I have heard happened to > >other users of Zip drives: The drive goes clicking when a Zip disk is > >inserted, and destroys all subsequent disks that are inserted. > >(Fortunately, I tested the drive with a blank disk after the clicking disk > >to avoid further data loss, as recommended on the Iomega web-pages). I have > >used 85+ disks without any problems since I bought my first Zip. > > > >I remember there was a thread about this last winter, but I am unable to > >locate it in the archives. So, is there any way to recover the data on the > >initial clicking disk ? > > ------------------------------------------------------------------------ > Geoffrey D. Guttmann, Ph.D _/_/_/_/ _/_/ _/_/_/_/ _/ _/ > Assistant Professor _/ _/ _/ _/ _/ _/ > Dept. of Anatomy and Cell Biology _/ _/ _/ _/ _/ > College of Medicine _/_/_/_/ _/_/_/_/ _/_/_/_/ _/_/ > University of Saskatchewan _/ _/ _/ _/ _/ _/ > A-315 Health Sciences Building _/ _/ _/ _/ _/ _/ > 107 Wiggins Road _/_/_/_/ _/ _/ _/_/_/_/ _/ _/ _/ > Saskatoon, SK S7N 5E5 > CANADA Voice:(306)966-4079 Fax:(306)966-4298 > E-mail:guttmann@duke.usask.ca > ------------------------------------------------------------------------ From nih-image-request@io.ece.drexel.edu Mon Aug 10 17:22 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA20030; Mon, 10 Aug 1998 17:22:06 -0400 (EDT) Resent-Date: Mon, 10 Aug 1998 17:22:06 -0400 (EDT) Message-ID: From: "Barwood, Henry" To: "'nih-image@biomed.drexel.edu'" Subject: Plot profile using Image-PC Date: Mon, 10 Aug 1998 16:07:40 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Encoding: 7 TEXT Resent-Message-ID: <"netns1.0.ue4.X2spr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/195 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 310 Status: O I have been running some profile plots using Scion's Image-PC (beta-3). Everything works and I can print the profiles, but I cannot save them as a .tif image like I could using Image for Mac. Does anyone have any suggestions of what I can do to save my plots? Thanks. Henry Barwood Indiana Geological Survey From nih-image-request@io.ece.drexel.edu Tue Aug 11 00:56 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id AAA20612; Tue, 11 Aug 1998 00:56:04 -0400 (EDT) Resent-Date: Tue, 11 Aug 1998 00:56:04 -0400 (EDT) Message-Id: <199808110441.AAA13261@mcfeely.concentric.net> Subject: Re: Clicking Zip disks Date: Mon, 10 Aug 98 21:49:26 -0800 From: Your Name To: Mime-Version: 1.0 Resent-Message-ID: <"mXLr32.0.wj4.njypr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/196 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 378 Status: O Hello, I had this clicking problem (about 40 clicks before it stopped) when I inserted my Zip disk into the drive. I sent my drive back to iomega and they gave me new Zip Drive. I have not had any problems since then (about 1.5 years, now). I was able to retrieve my Zip disk data using Norton Utilities. Good Luck, Wilfred Denetclaw Jr., Ph.D. Department Anatomy UCSF From nih-image-d-request@io.ece.drexel.edu Tue Aug 11 01:03 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id BAA21297; Tue, 11 Aug 1998 01:03:50 -0400 (EDT) Date: Tue, 11 Aug 1998 01:03:50 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808110503.BAA21297@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #33 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/33 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 15764 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 33 Today's Topics: Re: Skewed normal distribution [ Clive Washington ] ------------------------------ Date: Mon, 10 Aug 1998 11:35:53 +0100 From: Clive Washington To: nih-image@io.ece.drexel.edu Subject: Re: Skewed normal distribution Message-Id: Content-Type: text/plain; charset="us-ascii" >This problem is mathematical, but started in NIH Image. I described the >distribution of intensities in an ROI by the mean, standard deviation, and >skewness of the distribution of pixel intensities. Now, I would like to >generate the curve described by those 3 parameters. I've got the equation >for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know >how to put in the skewness term. I'm not sure about this but I think you'll find that you cannot reconstruct in this way. The normal distribution is unique so can be reconstructed knowing mean x and standard deviation. But there are an infinite number of different curves which can generate a particular skewedness. Admittedly they may not be smooth. For example if you take a normal and just pull up one channel a bit, the value of skewedness will increase. If you drop it down again and pull up another channel it will also increase similarly, and you won't be able to distinguish one from the other. So there is no unique solution. You might be better fitting a more explicit form to your data. The simplest skewed form is the lognormal, which has a tail to larger X. I haven't got the formula to hand but it's in the books. I expect there are others - consult the particle size literature, esp. Terry Allen's book 'particle size measurement' since particle people have to deal with this sort of data frequently. ////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// Dr. Clive Washington, Tel. 0115 9515034 Senior Lecturer in Pharmaceutics, Fax 0115 9515102 Department of Pharmaceutical Sciences, University of Nottingham, University Park, Email pazcw@unix.ccc.nottingham.ac.uk Nottingham NG7 2RD. http://reliant.pharm.nottingham.ac.uk/clive.html "It's mail, Jim, but not as we know it." ////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// ------------------------------ Date: Mon, 10 Aug 1998 13:00:01 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Clicking Zip disks Message-Id: Content-Type: text/plain; charset="us-ascii" Now it has finally happened, the dreaded thing I have heard happened to other users of Zip drives: The drive goes clicking when a Zip disk is inserted, and destroys all subsequent disks that are inserted. (Fortunately, I tested the drive with a blank disk after the clicking disk to avoid further data loss, as recommended on the Iomega web-pages). I have used 85+ disks without any problems since I bought my first Zip. I remember there was a thread about this last winter, but I am unable to locate it in the archives. So, is there any way to recover the data on the initial clicking disk ? +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Mon, 10 Aug 1998 10:19:13 -0300 From: rhawkes@mta.ca (Robert Hawkes) To: nih-image@io.ece.drexel.edu Subject: PowerBook, PCI Expansion and Frame Rate Message-Id: Content-Type: text/plain; charset="us-ascii" I have recently acquired a PowerBook G3 / 233 MHz with a Magma PCI expansion system (3 slot, portable) which we are using with a SCION LG-3 video digitizer. Even though the G3 should be faster than the 9600/233 we use in the lab, I can only get 12 fps from NIH (or Scion) Image, even with virtual memory and extensions turned off. I am using system 8.1. I would very much appreciate any suggestions. Bob Hawkes rhawkes@mta.ca ------------------------------ Date: Mon, 10 Aug 1998 16:30:50 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: PowerBook, PCI Expansion and Frame Rate Message-Id: Content-Type: text/plain; charset="us-ascii" >I have recently acquired a PowerBook G3 / 233 MHz with a Magma PCI >expansion system (3 slot, portable) which we are using with a SCION LG-3 >video digitizer. Even though the G3 should be faster than the 9600/233 we >use in the lab, I can only get 12 fps from NIH (or Scion) Image, even with >virtual memory and extensions turned off. I am using system 8.1. > >I would very much appreciate any suggestions. > >Bob Hawkes >rhawkes@mta.ca Try reducing the number of colors on the screen. Makes a big difference. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Mon, 10 Aug 1998 10:37:29 -0600 (CST) From: "Geoffrey D. Guttmann" To: nih-image@io.ece.drexel.edu Subject: Re: Clicking Zip disks Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi folks The same problem happened to me. The drive was in warranty so Iomega replaced the Zip drive. The cost to recover the data was US$425 but they offered a 50% discount since the drive was under warranty. Maybe somebody can set up a cheaper Zip disk recovery service. Cheers, geoff >Now it has finally happened, the dreaded thing I have heard happened to >other users of Zip drives: The drive goes clicking when a Zip disk is >inserted, and destroys all subsequent disks that are inserted. >(Fortunately, I tested the drive with a blank disk after the clicking disk >to avoid further data loss, as recommended on the Iomega web-pages). I have >used 85+ disks without any problems since I bought my first Zip. > >I remember there was a thread about this last winter, but I am unable to >locate it in the archives. So, is there any way to recover the data on the >initial clicking disk ? ------------------------------------------------------------------------ Geoffrey D. Guttmann, Ph.D _/_/_/_/ _/_/ _/_/_/_/ _/ _/ Assistant Professor _/ _/ _/ _/ _/ _/ Dept. of Anatomy and Cell Biology _/ _/ _/ _/ _/ College of Medicine _/_/_/_/ _/_/_/_/ _/_/_/_/ _/_/ University of Saskatchewan _/ _/ _/ _/ _/ _/ A-315 Health Sciences Building _/ _/ _/ _/ _/ _/ 107 Wiggins Road _/_/_/_/ _/ _/ _/_/_/_/ _/ _/ _/ Saskatoon, SK S7N 5E5 CANADA Voice:(306)966-4079 Fax:(306)966-4298 E-mail:guttmann@duke.usask.ca ------------------------------------------------------------------------ ------------------------------ Date: Mon, 10 Aug 1998 13:24:47 -0400 From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu Subject: Re: Skewed normal distribution Message-Id: Content-Type: text/plain; charset="us-ascii" >>This problem is mathematical, but started in NIH Image. I described the >>distribution of intensities in an ROI by the mean, standard deviation, and >>skewness of the distribution of pixel intensities. Now, I would like to >>generate the curve described by those 3 parameters. I've got the equation >>for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know >>how to put in the skewness term. > >I'm not sure about this but I think you'll find that you cannot reconstruct >in this way. The normal distribution is unique so can be reconstructed >knowing mean x and standard deviation. But there are an infinite number of >different curves which can generate a particular skewedness. Admittedly >they may not be smooth. For example if you take a normal and just pull up >one channel a bit, the value of skewedness will increase. If you drop it >down again and pull up another channel it will also increase similarly, and >you won't be able to distinguish one from the other. So there is no unique >solution. Thank you for your thought experiment with a normal curve. I believe that your logic applies to the SD of the the normal curve as well: there are an infinite number of actual distributions with the same mean and SD. What I'm looking for is a formula with 3 independent variables (mean, S.D. and skewness), which will generate a unique "standard" skewed normal (Gaussian) curve, the way mean and SD generate a standard normal curve. > >You might be better fitting a more explicit form to your data. The >simplest skewed form is the lognormal, which has a tail to larger X. I >haven't got the formula to hand but it's in the books. I expect there are >others - consult the particle size literature, esp. Terry Allen's book >'particle size measurement' since particle people have to deal with this >sort of data frequently. I'll try a log transformation, and also check the book. Thank you. Harry. > >////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// > >Dr. Clive Washington, Tel. 0115 9515034 >Senior Lecturer in Pharmaceutics, Fax 0115 9515102 >Department of Pharmaceutical Sciences, >University of Nottingham, >University Park, Email pazcw@unix.ccc.nottingham.ac.uk >Nottingham NG7 2RD. http://reliant.pharm.nottingham.ac.uk/clive.html > > "It's mail, Jim, but not as we know it." > >////////////////////////COLLOID ENGINEERING GROUP/////////////////////////// Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 ------------------------------ Date: Mon, 10 Aug 1998 11:31:19 -0600 From: "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: Clicking Zip disks Message-ID: <35CF2E67.A8656FE6@usa.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit My experieneces were with an internal IDE zip on a Wintel box, but they may be relavent: 1) when the drive started clicking, I was unable to read any disks on that drive, but had no problems reading them on other zip drives. 2) Taking the Zip drive out of the computer case and putting it back in cured the problem TEMPORARILY - I'd try gently knocking on the case of an external drive. However, the drive did eventually die and have to be replaced (in fact, the replacement was DOA, and had to be replaced as well...). 3) At this point, I think long and hard before buying any more Zip drives. First because at 100 - 200 MB of images per experiment Zips get used up fast, and second because CD-R disks are cheaper and less prone to being killed by a defective drive. Chris Tully Geoffrey D. Guttmann wrote: > > Hi folks > The same problem happened to me. The drive was in warranty so > Iomega replaced the Zip drive. The cost to recover the data was US$425 > but they offered a 50% discount since the drive was under warranty. Maybe > somebody can set up a cheaper Zip disk recovery service. > Cheers, geoff > > >Now it has finally happened, the dreaded thing I have heard happened to > >other users of Zip drives: The drive goes clicking when a Zip disk is > >inserted, and destroys all subsequent disks that are inserted. > >(Fortunately, I tested the drive with a blank disk after the clicking disk > >to avoid further data loss, as recommended on the Iomega web-pages). I have > >used 85+ disks without any problems since I bought my first Zip. > > > >I remember there was a thread about this last winter, but I am unable to > >locate it in the archives. So, is there any way to recover the data on the > >initial clicking disk ? > > ------------------------------------------------------------------------ > Geoffrey D. Guttmann, Ph.D _/_/_/_/ _/_/ _/_/_/_/ _/ _/ > Assistant Professor _/ _/ _/ _/ _/ _/ > Dept. of Anatomy and Cell Biology _/ _/ _/ _/ _/ > College of Medicine _/_/_/_/ _/_/_/_/ _/_/_/_/ _/_/ > University of Saskatchewan _/ _/ _/ _/ _/ _/ > A-315 Health Sciences Building _/ _/ _/ _/ _/ _/ > 107 Wiggins Road _/_/_/_/ _/ _/ _/_/_/_/ _/ _/ _/ > Saskatoon, SK S7N 5E5 > CANADA Voice:(306)966-4079 Fax:(306)966-4298 > E-mail:guttmann@duke.usask.ca > ------------------------------------------------------------------------ ------------------------------ Date: Mon, 10 Aug 1998 16:07:40 -0500 From: "Barwood, Henry" To: "'nih-image@biomed.drexel.edu'" Subject: Plot profile using Image-PC Message-ID: I have been running some profile plots using Scion's Image-PC (beta-3). Everything works and I can print the profiles, but I cannot save them as a .tif image like I could using Image for Mac. Does anyone have any suggestions of what I can do to save my plots? Thanks. Henry Barwood Indiana Geological Survey ------------------------------ Date: Mon, 10 Aug 98 21:49:26 -0800 From: Your Name To: Subject: Re: Clicking Zip disks Message-Id: <199808110441.AAA13261@mcfeely.concentric.net> Content-Type: text/plain; charset="US-ASCII" Hello, I had this clicking problem (about 40 clicks before it stopped) when I inserted my Zip disk into the drive. I sent my drive back to iomega and they gave me new Zip Drive. I have not had any problems since then (about 1.5 years, now). I was able to retrieve my Zip disk data using Norton Utilities. Good Luck, Wilfred Denetclaw Jr., Ph.D. Department Anatomy UCSF -------------------------------- End of nih-image-d Digest V98 Issue #33 *************************************** From nih-image-request@io.ece.drexel.edu Tue Aug 11 09:07 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA28155; Tue, 11 Aug 1998 09:06:54 -0400 (EDT) Resent-Date: Tue, 11 Aug 1998 09:06:54 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: Mime-Version: 1.0 Date: Tue, 11 Aug 1998 14:54:04 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Cross-platform incremental CD recording Resent-Message-ID: <"3wV7J.0.YV6.Rw3qr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/197 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2520 Status: O I am trying to figure out some flexible way to store images in a cross- platform (Mac-PC) compatible way. All images will be created and saved in NIH image on the Mac. I want to do this on writable CD-ROMs. I have purchased a Sony Storewell CD writer. I have tested it and it works well. The CD writer software, Adaptec Toast, can record in both Mac and Windows/Jouliet format, and the cross-platform compatible ISO format. The writer is also bundled with Adaptec DirectCD, which allows files to be moved, renamed and deleted while the CD is "open" using the cross-platform UDF format. This functionality is very important since I often need to reorganize files as the scope of a project changes. UDF drivers are available for Windows as well, so I have successfully been able to read disks written in this format on a PC. The problem is to get some way of automatically mapping file extensions to file types. The files are of PICT, TIFF, Excel and Word types. I want some way for the PC to read the Mac file type attributes and automatically add the proper extensions. For various reasons, it is quite impractical to add the extensions on the Mac side. I have purchased the utility program DataWiz MacOpener for opening Mac disks on a PC. MacOpener mounts Mac disks and adds extensions automatically as desired, but only on Mac formatted disks. If I am going to take advantage of the incremental and changeable UDF format, which is supported both by the Mac and the PC, MacOpener does not add the extensions as the CD is recognized by the system as a valid PC disk. So what I need is either some utility on the PC that will recognize Mac files as Mac files and add proper extensions, even when the disk is readable by the PC; or some flexible (incremental) way to write CDs in a hybrid format that automatically adds extensions to the filenames in the PC directory part of the shared data. The latter solution is probably the best since that would not require special drivers to be installed on the PC. Any suggestions are welcome. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Tue Aug 11 12:57 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA12988; Tue, 11 Aug 1998 12:56:55 -0400 (EDT) Resent-Date: Tue, 11 Aug 1998 12:56:55 -0400 (EDT) Message-ID: <19980811164333.27127.qmail@hotmail.com> X-Originating-IP: [198.14.48.122] From: "Paul Loftsgard" To: nih-image@io.ece.drexel.edu Subject: Fractal analysis macros Date: Tue, 11 Aug 1998 09:43:32 PDT Resent-Message-ID: <"9K4So1.0.ny2.WJ7qr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/198 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 687 Status: O Hello, I've been using the fractal analysis macros to analyze super critical sprays and I have two questions. 1. I currently use the method of subtracting the background(radius 50), thresholding, auto selecting, then applying the box method on the selections. The images still look similar to the originals, but I was wondering whether there is anything flawed with this technique. 2. If possible could somebody give me a good description of the EDM method. Is it anything like the area caliper method? Any help would be appreciated. Thank you, Paul Loftsgard ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Tue Aug 11 14:43 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA19000; Tue, 11 Aug 1998 14:42:47 -0400 (EDT) Resent-Date: Tue, 11 Aug 1998 14:42:47 -0400 (EDT) Mime-Version: 1.0 X-Sender: rwadkins@wwwctrc.fs.saci.org Message-Id: In-Reply-To: <199808110442.AAA19441@io.ECE.Drexel.EDU> Date: Tue, 11 Aug 1998 13:37:53 -0600 To: nih-image@io.ece.drexel.edu From: "Randy M. Wadkins" Subject: Re: Clicking Zip disks Resent-Message-ID: <"NIm9r3.0.8S4.ut8qr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/199 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1156 Status: O >3) At this point, I think long and hard before buying any more Zip >drives. First because at 100 - 200 MB of images per experiment Zips get >used up fast, and second because CD-R disks are cheaper and less prone >to being killed by a defective drive. > >Chris Tully > We are in the process of copying our Zips onto CD-R, and then plan to throw the drives in the trash. Our failure rate has been 50% on the drives (over a 3 year period), with the loss of about 20% of our storage media. I suppose we will try to go with MO drives from now on, but they are somewhat bulkier than Zips. --Randy ****************************************************************** "Fight House Resolution 3888, which legalizes spam! Go to: http://www.cauce.org/latest.html and contact the Commerce Committee Rep. from your area. Otherwise, say goodbye to e-mail." Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** From nih-image-request@io.ece.drexel.edu Tue Aug 11 15:16 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA21245; Tue, 11 Aug 1998 15:15:38 -0400 (EDT) Resent-Date: Tue, 11 Aug 1998 15:15:38 -0400 (EDT) X-Sender: d306604@nobel.si.uqam.ca Message-Id: In-Reply-To: <19980811164333.27127.qmail@hotmail.com> Mime-Version: 1.0 Date: Tue, 11 Aug 1998 15:05:59 -0400 To: nih-image@io.ece.drexel.edu From: Dominique Berube Subject: Re: Fractal analysis macros Resent-Message-ID: <"MSP8O3.0.525.dP9qr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/200 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 775 Status: O > >2. If possible could somebody give me a good description of the EDM >method. Is it anything like the area caliper method? > EDM method is similar to the dilation techniques except that is performs an isotropic dilation of an outline. It results in a Minkowski dimension which is mathamatically different from the Hausdorf dimension obtained with the caliper method. Some found that the Minkoski dimension was sometimes slightly higher than the Hausdorf one but I'm not so sure of that. I personnaly prefer the EDM method. It's easier to implement and I find the result to be much more consistent than with the box-counting method, partly because I can generate more data points. Of course, box-counting remains useful for image surfaces but less reliable for outlines. From nih-image-request@io.ece.drexel.edu Tue Aug 11 16:51 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA27140; Tue, 11 Aug 1998 16:50:49 -0400 (EDT) Resent-Date: Tue, 11 Aug 1998 16:50:49 -0400 (EDT) Mime-Version: 1.0 X-Sender: rwadkins@wwwctrc.fs.saci.org Message-Id: In-Reply-To: <199808110442.AAA19441@io.ECE.Drexel.EDU> Date: Tue, 11 Aug 1998 15:30:02 -0600 To: nih-image@io.ece.drexel.edu From: "Randy M. Wadkins" Subject: Re: Clicking Zip disks Resent-Message-ID: <"Xojj72.0.8S6.PmAqr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/201 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1347 Status: O >------------------------------ >Date: Mon, 10 Aug 1998 10:37:29 -0600 (CST) >From: "Geoffrey D. Guttmann" >To: nih-image@io.ece.drexel.edu >Subject: Re: Clicking Zip disks >Message-ID: >Content-Type: TEXT/PLAIN; charset=US-ASCII > >Hi folks > The same problem happened to me. The drive was in warranty so >Iomega replaced the Zip drive. The cost to recover the data was US$425 >but they offered a 50% discount since the drive was under warranty. Maybe >somebody can set up a cheaper Zip disk recovery service. >Cheers, geoff > BTW: there is now a company that specializes in recovering data from clicked Zips. They seem a little cheaper than Iomega. See: http://www.ontrack.com/hc/cod.asp --Randy ****************************************************************** "Fight House Resolution 3888, which legalizes spam! Go to: http://www.cauce.org/latest.html and contact the Commerce Committee Rep. from your area. Otherwise, say goodbye to e-mail." Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** From nih-image-d-request@io.ece.drexel.edu Wed Aug 12 06:13 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA28190; Wed, 12 Aug 1998 06:13:33 -0400 (EDT) Date: Wed, 12 Aug 1998 06:13:33 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808121013.GAA28190@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #34 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/34 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 8506 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 34 Today's Topics: Cross-platform incremental CD record [ Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Cross-platform incremental CD recording Message-Id: Content-Type: text/plain; charset="us-ascii" I am trying to figure out some flexible way to store images in a cross- platform (Mac-PC) compatible way. All images will be created and saved in NIH image on the Mac. I want to do this on writable CD-ROMs. I have purchased a Sony Storewell CD writer. I have tested it and it works well. The CD writer software, Adaptec Toast, can record in both Mac and Windows/Jouliet format, and the cross-platform compatible ISO format. The writer is also bundled with Adaptec DirectCD, which allows files to be moved, renamed and deleted while the CD is "open" using the cross-platform UDF format. This functionality is very important since I often need to reorganize files as the scope of a project changes. UDF drivers are available for Windows as well, so I have successfully been able to read disks written in this format on a PC. The problem is to get some way of automatically mapping file extensions to file types. The files are of PICT, TIFF, Excel and Word types. I want some way for the PC to read the Mac file type attributes and automatically add the proper extensions. For various reasons, it is quite impractical to add the extensions on the Mac side. I have purchased the utility program DataWiz MacOpener for opening Mac disks on a PC. MacOpener mounts Mac disks and adds extensions automatically as desired, but only on Mac formatted disks. If I am going to take advantage of the incremental and changeable UDF format, which is supported both by the Mac and the PC, MacOpener does not add the extensions as the CD is recognized by the system as a valid PC disk. So what I need is either some utility on the PC that will recognize Mac files as Mac files and add proper extensions, even when the disk is readable by the PC; or some flexible (incremental) way to write CDs in a hybrid format that automatically adds extensions to the filenames in the PC directory part of the shared data. The latter solution is probably the best since that would not require special drivers to be installed on the PC. Any suggestions are welcome. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Tue, 11 Aug 1998 09:43:32 PDT From: "Paul Loftsgard" To: nih-image@io.ece.drexel.edu Subject: Fractal analysis macros Message-ID: <19980811164333.27127.qmail@hotmail.com> Content-Type: text/plain Hello, I've been using the fractal analysis macros to analyze super critical sprays and I have two questions. 1. I currently use the method of subtracting the background(radius 50), thresholding, auto selecting, then applying the box method on the selections. The images still look similar to the originals, but I was wondering whether there is anything flawed with this technique. 2. If possible could somebody give me a good description of the EDM method. Is it anything like the area caliper method? Any help would be appreciated. Thank you, Paul Loftsgard ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Tue, 11 Aug 1998 13:37:53 -0600 From: "Randy M. Wadkins" To: nih-image@io.ece.drexel.edu Subject: Re: Clicking Zip disks Message-Id: Content-Type: text/plain; charset="us-ascii" >3) At this point, I think long and hard before buying any more Zip >drives. First because at 100 - 200 MB of images per experiment Zips get >used up fast, and second because CD-R disks are cheaper and less prone >to being killed by a defective drive. > >Chris Tully > We are in the process of copying our Zips onto CD-R, and then plan to throw the drives in the trash. Our failure rate has been 50% on the drives (over a 3 year period), with the loss of about 20% of our storage media. I suppose we will try to go with MO drives from now on, but they are somewhat bulkier than Zips. --Randy ****************************************************************** "Fight House Resolution 3888, which legalizes spam! Go to: http://www.cauce.org/latest.html and contact the Commerce Committee Rep. from your area. Otherwise, say goodbye to e-mail." Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** ------------------------------ Date: Tue, 11 Aug 1998 15:05:59 -0400 From: Dominique Berube To: nih-image@io.ece.drexel.edu Subject: Re: Fractal analysis macros Message-Id: Content-Type: text/plain; charset="us-ascii" > >2. If possible could somebody give me a good description of the EDM >method. Is it anything like the area caliper method? > EDM method is similar to the dilation techniques except that is performs an isotropic dilation of an outline. It results in a Minkowski dimension which is mathamatically different from the Hausdorf dimension obtained with the caliper method. Some found that the Minkoski dimension was sometimes slightly higher than the Hausdorf one but I'm not so sure of that. I personnaly prefer the EDM method. It's easier to implement and I find the result to be much more consistent than with the box-counting method, partly because I can generate more data points. Of course, box-counting remains useful for image surfaces but less reliable for outlines. ------------------------------ Date: Tue, 11 Aug 1998 15:30:02 -0600 From: "Randy M. Wadkins" To: nih-image@io.ece.drexel.edu Subject: Re: Clicking Zip disks Message-Id: Content-Type: text/plain; charset="us-ascii" >------------------------------ >Date: Mon, 10 Aug 1998 10:37:29 -0600 (CST) >From: "Geoffrey D. Guttmann" >To: nih-image@io.ece.drexel.edu >Subject: Re: Clicking Zip disks >Message-ID: >Content-Type: TEXT/PLAIN; charset=US-ASCII > >Hi folks > The same problem happened to me. The drive was in warranty so >Iomega replaced the Zip drive. The cost to recover the data was US$425 >but they offered a 50% discount since the drive was under warranty. Maybe >somebody can set up a cheaper Zip disk recovery service. >Cheers, geoff > BTW: there is now a company that specializes in recovering data from clicked Zips. They seem a little cheaper than Iomega. See: http://www.ontrack.com/hc/cod.asp --Randy ****************************************************************** "Fight House Resolution 3888, which legalizes spam! Go to: http://www.cauce.org/latest.html and contact the Commerce Committee Rep. from your area. Otherwise, say goodbye to e-mail." Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** -------------------------------- End of nih-image-d Digest V98 Issue #34 *************************************** From nih-image-request@io.ece.drexel.edu Wed Aug 12 11:34 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA22636; Wed, 12 Aug 1998 11:33:44 -0400 (EDT) Resent-Date: Wed, 12 Aug 1998 11:33:44 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Wed, 12 Aug 1998 11:15:39 -0400 To: nih-image@io.ece.drexel.edu From: Otter Subject: Help with counting agar clones... Resent-Message-ID: <"veO__3.0.dG5.GBRqr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/202 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 949 Status: O Hi everyone, I am a new NIH Image user (v1.61 MAC), so please forgive me if you have heard this question a million times already! I am trying to count agar clones by size and I am unable to figure it out. Here is what I would like to do. I would like to take about 16 representative shots of a culture dish containing the clones and then paste those 16 shots together (I can do this via Photoshop). After opening that image up in NIH Image, I would like to have NIH Image count how many clones are present of varying sizes (in diameter, not pixels). For example, I would like NIH Image to tell me that out of x many clones, 5 are less than 50 microns, 15 are between 50 and 100 microns, 22 are between 175 and 200 microns, and so on. Does anyone have any advice or help on how I can do this? Is there a Macro to perform this sort of calculation? Thanks for your time and help, Evan L. Kaplan Carcinogenesis Lab Michigan State University From nih-image-request@io.ece.drexel.edu Wed Aug 12 12:42 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA27327; Wed, 12 Aug 1998 12:42:39 -0400 (EDT) Resent-Date: Wed, 12 Aug 1998 12:42:39 -0400 (EDT) X-Sender: ad1054@unix.worldpath.net Message-Id: Mime-Version: 1.0 Date: Wed, 12 Aug 1998 12:33:19 -0400 To: nih-image@io.ece.drexel.edu From: ad1054@worldpath.net (Dr. Christopher Coulon) Subject: Re: Help with counting agar clones... Resent-Message-ID: <"te6dk1.0.fU6.aESqr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/203 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1604 Status: O Evan, It really depends on your image contrast. If the contrast is good, an autoThreshold should segment your cultures from the background. Then an analyzeParticles should do your counts (use rMajor[] to return the diameter, or if ellipses are significant, use the average of rMinor[] and rMajor[]). If you need help on this, let me know with a message to me off list. Chris >Hi everyone, > >I am a new NIH Image user (v1.61 MAC), so please forgive me if you have >heard this question a million times already! I am trying to count agar >clones by size and I am unable to figure it out. Here is what I would like >to do. I would like to take about 16 representative shots of a culture >dish containing the clones and then paste those 16 shots together (I can do >this via Photoshop). After opening that image up in NIH Image, I would >like to have NIH Image count how many clones are present of varying sizes >(in diameter, not pixels). For example, I would like NIH Image to tell me >that out of x many clones, 5 are less than 50 microns, 15 are between 50 >and 100 microns, 22 are between 175 and 200 microns, and so on. Does >anyone have any advice or help on how I can do this? Is there a Macro to >perform this sort of calculation? > >Thanks for your time and help, > >Evan L. Kaplan >Carcinogenesis Lab >Michigan State University * * * * * * * * * * * * * * * * * * * Dr. Christopher Hunt Coulon * * The GAIA Group * * 40 Chick Road * * Wolfeboro, New Hampshire 03894 * * 603 569-0028 * * * * * * * * * * * * * * * * * * * From nih-image-d-request@io.ece.drexel.edu Thu Aug 13 06:19 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA23533; Thu, 13 Aug 1998 06:19:51 -0400 (EDT) Date: Thu, 13 Aug 1998 06:19:51 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808131019.GAA23533@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #35 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/35 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3517 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 35 Today's Topics: Help with counting agar clones... [ Otter ] Re: Help with counting agar clones.. [ ad1054@worldpath.net (Dr. Christoph ] ------------------------------ Date: Wed, 12 Aug 1998 11:15:39 -0400 From: Otter To: nih-image@io.ece.drexel.edu Subject: Help with counting agar clones... Message-Id: Content-Type: text/plain; charset="us-ascii" Hi everyone, I am a new NIH Image user (v1.61 MAC), so please forgive me if you have heard this question a million times already! I am trying to count agar clones by size and I am unable to figure it out. Here is what I would like to do. I would like to take about 16 representative shots of a culture dish containing the clones and then paste those 16 shots together (I can do this via Photoshop). After opening that image up in NIH Image, I would like to have NIH Image count how many clones are present of varying sizes (in diameter, not pixels). For example, I would like NIH Image to tell me that out of x many clones, 5 are less than 50 microns, 15 are between 50 and 100 microns, 22 are between 175 and 200 microns, and so on. Does anyone have any advice or help on how I can do this? Is there a Macro to perform this sort of calculation? Thanks for your time and help, Evan L. Kaplan Carcinogenesis Lab Michigan State University ------------------------------ Date: Wed, 12 Aug 1998 12:33:19 -0400 From: ad1054@worldpath.net (Dr. Christopher Coulon) To: nih-image@io.ece.drexel.edu Subject: Re: Help with counting agar clones... Message-Id: Content-Type: text/plain; charset="us-ascii" Evan, It really depends on your image contrast. If the contrast is good, an autoThreshold should segment your cultures from the background. Then an analyzeParticles should do your counts (use rMajor[] to return the diameter, or if ellipses are significant, use the average of rMinor[] and rMajor[]). If you need help on this, let me know with a message to me off list. Chris >Hi everyone, > >I am a new NIH Image user (v1.61 MAC), so please forgive me if you have >heard this question a million times already! I am trying to count agar >clones by size and I am unable to figure it out. Here is what I would like >to do. I would like to take about 16 representative shots of a culture >dish containing the clones and then paste those 16 shots together (I can do >this via Photoshop). After opening that image up in NIH Image, I would >like to have NIH Image count how many clones are present of varying sizes >(in diameter, not pixels). For example, I would like NIH Image to tell me >that out of x many clones, 5 are less than 50 microns, 15 are between 50 >and 100 microns, 22 are between 175 and 200 microns, and so on. Does >anyone have any advice or help on how I can do this? Is there a Macro to >perform this sort of calculation? > >Thanks for your time and help, > >Evan L. Kaplan >Carcinogenesis Lab >Michigan State University * * * * * * * * * * * * * * * * * * * Dr. Christopher Hunt Coulon * * The GAIA Group * * 40 Chick Road * * Wolfeboro, New Hampshire 03894 * * 603 569-0028 * * * * * * * * * * * * * * * * * * * -------------------------------- End of nih-image-d Digest V98 Issue #35 *************************************** From nih-image-request@io.ece.drexel.edu Thu Aug 13 08:05 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA03818; Thu, 13 Aug 1998 08:05:09 -0400 (EDT) Resent-Date: Thu, 13 Aug 1998 08:05:09 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Thu, 13 Aug 1998 07:39:37 -0500 To: nih-image@io.ece.drexel.edu From: Laird Bloom Subject: Re:counting agar clones/measuring areas Resent-Message-ID: <"ZShRT.0.nH.V1jqr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/204 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1845 Status: O Hi Evan, This may not be quite what you want, but I've written a set of macros that make it easy to outline a set of regions on your image or series of images and save the areas in a data file. You can either do it on saved images or directly at the microscope, which I've found to be easier. It's still relatively time-consuming, since you have to outline individual areas, but at least you know what you're measuring. You can set the scale in Image to give you area in square mm, etc., instead of pixels, but at some point you have to figure out a conversion factor based on your microscope's magnification. The data files are easy to import into Microsoft Excel, which has a nice histogram-making function if you want to divide your population of colonies into size ranges. Please let me know if you want the code. Yours, Laird Bloom MIT Center for Cancer Research >Hi everyone, > >I am a new NIH Image user (v1.61 MAC), so please forgive me if you have >heard this question a million times already! I am trying to count agar >clones by size and I am unable to figure it out. Here is what I would like >to do. I would like to take about 16 representative shots of a culture >dish containing the clones and then paste those 16 shots together (I can do >this via Photoshop). After opening that image up in NIH Image, I would >like to have NIH Image count how many clones are present of varying sizes >(in diameter, not pixels). For example, I would like NIH Image to tell me >that out of x many clones, 5 are less than 50 microns, 15 are between 50 >and 100 microns, 22 are between 175 and 200 microns, and so on. Does >anyone have any advice or help on how I can do this? Is there a Macro to >perform this sort of calculation? > >Thanks for your time and help, > >Evan L. Kaplan >Carcinogenesis Lab >Michigan State University From nih-image-request@io.ece.drexel.edu Thu Aug 13 16:58 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA18366; Thu, 13 Aug 1998 16:57:19 -0400 (EDT) Resent-Date: Thu, 13 Aug 1998 16:57:19 -0400 (EDT) Message-ID: <35D35085.D5046081@usa.net> Date: Thu, 13 Aug 1998 14:45:58 -0600 From: "Christopher P. Tully" Reply-To: cptully@usa.net X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Help with counting agar clones... References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"uZD7z2.0.W84.y-qqr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/205 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2014 Status: O Evan- a simple outline to get the data you describe: 1) Collect and composite the images (compositing may be unnecessary, since totals from several images can be added together after analysis, thus saving the time to composite the images). 2) Open the image(s) in NIH-Image 3) Make sure the scale is set properly in Analyze > Set Scale... 4) Choose Anaylze > Options, and make sure that the appropriate measurements are selected (either use area, or ellipse major axis and ellpise minor axis) 5) Threshold the image (either manually, or using the auto threshold feature). 6) Use the Anaylze Particles feature to measure the thersholded objects 7) copy the results from the results table and past them into Excel 8) If you are using single images instead of a composite, repeat 2-7 for all images 9) in Excel, use the Histogram funbction under Analysis tools to generate a histogram of your size data. The histogram tool allows you to specify the number of bins and the range of each bin, etc. Chris Tully Otter wrote: > > Hi everyone, > > I am a new NIH Image user (v1.61 MAC), so please forgive me if you have > heard this question a million times already! I am trying to count agar > clones by size and I am unable to figure it out. Here is what I would like > to do. I would like to take about 16 representative shots of a culture > dish containing the clones and then paste those 16 shots together (I can do > this via Photoshop). After opening that image up in NIH Image, I would > like to have NIH Image count how many clones are present of varying sizes > (in diameter, not pixels). For example, I would like NIH Image to tell me > that out of x many clones, 5 are less than 50 microns, 15 are between 50 > and 100 microns, 22 are between 175 and 200 microns, and so on. Does > anyone have any advice or help on how I can do this? Is there a Macro to > perform this sort of calculation? > > Thanks for your time and help, > > Evan L. Kaplan > Carcinogenesis Lab > Michigan State University From nih-image-request@io.ece.drexel.edu Fri Aug 14 02:21 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA11643; Fri, 14 Aug 1998 02:21:22 -0400 (EDT) Resent-Date: Fri, 14 Aug 1998 02:21:22 -0400 (EDT) Message-ID: <35D3D443.AD84F5F2@caspur.it> Date: Fri, 14 Aug 1998 08:08:04 +0200 From: Leopoldo Silvestroni Organization: Università di Roma 'La Sapienza' X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: FFT question Content-Transfer-Encoding: 8bit Resent-Message-ID: <"YhrNF3.0.sd2.mNzqr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/206 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-1 Content-Length: 518 Status: O Hi everyone, I would greatly appreciate receiving your help as for: - a photoshop compatible FFT plugin - how to "apply" a fast Fourier transform to a square selection thank You all in advance Leopoldo Silvestroni, MD -- Leopoldo Silvestroni,MD Laboratorio di Biofluorimetria Dipartimento di Fisiopatologia Medica Policlinico Umberto I Università di Roma 'La Sapienza' 00161-Roma tel. +39 6 49970710 fax +39 6 4461450 e-mail: l.silvestroni@caspur.it WWW address: http://w3.uniroma1.it/MEDICFISIO/labpag1.html From nih-image-d-request@io.ece.drexel.edu Fri Aug 14 02:24 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA12248; Fri, 14 Aug 1998 02:24:57 -0400 (EDT) Date: Fri, 14 Aug 1998 02:24:57 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808140624.CAA12248@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #36 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/36 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 5731 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 36 Today's Topics: Re:counting agar clones/measuring ar [ Laird Bloom ] Re: Help with counting agar clones.. [ "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re:counting agar clones/measuring areas Message-Id: Content-Type: text/plain; charset="us-ascii" Hi Evan, This may not be quite what you want, but I've written a set of macros that make it easy to outline a set of regions on your image or series of images and save the areas in a data file. You can either do it on saved images or directly at the microscope, which I've found to be easier. It's still relatively time-consuming, since you have to outline individual areas, but at least you know what you're measuring. You can set the scale in Image to give you area in square mm, etc., instead of pixels, but at some point you have to figure out a conversion factor based on your microscope's magnification. The data files are easy to import into Microsoft Excel, which has a nice histogram-making function if you want to divide your population of colonies into size ranges. Please let me know if you want the code. Yours, Laird Bloom MIT Center for Cancer Research >Hi everyone, > >I am a new NIH Image user (v1.61 MAC), so please forgive me if you have >heard this question a million times already! I am trying to count agar >clones by size and I am unable to figure it out. Here is what I would like >to do. I would like to take about 16 representative shots of a culture >dish containing the clones and then paste those 16 shots together (I can do >this via Photoshop). After opening that image up in NIH Image, I would >like to have NIH Image count how many clones are present of varying sizes >(in diameter, not pixels). For example, I would like NIH Image to tell me >that out of x many clones, 5 are less than 50 microns, 15 are between 50 >and 100 microns, 22 are between 175 and 200 microns, and so on. Does >anyone have any advice or help on how I can do this? Is there a Macro to >perform this sort of calculation? > >Thanks for your time and help, > >Evan L. Kaplan >Carcinogenesis Lab >Michigan State University ------------------------------ Date: Thu, 13 Aug 1998 14:45:58 -0600 From: "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: Help with counting agar clones... Message-ID: <35D35085.D5046081@usa.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Evan- a simple outline to get the data you describe: 1) Collect and composite the images (compositing may be unnecessary, since totals from several images can be added together after analysis, thus saving the time to composite the images). 2) Open the image(s) in NIH-Image 3) Make sure the scale is set properly in Analyze > Set Scale... 4) Choose Anaylze > Options, and make sure that the appropriate measurements are selected (either use area, or ellipse major axis and ellpise minor axis) 5) Threshold the image (either manually, or using the auto threshold feature). 6) Use the Anaylze Particles feature to measure the thersholded objects 7) copy the results from the results table and past them into Excel 8) If you are using single images instead of a composite, repeat 2-7 for all images 9) in Excel, use the Histogram funbction under Analysis tools to generate a histogram of your size data. The histogram tool allows you to specify the number of bins and the range of each bin, etc. Chris Tully Otter wrote: > > Hi everyone, > > I am a new NIH Image user (v1.61 MAC), so please forgive me if you have > heard this question a million times already! I am trying to count agar > clones by size and I am unable to figure it out. Here is what I would like > to do. I would like to take about 16 representative shots of a culture > dish containing the clones and then paste those 16 shots together (I can do > this via Photoshop). After opening that image up in NIH Image, I would > like to have NIH Image count how many clones are present of varying sizes > (in diameter, not pixels). For example, I would like NIH Image to tell me > that out of x many clones, 5 are less than 50 microns, 15 are between 50 > and 100 microns, 22 are between 175 and 200 microns, and so on. Does > anyone have any advice or help on how I can do this? Is there a Macro to > perform this sort of calculation? > > Thanks for your time and help, > > Evan L. Kaplan > Carcinogenesis Lab > Michigan State University ------------------------------ Date: Fri, 14 Aug 1998 08:08:04 +0200 From: Leopoldo Silvestroni To: nih-image@io.ece.drexel.edu Subject: FFT question Message-ID: <35D3D443.AD84F5F2@caspur.it> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi everyone, I would greatly appreciate receiving your help as for: - a photoshop compatible FFT plugin - how to "apply" a fast Fourier transform to a square selection thank You all in advance Leopoldo Silvestroni, MD -- Leopoldo Silvestroni,MD Laboratorio di Biofluorimetria Dipartimento di Fisiopatologia Medica Policlinico Umberto I Università di Roma 'La Sapienza' 00161-Roma tel. +39 6 49970710 fax +39 6 4461450 e-mail: l.silvestroni@caspur.it WWW address: http://w3.uniroma1.it/MEDICFISIO/labpag1.html -------------------------------- End of nih-image-d Digest V98 Issue #36 *************************************** From nih-image-request@io.ece.drexel.edu Fri Aug 14 04:49 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id EAA26888; Fri, 14 Aug 1998 04:49:01 -0400 (EDT) Resent-Date: Fri, 14 Aug 1998 04:49:01 -0400 (EDT) From: tony.collins@bbsrc.ac.uk Message-Id: <9808140838.AA03332@mserv.iapc.bbsrc.ac.uk> To: nih-image@io.ece.drexel.edu Date: Fri, 14 Aug 1998 09:40:51 +0100 Subject: NIH macro conversion to Scion Image Priority: normal X-Mailer: Pegasus Mail for Win32 (v3.01b) MIME-Version: 1.0 Resent-Message-ID: <"QtwSj.0.xH6.pU_qr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/207 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 628 Status: O I'm not sure if this is the right forum to be asking this question if it's not I apologise in advance, I've only just joined the list. As I understand it, Scion's Image program *should* be able to use NIH Image macro (correct?). I find that it can't, the macro's are loaded correctly but they don't run correctly. Are there any rules to converting the macros from NIH to Scion's Image? Or is the macro interpreter a bit buggy in Scion's Beta software? Many thanks Tony Collins Dept. Neurobiology The Babraham Institute Babraham Hall Babraham Cambridge CB2 4AT UK tel. +44 (0) 1223 832312 fax. +44 (0) 1223 836614 From nih-image-request@io.ece.drexel.edu Fri Aug 14 07:05 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA10994; Fri, 14 Aug 1998 07:04:52 -0400 (EDT) Resent-Date: Fri, 14 Aug 1998 07:04:52 -0400 (EDT) From: DrJohnRuss@aol.com Message-ID: <1acbe6e7.35d41763@aol.com> Date: Fri, 14 Aug 1998 06:54:26 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: FFT question Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"l2-Ke2.0.uP2.LU1rr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/208 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 649 Status: O In a message dated 8/14/98 6:18:18 AM, Leopoldo Silvestroni, MD wrote: >I would greatly appreciate receiving your help as for: >- a photoshop compatible FFT plugin >- how to "apply" a fast Fourier transform to a square selection >thank You all in advance > The Image Processing Tool Kit (http://members.aol.com/ImagProcTK/) includes complete FFT routines as well as a comprehensive tutorial showing their use with a variety of images. If the region to be transformed is square and a power of two in size, the transform can be applied directly. If not, it should be padded to a larger size by pasting it into a medium grey blank image. John Russ From nih-image-request@io.ece.drexel.edu Fri Aug 14 18:12 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA11920; Fri, 14 Aug 1998 18:12:07 -0400 (EDT) Resent-Date: Fri, 14 Aug 1998 18:12:07 -0400 (EDT) Message-ID: <35D4B456.663E294A@usa.net> Date: Fri, 14 Aug 1998 16:04:07 -0600 From: "Christopher P. Tully" Reply-To: cptully@usa.net X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: NIH macro conversion to Scion Image References: <9808140838.AA03332@mserv.iapc.bbsrc.ac.uk> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"GZkB83.0.Tf2.BEBrr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/209 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1391 Status: O Tony- Scion may also respond to your questions, nut since they haven't yet: I believe that they did the port based on NIH-Image v1.57 source, so there are a few macro commands which were added after 1.57 that they have not yet implemented. Also, from what they have told me when I asked, the macro interpreter was the last item that they worked on, so it may still be incomplete. I would look for a change history to find out exactly which version of Image their port is based on, and what parts have been implemented or still need to be implemented. All of my comments above are based on the assumption that you are asking about Scion Image for Win95/NT. If not, ignore them. Chris Tully tony.collins@bbsrc.ac.uk wrote: > > I'm not sure if this is the right forum to be asking this question if it's > not I apologise in advance, I've only just joined the list. > As I understand it, Scion's Image program *should* be able to use > NIH Image macro (correct?). I find that it can't, the macro's are > loaded correctly but they don't run correctly. Are there any rules to > converting the macros from NIH to Scion's Image? Or is the macro > interpreter a bit buggy in Scion's Beta software? > Many thanks > > Tony Collins > > Dept. Neurobiology > The Babraham Institute > Babraham Hall > Babraham > Cambridge CB2 4AT > UK > > tel. +44 (0) 1223 832312 > fax. +44 (0) 1223 836614 From nih-image-request@io.ece.drexel.edu Fri Aug 14 19:03 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id TAA16272; Fri, 14 Aug 1998 19:03:29 -0400 (EDT) Resent-Date: Fri, 14 Aug 1998 19:03:29 -0400 (EDT) Date: Fri, 14 Aug 1998 12:54:19 -1000 From: Kathleen Annikki Moore X-Sender: moorekat@uhunix5 To: nih-image@io.ece.drexel.edu Subject: solution for acquistion with Mac G3 powerbook? Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"GxmnP1.0.bm3.m0Crr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/210 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 458 Status: O I'm beginning. Any helpful acquisition suggestions would be welcome. Will NIH image + plug-in digitizer(operating on a Mac G3 powerbook which is on order) software capture bone microscopy images with adequate image quality from a hitachi KPC-500 video attached to brightfield or fluorescent microscope. Is a single freeze frame adequate data for an image analysis? or is averaging "X" amount of frames necessary. Very grateful for responses. Kathleen Moore From nih-image-d-request@io.ece.drexel.edu Sat Aug 15 06:15 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA15577; Sat, 15 Aug 1998 06:15:49 -0400 (EDT) Date: Sat, 15 Aug 1998 06:15:49 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808151015.GAA15577@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #37 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/37 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4829 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 37 Today's Topics: NIH macro conversion to Scion Image [ tony.collins@bbsrc.ac.uk ] Re: FFT question [ DrJohnRuss@aol.com ] Re: NIH macro conversion to Scion Im [ "Christopher P. Tully" Content-Type: text/plain; charset="US-ASCII" I'm not sure if this is the right forum to be asking this question if it's not I apologise in advance, I've only just joined the list. As I understand it, Scion's Image program *should* be able to use NIH Image macro (correct?). I find that it can't, the macro's are loaded correctly but they don't run correctly. Are there any rules to converting the macros from NIH to Scion's Image? Or is the macro interpreter a bit buggy in Scion's Beta software? Many thanks Tony Collins Dept. Neurobiology The Babraham Institute Babraham Hall Babraham Cambridge CB2 4AT UK tel. +44 (0) 1223 832312 fax. +44 (0) 1223 836614 ------------------------------ Date: Fri, 14 Aug 1998 06:54:26 EDT From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: FFT question Message-ID: <1acbe6e7.35d41763@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 8/14/98 6:18:18 AM, Leopoldo Silvestroni, MD wrote: >I would greatly appreciate receiving your help as for: >- a photoshop compatible FFT plugin >- how to "apply" a fast Fourier transform to a square selection >thank You all in advance > The Image Processing Tool Kit (http://members.aol.com/ImagProcTK/) includes complete FFT routines as well as a comprehensive tutorial showing their use with a variety of images. If the region to be transformed is square and a power of two in size, the transform can be applied directly. If not, it should be padded to a larger size by pasting it into a medium grey blank image. John Russ ------------------------------ Date: Fri, 14 Aug 1998 16:04:07 -0600 From: "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: NIH macro conversion to Scion Image Message-ID: <35D4B456.663E294A@usa.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Tony- Scion may also respond to your questions, nut since they haven't yet: I believe that they did the port based on NIH-Image v1.57 source, so there are a few macro commands which were added after 1.57 that they have not yet implemented. Also, from what they have told me when I asked, the macro interpreter was the last item that they worked on, so it may still be incomplete. I would look for a change history to find out exactly which version of Image their port is based on, and what parts have been implemented or still need to be implemented. All of my comments above are based on the assumption that you are asking about Scion Image for Win95/NT. If not, ignore them. Chris Tully tony.collins@bbsrc.ac.uk wrote: > > I'm not sure if this is the right forum to be asking this question if it's > not I apologise in advance, I've only just joined the list. > As I understand it, Scion's Image program *should* be able to use > NIH Image macro (correct?). I find that it can't, the macro's are > loaded correctly but they don't run correctly. Are there any rules to > converting the macros from NIH to Scion's Image? Or is the macro > interpreter a bit buggy in Scion's Beta software? > Many thanks > > Tony Collins > > Dept. Neurobiology > The Babraham Institute > Babraham Hall > Babraham > Cambridge CB2 4AT > UK > > tel. +44 (0) 1223 832312 > fax. +44 (0) 1223 836614 ------------------------------ Date: Fri, 14 Aug 1998 12:54:19 -1000 From: Kathleen Annikki Moore To: nih-image@io.ece.drexel.edu Subject: solution for acquistion with Mac G3 powerbook? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I'm beginning. Any helpful acquisition suggestions would be welcome. Will NIH image + plug-in digitizer(operating on a Mac G3 powerbook which is on order) software capture bone microscopy images with adequate image quality from a hitachi KPC-500 video attached to brightfield or fluorescent microscope. Is a single freeze frame adequate data for an image analysis? or is averaging "X" amount of frames necessary. Very grateful for responses. Kathleen Moore -------------------------------- End of nih-image-d Digest V98 Issue #37 *************************************** From nih-image-request@io.ece.drexel.edu Mon Aug 17 08:16 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA14483; Mon, 17 Aug 1998 08:16:19 -0400 (EDT) Resent-Date: Mon, 17 Aug 1998 08:16:19 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Mon, 17 Aug 1998 08:04:08 -0500 To: nih-image@io.ece.drexel.edu From: Laird Bloom Subject: code for area measurement macros Resent-Message-ID: <"HkOnm1.0.JD3.Sm1sr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/211 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 9680 Status: O I've had several requests for the code for macros to record area measurement data from regions you outline with a mouse. Here is the code for two versions, one for use with saved images, and one that works well for live images. Please contact me if you have questions. Laird Bloom MIT Center for Cancer Research Times{The following is a set of instructions for the setup with our microscope; you should copy the two sets of macros below into separate Image files before use. We use Scion Image 1.62, essentially the same as NIH Image 1.61. You may need to modify the StartCapturing and StopCapturing commands if the "measure areas on scope" macro, depending on the source of your input. Area measurement macros This set of macros will allow you to measure the area of a region you draw, as described above, to get an average of all the areas you measure, and to save the data in a text file and a modified version of your image with the areas drawn in . The output can be imported to Excel for analysis but requires some editing to work efficiently. If you use a lot of saved images, you may want to modify the data output features of the "Area measurement macro" set to be more like that of the "Measure areas on scope" set. >From Scion Image "Special" menu, select "Load Macros" and open the "Area measurement macros" file in the Scion Image folder on the desktop. Then open your first image. Type "S" or select "Set up area measurements" in Special menu. The computer will ask you to name a file for your results. Use one of the outlining tools from the tools palette to outline the region you want to measure. The heart-shaped dotted line allows you to draw freehand regions with the mouse. Then type "M" (or select "Measure area" in the Special menu), and the computer will draw a line around what you just outlined, give the region a number, print the area in pixels in the center of the region, and enter the area in the results file, shown at the bottom of the screen. You can do this repeatedly on the same image. The total area of the image will also be given in the results file. When you have finished with an image, type "F" or select "Finish area measurements" in the Special menu, and the computer will average all of the measurements you made, save the modified image file with a new name ("[your file name] + area measurements"), and ask you which file to open next. (At this point, you need to save the modified images. Just delete them later if you don't want them.) Click on cancel if you don't want to measure other samples. "Measure areas on scope" macro It is sometimes convenient to measure areas on many parts of a sample without having to save each image and reopen it. To do this and save the areas as a set of numbers suitable for import into Excel, load the "Measure areas on scope" macro file. Data are saved as a single column of numbers for each sample, which can be copied and pasted into a single column in Excel. To start, be sure to close the video camera window. Then type P or pull down the "Set up measurement parameters" macro. It will ask you whether you want to save each image before and after labeling areas, and then it will ask you for the name of your first sample and begin showing live video images. When you have found the image you want, click the mouse button or press the shift, option, or control keys. (You may have to hold the key or mouse button down for a fraction of a second or push it a second time.) Then select a drawing tool, draw around an area you wish to measure, and press the M key when you're ready. The area of each region in pixels (this can be changed to mm, etc from the pulldown menus) will show up in a text file on the right of the screen and is saved after each entry. Be careful if you modify this file while adding data to it (e.g., if the font is too large to let you see all your data); if the text is still highlighted when you measure your next area, all of the highlighted data will be deleted (based on sad but true experience). Keep drawing and pressing M until you're done with that image. Then press V (or pull down "New view of this sample" macro), get your next image, and continue. To score another sample (and save the counts in a new file), press S or pull down "Score next sample" macro. You can open this file in Excel, or copy and paste as a single column into a single Excel file for all of you data (more convenient).} {"Measure areas on scope" macro file follows: modified area measurement macro--use while measuring areas while at microscope. Saves data for each sample in a separate file as a column of numbers; import into Excel for analysis. } var {Global variables} n,d,nLines,j,total,TotalArea:integer; mean:real; SaveMod,nSave,nSample,SampleName,ImageName:string; procedure GetImageToMeasure; begin StartCapturing; Repeat Wait(.1); Until Button or KeyDown('shift') or KeyDown('option') or KeyDown('control'); StopCapturing; SetPicName(nSample,' Image'); SelectWindow(nSample,' Image'); if nSave='Yes' then Save; end procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetBackgroundColor(1); SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('With Background'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nSample); If j=1 then writeln (nSample); SetFont('Times'); SetFontSize(12); Writeln(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set parameters for area measurements [P]'; var width,height:integer; begin nSave:=GetString('Save each image as a 1.2 MB file?','Yes'); SaveMod:=GetString('Save each image with areas marked?','Yes'); nSample:=GetString('name of first sample'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; macro 'New view of current sample [v]'; begin SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); DisposeAll; GetImageToMeasure; end; macro 'New Sample [S]'; begin If j=0 then j:=1; SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); Dispose; SelectWindow(nSample); mean:=total/j; writeln('Mean ='); write(mean); save; dispose; nSample:=GetString('Name of next sample:'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; {"Area measurement macros": The following set of macros should be in a separate Image file from the preceding set. It was designed for measuring areas on saved files.} { modified area measurement macro; please do not change this file. Each macro uses the global variables listed at the top. } var {Global variable, initially zero} n,d,nLines,j,total,TotalArea:integer; mean:real; nOut,SampleName,ImageName:string; procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; {Fill; Invert; KillRoi;} x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('WithBackground'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; procedure EndProcedure; begin DisposeAll; mean:=total/j; SelectWindow(nOut); Writeln(' Mean area = ',mean:0); Save; {nLines:=nLines+10; Open(nOut); MoveWindow(120,nLines);} Open(' '); total:=0; j:=0; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nOut); Moveto(120,560); If j=1 then write (ImageName,' (image area =',TotalArea,') '); SetFont('Times'); SetFontSize(12); Write(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set Up Area Measurements [S]'; var width,height:integer; begin ImageName:=WindowTitle; nOut:=GetString('name for results file','Results'); NewTextWindow(nOut); MoveWindow(120,550); total:=0; j:=0; SelectWindow(ImageName); SelectAll; Measure; TotalArea:=rArea[rCount]; KillRoi; end; macro 'Finish Area Measurement [F]'; var nSave:string; begin If j=0 then j:=1; SaveAs(ImageName,' + area measurements'); EndProcedure; end; From nih-image-request@io.ece.drexel.edu Mon Aug 17 08:45 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA17041; Mon, 17 Aug 1998 08:45:12 -0400 (EDT) Resent-Date: Mon, 17 Aug 1998 08:45:12 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Mon, 17 Aug 1998 08:36:21 -0500 To: nih-image@io.ece.drexel.edu From: Laird Bloom Subject: Macro for counting cells, saving data Resent-Message-ID: <"wZc9d3.0.rw3.oE2sr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/212 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 4928 Status: O TimesTo NIH Image users: This macro is modified from the cell counting macro available on the NIH Image web site. It's designed to save data to a text file while collecting multiple data points per sample at the microscope. It works well for cells labeled with DAPI, propidium iodide, or octadecyl rhodamine--brightly fluorescent cells on a dark background--but is probably OK for non-fluorescent stains as well. DAPI is particularly nice because it stains only nuclei, and is therefore doesn't change much when cells spread out. Cytoplasmic or membrane stains (e.g. octadecyl rhodamine or FITC variants) are dimmer on spread cells than on rounded cells, and this macro sometimes has trouble seeing dimmer spread cells labeled this way. The macro is written to use only the red, green, or blue channel (gets rid of background prior to threshholding), but that could be modified. Code is written for Scion Image 1.62. Points at which there are Scion-specific commands are noted. Please contact me if you have questions. Laird Bloom MIT Center for Cancer Research var {Global variable, initially zero} nAvg,Threshold:integer; {range: 10-150} procedure DoGammaTransform(gamma:real); var i,v:integer; n,mode,min,max:integer mean:real; begin measure; GetResults(n,mean,mode,min,max); ShowMessage('min=',min:1,'\max=',max:1); for i:=1 to 254 DO begin if (i>min) and (i<Acquire menu. StartCapturing and StopCapturing may be Scion Image 1.62-specific macro commands. } {Acquire('Plug-In Digitizer');} StartCapturing; Repeat Wait(.1); Until Button; StopCapturing; SetPicName(nWell,'.',j:2); if nSave='Yes' then SaveAs(''); {Using just the main color of your chromophore seems to make the image cleaner. The Bit24toRGBColor command may be specific to Scion Image 1.62.} Bit24toRGBColor; SelectSlice(color); Threshold:=0; CountCells(false); dispose; SelectWindow(nOut); d:=520-nLines; MoveWindow(20,d); Write(rCount,' '); rUser1[j]:=rCount; total:=total+rCount end; mean:=total/j; SelectWindow(nOut) Writeln(' T = ',total:2,' M ='mean:2,' '); Save; nLines:=nLines+10; nNext:=GetString('Score another sample? (type no to end)','yes'); until not (nNext='yes'); SelectWindow(nOut); Save; end; end; From nih-image-request@io.ece.drexel.edu Mon Aug 17 11:25 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA29596; Mon, 17 Aug 1998 11:25:32 -0400 (EDT) Resent-Date: Mon, 17 Aug 1998 11:25:32 -0400 (EDT) Content-Return: allowed Date: Mon, 17 Aug 1998 11:05:52 -0400 From: "Dibble, Nicole A" Subject: LG-3 NuBus To: "'nih-image@biomed.drexel.edu'" Message-Id: <215D10CDFC93D111A11600805FBB7C28211D58@BILLHALEY> Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1460.8) Resent-Message-ID: <"HHYpB1.0.Tv6.QV4sr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/213 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 117 Status: O I currently have a LG-3 NuBus framegrabber for Macintosh for sale. Anyone interested??? Make me an offer. Nicole From nih-image-request@io.ece.drexel.edu Mon Aug 17 11:51 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA02083; Mon, 17 Aug 1998 11:51:22 -0400 (EDT) Resent-Date: Mon, 17 Aug 1998 11:51:22 -0400 (EDT) Date: Mon, 17 Aug 1998 11:37:56 -0400 From: iskanderys@ornl.gov (Yousef S. Iskander) Subject: unsubscribe In-reply-to: <215D10CDFC93D111A11600805FBB7C28211D58@BILLHALEY> X-Sender: q1u@cosmail1.ctd.ornl.gov To: nih-image@io.ece.drexel.edu Message-id: <4.0.1.19980817113710.00f42520@cosmail1.ctd.ornl.gov> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Resent-Message-ID: <"xW4mx.0.PC.ev4sr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/214 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 268 Status: O --------------------------------------------------------- Yousef S. Iskander Oak Ridge National Laboratory Metals and Ceramics Division P.O. Box 2008, Bldg. 5500, MS 6376 Oak Ridge, TN 37831-6376 Phone: (423) 574-5096, (423) 576-7340 e-mail: iskanderys@ornl.gov From nih-image-request@io.ece.drexel.edu Mon Aug 17 18:02 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA02254; Mon, 17 Aug 1998 18:01:46 -0400 (EDT) Resent-Date: Mon, 17 Aug 1998 18:01:46 -0400 (EDT) Message-Id: In-Reply-To: <4.0.1.19980817113710.00f42520@cosmail1.ctd.ornl.gov> References: <215D10CDFC93D111A11600805FBB7C28211D58@BILLHALEY> Mime-Version: 1.0 Date: Mon, 17 Aug 1998 16:47:37 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Re: unsubscribe Resent-Message-ID: <"1QpK.0.mG.-JAsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/215 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 1221 Status: O TimesAn administrative reminder. To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe do not send it to the mail list itself. Thanks. ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Mon Aug 17 21:44 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA18812; Mon, 17 Aug 1998 21:44:18 -0400 (EDT) Resent-Date: Mon, 17 Aug 1998 21:44:18 -0400 (EDT) Date: Mon, 17 Aug 1998 21:31:23 -0400 X-Sender: hmthomas@med.cornell.edu (Unverified) Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: Capture max intensity during TIFF import Resent-Message-ID: <"63hRU1.0.NK4.qbDsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/216 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 735 Status: O As I Import a stack of TIFF images (output from a PC program), the Information Window shows the max intensity of each slice (briefly). Is there a way to capture these values (and thus get the largest max value) with the Image macro language? If so, I can Import the stack again with a fixed scale, using the captured largest max value from the stack. [At present, I obtain the value from the PC program and type it into the Import subdialogue box "Set".] Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 From nih-image-d-request@io.ece.drexel.edu Tue Aug 18 06:26 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA28008; Tue, 18 Aug 1998 06:26:41 -0400 (EDT) Date: Tue, 18 Aug 1998 06:26:41 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808181026.GAA28008@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #38 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/38 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 19417 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 38 Today's Topics: code for area measurement macros [ Laird Bloom ] Macro for counting cells, saving dat [ Laird Bloom ] LG-3 NuBus [ "Dibble, Nicole A" To: nih-image@io.ece.drexel.edu Subject: code for area measurement macros Message-Id: Content-Type: text/enriched; charset="us-ascii" I've had several requests for the code for macros to record area measurement data from regions you outline with a mouse. Here is the code for two versions, one for use with saved images, and one that works well for live images. Please contact me if you have questions. Laird Bloom MIT Center for Cancer Research Times{The following is a set of instructions for the setup with our microscope; you should copy the two sets of macros below into separate Image files before use. We use Scion Image 1.62, essentially the same as NIH Image 1.61. You may need to modify the StartCapturing and StopCapturing commands if the "measure areas on scope" macro, depending on the source of your input. Area measurement macros This set of macros will allow you to measure the area of a region you draw, as described above, to get an average of all the areas you measure, and to save the data in a text file and a modified version of your image with the areas drawn in . The output can be imported to Excel for analysis but requires some editing to work efficiently. If you use a lot of saved images, you may want to modify the data output features of the "Area measurement macro" set to be more like that of the "Measure areas on scope" set. >From Scion Image "Special" menu, select "Load Macros" and open the "Area measurement macros" file in the Scion Image folder on the desktop. Then open your first image. Type "S" or select "Set up area measurements" in Special menu. The computer will ask you to name a file for your results. Use one of the outlining tools from the tools palette to outline the region you want to measure. The heart-shaped dotted line allows you to draw freehand regions with the mouse. Then type "M" (or select "Measure area" in the Special menu), and the computer will draw a line around what you just outlined, give the region a number, print the area in pixels in the center of the region, and enter the area in the results file, shown at the bottom of the screen. You can do this repeatedly on the same image. The total area of the image will also be given in the results file. When you have finished with an image, type "F" or select "Finish area measurements" in the Special menu, and the computer will average all of the measurements you made, save the modified image file with a new name ("[your file name] + area measurements"), and ask you which file to open next. (At this point, you need to save the modified images. Just delete them later if you don't want them.) Click on cancel if you don't want to measure other samples. "Measure areas on scope" macro It is sometimes convenient to measure areas on many parts of a sample without having to save each image and reopen it. To do this and save the areas as a set of numbers suitable for import into Excel, load the "Measure areas on scope" macro file. Data are saved as a single column of numbers for each sample, which can be copied and pasted into a single column in Excel. To start, be sure to close the video camera window. Then type P or pull down the "Set up measurement parameters" macro. It will ask you whether you want to save each image before and after labeling areas, and then it will ask you for the name of your first sample and begin showing live video images. When you have found the image you want, click the mouse button or press the shift, option, or control keys. (You may have to hold the key or mouse button down for a fraction of a second or push it a second time.) Then select a drawing tool, draw around an area you wish to measure, and press the M key when you're ready. The area of each region in pixels (this can be changed to mm, etc from the pulldown menus) will show up in a text file on the right of the screen and is saved after each entry. Be careful if you modify this file while adding data to it (e.g., if the font is too large to let you see all your data); if the text is still highlighted when you measure your next area, all of the highlighted data will be deleted (based on sad but true experience). Keep drawing and pressing M until you're done with that image. Then press V (or pull down "New view of this sample" macro), get your next image, and continue. To score another sample (and save the counts in a new file), press S or pull down "Score next sample" macro. You can open this file in Excel, or copy and paste as a single column into a single Excel file for all of you data (more convenient).} {"Measure areas on scope" macro file follows: modified area measurement macro--use while measuring areas while at microscope. Saves data for each sample in a separate file as a column of numbers; import into Excel for analysis. } var {Global variables} n,d,nLines,j,total,TotalArea:integer; mean:real; SaveMod,nSave,nSample,SampleName,ImageName:string; procedure GetImageToMeasure; begin StartCapturing; Repeat Wait(.1); Until Button or KeyDown('shift') or KeyDown('option') or KeyDown('control'); StopCapturing; SetPicName(nSample,' Image'); SelectWindow(nSample,' Image'); if nSave='Yes' then Save; end procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetBackgroundColor(1); SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('With Background'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nSample); If j=1 then writeln (nSample); SetFont('Times'); SetFontSize(12); Writeln(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set parameters for area measurements [P]'; var width,height:integer; begin nSave:=GetString('Save each image as a 1.2 MB file?','Yes'); SaveMod:=GetString('Save each image with areas marked?','Yes'); nSample:=GetString('name of first sample'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; macro 'New view of current sample [v]'; begin SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); DisposeAll; GetImageToMeasure; end; macro 'New Sample [S]'; begin If j=0 then j:=1; SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); Dispose; SelectWindow(nSample); mean:=total/j; writeln('Mean ='); write(mean); save; dispose; nSample:=GetString('Name of next sample:'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; {"Area measurement macros": The following set of macros should be in a separate Image file from the preceding set. It was designed for measuring areas on saved files.} { modified area measurement macro; please do not change this file. Each macro uses the global variables listed at the top. } var {Global variable, initially zero} n,d,nLines,j,total,TotalArea:integer; mean:real; nOut,SampleName,ImageName:string; procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; {Fill; Invert; KillRoi;} x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('WithBackground'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; procedure EndProcedure; begin DisposeAll; mean:=total/j; SelectWindow(nOut); Writeln(' Mean area = ',mean:0); Save; {nLines:=nLines+10; Open(nOut); MoveWindow(120,nLines);} Open(' '); total:=0; j:=0; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nOut); Moveto(120,560); If j=1 then write (ImageName,' (image area =',TotalArea,') '); SetFont('Times'); SetFontSize(12); Write(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set Up Area Measurements [S]'; var width,height:integer; begin ImageName:=WindowTitle; nOut:=GetString('name for results file','Results'); NewTextWindow(nOut); MoveWindow(120,550); total:=0; j:=0; SelectWindow(ImageName); SelectAll; Measure; TotalArea:=rArea[rCount]; KillRoi; end; macro 'Finish Area Measurement [F]'; var nSave:string; begin If j=0 then j:=1; SaveAs(ImageName,' + area measurements'); EndProcedure; end; ------------------------------ Date: Mon, 17 Aug 1998 08:36:21 -0500 From: Laird Bloom To: nih-image@io.ece.drexel.edu Subject: Macro for counting cells, saving data Message-Id: Content-Type: text/enriched; charset="us-ascii" TimesTo NIH Image users: This macro is modified from the cell counting macro available on the NIH Image web site. It's designed to save data to a text file while collecting multiple data points per sample at the microscope. It works well for cells labeled with DAPI, propidium iodide, or octadecyl rhodamine--brightly fluorescent cells on a dark background--but is probably OK for non-fluorescent stains as well. DAPI is particularly nice because it stains only nuclei, and is therefore doesn't change much when cells spread out. Cytoplasmic or membrane stains (e.g. octadecyl rhodamine or FITC variants) are dimmer on spread cells than on rounded cells, and this macro sometimes has trouble seeing dimmer spread cells labeled this way. The macro is written to use only the red, green, or blue channel (gets rid of background prior to threshholding), but that could be modified. Code is written for Scion Image 1.62. Points at which there are Scion-specific commands are noted. Please contact me if you have questions. Laird Bloom MIT Center for Cancer Research var {Global variable, initially zero} nAvg,Threshold:integer; {range: 10-150} procedure DoGammaTransform(gamma:real); var i,v:integer; n,mode,min,max:integer mean:real; begin measure; GetResults(n,mean,mode,min,max); ShowMessage('min=',min:1,'\max=',max:1); for i:=1 to 254 DO begin if (i>min) and (i<Acquire menu. StartCapturing and StopCapturing may be Scion Image 1.62-specific macro commands. } {Acquire('Plug-In Digitizer');} StartCapturing; Repeat Wait(.1); Until Button; StopCapturing; SetPicName(nWell,'.',j:2); if nSave='Yes' then SaveAs(''); {Using just the main color of your chromophore seems to make the image cleaner. The Bit24toRGBColor command may be specific to Scion Image 1.62.} Bit24toRGBColor; SelectSlice(color); Threshold:=0; CountCells(false); dispose; SelectWindow(nOut); d:=520-nLines; MoveWindow(20,d); Write(rCount,' '); rUser1[j]:=rCount; total:=total+rCount end; mean:=total/j; SelectWindow(nOut) Writeln(' T = ',total:2,' M ='mean:2,' '); Save; nLines:=nLines+10; nNext:=GetString('Score another sample? (type no to end)','yes'); until not (nNext='yes'); SelectWindow(nOut); Save; end; end; ------------------------------ Date: Mon, 17 Aug 1998 11:05:52 -0400 From: "Dibble, Nicole A" To: "'nih-image@biomed.drexel.edu'" Subject: LG-3 NuBus Message-Id: <215D10CDFC93D111A11600805FBB7C28211D58@BILLHALEY> Content-Return: allowed Content-Type: text/plain I currently have a LG-3 NuBus framegrabber for Macintosh for sale. Anyone interested??? Make me an offer. Nicole ------------------------------ Date: Mon, 17 Aug 1998 11:37:56 -0400 From: iskanderys@ornl.gov (Yousef S. Iskander) To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-id: <4.0.1.19980817113710.00f42520@cosmail1.ctd.ornl.gov> Content-type: text/plain; charset="us-ascii" --------------------------------------------------------- Yousef S. Iskander Oak Ridge National Laboratory Metals and Ceramics Division P.O. Box 2008, Bldg. 5500, MS 6376 Oak Ridge, TN 37831-6376 Phone: (423) 574-5096, (423) 576-7340 e-mail: iskanderys@ornl.gov ------------------------------ Date: Mon, 17 Aug 1998 16:47:37 -0500 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Re: unsubscribe Message-Id: Content-Type: text/enriched; charset="us-ascii" TimesAn administrative reminder. To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe do not send it to the mail list itself. Thanks. ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- ------------------------------ Date: Mon, 17 Aug 1998 21:31:23 -0400 From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) Subject: Capture max intensity during TIFF import Message-Id: Content-Type: text/plain; charset="us-ascii" As I Import a stack of TIFF images (output from a PC program), the Information Window shows the max intensity of each slice (briefly). Is there a way to capture these values (and thus get the largest max value) with the Image macro language? If so, I can Import the stack again with a fixed scale, using the captured largest max value from the stack. [At present, I obtain the value from the PC program and type it into the Import subdialogue box "Set".] Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 -------------------------------- End of nih-image-d Digest V98 Issue #38 *************************************** From nih-image-request@io.ece.drexel.edu Tue Aug 18 09:29 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA12005; Tue, 18 Aug 1998 09:29:18 -0400 (EDT) Resent-Date: Tue, 18 Aug 1998 09:29:18 -0400 (EDT) X-Authentication-Warning: pagan.vims.edu: cutter owned process doing -bs Date: Tue, 18 Aug 1998 09:13:24 -0400 (EDT) From: Randy Cutter Reply-To: Randy Cutter To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #29 In-Reply-To: <199808051012.GAA20092@io.ECE.Drexel.EDU> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"xTCfU2.0.4X2.rqNsr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/217 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 346 Status: O Has the version of Object-Image with the color segmentation routine mentioned Aug. 5 by Jeremy Brown been posted on the NIH website? --------------------- Randy Cutter Virginia Institute of Marine Science Route 1208 Gloucester Point, VA 23062 USA phone 804 684-7365 fax 804 684-7399 or 7045 email: cutter@vims.edu --------------------- From nih-image-request@io.ece.drexel.edu Tue Aug 18 11:19 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA20172; Tue, 18 Aug 1998 11:19:31 -0400 (EDT) Resent-Date: Tue, 18 Aug 1998 11:19:31 -0400 (EDT) Message-ID: <35D9991D.DEDDAF10@usa.net> Date: Tue, 18 Aug 1998 09:09:17 -0600 From: "Christopher P. Tully" Reply-To: cptully@usa.net X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Capture max intensity during TIFF import References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"VaQZV2.0.3h4.BXPsr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/218 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1434 Status: O Henry- Here is a simple macro to collect max values of a stack. It will record the maximum value of each slice in a stck to a tab delimited text window (run it with your stack already opened): macro 'max values'; var i:integer; n,mean,mode,min,max:integer; StackPID:integer; tab:integer; begin tab:=chr(9); StackPID:=PidNumber; NewTextWindow('Max Values',100,200); Writeln('Slice',tab,'Max Value'); for i := 1 to nSlices do begin SelectPic(StackPID); SelectSlice(i); SelectAll; Measure; GetResults(n,mean,mode,min,max); SelectWindow('Max Values'); Writeln(i,tab,max); end; end; Chris Tully Henry M. Thomas wrote: > > As I Import a stack of TIFF images (output from a PC program), the > Information Window shows the max intensity of each slice (briefly). Is > there a way to capture these values (and thus get the largest max value) > with the Image macro language? > > If so, I can Import the stack again with a fixed scale, using the captured > largest max value from the stack. [At present, I obtain the value from the > PC program and type it into the Import subdialogue box "Set".] > > Henry M. Thomas, III MD (Harry) > Professor of Clinical Medicine, Pulmonary and Critical Care Division > Department of Medicine, Cornell Univ. Medical School > Director, Pulmonary Research, Burke Rehabilitation Hospital > 785 Mamaroneck Ave. White Plains, NY 10605 > (914) 597-2141 From nih-image-request@io.ece.drexel.edu Tue Aug 18 11:27 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA20977; Tue, 18 Aug 1998 11:27:38 -0400 (EDT) Resent-Date: Tue, 18 Aug 1998 11:27:38 -0400 (EDT) X-OpenMail-Hops: 1 Date: Tue, 18 Aug 1998 11:09:55 -0400 Message-Id: Subject: Printer for gel documentation MIME-Version: 1.0 From: "Michael King" TO: nih-image@io.ece.drexel.edu X-Bad-Content-Type: text/plain; charset=US-ASCII; name="Printer" Content-Disposition: inline; filename="Printer" Content-Transfer-Encoding: 7bit Resent-Message-ID: <"V-NQS2.0.wo4.4ePsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/219 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 427 Status: O What are the current recommendations for monochrome thermal printers for use in gel documentation systems? Ideally, we would like to keep the cost to about $0.10 per print. This would exclude printers such as the Kodak SP700. I have seen previous postings where people utilize the Mitsubishi P-90 printer. What other printers are people using? Are there newer printers that we should investigate? Thanks, Michael King From nih-image-request@io.ece.drexel.edu Tue Aug 18 13:18 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA27538; Tue, 18 Aug 1998 13:18:01 -0400 (EDT) Resent-Date: Tue, 18 Aug 1998 13:18:01 -0400 (EDT) Date: Tue, 18 Aug 98 10:02:54 PDT From: Walter Wolf To: nih-image@io.ece.drexel.edu Cc: wwolfw@hsc.usc.edu, hkim@hsc.usc.edu Subject: Is there a macro for automating ROI analysis? Message-ID: Resent-Message-ID: <"d7N1q1.0.eU6.4FRsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/220 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1228 Status: O Is there a macro anyone has written that allows a definition of a region-of-interest, and once defined, can analyze each of the pixels in that stack? Basically, what I am looking for is using the macro "Plot Z-Axis Profile [Z]" together with another macro (or a modification of Plot Z-Axis Profile [Z]) to plot each of the pixels in a ROI, and save the results to measurement files. ====================================================================== | Professor Walter Wolf, Ph.D. E-Mail: wwolfw@hsc.usc.edu | | Distinguished Professor of Pharmaceutical Sciences | | Director, Pharmacokinetic Imaging Program | | Department of Pharmaceutical Sciences, School of Pharmacy | | University of Southern California Telephone: 323-442-1405 | | 1985 Zonal Ave., Los Angeles, CA 90033 Fax: 323-442-9804 | | | |Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute| | MRI at St. Vincent Medical Center Telephone: 213-484-7235 | | 2131 Third St., Los Angeles, CA 90057 Fax: 213-484-7447 | ====================================================================== From nih-image-request@io.ece.drexel.edu Tue Aug 18 15:36 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA06325; Tue, 18 Aug 1998 15:35:47 -0400 (EDT) Resent-Date: Tue, 18 Aug 1998 15:35:47 -0400 (EDT) Message-ID: <35D9C637.2427A25A@umn.edu> Date: Tue, 18 Aug 1998 13:21:43 -0500 From: Paul Morin X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: white bars in the histogram Content-Transfer-Encoding: 7bit Resent-Message-ID: <"rDfo51.0.iF1.yGTsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/221 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 241 Status: O I'm calculating a histogram of a ROI and exporting the data to a file. When I look at the file I find that about every 10 values is a zero when it shouldn't be. Is there a way to turn this feature off? Paul Morin University of Minnesota From nih-image-request@io.ece.drexel.edu Tue Aug 18 17:20 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA13661; Tue, 18 Aug 1998 17:19:50 -0400 (EDT) Resent-Date: Tue, 18 Aug 1998 17:19:50 -0400 (EDT) Message-Id: <3.0.5.32.19980818220452.00937a10@pop.uea.ac.uk> X-Sender: b143@pop.uea.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Tue, 18 Aug 1998 22:04:52 +0100 To: nih-image@io.ece.drexel.edu From: Gregoire Thomas Subject: Re: code for area measurement macros In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"xEqM.0.f33.eoUsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/222 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 516 Status: O you could also try the software available on: http://www.draak.demon.co.uk/imagine/ It provides a range of tools for the selection of regions with the mouse and a 'friendly' interface. Greg At 08:04 17/08/98 -0500, you wrote: >I've had several requests for the code for macros to record area >measurement data from regions you outline with a mouse. Here is the code >for two versions, one for use with saved images, and one that works well >for live images. Please contact me if you have questions. >Laird Bloom From nih-image-request@io.ece.drexel.edu Tue Aug 18 20:30 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA27767; Tue, 18 Aug 1998 20:30:41 -0400 (EDT) Resent-Date: Tue, 18 Aug 1998 20:30:41 -0400 (EDT) Date: Tue, 18 Aug 1998 19:13:59 -0500 From: scidi Subject: Help with Imaging System To: nih-image@io.ece.drexel.edu Reply-to: scidi@mci2000.com Message-id: <0EXW00MGHUDJFU@PM06SM.PMM.MCI.NET> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1161 Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-Priority: 3 Resent-Message-ID: <"3uOqM2.0.zb6.ihXsr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/223 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 1279 Status: O I am in need of some help with an imaging system that I am installing. The system utilizes the old LG-3/TV-3 combination as an old IIci that was laying around is being used solely for this imaging system. I tested the cards and Cohu camera out on a PowerMac 7100. Utilizing NIH Image, I got great, crisp pictures. I was using version 1.62a of NIH Image. I then went to install on the Mac IIci. I was using version 1.55 of NIH Image, since 1.62a needs a PowerMac. Upon attempting to capture an image I get a highly grainy and image that has quite a bit of snow. Obviously not crisp at all. The gain on the camera is 0, and all of the other settings are as they should be according to Cohu and Scion. I remember some things a while ago concerning the FPU and non-FPU versions of Image. If I recall I need to use the FPU version on the IIci???? Is this my problem?? The reason I think it is a software thing is because it works great on my PowerMac. Virtual memory is OFF and 32 bit addressing was tried both on and off with no change in the picture. If anyone could help I would be most appreciative. Thank you. Mark R. Molenda, Owner Scientific Digital Imaging 1407 S 59th St. Milwaukee, WI 53214 phone (414) 476-2694 fax (414) 645-8037 scidi@mci2000.com From nih-image-request@io.ece.drexel.edu Tue Aug 18 21:50 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA04191; Tue, 18 Aug 1998 21:49:56 -0400 (EDT) Resent-Date: Tue, 18 Aug 1998 21:49:56 -0400 (EDT) Date: Tue, 18 Aug 1998 20:31:54 -0500 From: scidi Subject: Help with Imaging Systems, cont. To: nih-image@io.ece.drexel.edu Reply-to: scidi@mci2000.com Message-id: <0EXW00BC6XZJ7F@PM04SM.PMM.MCI.NET> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1161 Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-Priority: 3 Resent-Message-ID: <"FRcat3.0.zp.qqYsr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/224 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 1055 Status: O One thing I forgot to mention.....On the IIci, it says that the camera is capturing at 0.45 frames/second. It is extremely delayed. It has to be something with the software somewhere. I just know it is a click of a button or a turn of a switch or something. Any ideas????? Mark R. Molenda, Owner Scientific Digital Imaging 1407 S 59th St. Milwaukee, WI 53214 phone (414) 476-2694 fax (414) 645-8037 scidi@mci2000.com ---------- > From: Michael King > To: nih-image@io.ece.drexel.edu > Subject: Printer for gel documentation > Date: Tuesday, August 18, 1998 10:09 AM > > What are the current recommendations for monochrome thermal printers for > use in gel documentation systems? > Ideally, we would like to keep the cost to about $0.10 per print. This > would exclude printers such as the Kodak SP700. > I have seen previous postings where people utilize the Mitsubishi P-90 > printer. What other printers are people using? > Are there newer printers that we should investigate? > > Thanks, > Michael King From nih-image-request@io.ece.drexel.edu Tue Aug 18 23:09 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id XAA10617; Tue, 18 Aug 1998 23:09:45 -0400 (EDT) Resent-Date: Tue, 18 Aug 1998 23:09:45 -0400 (EDT) Message-ID: <35DA40E5.4FB7ED7D@usa.net> Date: Tue, 18 Aug 1998 21:05:10 -0600 From: "Christopher P. Tully" Reply-To: cptully@usa.net X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: NIH-Image Subject: Re: Capture max intensity during TIFF import References: <62795CD06F8@rna.bio.mq.edu.au> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"QA54a1.0.CP2.K0asr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/225 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1534 Status: O Greg (and Henry)- Oops, I guess I missed that part. Not having a Mac handy at the moment, I can't test your theory, but the implication from Henry's original message is that he's been importing stacks with a maximum value set, so here's a modified macro (untested): macro 'max values v2'; var i:integer; n,mean,mode,min,max:integer; stackmax:integer; StackPID:integer; tab:integer; path:string; begin tab:=chr(9); StackPID:=PidNumber; path:=GetPath('window'); NewTextWindow('Max Values',100,200); Writeln('Slice',tab,'Max Value'); stackmax:=0; for i := 1 to nSlices do begin SelectPic(StackPID); SelectSlice(i); SelectAll; Measure; GetResults(n,mean,mode,min,max); SelectWindow('Max Values'); Writeln(i,tab,max); If stackmax < max then stackmax:=max; end; SelectPic(StackPid); Dispose; SetImportMinMax(0,stackmax); SetImport('TIFF'); Import(path); end; As I said, this macro is untested. It may work as is, or (more likely) it may need some tweeking. Please let me know how it works. Chris Tully GJOSS@rna.bio.mq.edu.au wrote: > Yes Chris, you report max stack value; but will this allow him to: > "If so, I can Import the stack again with a fixed scale, using the captured > largest max value from the stack. [At present, I obtain the value from the > PC program and type it into the Import subdialogue box "Set".]" > > ? ? :-) > > as far as I can determine, setting max value in import dialogue for 8bit Tiff > stack will be ignored on import. From nih-image-d-request@io.ece.drexel.edu Wed Aug 19 06:15 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA15027; Wed, 19 Aug 1998 06:15:22 -0400 (EDT) Date: Wed, 19 Aug 1998 06:15:22 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808191015.GAA15027@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #39 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/39 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 11741 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 39 Today's Topics: Re: nih-image-d Digest V98 #29 [ Randy Cutter ] Re: Capture max intensity during TIF [ "Christopher P. Tully" ] white bars in the histogram [ Paul Morin ] Re: code for area measurement macros [ Gregoire Thomas ] Help with Imaging Systems, cont. [ scidi ] Re: Capture max intensity during TIF [ "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #29 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Has the version of Object-Image with the color segmentation routine mentioned Aug. 5 by Jeremy Brown been posted on the NIH website? --------------------- Randy Cutter Virginia Institute of Marine Science Route 1208 Gloucester Point, VA 23062 USA phone 804 684-7365 fax 804 684-7399 or 7045 email: cutter@vims.edu --------------------- ------------------------------ Date: Tue, 18 Aug 1998 09:09:17 -0600 From: "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: Capture max intensity during TIFF import Message-ID: <35D9991D.DEDDAF10@usa.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Henry- Here is a simple macro to collect max values of a stack. It will record the maximum value of each slice in a stck to a tab delimited text window (run it with your stack already opened): macro 'max values'; var i:integer; n,mean,mode,min,max:integer; StackPID:integer; tab:integer; begin tab:=chr(9); StackPID:=PidNumber; NewTextWindow('Max Values',100,200); Writeln('Slice',tab,'Max Value'); for i := 1 to nSlices do begin SelectPic(StackPID); SelectSlice(i); SelectAll; Measure; GetResults(n,mean,mode,min,max); SelectWindow('Max Values'); Writeln(i,tab,max); end; end; Chris Tully Henry M. Thomas wrote: > > As I Import a stack of TIFF images (output from a PC program), the > Information Window shows the max intensity of each slice (briefly). Is > there a way to capture these values (and thus get the largest max value) > with the Image macro language? > > If so, I can Import the stack again with a fixed scale, using the captured > largest max value from the stack. [At present, I obtain the value from the > PC program and type it into the Import subdialogue box "Set".] > > Henry M. Thomas, III MD (Harry) > Professor of Clinical Medicine, Pulmonary and Critical Care Division > Department of Medicine, Cornell Univ. Medical School > Director, Pulmonary Research, Burke Rehabilitation Hospital > 785 Mamaroneck Ave. White Plains, NY 10605 > (914) 597-2141 ------------------------------ Date: Tue, 18 Aug 1998 11:09:55 -0400 From: "Michael King" TO: nih-image@io.ece.drexel.edu Subject: Printer for gel documentation Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline; filename="Printer" Content-Transfer-Encoding: 7bit What are the current recommendations for monochrome thermal printers for use in gel documentation systems? Ideally, we would like to keep the cost to about $0.10 per print. This would exclude printers such as the Kodak SP700. I have seen previous postings where people utilize the Mitsubishi P-90 printer. What other printers are people using? Are there newer printers that we should investigate? Thanks, Michael King ------------------------------ Date: Tue, 18 Aug 98 10:02:54 PDT From: Walter Wolf To: nih-image@io.ece.drexel.edu Cc: wwolfw@hsc.usc.edu, hkim@hsc.usc.edu Subject: Is there a macro for automating ROI analysis? Message-ID: Is there a macro anyone has written that allows a definition of a region-of-interest, and once defined, can analyze each of the pixels in that stack? Basically, what I am looking for is using the macro "Plot Z-Axis Profile [Z]" together with another macro (or a modification of Plot Z-Axis Profile [Z]) to plot each of the pixels in a ROI, and save the results to measurement files. ====================================================================== | Professor Walter Wolf, Ph.D. E-Mail: wwolfw@hsc.usc.edu | | Distinguished Professor of Pharmaceutical Sciences | | Director, Pharmacokinetic Imaging Program | | Department of Pharmaceutical Sciences, School of Pharmacy | | University of Southern California Telephone: 323-442-1405 | | 1985 Zonal Ave., Los Angeles, CA 90033 Fax: 323-442-9804 | | | |Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute| | MRI at St. Vincent Medical Center Telephone: 213-484-7235 | | 2131 Third St., Los Angeles, CA 90057 Fax: 213-484-7447 | ====================================================================== ------------------------------ Date: Tue, 18 Aug 1998 13:21:43 -0500 From: Paul Morin To: nih-image@io.ece.drexel.edu Subject: white bars in the histogram Message-ID: <35D9C637.2427A25A@umn.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I'm calculating a histogram of a ROI and exporting the data to a file. When I look at the file I find that about every 10 values is a zero when it shouldn't be. Is there a way to turn this feature off? Paul Morin University of Minnesota ------------------------------ Date: Tue, 18 Aug 1998 22:04:52 +0100 From: Gregoire Thomas To: nih-image@io.ece.drexel.edu Subject: Re: code for area measurement macros Message-Id: <3.0.5.32.19980818220452.00937a10@pop.uea.ac.uk> Content-Type: text/plain; charset="us-ascii" you could also try the software available on: http://www.draak.demon.co.uk/imagine/ It provides a range of tools for the selection of regions with the mouse and a 'friendly' interface. Greg At 08:04 17/08/98 -0500, you wrote: >I've had several requests for the code for macros to record area >measurement data from regions you outline with a mouse. Here is the code >for two versions, one for use with saved images, and one that works well >for live images. Please contact me if you have questions. >Laird Bloom ------------------------------ Date: Tue, 18 Aug 1998 19:13:59 -0500 From: scidi To: nih-image@io.ece.drexel.edu Subject: Help with Imaging System Message-id: <0EXW00MGHUDJFU@PM06SM.PMM.MCI.NET> Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit I am in need of some help with an imaging system that I am installing. The system utilizes the old LG-3/TV-3 combination as an old IIci that was laying around is being used solely for this imaging system. I tested the cards and Cohu camera out on a PowerMac 7100. Utilizing NIH Image, I got great, crisp pictures. I was using version 1.62a of NIH Image. I then went to install on the Mac IIci. I was using version 1.55 of NIH Image, since 1.62a needs a PowerMac. Upon attempting to capture an image I get a highly grainy and image that has quite a bit of snow. Obviously not crisp at all. The gain on the camera is 0, and all of the other settings are as they should be according to Cohu and Scion. I remember some things a while ago concerning the FPU and non-FPU versions of Image. If I recall I need to use the FPU version on the IIci???? Is this my problem?? The reason I think it is a software thing is because it works great on my PowerMac. Virtual memory is OFF and 32 bit addressing was tried both on and off with no change in the picture. If anyone could help I would be most appreciative. Thank you. Mark R. Molenda, Owner Scientific Digital Imaging 1407 S 59th St. Milwaukee, WI 53214 phone (414) 476-2694 fax (414) 645-8037 scidi@mci2000.com ------------------------------ Date: Tue, 18 Aug 1998 20:31:54 -0500 From: scidi To: nih-image@io.ece.drexel.edu Subject: Help with Imaging Systems, cont. Message-id: <0EXW00BC6XZJ7F@PM04SM.PMM.MCI.NET> Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit One thing I forgot to mention.....On the IIci, it says that the camera is capturing at 0.45 frames/second. It is extremely delayed. It has to be something with the software somewhere. I just know it is a click of a button or a turn of a switch or something. Any ideas????? Mark R. Molenda, Owner Scientific Digital Imaging 1407 S 59th St. Milwaukee, WI 53214 phone (414) 476-2694 fax (414) 645-8037 scidi@mci2000.com ---------- > From: Michael King > To: nih-image@io.ece.drexel.edu > Subject: Printer for gel documentation > Date: Tuesday, August 18, 1998 10:09 AM > > What are the current recommendations for monochrome thermal printers for > use in gel documentation systems? > Ideally, we would like to keep the cost to about $0.10 per print. This > would exclude printers such as the Kodak SP700. > I have seen previous postings where people utilize the Mitsubishi P-90 > printer. What other printers are people using? > Are there newer printers that we should investigate? > > Thanks, > Michael King ------------------------------ Date: Tue, 18 Aug 1998 21:05:10 -0600 From: "Christopher P. Tully" To: NIH-Image Subject: Re: Capture max intensity during TIFF import Message-ID: <35DA40E5.4FB7ED7D@usa.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greg (and Henry)- Oops, I guess I missed that part. Not having a Mac handy at the moment, I can't test your theory, but the implication from Henry's original message is that he's been importing stacks with a maximum value set, so here's a modified macro (untested): macro 'max values v2'; var i:integer; n,mean,mode,min,max:integer; stackmax:integer; StackPID:integer; tab:integer; path:string; begin tab:=chr(9); StackPID:=PidNumber; path:=GetPath('window'); NewTextWindow('Max Values',100,200); Writeln('Slice',tab,'Max Value'); stackmax:=0; for i := 1 to nSlices do begin SelectPic(StackPID); SelectSlice(i); SelectAll; Measure; GetResults(n,mean,mode,min,max); SelectWindow('Max Values'); Writeln(i,tab,max); If stackmax < max then stackmax:=max; end; SelectPic(StackPid); Dispose; SetImportMinMax(0,stackmax); SetImport('TIFF'); Import(path); end; As I said, this macro is untested. It may work as is, or (more likely) it may need some tweeking. Please let me know how it works. Chris Tully GJOSS@rna.bio.mq.edu.au wrote: > Yes Chris, you report max stack value; but will this allow him to: > "If so, I can Import the stack again with a fixed scale, using the captured > largest max value from the stack. [At present, I obtain the value from the > PC program and type it into the Import subdialogue box "Set".]" > > ? ? :-) > > as far as I can determine, setting max value in import dialogue for 8bit Tiff > stack will be ignored on import. -------------------------------- End of nih-image-d Digest V98 Issue #39 *************************************** From nih-image-request@io.ece.drexel.edu Wed Aug 19 08:11 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA24733; Wed, 19 Aug 1998 08:11:18 -0400 (EDT) Resent-Date: Wed, 19 Aug 1998 08:11:18 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Wed, 19 Aug 1998 08:11:25 -0400 From: "Michael Shrout" To: nih-image@io.ece.drexel.edu Subject: Morphologic Operations and NIH Image Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id HAA23503 Resent-Message-ID: <"pCuuK.0.Ul5.Xuhsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/226 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1445 Status: O I am attempting to use the Binary menu to simplify and measure bone changes. The program states that "Erode and Dilate do not perform erosion and dilation with structuring elements as described in the literature of classical mathematical morphology." I'm trying to understand what I am doing when I use the Binary submenu. The program defines these procedures: Erode - Removes pixels from the edges of objects in a binary images, where contiguous black areas in the image are considered objects, and background is assumed to be white. A pixel is removed (set to white) if four or more of its eight neighbors are white. Erosion separates objects that are touching and removes isolated pixels. Dilate - Adds pixels to the edges of objects in a binary images. A pixel is added (set to black) if four or more of its eight neighbors are black. Dilation connects discontinuous objects and fills in holes. Does Image do morphologic operations? Is if fair to say a morphologic operation is the net change to an image, regardless of the technique used to get there? In other words, does it matter if I skeletonize an image with Image or, say, Alice [Dip Station] which apparently uses different mathematical structuring elements? If they are different, can I use the morphologic operator literature to justify a technique I develop using Image? I'd appreciate any input I can get! Mike Shrout Associate Professor Medical College of Georgia From nih-image-request@io.ece.drexel.edu Wed Aug 19 09:50 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA03097; Wed, 19 Aug 1998 09:49:56 -0400 (EDT) Resent-Date: Wed, 19 Aug 1998 09:49:56 -0400 (EDT) Message-ID: <35DAE297.5C5F372@netmatters.co.uk> Date: Wed, 19 Aug 1998 14:35:10 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: EDINBURGH LOCAL FORUM? References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"GgD3X1.0.fO.1Ijsr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/227 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 314 Status: O Would anyone in the Edinburgh Area, or Scotland come to that, be interested in some kind of local NIH/Object/Scion Image forum? Jeremy *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html From nih-image-request@io.ece.drexel.edu Wed Aug 19 11:52 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA12778; Wed, 19 Aug 1998 11:52:37 -0400 (EDT) Resent-Date: Wed, 19 Aug 1998 11:52:37 -0400 (EDT) Date: Wed, 19 Aug 1998 11:33:06 -0400 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: Re: Capture max intensity during TIFF import Resent-Message-ID: <"HpC_S1.0.Zj2.-0lsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/228 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1893 Status: O Thanks for the help. Using IMPORT repeatedly gives flexibility in the Import command. Greg's Measure (the max intensity in each of 5 slices) works fine. Wayne's cvalue(1) is more elegant, but I kept getting 1 for cValue(1); I'm sure it can be worked out. Here is the code that works for me. Appreciatively, Harry var LargestMax,sliceno,width,height,lower,upper:integer; {Global variable, initially zero} OldStackTitle,NewStackTitle,NewerStackTitle,NewWindowTitle:string; procedure procIMPORT begin {Import 1st time and discard. Image's automatic TIFF file detection gets height & Width from a 16 bit Scanalytics Cellscan PC 5 slice TIFF} Import(''); {1st time you run program, default no. slices is 1} GetPicSize(width,height); {only necessary cause SetCustom requires it} Dispose; {Import 2nd time (and discard) with dummy fixed scale to get the largest calibrated value in the 5 slices; "custom' uses the height,width and offset from the previous Import } SetImport('custom,16-bits unsigned,swap bytes,calibrate'); SetImportMinMax(0,32767); SetCustom(width,height,8,5); {1st time program runs, you need to set slices to 5} Import(''); largestMax := 0; ResetCounter; for i:=1 to nSlices do begin selectSlice(i); Measure; if rMax[i] >largestMax then largestMax:= rMax[i]; end; Dispose; {Import 3rd time with fixed scale using largest calibrated value in the 5 slices as max} SetImport('custom,16-bits unsigned,swap bytes,calibrate'); SetImportMinMax(0,largestMax); Import(''); SetScale(1,'pixel'); end Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 From nih-image-request@io.ece.drexel.edu Wed Aug 19 11:54 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA12968; Wed, 19 Aug 1998 11:54:31 -0400 (EDT) Resent-Date: Wed, 19 Aug 1998 11:54:31 -0400 (EDT) Date: Wed, 19 Aug 1998 11:42:21 -0400 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: Macro command for Scale to fit Window? Resent-Message-ID: <"D6hp92.0.Vw2.f9lsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/229 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 769 Status: O I want to paste into the middle of a 1500 by 800 pixel window, which doesn' fit on the screen. Pasting into the scrollable, regular window pastes at, roughly (and unpredictably by me) 250,250, whereas pasting into the scaled-to-fit-window window pastes reliably at 750,400. Then I can move the ROI by macro. Scale to Fit Window is in the Options Menu. I can't find a macro equivalent. If not, how can I reliably move the upper left corner of the pasted ROI to, say 20,20? Thanks, Harry Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 From nih-image-request@io.ece.drexel.edu Wed Aug 19 12:23 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA15192; Wed, 19 Aug 1998 12:23:24 -0400 (EDT) Resent-Date: Wed, 19 Aug 1998 12:23:24 -0400 (EDT) Date: Wed, 19 Aug 1998 09:05:31 -0700 From: "Mark N. Rand" Reply-To: mnr@u.washington.edu Subject: Re: Is there a macro for automating ROI analysis? To: nih-image@io.ece.drexel.edu In-Reply-To: <199808191016.GAA15108@io.ECE.Drexel.EDU> Message-ID: X-Authenticated: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by io.ECE.Drexel.EDU id MAA13901 Resent-Message-ID: <"YXgeM2.0.SP3.bWlsr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/230 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=ISO-8859-1 Content-Length: 2184 Status: O On Wed, 19 Aug 1998 06:16:09 -0400 (EDT) nih-image-d-request@io.ece.drexel.edu wrote: >Date: Tue, 18 Aug 98 10:02:54 PDT >From: Walter Wolf >To: nih-image@io.ece.drexel.edu >Cc: wwolfw@hsc.usc.edu, hkim@hsc.usc.edu >Subject: Is there a macro for automating ROI analysis? >Message-ID: > >Is there a macro anyone has written that allows a definition of a >region-of-interest, and once defined, can analyze each of the pixels in >that stack? Basically, what I am looking for is using the macro "Plot Z-Axis >Profile [Z]" together with another macro (or a modification of Plot >Z-Axis Profile [Z]) to plot each of the pixels in a ROI, and save the results >to measurement files. > I'm not sure about analyzing *each* of the pixels in the ROI through the stack, but if you want to measure the *average* values of pixels in the ROI this macro should do the trick: Procedure CheckForStack; begin if nPics = 0 then begin PutMessage('This macro requires a stack!'); exit; end; if nSlices = 0 then begin PutMessage('This window is not a stack!'); exit; end; end; macro 'ROI Stack Measurement [R]'; { Takes a stack and outputs measurements of the selected ROI from each frame in the stack. } var i, oldSliceNum: integer; begin CheckForStack; ResetCounter; oldSliceNum := SliceNumber; SaveState; for i := 1 to nSlices do begin ChooseSlice(i); RestoreROI; Measure; end; UpdateResults; SelectSlice(oldSliceNum); RestoreState; end; (The CheckForStack procedure is from the standard Stack Macros file that comes with NIH-Image; omit it if you paste the ROI Stack Measurement macro into the Stack Macros file.) If you actually do want to measure and plot each pixel in the ROI you could select each pixel manually and run the macro repeatedly for all of the pixels in the region you want to measure, although this might prove tedious. Mark N. Rand, Ph.D. U.W. Dept. Neurology, School of Medicine 1959 NE Pacific St., Box 356465 Seattle WA 98195-6465 fax: (206) 616-8272 vox: (206) 616-5153 <°){{{{>< <°){{{{>< <°){{{{>< <°){{{{>< <°){{{{>< <°){{{{>< From nih-image-request@io.ece.drexel.edu Wed Aug 19 12:34 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA16110; Wed, 19 Aug 1998 12:34:08 -0400 (EDT) Resent-Date: Wed, 19 Aug 1998 12:34:08 -0400 (EDT) Message-ID: <35DB09DC.96BEFFC8@netmatters.co.uk> Date: Wed, 19 Aug 1998 17:22:39 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Macro command for Scale to fit Window? References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"5zuKt.0.Aj3.ullsr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/231 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1251 Status: O Henry M. Thomas wrote: > I want to paste into the middle of a 1500 by 800 pixel window, which doesn' > fit on the screen. Pasting into the scrollable, regular window pastes at, > roughly (and unpredictably by me) 250,250, whereas pasting into the > scaled-to-fit-window window pastes reliably at 750,400. Then I can move > the ROI by macro. > > Scale to Fit Window is in the Options Menu. I can't find a macro > equivalent. If not, how can I reliably move the upper left corner of the > pasted ROI to, say 20,20? > > Thanks, Harry > > Henry M. Thomas, III MD (Harry) > Professor of Clinical Medicine, Pulmonary and Critical Care Division > Department of Medicine, Cornell Univ. Medical School > Director, Pulmonary Research, Burke Rehabilitation Hospital > 785 Mamaroneck Ave. White Plains, NY 10605 > (914) 597-2141 Harry, Hope this is what you need..... Macro 'Paste Selection 20,20' Var left,top,width,height:integer; begin GetRoi(left,top,width,height); Copy; SetNewSize(1500,800); MakeNewWindow('1500x800'); MakeROI(20,20,width,height); Paste; end; Jeremy *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html From nih-image-request@io.ece.drexel.edu Wed Aug 19 15:47 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA29871; Wed, 19 Aug 1998 15:47:06 -0400 (EDT) Resent-Date: Wed, 19 Aug 1998 15:47:06 -0400 (EDT) X-Sender: cozturk@tempest.bme-mri.jhu.edu Message-Id: In-Reply-To: <35D9C637.2427A25A@umn.edu> Mime-Version: 1.0 Date: Wed, 19 Aug 1998 15:40:10 -0400 To: nih-image@io.ece.drexel.edu From: Cengizhan Ozturk Subject: Re: white bars in the histogram Resent-Message-ID: <"pcapv.0.Kx6.yTosr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/232 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 658 Status: O >I'm calculating a histogram of a ROI and exporting the data to a file. >When I look at the file I find that about every 10 values is a zero when >it shouldn't be. Is there a way to turn this feature off? > >Paul Morin > >University of Minnesota It might not be applied to your case, If you had imported the image and used a scale these things can happen. Cengizhan Dr. Cengizhan Ozturk ======================= Johns Hopkins University - Medical Imaging Lab 407 Traylor Building / 720 Rutland Av. Baltimore, MD 21205-2196 Phone: (410) 614 5292 Fax: (410) 502 6915 E-mail: cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk/ ======================= From nih-image-request@io.ece.drexel.edu Wed Aug 19 16:33 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA03341; Wed, 19 Aug 1998 16:33:13 -0400 (EDT) Resent-Date: Wed, 19 Aug 1998 16:33:13 -0400 (EDT) X-Sender: a_team@pop.dds.nl Message-Id: In-Reply-To: <199808191001.GAA13739@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Wed, 19 Aug 1998 22:23:51 +0200 To: nih-image@io.ece.drexel.edu From: "Anneke M.Th. Harbers and Ard Jonker" Subject: Re: Capture max intensity during TIFF import Resent-Message-ID: <"tA8ol2.0.8d.RHpsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/233 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 754 Status: O >Greg (and Henry)- I would advocate to set another variable (min) to be taken: ...,stackmin:integer; ... stackmin:=65536; for i := 1 to nSlices do begin SelectPic(StackPID); SelectSlice(i); SelectAll; Measure; GetResults(n,mean,mode,min,max); Writeln(i,tab,max); If stackmax < max then stackmax:=max; If stackmin < min then stackmin:=min; end; SetImportMinMax(min,stackmax); SetImport('TIFF'); Import(path); end; This prevents that you waste probably unused lower values. If the 16 bit stack contains values of e.g. 10.000 to 40.000, you have gained some precision, as greyvalue 0 will be assigned to 10.000 rather than to 0. The range will be 10.000...40.000 rather than 0...40.000 spread over 256 greyvalues. Ard From nih-image-request@io.ece.drexel.edu Wed Aug 19 21:13 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA25837; Wed, 19 Aug 1998 21:13:41 -0400 (EDT) Resent-Date: Wed, 19 Aug 1998 21:13:41 -0400 (EDT) Message-Id: In-Reply-To: <35C878D7.8A6A83F1@netreach.net> Mime-Version: 1.0 Date: Wed, 19 Aug 1998 21:01:08 -0400 To: nih-image@io.ece.drexel.edu From: kwb Subject: NIH Quicktimes in PowerPoint Presentations. Resent-Message-ID: <"08osf3.0.K56.4Ptsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/234 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 480 Status: O I've created quicktime animations using NIH Image 1.62 and have no problem viewing them using PowerPoint on the Mac. I haven't been as successful using the PC version. Has anybody had any success presenting quicktime animations using PowerPoint on a PC platform and is there a particular variety of quicktime (video, cinepak, animation?) that might be best suited to this purpose? Thank you in advance for any comments or suggestions. Regards, Ken Baker kwb@bserv.com From nih-image-d-request@io.ece.drexel.edu Thu Aug 20 04:18 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id EAA02179; Thu, 20 Aug 1998 04:18:32 -0400 (EDT) Date: Thu, 20 Aug 1998 04:18:32 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808200818.EAA02179@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #40 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/40 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 14587 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 40 Today's Topics: Morphologic Operations and NIH Image [ "Michael Shrout" ] Method for analyzing many particles [ "KUNITOMO,Junko" To: nih-image@io.ece.drexel.edu Subject: Morphologic Operations and NIH Image Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit I am attempting to use the Binary menu to simplify and measure bone changes. The program states that "Erode and Dilate do not perform erosion and dilation with structuring elements as described in the literature of classical mathematical morphology." I'm trying to understand what I am doing when I use the Binary submenu. The program defines these procedures: Erode - Removes pixels from the edges of objects in a binary images, where contiguous black areas in the image are considered objects, and background is assumed to be white. A pixel is removed (set to white) if four or more of its eight neighbors are white. Erosion separates objects that are touching and removes isolated pixels. Dilate - Adds pixels to the edges of objects in a binary images. A pixel is added (set to black) if four or more of its eight neighbors are black. Dilation connects discontinuous objects and fills in holes. Does Image do morphologic operations? Is if fair to say a morphologic operation is the net change to an image, regardless of the technique used to get there? In other words, does it matter if I skeletonize an image with Image or, say, Alice [Dip Station] which apparently uses different mathematical structuring elements? If they are different, can I use the morphologic operator literature to justify a technique I develop using Image? I'd appreciate any input I can get! Mike Shrout Associate Professor Medical College of Georgia ------------------------------ Date: Wed, 19 Aug 1998 14:35:10 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: EDINBURGH LOCAL FORUM? Message-ID: <35DAE297.5C5F372@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Would anyone in the Edinburgh Area, or Scotland come to that, be interested in some kind of local NIH/Object/Scion Image forum? Jeremy *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html ------------------------------ Date: Wed, 19 Aug 1998 11:33:06 -0400 From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) Subject: Re: Capture max intensity during TIFF import Message-Id: Content-Type: text/plain; charset="us-ascii" Thanks for the help. Using IMPORT repeatedly gives flexibility in the Import command. Greg's Measure (the max intensity in each of 5 slices) works fine. Wayne's cvalue(1) is more elegant, but I kept getting 1 for cValue(1); I'm sure it can be worked out. Here is the code that works for me. Appreciatively, Harry var LargestMax,sliceno,width,height,lower,upper:integer; {Global variable, initially zero} OldStackTitle,NewStackTitle,NewerStackTitle,NewWindowTitle:string; procedure procIMPORT begin {Import 1st time and discard. Image's automatic TIFF file detection gets height & Width from a 16 bit Scanalytics Cellscan PC 5 slice TIFF} Import(''); {1st time you run program, default no. slices is 1} GetPicSize(width,height); {only necessary cause SetCustom requires it} Dispose; {Import 2nd time (and discard) with dummy fixed scale to get the largest calibrated value in the 5 slices; "custom' uses the height,width and offset from the previous Import } SetImport('custom,16-bits unsigned,swap bytes,calibrate'); SetImportMinMax(0,32767); SetCustom(width,height,8,5); {1st time program runs, you need to set slices to 5} Import(''); largestMax := 0; ResetCounter; for i:=1 to nSlices do begin selectSlice(i); Measure; if rMax[i] >largestMax then largestMax:= rMax[i]; end; Dispose; {Import 3rd time with fixed scale using largest calibrated value in the 5 slices as max} SetImport('custom,16-bits unsigned,swap bytes,calibrate'); SetImportMinMax(0,largestMax); Import(''); SetScale(1,'pixel'); end Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 ------------------------------ Date: Wed, 19 Aug 1998 11:42:21 -0400 From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) Subject: Macro command for Scale to fit Window? Message-Id: Content-Type: text/plain; charset="us-ascii" I want to paste into the middle of a 1500 by 800 pixel window, which doesn' fit on the screen. Pasting into the scrollable, regular window pastes at, roughly (and unpredictably by me) 250,250, whereas pasting into the scaled-to-fit-window window pastes reliably at 750,400. Then I can move the ROI by macro. Scale to Fit Window is in the Options Menu. I can't find a macro equivalent. If not, how can I reliably move the upper left corner of the pasted ROI to, say 20,20? Thanks, Harry Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 ------------------------------ Date: Wed, 19 Aug 1998 09:05:31 -0700 From: "Mark N. Rand" To: nih-image@io.ece.drexel.edu Subject: Re: Is there a macro for automating ROI analysis? Message-ID: Content-Type: TEXT/PLAIN; CHARSET=ISO-8859-1 Content-Transfer-Encoding: 8bit On Wed, 19 Aug 1998 06:16:09 -0400 (EDT) nih-image-d-request@io.ece.drexel.edu wrote: >Date: Tue, 18 Aug 98 10:02:54 PDT >From: Walter Wolf >To: nih-image@io.ece.drexel.edu >Cc: wwolfw@hsc.usc.edu, hkim@hsc.usc.edu >Subject: Is there a macro for automating ROI analysis? >Message-ID: > >Is there a macro anyone has written that allows a definition of a >region-of-interest, and once defined, can analyze each of the pixels in >that stack? Basically, what I am looking for is using the macro "Plot Z-Axis >Profile [Z]" together with another macro (or a modification of Plot >Z-Axis Profile [Z]) to plot each of the pixels in a ROI, and save the results >to measurement files. > I'm not sure about analyzing *each* of the pixels in the ROI through the stack, but if you want to measure the *average* values of pixels in the ROI this macro should do the trick: Procedure CheckForStack; begin if nPics = 0 then begin PutMessage('This macro requires a stack!'); exit; end; if nSlices = 0 then begin PutMessage('This window is not a stack!'); exit; end; end; macro 'ROI Stack Measurement [R]'; { Takes a stack and outputs measurements of the selected ROI from each frame in the stack. } var i, oldSliceNum: integer; begin CheckForStack; ResetCounter; oldSliceNum := SliceNumber; SaveState; for i := 1 to nSlices do begin ChooseSlice(i); RestoreROI; Measure; end; UpdateResults; SelectSlice(oldSliceNum); RestoreState; end; (The CheckForStack procedure is from the standard Stack Macros file that comes with NIH-Image; omit it if you paste the ROI Stack Measurement macro into the Stack Macros file.) If you actually do want to measure and plot each pixel in the ROI you could select each pixel manually and run the macro repeatedly for all of the pixels in the region you want to measure, although this might prove tedious. Mark N. Rand, Ph.D. U.W. Dept. Neurology, School of Medicine 1959 NE Pacific St., Box 356465 Seattle WA 98195-6465 fax: (206) 616-8272 vox: (206) 616-5153 <°){{{{>< <°){{{{>< <°){{{{>< <°){{{{>< <°){{{{>< <°){{{{>< ------------------------------ Date: Wed, 19 Aug 1998 17:22:39 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: Macro command for Scale to fit Window? Message-ID: <35DB09DC.96BEFFC8@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Henry M. Thomas wrote: > I want to paste into the middle of a 1500 by 800 pixel window, which doesn' > fit on the screen. Pasting into the scrollable, regular window pastes at, > roughly (and unpredictably by me) 250,250, whereas pasting into the > scaled-to-fit-window window pastes reliably at 750,400. Then I can move > the ROI by macro. > > Scale to Fit Window is in the Options Menu. I can't find a macro > equivalent. If not, how can I reliably move the upper left corner of the > pasted ROI to, say 20,20? > > Thanks, Harry > > Henry M. Thomas, III MD (Harry) > Professor of Clinical Medicine, Pulmonary and Critical Care Division > Department of Medicine, Cornell Univ. Medical School > Director, Pulmonary Research, Burke Rehabilitation Hospital > 785 Mamaroneck Ave. White Plains, NY 10605 > (914) 597-2141 Harry, Hope this is what you need..... Macro 'Paste Selection 20,20' Var left,top,width,height:integer; begin GetRoi(left,top,width,height); Copy; SetNewSize(1500,800); MakeNewWindow('1500x800'); MakeROI(20,20,width,height); Paste; end; Jeremy *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html ------------------------------ Date: Wed, 19 Aug 1998 15:40:10 -0400 From: Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Re: white bars in the histogram Message-Id: Content-Type: text/plain; charset="us-ascii" >I'm calculating a histogram of a ROI and exporting the data to a file. >When I look at the file I find that about every 10 values is a zero when >it shouldn't be. Is there a way to turn this feature off? > >Paul Morin > >University of Minnesota It might not be applied to your case, If you had imported the image and used a scale these things can happen. Cengizhan Dr. Cengizhan Ozturk ======================= Johns Hopkins University - Medical Imaging Lab 407 Traylor Building / 720 Rutland Av. Baltimore, MD 21205-2196 Phone: (410) 614 5292 Fax: (410) 502 6915 E-mail: cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk/ ======================= ------------------------------ Date: Wed, 19 Aug 1998 22:23:51 +0200 From: "Anneke M.Th. Harbers and Ard Jonker" To: nih-image@io.ece.drexel.edu Subject: Re: Capture max intensity during TIFF import Message-Id: Content-Type: text/plain; charset="us-ascii" >Greg (and Henry)- I would advocate to set another variable (min) to be taken: ...,stackmin:integer; ... stackmin:=65536; for i := 1 to nSlices do begin SelectPic(StackPID); SelectSlice(i); SelectAll; Measure; GetResults(n,mean,mode,min,max); Writeln(i,tab,max); If stackmax < max then stackmax:=max; If stackmin < min then stackmin:=min; end; SetImportMinMax(min,stackmax); SetImport('TIFF'); Import(path); end; This prevents that you waste probably unused lower values. If the 16 bit stack contains values of e.g. 10.000 to 40.000, you have gained some precision, as greyvalue 0 will be assigned to 10.000 rather than to 0. The range will be 10.000...40.000 rather than 0...40.000 spread over 256 greyvalues. Ard ------------------------------ Date: Wed, 19 Aug 1998 21:01:08 -0400 From: kwb To: nih-image@io.ece.drexel.edu Subject: NIH Quicktimes in PowerPoint Presentations. Message-Id: Content-Type: text/plain; charset="us-ascii" I've created quicktime animations using NIH Image 1.62 and have no problem viewing them using PowerPoint on the Mac. I haven't been as successful using the PC version. Has anybody had any success presenting quicktime animations using PowerPoint on a PC platform and is there a particular variety of quicktime (video, cinepak, animation?) that might be best suited to this purpose? Thank you in advance for any comments or suggestions. Regards, Ken Baker kwb@bserv.com ------------------------------ Date: Thu, 20 Aug 1998 17:04:39 +0900 From: "KUNITOMO,Junko" To: nih-image@io.ece.drexel.edu Subject: Method for analyzing many particles Message-Id: <199808200804.RAA14195@region.envi.osakafu-u.ac.jp> Content-Type: text/plain; charset="ISO-2022-JP" Content-Transfer-Encoding: 7bit I need some help with analysis of particles. I would like to count and measure more than 8000(Max Measurements) particles and long perimeter particles. Please let me know if there is a method for analyzing many particles for example particle count and perimeter? *************************************** $BT"M'=_;R!J(JKUNITOMO,Junko) Osaka Prefecture University Gakuen cho 1-1,Sakai city,Osaka,Japan Tel$B!'(J+81-722-54-9444 Fax$B!'(J+81-722-54-9918 E-mail$B!'(Jkunitomo@envi.osakafu-u.ac.jp -------------------------------- End of nih-image-d Digest V98 Issue #40 *************************************** From nih-image-request@io.ece.drexel.edu Thu Aug 20 04:19 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id EAA02099; Thu, 20 Aug 1998 04:18:05 -0400 (EDT) Resent-Date: Thu, 20 Aug 1998 04:18:05 -0400 (EDT) Message-Id: <199808200804.RAA14195@region.envi.osakafu-u.ac.jp> X-Sender: kunitomo@region.envi.osakafu-u.ac.jp X-Mailer: Macintosh Eudora Pro Version 3.1.1-J Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Date: Thu, 20 Aug 1998 17:04:39 +0900 To: nih-image@io.ece.drexel.edu From: "KUNITOMO,Junko" Subject: Method for analyzing many particles Resent-Message-ID: <"8m9aZ2.0.RA.xYzsr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/235 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="ISO-2022-JP" Content-Length: 504 Status: O I need some help with analysis of particles. I would like to count and measure more than 8000(Max Measurements) particles and long perimeter particles. Please let me know if there is a method for analyzing many particles for example particle count and perimeter? *************************************** $BT"M'=_;R!J(JKUNITOMO,Junko) Osaka Prefecture University Gakuen cho 1-1,Sakai city,Osaka,Japan Tel$B!'(J+81-722-54-9444 Fax$B!'(J+81-722-54-9918 E-mail$B!'(Jkunitomo@envi.osakafu-u.ac.jp From nih-image-request@io.ece.drexel.edu Thu Aug 20 06:47 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA15257; Thu, 20 Aug 1998 06:47:53 -0400 (EDT) Resent-Date: Thu, 20 Aug 1998 06:47:53 -0400 (EDT) Message-ID: <35DC7BD4.3B92@cris.enel.it> Date: Thu, 20 Aug 1998 12:41:08 -0700 From: "Zuccala David" Reply-To: zuccala@cris.enel.it Organization: ENEL Ricerca - Polo Idraulico e Strutturale X-Mailer: Mozilla 3.01Gold (Win16; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Morphologic Operations and NIH Image References: <199808200815.EAA01819@io.ECE.Drexel.EDU> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"ubRGs2.0.OP3.ql_sr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/236 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1685 Status: O > Does Image do morphologic operations? Is if fair to say a morphologic operation is the > net change to an image, regardless of the technique used to get there? In other words, > does it matter if I skeletonize an image with Image or, say, Alice [Dip Station] which > apparently uses different mathematical structuring elements? If they are different, can I > use the morphologic operator literature to justify a technique I develop using Image? > Dear Mike, I used for some time NIH-Image and DIP Station (Alice didn't existed yet, but I assume that it is not less powerful). DIP Station implements grey-level morphology, that is more general than binary morphology used by NIH-Image. Moreover, DIP Station allows you to define your own structuring elements. Anyway, if you try DIP Station morphology with binary images, you should get the same results of NIH-Image morphology, as far as the structuring elements are the same. For instance, NIH-Image structuring element with 4 neighbours should be * *** * and with 8 neighbours *** *** *** Be careful because DIP Station allows you to define also the centre of the structuring element, that does change the result. Also check blacks and whites because NIH-Image erosion may be DIP Station dilation and vice-versa. If you have more questions, I'll be at work tomorrow (Friday) and then after September 15th. Hope this helps. David ********************************************************** David Zuccala' ENEL RICERCA - Polo Idraulico e Strutturale v. Pozzobonelli, 6 ph.: + 39 02 7224.8487 I - 20162 Milano fax: + 39 02 7224.8430 e-mail: zuccala@cris.enel.it From nih-image-request@io.ece.drexel.edu Thu Aug 20 15:32 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA23766; Thu, 20 Aug 1998 15:30:28 -0400 (EDT) Resent-Date: Thu, 20 Aug 1998 15:30:28 -0400 (EDT) X-Sender: cozturk@tempest.bme-mri.jhu.edu Message-Id: In-Reply-To: References: <35C878D7.8A6A83F1@netreach.net> Mime-Version: 1.0 Date: Thu, 20 Aug 1998 15:09:29 -0400 To: nih-image@io.ece.drexel.edu From: Cengizhan Ozturk Subject: Re: NIH Quicktimes in PowerPoint Presentations. Resent-Message-ID: <"y2_PE2.0.fR5.sK7tr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/237 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1267 Status: O >I've created quicktime animations using NIH Image 1.62 and have no problem >viewing them using PowerPoint on the Mac. I haven't been as successful >using the PC version. >Has anybody had any success presenting quicktime animations using >PowerPoint on a PC platform and is there a particular variety of quicktime >(video, cinepak, animation?) that might be best suited to this purpose? >Thank you in advance for any comments or suggestions. > > Regards, > Ken Baker >kwb@bserv.com I was successfull in MAC-PC Quicktime presentations. Couple of pointers: 1. Get the latest Quicktime (3.x) for windozz from apple and carry it with your presentation. 2. Do not use any compression schemes unless you have to. The choice will depend on your movie. 3. Flatten the quicktime movies (latest movie player takes care of it, non mac platform save option, also make it self contained ) 4. I usually burn a CD (ISO 9660) then you can carry it around easily. Good Luck. Cengizhan Dr. Cengizhan Ozturk ======================= Johns Hopkins University - Medical Imaging Lab 407 Traylor Building / 720 Rutland Av. Baltimore, MD 21205-2196 Phone: (410) 614 5292 Fax: (410) 502 6915 E-mail: cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk/ ======================= From nih-image-request@io.ece.drexel.edu Thu Aug 20 21:38 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA18468; Thu, 20 Aug 1998 21:37:58 -0400 (EDT) Resent-Date: Thu, 20 Aug 1998 21:37:58 -0400 (EDT) Message-Id: <3.0.1.32.19980821114439.0069b3f0@email.aims.gov.au> X-Sender: msalmon@email.aims.gov.au X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Fri, 21 Aug 1998 11:44:39 +1000 To: nih-image@io.ece.drexel.edu From: Matt Salmon Subject: Questions on NIH-image Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Resent-Message-ID: <"sFZ0D2.0.mL4.4tCtr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/238 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="iso-8859-1" Content-Length: 3161 Status: O Hi, I have just subscribed to your mailing list so I hope that this message gets through. I am currently using NIH-image to determine egg numbers from samples taken from female broodstock tiger prawns after spawning. =20 Firstly, I should give you some background information of how I am using this program. At AIMS (The Australian Institute of Marine Science) Mariculture facility an average experiment can involve anything up to 100 female broodstock. When a female spawns we subsample her eggs (five replicates per sample) to detemine fecundity. Currently these samples are manually counted and if each female spawns twice (although she can spawn up to five times during an experiment) that's a minimum of 400 samples (of which each replicate can contain up to 300 individual eggs) that need to be counted. That's a lot of counting, labour and time. I have just started to use NIH-image and I am still learning about it's limits and functions with the help of your manual and general use of the program. =20 I have several problems which I have encountered. The prawn eggs are between 100-150um in size and I can clearly see the eggs on the computer monitor. Unfortunately when the egg samples are collected they are fixed in alcohol and this sometimes produces a precipitate and other floculative material which ranges in size and shape. =20 1) Is their a way that I can tell the computer to look for spherical eggs within a given pixel range? At the moment when I define a given pixel size/range the computer detects other particles within this range which are not eggs. The eggs are always spherical and do not resemble any other floculative material. 2) Another problem is that sometimes the eggs clump and are not detected because they are larger than the defined pixel range. I am currently testing different detergents which have only partially resolved the problem. My question is, is their some way of telling the program to measure the area (in the field of view) which is shaded by the eggs and given the size of the eggs accuratley working out the number of eggs which correlate to the shaded area within the given field of view? For example, If a their is a clump of eggs the program measures the area they occupy and knowing that one egg is so many pixels in size determines that their is 4 eggs within that clump. Are these solvable problems or am I hoping for too much out of this program? If this can be done, is their also a way of getting the program to differentiate between an egg and other particles? Can you tell the program to take a picture of an egg and only count paricles which conform to it's size and shape? The eggs are quite distinct, spherical and can be seen easily with the naked=20 eye. I know that some of these questions may be too complex but I hope that you can shed some light as this program would be a huge benefit if I can implement an accurate automated process for counting egg samples. I'm sure you will be hearing from me regularly but I hope I don't become to much of a nuisance. Yours Sincerely, Matt Salmon BSc. From nih-image-request@io.ece.drexel.edu Thu Aug 20 23:18 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id XAA25965; Thu, 20 Aug 1998 23:18:47 -0400 (EDT) Resent-Date: Thu, 20 Aug 1998 23:18:47 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: m.salmon@aims.gov.au, nih-image@io.ece.drexel.edu Date: Fri, 21 Aug 1998 13:13:36 GMT+1000 Subject: Re: Questions on NIH-image Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <6583BB8361F@rna.bio.mq.edu.au> Resent-Message-ID: <"lrI3e2.0.i66.DLEtr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/239 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2101 Status: O >Date: Fri, 21 Aug 1998 11:44:39 +1000 >From: Matt Salmon >Subject: Questions on NIH-image >............ I am currently using NIH-image to determine egg >numbers from samples taken from female broodstock tiger prawns after >spawning. >.......................... Matt, You can be quite confident that your project could be quite well done with NIH-Image and macros. You should have some particular advantages with counting your eggs as they are both spherial and relatively uniform in size. Your approach to attempt to have eggs separated (non-clumped) as far a possible I think is the correct one. It is easier to count analyse image of separate eggs than to separate eggs in the image :-) but there is a balance in that you want to maintain a reasonable egg density / field size / resolution. Assuming you are using a PAL video camera 768x512 pixels and 100um eggs are say minimum 16 pixel diameter to allow adequate circularity test, you might expect eggs at say 32 pixel centers 24x16=384 eggs per field (5x3 mm) ....matches 300 per sample quite well. A ring-light illuminator to give you a dark field background with low angle incident light scatter from eggs to a dissecting microscope should give good contrast. The tack I would take would be to analyzeParticles for eggsize particle range and then do a macro pass of each egg rMajor/rMinor axis to check near 1 and rMax[]~=rMin[] for uniform color. More stringent qualification of particles could be done using autoOutline(rX[i],rY[i]) ie automated "wand"ing of each "particle" to allow detail analysis of shape. You would then have data for a size histogram. Larger "particles" or clumps could then be estimated on the basis of rArea[clump]/modal rArea[egg] A circular Hough transform could be used to emphasise circular objects (in clumps) but I would expect this to be an unnecessary complication in your case. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Thu Aug 20 23:21 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id XAA26301; Thu, 20 Aug 1998 23:21:46 -0400 (EDT) Date: Thu, 20 Aug 1998 23:21:46 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808210321.XAA26301@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #41 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/41 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 9957 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 41 Today's Topics: Re: Morphologic Operations and NIH I [ "Zuccala David" ] Re: Questions on NIH-image [ GJOSS@rna.bio.mq.edu.au ] ------------------------------ Date: Thu, 20 Aug 1998 12:41:08 -0700 From: "Zuccala David" To: nih-image@io.ece.drexel.edu Subject: Re: Morphologic Operations and NIH Image Message-ID: <35DC7BD4.3B92@cris.enel.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Does Image do morphologic operations? Is if fair to say a morphologic operation is the > net change to an image, regardless of the technique used to get there? In other words, > does it matter if I skeletonize an image with Image or, say, Alice [Dip Station] which > apparently uses different mathematical structuring elements? If they are different, can I > use the morphologic operator literature to justify a technique I develop using Image? > Dear Mike, I used for some time NIH-Image and DIP Station (Alice didn't existed yet, but I assume that it is not less powerful). DIP Station implements grey-level morphology, that is more general than binary morphology used by NIH-Image. Moreover, DIP Station allows you to define your own structuring elements. Anyway, if you try DIP Station morphology with binary images, you should get the same results of NIH-Image morphology, as far as the structuring elements are the same. For instance, NIH-Image structuring element with 4 neighbours should be * *** * and with 8 neighbours *** *** *** Be careful because DIP Station allows you to define also the centre of the structuring element, that does change the result. Also check blacks and whites because NIH-Image erosion may be DIP Station dilation and vice-versa. If you have more questions, I'll be at work tomorrow (Friday) and then after September 15th. Hope this helps. David ********************************************************** David Zuccala' ENEL RICERCA - Polo Idraulico e Strutturale v. Pozzobonelli, 6 ph.: + 39 02 7224.8487 I - 20162 Milano fax: + 39 02 7224.8430 e-mail: zuccala@cris.enel.it ------------------------------ Date: Thu, 20 Aug 1998 15:09:29 -0400 From: Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Re: NIH Quicktimes in PowerPoint Presentations. Message-Id: Content-Type: text/plain; charset="us-ascii" >I've created quicktime animations using NIH Image 1.62 and have no problem >viewing them using PowerPoint on the Mac. I haven't been as successful >using the PC version. >Has anybody had any success presenting quicktime animations using >PowerPoint on a PC platform and is there a particular variety of quicktime >(video, cinepak, animation?) that might be best suited to this purpose? >Thank you in advance for any comments or suggestions. > > Regards, > Ken Baker >kwb@bserv.com I was successfull in MAC-PC Quicktime presentations. Couple of pointers: 1. Get the latest Quicktime (3.x) for windozz from apple and carry it with your presentation. 2. Do not use any compression schemes unless you have to. The choice will depend on your movie. 3. Flatten the quicktime movies (latest movie player takes care of it, non mac platform save option, also make it self contained ) 4. I usually burn a CD (ISO 9660) then you can carry it around easily. Good Luck. Cengizhan Dr. Cengizhan Ozturk ======================= Johns Hopkins University - Medical Imaging Lab 407 Traylor Building / 720 Rutland Av. Baltimore, MD 21205-2196 Phone: (410) 614 5292 Fax: (410) 502 6915 E-mail: cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk/ ======================= ------------------------------ Date: Fri, 21 Aug 1998 11:44:39 +1000 From: Matt Salmon To: nih-image@io.ece.drexel.edu Subject: Questions on NIH-image Message-Id: <3.0.1.32.19980821114439.0069b3f0@email.aims.gov.au> Content-Type: text/enriched; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I have just subscribed to your mailing list so I hope that this message gets through. I am currently using NIH-image to determine egg numbers from samples taken from female broodstock tiger prawns after spawning. =20 Firstly, I should give you some background information of how I am using this program. At AIMS (The Australian Institute of Marine Science) Mariculture facility an average experiment can involve anything up to 100 female broodstock. When a female spawns we subsample her eggs (five replicates per sample) to detemine fecundity. Currently these samples are manually counted and if each female spawns twice (although she can spawn up to five times during an experiment) that's a minimum of 400 samples (of which each replicate can contain up to 300 individual eggs) that need to be counted. That's a lot of counting, labour and time. I have just started to use NIH-image and I am still learning about it's limits and functions with the help of your manual and general use of the program. =20 I have several problems which I have encountered. The prawn eggs are between 100-150um in size and I can clearly see the eggs on the computer monitor. Unfortunately when the egg samples are collected they are fixed in alcohol and this sometimes produces a precipitate and other floculative material which ranges in size and shape. =20 1) Is their a way that I can tell the computer to look for spherical eggs within a given pixel range? At the moment when I define a given pixel size/range the computer detects other particles within this range which are not eggs. The eggs are always spherical and do not resemble any other floculative material. 2) Another problem is that sometimes the eggs clump and are not detected because they are larger than the defined pixel range. I am currently testing different detergents which have only partially resolved the problem. My question is, is their some way of telling the program to measure the area (in the field of view) which is shaded by the eggs and given the size of the eggs accuratley working out the number of eggs which correlate to the shaded area within the given field of view? For example, If a their is a clump of eggs the program measures the area they occupy and knowing that one egg is so many pixels in size determines that their is 4 eggs within that clump. Are these solvable problems or am I hoping for too much out of this program? If this can be done, is their also a way of getting the program to differentiate between an egg and other particles? Can you tell the program to take a picture of an egg and only count paricles which conform to it's size and shape? The eggs are quite distinct, spherical and can be seen easily with the naked=20 eye. I know that some of these questions may be too complex but I hope that you can shed some light as this program would be a huge benefit if I can implement an accurate automated process for counting egg samples. I'm sure you will be hearing from me regularly but I hope I don't become to much of a nuisance. Yours Sincerely, Matt Salmon BSc. ------------------------------ Date: Fri, 21 Aug 1998 13:13:36 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: m.salmon@aims.gov.au, nih-image@io.ece.drexel.edu Subject: Re: Questions on NIH-image Message-ID: <6583BB8361F@rna.bio.mq.edu.au> >Date: Fri, 21 Aug 1998 11:44:39 +1000 >From: Matt Salmon >Subject: Questions on NIH-image >............ I am currently using NIH-image to determine egg >numbers from samples taken from female broodstock tiger prawns after >spawning. >.......................... Matt, You can be quite confident that your project could be quite well done with NIH-Image and macros. You should have some particular advantages with counting your eggs as they are both spherial and relatively uniform in size. Your approach to attempt to have eggs separated (non-clumped) as far a possible I think is the correct one. It is easier to count analyse image of separate eggs than to separate eggs in the image :-) but there is a balance in that you want to maintain a reasonable egg density / field size / resolution. Assuming you are using a PAL video camera 768x512 pixels and 100um eggs are say minimum 16 pixel diameter to allow adequate circularity test, you might expect eggs at say 32 pixel centers 24x16=384 eggs per field (5x3 mm) ....matches 300 per sample quite well. A ring-light illuminator to give you a dark field background with low angle incident light scatter from eggs to a dissecting microscope should give good contrast. The tack I would take would be to analyzeParticles for eggsize particle range and then do a macro pass of each egg rMajor/rMinor axis to check near 1 and rMax[]~=rMin[] for uniform color. More stringent qualification of particles could be done using autoOutline(rX[i],rY[i]) ie automated "wand"ing of each "particle" to allow detail analysis of shape. You would then have data for a size histogram. Larger "particles" or clumps could then be estimated on the basis of rArea[clump]/modal rArea[egg] A circular Hough transform could be used to emphasise circular objects (in clumps) but I would expect this to be an unnecessary complication in your case. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #41 *************************************** From nih-image-request@io.ece.drexel.edu Fri Aug 21 03:05 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id DAA11705; Fri, 21 Aug 1998 03:04:59 -0400 (EDT) Resent-Date: Fri, 21 Aug 1998 03:04:59 -0400 (EDT) Message-ID: From: "Goldsmith, Noel" To: "'Matt Salmon'" , "'Image Mailing List'" Subject: RE: Questions on NIH-image Date: Fri, 21 Aug 1998 16:57:15 +1000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"sldzZ2.0.yh2.OfHtr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/240 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 5276 Status: O Matt, Hi, Well you have a few good questions. 1. Image analysis is better if your samples are perfect. But you know that already. 2. The eggs are little spheres but what you see on the monitor is circles. 3. Is there some filtering you might do to pick out circles of a certain size range? I have some suggestions. 1 Try some FFT filterings using low or high pass filters. 2. Take an image of 1 egg all by itself and FFT this and then use this as a mask for an image of many eggs. This is based on the idea that is seen in John Russ's book The Image Processing handbook, in which a page of text is processed using a template or mask made from one letter, in the case illustrated an "e" I think. If you use a mask which passes the frequency you should pick out all the 'e''s whereas if you filter out the frequencies associated with the 'e''s you should remove them. 3. Try some convolution filters. Variables to try. Filter size can vary from 3x3 up to 63x63. Values in each of the filter cells can be between 0-255. Try with scaled convolutions on and off. To try all of the possibilities can take quite a while. ie with a 3x3 filter there are 9x256 arrangements, some of which would be symmetrically equivalent. Why it might be good. With a suitable convolution mask which is circular (use zeros to pad it out to the square) and of the same size as the circles in question then a useful effect might be had. 4. Try some background subtractions which can be used to remove small bits from the field. 5. Try the ideas of masking the image with a thresholded image etc. 6. I guess the eggs are the same density grey as the other materials, if not thresholding might help. 7. If you know the size of one egg and then write a macro it could be used to determine the number of eggs in a mass of nicely packed eggs. You would of course need to calibrate by counting a few hundred and dividing by the appropriate number. Best regards Noel > ---------- > From: Matt Salmon > Sent: Friday, 21 August 1998 11:44 AM > To: nih-image@io.ece.drexel.edu > Subject: Questions on NIH-image > > Hi, I have just subscribed to your mailing list so I hope that this > message gets through. I am currently using NIH-image to determine egg > numbers from samples taken from female broodstock tiger prawns after > spawning. > Firstly, I should give you some background information of how I am > using this program. At AIMS (The Australian Institute of Marine > Science) Mariculture facility an average experiment can involve > anything up to 100 female broodstock. When a female spawns we > subsample her eggs (five replicates per sample) to detemine fecundity. > Currently these samples are manually counted and if each female spawns > twice (although she can spawn up to five times during an experiment) > that's a minimum of 400 samples (of which each replicate can contain > up to 300 individual eggs) that need to be counted. That's a lot of > counting, labour and time. I have just started to use NIH-image and I > am still learning about it's limits and functions with the help of > your manual and general use of the program. > I have several problems which I have encountered. The prawn eggs are > between 100-150um in size and I can clearly see the eggs on the > computer monitor. Unfortunately when the egg samples are collected > they are fixed in alcohol and this sometimes produces a precipitate > and other floculative material which ranges in size and shape. > 1) Is their a way that I can tell the computer to look for spherical > eggs within a given pixel range? At the moment when I define a given > pixel size/range the computer detects other particles within this > range which are not eggs. The eggs are always spherical and do not > resemble any other floculative material. > 2) Another problem is that sometimes the eggs clump and are not > detected because they are larger than the defined pixel range. I am > currently testing different detergents which have only partially > resolved the problem. My question is, is their some way of telling > the program to measure the area (in the field of view) which is shaded > by the eggs and given the size of the eggs accuratley working out the > number of eggs which correlate to the shaded area within the given > field of view? For example, If a their is a clump of eggs the program > measures the area they occupy and knowing that one egg is so many > pixels in size determines that their is 4 eggs within that clump. Are > these solvable problems or am I hoping for too much out of this > program? If this can be done, is their also a way of getting the > program to differentiate between an egg and other particles? Can you > tell the program to take a picture of an egg and only count paricles > which conform to it's size and shape? The eggs are quite distinct, > spherical and can be seen easily with the naked eye. > I know that some of these questions may be too complex but I hope that > you can shed some light as this program would be a huge benefit if I > can implement an accurate automated process for counting egg samples. > I'm sure you will be hearing from me regularly but I hope I don't > become to much of a nuisance. > > Yours Sincerely, > > Matt Salmon BSc. > From nih-image-request@io.ece.drexel.edu Fri Aug 21 16:27 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA06260; Fri, 21 Aug 1998 16:26:52 -0400 (EDT) Resent-Date: Fri, 21 Aug 1998 16:26:52 -0400 (EDT) Message-ID: <19980821200230.19206.qmail@hotmail.com> X-Originating-IP: [198.14.50.104] From: "Paul Loftsgard" To: nih-image@io.ece.drexel.edu Subject: fractal analysis Date: Fri, 21 Aug 1998 13:02:30 PDT Resent-Message-ID: <"eal-g.0.651.x9Ttr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/241 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 810 Status: O I have another question about the fractal analysis macros(I wrote a couple weeks ago about edm). Anyway my question is this: Does area play a factor in determing fractal dimension with either the box counting or edm method? I am finding the dimensions of sprays and at the top and bottom of each spray is a flat side(the end of the cameras field of view). I was wondering whether or not I can just remove the center portion of the spray, attach the two sides and determine the dimension of the new image. This results in about half of the total area of the spray being eliminated. Any help would be appreciated(or ideas on how to get around the flat sides) Thanks, Paul Loftsgard ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Fri Aug 21 16:44 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA07539; Fri, 21 Aug 1998 16:44:34 -0400 (EDT) Resent-Date: Fri, 21 Aug 1998 16:44:34 -0400 (EDT) X-Sender: d306604@nobel.si.uqam.ca Message-Id: In-Reply-To: <19980821200230.19206.qmail@hotmail.com> Mime-Version: 1.0 Date: Fri, 21 Aug 1998 16:23:33 -0400 To: nih-image@io.ece.drexel.edu From: Dominique Berube Subject: Re: fractal analysis Resent-Message-ID: <"4qmRX1.0.0U1.EUTtr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/242 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1794 Status: O >I have another question about the fractal analysis macros(I wrote a >couple weeks ago about edm). Anyway my question is this: > >Does area play a factor in determing fractal dimension with either the >box counting or edm method? My own experience showed that size is of the most importance with box-counting. Fractal dimension varies greatly with size, because of the limited amount of data generated with that method. That is the primary reason why I never use this method on boundaries. The scale of the study is too limited to use it. With EDM, I manage to produce consistant fractal dimensions (variations of 0.03 max) for particle sizes between 10000 and 400000 pixels. This was tested on a few particles, by varying the resolution of the image (at the time of the acquisition, of course!). > >I am finding the dimensions of sprays and at the top and bottom of each >spray is a flat side(the end of the cameras field of view). I was >wondering whether or not I can just remove the center portion of the >spray, attach the two sides and determine the dimension of the new >image. This results in about half of the total area of the spray being >eliminated. >Any help would be appreciated(or ideas on how to get around the flat >sides) > Well. I'm not so sure about this one. If your image could be limited to just your two side lines (not the straignt ones), I don't see the problem with the fractal analysis. You could crop your image to eliminate the two flat sizes (if they are at the top and bottom of the image). Fractal analysis would then be limited to the two lines still on the picture. OK, I'm not sure enough here so I'll stop! :) Dominique Dominique Berube Ph.D Environmental Sciences, UQAM Email: d306604@er.uqam.ca Phone: (514) 987-3000 (3986) Fax: (514) 987-7749 From nih-image-d-request@io.ece.drexel.edu Sat Aug 22 06:12 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA09495; Sat, 22 Aug 1998 06:12:25 -0400 (EDT) Date: Sat, 22 Aug 1998 06:12:25 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808221012.GAA09495@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #42 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/42 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 9284 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 42 Today's Topics: RE: Questions on NIH-image [ "Goldsmith, Noel" To: "'Matt Salmon'" , "'Image Mailing List'" Subject: RE: Questions on NIH-image Message-ID: Content-Type: text/plain; charset="iso-8859-1" Matt, Hi, Well you have a few good questions. 1. Image analysis is better if your samples are perfect. But you know that already. 2. The eggs are little spheres but what you see on the monitor is circles. 3. Is there some filtering you might do to pick out circles of a certain size range? I have some suggestions. 1 Try some FFT filterings using low or high pass filters. 2. Take an image of 1 egg all by itself and FFT this and then use this as a mask for an image of many eggs. This is based on the idea that is seen in John Russ's book The Image Processing handbook, in which a page of text is processed using a template or mask made from one letter, in the case illustrated an "e" I think. If you use a mask which passes the frequency you should pick out all the 'e''s whereas if you filter out the frequencies associated with the 'e''s you should remove them. 3. Try some convolution filters. Variables to try. Filter size can vary from 3x3 up to 63x63. Values in each of the filter cells can be between 0-255. Try with scaled convolutions on and off. To try all of the possibilities can take quite a while. ie with a 3x3 filter there are 9x256 arrangements, some of which would be symmetrically equivalent. Why it might be good. With a suitable convolution mask which is circular (use zeros to pad it out to the square) and of the same size as the circles in question then a useful effect might be had. 4. Try some background subtractions which can be used to remove small bits from the field. 5. Try the ideas of masking the image with a thresholded image etc. 6. I guess the eggs are the same density grey as the other materials, if not thresholding might help. 7. If you know the size of one egg and then write a macro it could be used to determine the number of eggs in a mass of nicely packed eggs. You would of course need to calibrate by counting a few hundred and dividing by the appropriate number. Best regards Noel > ---------- > From: Matt Salmon > Sent: Friday, 21 August 1998 11:44 AM > To: nih-image@io.ece.drexel.edu > Subject: Questions on NIH-image > > Hi, I have just subscribed to your mailing list so I hope that this > message gets through. I am currently using NIH-image to determine egg > numbers from samples taken from female broodstock tiger prawns after > spawning. > Firstly, I should give you some background information of how I am > using this program. At AIMS (The Australian Institute of Marine > Science) Mariculture facility an average experiment can involve > anything up to 100 female broodstock. When a female spawns we > subsample her eggs (five replicates per sample) to detemine fecundity. > Currently these samples are manually counted and if each female spawns > twice (although she can spawn up to five times during an experiment) > that's a minimum of 400 samples (of which each replicate can contain > up to 300 individual eggs) that need to be counted. That's a lot of > counting, labour and time. I have just started to use NIH-image and I > am still learning about it's limits and functions with the help of > your manual and general use of the program. > I have several problems which I have encountered. The prawn eggs are > between 100-150um in size and I can clearly see the eggs on the > computer monitor. Unfortunately when the egg samples are collected > they are fixed in alcohol and this sometimes produces a precipitate > and other floculative material which ranges in size and shape. > 1) Is their a way that I can tell the computer to look for spherical > eggs within a given pixel range? At the moment when I define a given > pixel size/range the computer detects other particles within this > range which are not eggs. The eggs are always spherical and do not > resemble any other floculative material. > 2) Another problem is that sometimes the eggs clump and are not > detected because they are larger than the defined pixel range. I am > currently testing different detergents which have only partially > resolved the problem. My question is, is their some way of telling > the program to measure the area (in the field of view) which is shaded > by the eggs and given the size of the eggs accuratley working out the > number of eggs which correlate to the shaded area within the given > field of view? For example, If a their is a clump of eggs the program > measures the area they occupy and knowing that one egg is so many > pixels in size determines that their is 4 eggs within that clump. Are > these solvable problems or am I hoping for too much out of this > program? If this can be done, is their also a way of getting the > program to differentiate between an egg and other particles? Can you > tell the program to take a picture of an egg and only count paricles > which conform to it's size and shape? The eggs are quite distinct, > spherical and can be seen easily with the naked eye. > I know that some of these questions may be too complex but I hope that > you can shed some light as this program would be a huge benefit if I > can implement an accurate automated process for counting egg samples. > I'm sure you will be hearing from me regularly but I hope I don't > become to much of a nuisance. > > Yours Sincerely, > > Matt Salmon BSc. > ------------------------------ Date: Fri, 21 Aug 1998 13:02:30 PDT From: "Paul Loftsgard" To: nih-image@io.ece.drexel.edu Subject: fractal analysis Message-ID: <19980821200230.19206.qmail@hotmail.com> Content-Type: text/plain I have another question about the fractal analysis macros(I wrote a couple weeks ago about edm). Anyway my question is this: Does area play a factor in determing fractal dimension with either the box counting or edm method? I am finding the dimensions of sprays and at the top and bottom of each spray is a flat side(the end of the cameras field of view). I was wondering whether or not I can just remove the center portion of the spray, attach the two sides and determine the dimension of the new image. This results in about half of the total area of the spray being eliminated. Any help would be appreciated(or ideas on how to get around the flat sides) Thanks, Paul Loftsgard ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Fri, 21 Aug 1998 16:23:33 -0400 From: Dominique Berube To: nih-image@io.ece.drexel.edu Subject: Re: fractal analysis Message-Id: Content-Type: text/plain; charset="us-ascii" >I have another question about the fractal analysis macros(I wrote a >couple weeks ago about edm). Anyway my question is this: > >Does area play a factor in determing fractal dimension with either the >box counting or edm method? My own experience showed that size is of the most importance with box-counting. Fractal dimension varies greatly with size, because of the limited amount of data generated with that method. That is the primary reason why I never use this method on boundaries. The scale of the study is too limited to use it. With EDM, I manage to produce consistant fractal dimensions (variations of 0.03 max) for particle sizes between 10000 and 400000 pixels. This was tested on a few particles, by varying the resolution of the image (at the time of the acquisition, of course!). > >I am finding the dimensions of sprays and at the top and bottom of each >spray is a flat side(the end of the cameras field of view). I was >wondering whether or not I can just remove the center portion of the >spray, attach the two sides and determine the dimension of the new >image. This results in about half of the total area of the spray being >eliminated. >Any help would be appreciated(or ideas on how to get around the flat >sides) > Well. I'm not so sure about this one. If your image could be limited to just your two side lines (not the straignt ones), I don't see the problem with the fractal analysis. You could crop your image to eliminate the two flat sizes (if they are at the top and bottom of the image). Fractal analysis would then be limited to the two lines still on the picture. OK, I'm not sure enough here so I'll stop! :) Dominique Dominique Berube Ph.D Environmental Sciences, UQAM Email: d306604@er.uqam.ca Phone: (514) 987-3000 (3986) Fax: (514) 987-7749 -------------------------------- End of nih-image-d Digest V98 Issue #42 *************************************** From nih-image-request@io.ece.drexel.edu Mon Aug 24 16:55 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA21326; Mon, 24 Aug 1998 16:53:24 -0400 (EDT) Resent-Date: Mon, 24 Aug 1998 16:53:24 -0400 (EDT) Message-ID: From: "Plylar, Tracy A. [C]" To: "'nih-image@biomed.drexel.edu'" Subject: NIH-Image Year 2000 compatible? Date: Mon, 24 Aug 1998 16:29:32 -0400 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1458.49) Resent-Message-ID: <"FmFcz1.0.ll4.jrSur"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/243 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 342 I need to know if NIH-Image has Y2K compatible issues? Of course there are no dates calculations involved in this software, (and if so, the OS would be responsible) but the vendors need to issue a written statement acknowledging this. Can anyone direct me to the URL where NIH states what version of NIH-Image is Y2K compatible? thanks TP From nih-image-request@io.ece.drexel.edu Mon Aug 24 17:53 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA25400; Mon, 24 Aug 1998 17:52:48 -0400 (EDT) Resent-Date: Mon, 24 Aug 1998 17:52:48 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 24 Aug 1998 17:43:30 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: NIH-Image Year 2000 compatible? Resent-Message-ID: <"Jl2uj2.0.Cy5.7rTur"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/244 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 434 >I need to know if NIH-Image has Y2K compatible issues? >Of course there are no dates calculations involved in this software, >(and if so, the OS would be responsible) but the vendors need to issue a >written statement acknowledging this. Can anyone direct me to the URL >where NIH states what version of NIH-Image is Y2K compatible? thanks TP http://rsb.info.nih.gov/nih-image/manual/faq.html (as of this afternoon) -wayne From nih-image-request@io.ece.drexel.edu Tue Aug 25 01:02 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id BAA28207; Tue, 25 Aug 1998 01:01:51 -0400 (EDT) Resent-Date: Tue, 25 Aug 1998 01:01:51 -0400 (EDT) Date: Tue, 25 Aug 1998 14:51:34 +1000 (EST) Message-Id: <199808250451.OAA32367@topaz.cqu.edu.au> X-Sender: mccannc@topaz.cqu.edu.au X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Cormac Subject: Frame grabber cards Resent-Message-ID: <"XMb1d3.0.yd6.aBaur"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/245 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 678 Hi there, there is a power pc set up here on campus which I am using for my project. I need to capture some images from a camera which is connected to the computer except the computer insists that I need a frame grabber card to do so. I know for a fact that there is already a frame grabber card installed in the machine but I have been unsuccessful in enabling it. I have followed instructions and used the sub-menu function 'Acquire' in order to try and launch it but it hasn't worked. Any suggestions would be appreciated. Please keep in mind that I am fairly unfamiliar with the Apple Mac computer. Cormac McCann Final Year Mechanical Engineering student. From nih-image-d-request@io.ece.drexel.edu Tue Aug 25 09:22 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA11236; Tue, 25 Aug 1998 09:22:33 -0400 (EDT) Date: Tue, 25 Aug 1998 09:22:33 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808251322.JAA11236@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #43 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/43 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3130 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 43 Today's Topics: NIH-Image Year 2000 compatible? [ "Plylar, Tracy A. [C]" ] Frame grabber cards [ Cormac ] unsubscribe [ "Dale H." ] ------------------------------ Date: Mon, 24 Aug 1998 16:29:32 -0400 From: "Plylar, Tracy A. [C]" To: "'nih-image@biomed.drexel.edu'" Subject: NIH-Image Year 2000 compatible? Message-ID: Content-Type: text/plain I need to know if NIH-Image has Y2K compatible issues? Of course there are no dates calculations involved in this software, (and if so, the OS would be responsible) but the vendors need to issue a written statement acknowledging this. Can anyone direct me to the URL where NIH states what version of NIH-Image is Y2K compatible? thanks TP ------------------------------ Date: Mon, 24 Aug 1998 17:43:30 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: NIH-Image Year 2000 compatible? Message-Id: Content-Type: text/plain; charset="us-ascii" >I need to know if NIH-Image has Y2K compatible issues? >Of course there are no dates calculations involved in this software, >(and if so, the OS would be responsible) but the vendors need to issue a >written statement acknowledging this. Can anyone direct me to the URL >where NIH states what version of NIH-Image is Y2K compatible? thanks TP http://rsb.info.nih.gov/nih-image/manual/faq.html (as of this afternoon) -wayne ------------------------------ Date: Tue, 25 Aug 1998 14:51:34 +1000 (EST) From: Cormac To: nih-image@io.ece.drexel.edu Subject: Frame grabber cards Message-Id: <199808250451.OAA32367@topaz.cqu.edu.au> Content-Type: text/plain; charset="us-ascii" Hi there, there is a power pc set up here on campus which I am using for my project. I need to capture some images from a camera which is connected to the computer except the computer insists that I need a frame grabber card to do so. I know for a fact that there is already a frame grabber card installed in the machine but I have been unsuccessful in enabling it. I have followed instructions and used the sub-menu function 'Acquire' in order to try and launch it but it hasn't worked. Any suggestions would be appreciated. Please keep in mind that I am fairly unfamiliar with the Apple Mac computer. Cormac McCann Final Year Mechanical Engineering student. ------------------------------ Date: Tue, 25 Aug 1998 09:06:21 -0400 From: "Dale H." To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <3.0.1.32.19980825090621.0071b500@email.psu.edu> Content-Type: text/plain; charset="us-ascii" -------------------------------- End of nih-image-d Digest V98 Issue #43 *************************************** From nih-image-request@io.ece.drexel.edu Tue Aug 25 09:23 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA11374; Tue, 25 Aug 1998 09:23:36 -0400 (EDT) Resent-Date: Tue, 25 Aug 1998 09:23:36 -0400 (EDT) Message-Id: <3.0.1.32.19980825090621.0071b500@email.psu.edu> X-Sender: dah13@email.psu.edu X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Tue, 25 Aug 1998 09:06:21 -0400 To: nih-image@io.ece.drexel.edu From: "Dale H." Subject: unsubscribe Mime-Version: 1.0 Resent-Message-ID: <"FWFBd3.0.HM2.wRhur"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/246 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1 From nih-image-request@io.ece.drexel.edu Tue Aug 25 13:19 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA27737; Tue, 25 Aug 1998 13:19:11 -0400 (EDT) Resent-Date: Tue, 25 Aug 1998 13:19:11 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Tue, 25 Aug 1998 12:05:27 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: ADMINISTRATA Resent-Message-ID: <"zqUfI2.0.LX6.Qxkur"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/247 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 1685 TimesHi everyone. The following is a reminder to everyone regarding administrative issues on the list. To unsubscribe follow these instructions: Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- And remember, the early bird may get the worm, but the second mouse gets the cheese. From nih-image-request@io.ece.drexel.edu Tue Aug 25 14:56 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA04837; Tue, 25 Aug 1998 14:55:46 -0400 (EDT) Resent-Date: Tue, 25 Aug 1998 14:55:46 -0400 (EDT) Message-Id: <9808251841.AA26518@acs1.acs.ucalgary.ca> Subject: Re: Frame grabber cards To: nih-image@io.ece.drexel.edu Date: Tue, 25 Aug 98 12:41:15 MDT From: "Doug S. Phillips" Cc: mccannc@topaz.cqu.edu.au In-Reply-To: <199808251307.JAA09662@io.ECE.Drexel.EDU>; from "nih-image-d-request@io.ece.drexel.edu" at Aug 25, 1998 9:07 am X-Mailer: ELM [version 2.3 PL11K] Mime-Version: 1.0 Resent-Message-ID: <"eP5Bd3.0.Mv.qLmur"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/248 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/mixed; boundary="----------------------------" Content-Length: 1915 ------------------------------ Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Cormac: Cormac wrote: > there is a power pc set up here on campus which I am using for my > project. I need to capture some images from a camera which is connected to > the computer except the computer insists that I need a frame grabber card to >do so. I know for a fact that there is already a frame grabber card >installed in the machine but I have been unsuccessful in enabling it. In the frame grabber appendix of the online manual for NIH-Image (at http://rsb.info.nih.gov/nih-image/manual/Appendices/frame.html ) it is stated that: > Using VDIGs (QuickTime Video Digitizer extensions), Image also supports > QuickTime compatible video digitizers such as those built into "AV" Macs and > the PowerMac7500/8500. >From http://ipt.lpl.arizona.edu/IPT/Help/helpmeister.html#13, there is the following information: > There are two main software components: digitizing software, and a system > extension called a VDIG (video digitizer), which tells the computer how to > communicate with the digitizing hardware. The VDIG for the AV Macs is called > AV Digitizer Options, and it belongs in the Extensions folder in the System > folder. If you need to install it manually, drag it to the closed System > folder and it will automatically be placed in the proper location. I saw another reference that indicated that the AV Digitizer Options was in the Info-Mac archive, but, checking there now, I can't find it. If someone else can complete the story here, I would interested in finding out the answer to the original question. Thanks. Doug S. Phillips Internet: phillips@ucalgary.ca University Computing Services Phone:(403)220-8445 FAX:(403)282-9199 The University of Calgary WWW: http://www.acs.ucalgary.ca/~phillips/ -------------------------------- From nih-image-d-request@io.ece.drexel.edu Wed Aug 26 06:11 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA19714; Wed, 26 Aug 1998 06:11:50 -0400 (EDT) Date: Wed, 26 Aug 1998 06:11:50 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808261011.GAA19714@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #44 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/44 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4571 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 44 Today's Topics: ADMINISTRATA [ Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: ADMINISTRATA Message-Id: Content-Type: text/enriched; charset="us-ascii" TimesHi everyone. The following is a reminder to everyone regarding administrative issues on the list. To unsubscribe follow these instructions: Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- And remember, the early bird may get the worm, but the second mouse gets the cheese. ------------------------------ Date: Tue, 25 Aug 98 12:41:15 MDT From: "Doug S. Phillips" To: nih-image@io.ece.drexel.edu Cc: mccannc@topaz.cqu.edu.au Subject: Re: Frame grabber cards Message-Id: <9808251841.AA26518@acs1.acs.ucalgary.ca> Content-Type: multipart/mixed; boundary="----------------------------" Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Cormac: Cormac wrote: > there is a power pc set up here on campus which I am using for my > project. I need to capture some images from a camera which is connected to > the computer except the computer insists that I need a frame grabber card to >do so. I know for a fact that there is already a frame grabber card >installed in the machine but I have been unsuccessful in enabling it. In the frame grabber appendix of the online manual for NIH-Image (at http://rsb.info.nih.gov/nih-image/manual/Appendices/frame.html ) it is stated that: > Using VDIGs (QuickTime Video Digitizer extensions), Image also supports > QuickTime compatible video digitizers such as those built into "AV" Macs and > the PowerMac7500/8500. >From http://ipt.lpl.arizona.edu/IPT/Help/helpmeister.html#13, there is the following information: > There are two main software components: digitizing software, and a system > extension called a VDIG (video digitizer), which tells the computer how to > communicate with the digitizing hardware. The VDIG for the AV Macs is called > AV Digitizer Options, and it belongs in the Extensions folder in the System > folder. If you need to install it manually, drag it to the closed System > folder and it will automatically be placed in the proper location. I saw another reference that indicated that the AV Digitizer Options was in the Info-Mac archive, but, checking there now, I can't find it. If someone else can complete the story here, I would interested in finding out the answer to the original question. Thanks. Doug S. Phillips Internet: phillips@ucalgary.ca University Computing Services Phone:(403)220-8445 FAX:(403)282-9199 The University of Calgary WWW: http://www.acs.ucalgary.ca/~phillips/ - ------------------------------ -------------------------------- End of nih-image-d Digest V98 Issue #44 *************************************** From nih-image-request@io.ece.drexel.edu Wed Aug 26 14:16 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA24928; Wed, 26 Aug 1998 14:16:04 -0400 (EDT) Resent-Date: Wed, 26 Aug 1998 14:16:04 -0400 (EDT) Subject: Re: unsubscribe Date: Wed, 26 Aug 98 13:58:22 -0400 x-sender: jlr$biol.biol.qc@qc1.qc.edu x-mailer: Claris Emailer 1.1 From: "Jared L. Rifkin" To: Mime-Version: 1.0 Message-ID: <2B7245D57A8@qc1.qc.edu> Resent-Message-ID: <"qYis_2.0.vj5.ep4vr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/249 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 58 why did i get this msg?????????????? check your address! From nih-image-request@io.ece.drexel.edu Wed Aug 26 14:37 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA26666; Wed, 26 Aug 1998 14:36:45 -0400 (EDT) Resent-Date: Wed, 26 Aug 1998 14:36:45 -0400 (EDT) Date: Wed, 26 Aug 1998 19:18:31 +0100 (BST) From: Jan Kreft X-Sender: sabjk@thor To: nih-image@io.ece.drexel.edu Subject: Q: Video or digital camera? Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"QhyTW1.0.S96.a65vr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/250 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 563 Dear all, we intend to buy some hardware to capture images from a phase contrast microscope. We can't spend more than $5000 and would rather less. We have a framegrabber anyway. Does anybody have experience with using both digital cameras and video cameras and could comment on which method gives the best image quality? The highest resolution? Many thanks, Jan. Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036 School of Pure and Applied Biology Fax +44 1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK From nih-image-request@io.ece.drexel.edu Wed Aug 26 16:17 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA03598; Wed, 26 Aug 1998 16:17:13 -0400 (EDT) Resent-Date: Wed, 26 Aug 1998 16:17:13 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Wed, 26 Aug 1998 14:55:24 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Re: Q: Video or digital camera? Resent-Message-ID: <"_yKlU2.0.sX.vW6vr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/251 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3139 >Dear all, > >we intend to buy some hardware to capture images from a phase contrast >microscope. We can't spend more than $5000 and would rather less. We have >a framegrabber anyway. Does anybody have experience with using both >digital cameras and video cameras and could comment on which method gives >the best image quality? The highest resolution? > The consumer model digital cameras have a fixed lens and so cannot be attached to a scope. Higher end professional systems consists of digital backs on SLR bodies and so, I believe could be readily mounted-you'll want an extension tube (Kodak makes models with Canon and Nikon bodies). The latter also provide manual overrides and better light meters. If you are not limited by low light intensity these provide a good system. They start at the $4k or so (Minolta RD-175) and go up to the stratosphere (20k for DCS 460-a beauty with 3kx2k pixels). On the Minolta you get a 3-chip system with the resolution achieved in part by software interpolation. Another option that is a relatively inexpensive solution, 6k, is the Leaf line camera which gives very high real resolution color images but with slow acquisition time. All these systems do not require a framegrabber. The spatial resolution you need obviously depends on application. Another concern to keep in mind is densitometric accuracy. If you are intending on performing densitometric measurements or segmentation, then consumer level systems are unlikely to be sufficiently accurate. The professional systems I suspect would do fine. A low cost monochrome solution is the Sony XC77. For 1k you get an accurate CCD camera albiet a low resolution one. Other systems exist that use the same chip and give you more electronic control. Color low cost system such as Cohu's cameras exist though have disappointing color matching-not suitable for publication. >From the DV camcorder market, spatial resolution is a major issue-its low, light sensitivity is often exasperatingly poor, and again mounting is a problem. Canon has a new system, the XL1. I would love to hear anyone's experience with this system. Its under 5k, 3 chip with interchangeable lenses. Its a NTSC system-so don't expect much resolution wise. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. From nih-image-request@io.ece.drexel.edu Wed Aug 26 17:02 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA06730; Wed, 26 Aug 1998 17:02:19 -0400 (EDT) Resent-Date: Wed, 26 Aug 1998 17:02:19 -0400 (EDT) Message-ID: From: "Barwood, Henry" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Q: Video or digital camera? Date: Wed, 26 Aug 1998 15:47:09 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Encoding: 8 TEXT Resent-Message-ID: <"3_RXw3.0.TI1.vE7vr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/252 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 256 Does anyone know if the new camcorders with "0" lux (infrared) capability are offered in a package with "C" mount lenses? I'm curious how the IR imaging would work on a microscope. Anyone tried one of these yet? Henry Barwood Indiana Geological Survey > From nih-image-request@io.ece.drexel.edu Wed Aug 26 23:16 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id XAA08591; Wed, 26 Aug 1998 23:15:56 -0400 (EDT) Resent-Date: Wed, 26 Aug 1998 23:15:56 -0400 (EDT) Message-ID: <35E4CDA4.37658712@usa.net> Date: Wed, 26 Aug 1998 21:08:20 -0600 From: "Christopher P. Tully" Reply-To: cptully@usa.net X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Q: Video or digital camera? References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"ik0t61.0.Im1.5pCvr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/253 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2332 Jan- Video cameras are nice because they output images at ~30 frames per second (fps) which allows easy positioning and focusing of your sample on the video screen. However, the trade off is that you only get 640 x 480 pixels (slightly more if you use a PAL camera instead of NTSC). Also, there are video cameras in a wide range of prices, and functionalities. Video cameras range from monochrome to single and three chip color cameras. And some have the ability to do on-chip integration for detecting very weak signals. You also have the option of getting most cameras in cooled or uncooled versions. As for digital cameras, I am only familiar with the high end scientific cameras such as the Photometrics Sensys, and the Diagnostic Instruments Spot. These cameras are nice in that they provide a much higher resolution image (1kx1k or better) that maps 1 image pixel to one ccd pixel. However, they are SLOW (3 fps at full resolution, faster with binning, or lower resolution, but I don't think they ever get upto video rates), and they are only monochrome. There is a solution for capturing color images with the Sensys that uses an LCD filter to filter the image for RGB and capture 3 images that are then merged to form the color image, but that takes even longer, and usually requires some fiddling to get the capture times right so that the colors come out right. Finally, the biggest disadvantage for you is that they run in the $15k+ range. Unless your project truely requires the high resolution of a digital camera, a video camera will be cheaper and easier to setup and use. Chris Tully Image Processing Consultant S&M Microscopes Colorado Springs, CO Jan Kreft wrote: > > Dear all, > > we intend to buy some hardware to capture images from a phase contrast > microscope. We can't spend more than $5000 and would rather less. We have > a framegrabber anyway. Does anybody have experience with using both > digital cameras and video cameras and could comment on which method gives > the best image quality? The highest resolution? > > Many thanks, > > Jan. > > Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036 > School of Pure and Applied Biology Fax +44 1222 874305 > Cardiff University E-mail Kreft@cardiff.ac.uk > PO Box 915, Cardiff CF1 3TL, UK From nih-image-request@io.ece.drexel.edu Wed Aug 26 23:35 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id XAA10611; Wed, 26 Aug 1998 23:34:56 -0400 (EDT) Resent-Date: Wed, 26 Aug 1998 23:34:56 -0400 (EDT) Date: Wed, 26 Aug 1998 17:20:57 -1000 From: Kathleen Annikki Moore X-Sender: moorekat@uhunix5 To: nih-image@io.ece.drexel.edu Subject: Is there a PCI external device for framegrabbing available for Mac G3 powerbook? Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"leI863.0.tE2.u2Dvr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/254 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 332 Is there PCI external device for framegrabbing available for Mac G3 powerbook that is adequate for acquistion of scientific data? Are pc products such as Snappy or Nogatech Capture Vision adequate to capture scientific data? Is there an adaptor for Macs? I'm beginning any suggestions would be quite helpful. Kathleen Moore From nih-image-request@io.ece.drexel.edu Thu Aug 27 02:40 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA26919; Thu, 27 Aug 1998 02:39:56 -0400 (EDT) Resent-Date: Thu, 27 Aug 1998 02:39:56 -0400 (EDT) Message-ID: <35E4F9F0.6A0B7DA@caspur.it> Date: Thu, 27 Aug 1998 08:17:20 +0200 From: Leopoldo Silvestroni Organization: Università di Roma 'La Sapienza' X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Q: Video or digital camera? References: Content-Transfer-Encoding: 8bit Resent-Message-ID: <"vtvpq3.0.jD6.5lFvr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/255 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-1 Content-Length: 658 Henry, many commercial b/w CCD cameras are sensitive to IR. To ascertain whether yours does, simply "illuminate" the CCD with a TV controller. IR sensitivity is testified by monitor sparking (due to pulsed IR emission from controller). IR microscopy is useful to visualize biological material when photodamage produced by visible light has to be reduced. best regards, Leopoldo Silvestroni,MD -- Laboratorio di Biofluorimetria Dipartimento di Fisiopatologia Medica Policlinico Umberto I Università di Roma 'La Sapienza' 00161-Roma tel. +39 6 49970710 fax +39 6 4461450 e-mail: l.silvestroni@caspur.it WWW: http://w3.uniroma1.it/MEDICFISIO/labpag1.html From nih-image-d-request@io.ece.drexel.edu Thu Aug 27 06:14 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA16001; Thu, 27 Aug 1998 06:14:40 -0400 (EDT) Date: Thu, 27 Aug 1998 06:14:40 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808271014.GAA16001@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #45 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/45 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 10260 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 45 Today's Topics: Re: unsubscribe [ "Jared L. Rifkin" ] Re: Q: Video or digital camera? [ Jonathan Nissanov To: Subject: Re: unsubscribe Message-ID: <2B7245D57A8@qc1.qc.edu> Content-Type: text/plain; charset="US-ASCII" why did i get this msg?????????????? check your address! ------------------------------ Date: Wed, 26 Aug 1998 19:18:31 +0100 (BST) From: Jan Kreft To: nih-image@io.ece.drexel.edu Subject: Q: Video or digital camera? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, we intend to buy some hardware to capture images from a phase contrast microscope. We can't spend more than $5000 and would rather less. We have a framegrabber anyway. Does anybody have experience with using both digital cameras and video cameras and could comment on which method gives the best image quality? The highest resolution? Many thanks, Jan. Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036 School of Pure and Applied Biology Fax +44 1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK ------------------------------ Date: Wed, 26 Aug 1998 14:55:24 -0500 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Re: Q: Video or digital camera? Message-Id: Content-Type: text/plain; charset="us-ascii" >Dear all, > >we intend to buy some hardware to capture images from a phase contrast >microscope. We can't spend more than $5000 and would rather less. We have >a framegrabber anyway. Does anybody have experience with using both >digital cameras and video cameras and could comment on which method gives >the best image quality? The highest resolution? > The consumer model digital cameras have a fixed lens and so cannot be attached to a scope. Higher end professional systems consists of digital backs on SLR bodies and so, I believe could be readily mounted-you'll want an extension tube (Kodak makes models with Canon and Nikon bodies). The latter also provide manual overrides and better light meters. If you are not limited by low light intensity these provide a good system. They start at the $4k or so (Minolta RD-175) and go up to the stratosphere (20k for DCS 460-a beauty with 3kx2k pixels). On the Minolta you get a 3-chip system with the resolution achieved in part by software interpolation. Another option that is a relatively inexpensive solution, 6k, is the Leaf line camera which gives very high real resolution color images but with slow acquisition time. All these systems do not require a framegrabber. The spatial resolution you need obviously depends on application. Another concern to keep in mind is densitometric accuracy. If you are intending on performing densitometric measurements or segmentation, then consumer level systems are unlikely to be sufficiently accurate. The professional systems I suspect would do fine. A low cost monochrome solution is the Sony XC77. For 1k you get an accurate CCD camera albiet a low resolution one. Other systems exist that use the same chip and give you more electronic control. Color low cost system such as Cohu's cameras exist though have disappointing color matching-not suitable for publication. >From the DV camcorder market, spatial resolution is a major issue-its low, light sensitivity is often exasperatingly poor, and again mounting is a problem. Canon has a new system, the XL1. I would love to hear anyone's experience with this system. Its under 5k, 3 chip with interchangeable lenses. Its a NTSC system-so don't expect much resolution wise. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. ------------------------------ Date: Wed, 26 Aug 1998 15:47:09 -0500 From: "Barwood, Henry" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Q: Video or digital camera? Message-ID: Does anyone know if the new camcorders with "0" lux (infrared) capability are offered in a package with "C" mount lenses? I'm curious how the IR imaging would work on a microscope. Anyone tried one of these yet? Henry Barwood Indiana Geological Survey > ------------------------------ Date: Wed, 26 Aug 1998 21:08:20 -0600 From: "Christopher P. Tully" To: nih-image@io.ece.drexel.edu Subject: Re: Q: Video or digital camera? Message-ID: <35E4CDA4.37658712@usa.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jan- Video cameras are nice because they output images at ~30 frames per second (fps) which allows easy positioning and focusing of your sample on the video screen. However, the trade off is that you only get 640 x 480 pixels (slightly more if you use a PAL camera instead of NTSC). Also, there are video cameras in a wide range of prices, and functionalities. Video cameras range from monochrome to single and three chip color cameras. And some have the ability to do on-chip integration for detecting very weak signals. You also have the option of getting most cameras in cooled or uncooled versions. As for digital cameras, I am only familiar with the high end scientific cameras such as the Photometrics Sensys, and the Diagnostic Instruments Spot. These cameras are nice in that they provide a much higher resolution image (1kx1k or better) that maps 1 image pixel to one ccd pixel. However, they are SLOW (3 fps at full resolution, faster with binning, or lower resolution, but I don't think they ever get upto video rates), and they are only monochrome. There is a solution for capturing color images with the Sensys that uses an LCD filter to filter the image for RGB and capture 3 images that are then merged to form the color image, but that takes even longer, and usually requires some fiddling to get the capture times right so that the colors come out right. Finally, the biggest disadvantage for you is that they run in the $15k+ range. Unless your project truely requires the high resolution of a digital camera, a video camera will be cheaper and easier to setup and use. Chris Tully Image Processing Consultant S&M Microscopes Colorado Springs, CO Jan Kreft wrote: > > Dear all, > > we intend to buy some hardware to capture images from a phase contrast > microscope. We can't spend more than $5000 and would rather less. We have > a framegrabber anyway. Does anybody have experience with using both > digital cameras and video cameras and could comment on which method gives > the best image quality? The highest resolution? > > Many thanks, > > Jan. > > Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036 > School of Pure and Applied Biology Fax +44 1222 874305 > Cardiff University E-mail Kreft@cardiff.ac.uk > PO Box 915, Cardiff CF1 3TL, UK ------------------------------ Date: Wed, 26 Aug 1998 17:20:57 -1000 From: Kathleen Annikki Moore To: nih-image@io.ece.drexel.edu Subject: Is there a PCI external device for framegrabbing available for Mac G3 powerbook? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Is there PCI external device for framegrabbing available for Mac G3 powerbook that is adequate for acquistion of scientific data? Are pc products such as Snappy or Nogatech Capture Vision adequate to capture scientific data? Is there an adaptor for Macs? I'm beginning any suggestions would be quite helpful. Kathleen Moore ------------------------------ Date: Thu, 27 Aug 1998 08:17:20 +0200 From: Leopoldo Silvestroni To: nih-image@io.ece.drexel.edu Subject: Re: Q: Video or digital camera? Message-ID: <35E4F9F0.6A0B7DA@caspur.it> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Henry, many commercial b/w CCD cameras are sensitive to IR. To ascertain whether yours does, simply "illuminate" the CCD with a TV controller. IR sensitivity is testified by monitor sparking (due to pulsed IR emission from controller). IR microscopy is useful to visualize biological material when photodamage produced by visible light has to be reduced. best regards, Leopoldo Silvestroni,MD -- Laboratorio di Biofluorimetria Dipartimento di Fisiopatologia Medica Policlinico Umberto I Università di Roma 'La Sapienza' 00161-Roma tel. +39 6 49970710 fax +39 6 4461450 e-mail: l.silvestroni@caspur.it WWW: http://w3.uniroma1.it/MEDICFISIO/labpag1.html -------------------------------- End of nih-image-d Digest V98 Issue #45 *************************************** From nih-image-request@io.ece.drexel.edu Thu Aug 27 12:30 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA17472; Thu, 27 Aug 1998 12:30:37 -0400 (EDT) Resent-Date: Thu, 27 Aug 1998 12:30:37 -0400 (EDT) Message-ID: From: "Barwood, Henry" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Q: Video or digital camera? Date: Thu, 27 Aug 1998 11:17:11 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Encoding: 15 TEXT Resent-Message-ID: <"T3T_t2.0.jy3.nNOvr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/256 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 466 You wrote: >many commercial b/w CCD cameras are sensitive to IR. To ascertain whether >yours does, simply "illuminate" the CCD with a TV controller. IR sensitivity >is testified by monitor sparking (due to pulsed IR emission from >controller). > >IR microscopy is useful to visualize biological material when photodamage >produced by visible light has to be reduced. > Thanks for this advice. I'll check a few cameras and see if I can find a suitable one. Henry From nih-image-request@io.ece.drexel.edu Thu Aug 27 14:44 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA26842; Thu, 27 Aug 1998 14:44:16 -0400 (EDT) Resent-Date: Thu, 27 Aug 1998 14:44:16 -0400 (EDT) Message-ID: <35E5B402.1511@ucdavis.edu> Date: Thu, 27 Aug 1998 11:31:17 -0800 From: "S. Patricia Stock" Organization: University of California, Davis X-Mailer: Mozilla 3.02 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: set scales and callibrate Content-Transfer-Encoding: 7bit Resent-Message-ID: <"kw46D3.0.f76.wGQvr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/257 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 540 Dear NIH-Imagers: We have recntly aquire the NIH image software (Scion Image 1.62a) andf I'm trying to get familiar with it, and still need to learn a lot. However, there is a primary question to ask you. we basically need to take measurements (only length and width) and haven't been able to figure our how you callibrate and set to scale whatever I need to measure. My units should be in micrometers, but I do not know what I need to know in order to calibrate this with the pixels? I'll appreciate your help a lot!! Thanks, Patricia From nih-image-request@io.ece.drexel.edu Thu Aug 27 16:20 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA03691; Thu, 27 Aug 1998 16:19:56 -0400 (EDT) Resent-Date: Thu, 27 Aug 1998 16:19:56 -0400 (EDT) Date: Thu, 27 Aug 1998 16:04:21 -0400 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: Pausing a macro to draw a freehand ROI Resent-Message-ID: <"zW3gz2.0.jd.JlRvr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/258 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 847 Is there a way to pause in the middle of a macro, draw a freehand ROI, then continue the macro? At present, I exit the macro, draw, then start the macro again at the beginning; this leads to clumsy programming. Example: a stack of 5 images. I want to outline a cell, measure,select the next slice, outline the slightly differently bordered cell, measure, select the next slice, etc. (At present, my macro F2 PutMessages "outline a cell, then hit F3", and then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit F3, etc.) Thanks in advance, Harry Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 From nih-image-request@io.ece.drexel.edu Thu Aug 27 17:05 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA06985; Thu, 27 Aug 1998 17:05:06 -0400 (EDT) Resent-Date: Thu, 27 Aug 1998 17:05:06 -0400 (EDT) Date: Thu, 27 Aug 1998 15:00:00 -0700 From: lpaul@darcy.geo.umn.edu (Paul Morin) Message-Id: <199808272200.OAA10589@darcy.geo.umn.edu> Apparently-To: nih-image@io.ece.drexel.edu Resent-Message-ID: <"FFHUA3.0.sT1.oTSvr"@io> To: nih-image@io.ece.drexel.edu Resent-From: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/259 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 178 When I ask analyze partcles to label the particles I get images without labels on them. I'm using NIH Image 1.61/ppc. Any ideas? Paul Morin University of Minnesota Geology From nih-image-request@io.ece.drexel.edu Thu Aug 27 18:43 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA12951; Thu, 27 Aug 1998 18:43:50 -0400 (EDT) Resent-Date: Thu, 27 Aug 1998 18:43:50 -0400 (EDT) Message-Id: <3.0.5.32.19980827163118.009379f0@mailhost.nmt.edu> X-Sender: grawling@mailhost.nmt.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Thu, 27 Aug 1998 16:31:18 -0600 To: nih-image@io.ece.drexel.edu From: Geff Rawling Subject: petrographic image ssytem Mime-Version: 1.0 Resent-Message-ID: <"LnNMI1.0.Oz2.dvTvr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/260 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 873 Hi imagers, I'm a geologist looking for advice in setting up an imaging system on a Nikon petrographic microscope for quantitative analysis of textures in thin sections of porous rocks. We have about $4-5k to spend, on a camera/frame grabber combination. We need color images and as high a resolution as possible. Image analysis will be done with Scion Image on a PC. There's a thread from about three years ago on this topic, but prices and products have probably changed since then. I will be happy to summarize any info I get for the list. Thanks a lot! Geff ********************************************* Geoffrey C. Rawling Department of Earth and Environmental Science New Mexico Tech P.O. Box 2217 Socorro, NM 87801 505-835-5952 grawling@nmt.edu ********************************************* From nih-image-request@io.ece.drexel.edu Fri Aug 28 03:46 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id DAA20614; Fri, 28 Aug 1998 03:46:36 -0400 (EDT) Resent-Date: Fri, 28 Aug 1998 03:46:36 -0400 (EDT) Message-ID: <35E66CC2.1932@dv.kp.dlr.de> Date: Fri, 28 Aug 1998 09:39:30 +0100 From: Stephan Sous Organization: DLR X-Mailer: Mozilla 3.01 [de] (Macintosh; I; 68K) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Pausing a Macro Content-Transfer-Encoding: 7bit Resent-Message-ID: <"w55vO.0.on4.xubvr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/261 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2723 Dear Mr. Thomas, I am writing a macro based on the macro 'Open Files From List ....' (Input/Output-Macro, comes with NIH-Image): cut----------------------------------------------------------------- var i: integer; ListName, ImageName,spath,pa: string; function GetName(ListName: string; i: integer): string; {Returns the the ith line from a text file that has been read into a one line image named 'ListName'.} var loc, ch: integer; name: string; begin SelectWindow(ListName); loc := -1; for i := 2 to i do repeat loc := loc + 1; ch := GetPixel(loc, 0) until ch < 32; {return or linefeed} name := ''; repeat loc := loc + 1; ch := GetPixel(loc, 0); if ch >= 32 then name := concat(name, chr(ch)); until ch < 32; GetName := name; end; Macro 'Start /<'; {Opens a series of files from a list stored in a text file.} var path, FileType: string; FileSize: integer; begin ListName := 'file-list.txt'; spath:=GetPath('window'); path := concat(GetPath('window'), ListName); GetFileInfo(path, FileType, FileSize); if FileSize < 0 then begin PutMessage('The file "', ListName, '" could not be found in the same folder as images.'); exit; end; SetImport('8-bit'); SetCustom(FileSize, 1, 0); Import(path); i:=1; ImageName := GetName(ListName, i); if ImageName = '' then begin SelectWindow(ListName); close; exit; end; pa:=concat(spath,ImageName); open(pa); ShowMessage(i); SetForegroundColor(255); SelectTool('freehand'); end; Macro '(-' begin end; Macro 'Open [F1]'; begin i:=i+1; ImageName := GetName(ListName, i); if ImageName = '' then begin SelectWindow(ListName); close; exit; end; pa:=concat(spath,ImageName); open(pa); ShowMessage(i'\'pa); SetForegroundColor(255); SelectTool('freehand'); end; Macro 'Close [F2]'; begin SetSaveAs('TIFF'); pa:=concat(spath,ImageName,'Z'); SaveAs( pa); Dispose; end; cut-------------------------------------------------------------------- I hope that I understand your question right. 1. Write a text-file named 'file-list.txt'. Put in the name of your images: Image1.tif Image2.tif . . ImageN.tif 2. The macro the text-file and the images must be in the same folder. 3. Start the start-macro. At the end of this macro you can adapt parts of your own macro. 4. Start the open-macro. Here you can adapt your own macro. 5. Start the Close-macro to save the modified images (*.tifz). I hope this macro will help you. Stephan From nih-image-d-request@io.ece.drexel.edu Fri Aug 28 03:47 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id DAA20810; Fri, 28 Aug 1998 03:47:54 -0400 (EDT) Date: Fri, 28 Aug 1998 03:47:54 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808280747.DAA20810@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #46 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/46 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 8098 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 46 Today's Topics: RE: Q: Video or digital camera? [ "Barwood, Henry" ] Re: Pausing a Macro [ Stephan Sous ] ------------------------------ Date: Thu, 27 Aug 1998 11:17:11 -0500 From: "Barwood, Henry" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Q: Video or digital camera? Message-ID: You wrote: >many commercial b/w CCD cameras are sensitive to IR. To ascertain whether >yours does, simply "illuminate" the CCD with a TV controller. IR sensitivity >is testified by monitor sparking (due to pulsed IR emission from >controller). > >IR microscopy is useful to visualize biological material when photodamage >produced by visible light has to be reduced. > Thanks for this advice. I'll check a few cameras and see if I can find a suitable one. Henry ------------------------------ Date: Thu, 27 Aug 1998 11:31:17 -0800 From: "S. Patricia Stock" To: nih-image@io.ece.drexel.edu Subject: set scales and callibrate Message-ID: <35E5B402.1511@ucdavis.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear NIH-Imagers: We have recntly aquire the NIH image software (Scion Image 1.62a) andf I'm trying to get familiar with it, and still need to learn a lot. However, there is a primary question to ask you. we basically need to take measurements (only length and width) and haven't been able to figure our how you callibrate and set to scale whatever I need to measure. My units should be in micrometers, but I do not know what I need to know in order to calibrate this with the pixels? I'll appreciate your help a lot!! Thanks, Patricia ------------------------------ Date: Thu, 27 Aug 1998 16:04:21 -0400 From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) Subject: Pausing a macro to draw a freehand ROI Message-Id: Content-Type: text/plain; charset="us-ascii" Is there a way to pause in the middle of a macro, draw a freehand ROI, then continue the macro? At present, I exit the macro, draw, then start the macro again at the beginning; this leads to clumsy programming. Example: a stack of 5 images. I want to outline a cell, measure,select the next slice, outline the slightly differently bordered cell, measure, select the next slice, etc. (At present, my macro F2 PutMessages "outline a cell, then hit F3", and then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit F3, etc.) Thanks in advance, Harry Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 ------------------------------ Date: Thu, 27 Aug 1998 15:00:00 -0700 From: lpaul@darcy.geo.umn.edu (Paul Morin) To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-Id: <199808272200.OAA10589@darcy.geo.umn.edu> When I ask analyze partcles to label the particles I get images without labels on them. I'm using NIH Image 1.61/ppc. Any ideas? Paul Morin University of Minnesota Geology ------------------------------ Date: Thu, 27 Aug 1998 16:31:18 -0600 From: Geff Rawling To: nih-image@io.ece.drexel.edu Subject: petrographic image ssytem Message-Id: <3.0.5.32.19980827163118.009379f0@mailhost.nmt.edu> Content-Type: text/plain; charset="us-ascii" Hi imagers, I'm a geologist looking for advice in setting up an imaging system on a Nikon petrographic microscope for quantitative analysis of textures in thin sections of porous rocks. We have about $4-5k to spend, on a camera/frame grabber combination. We need color images and as high a resolution as possible. Image analysis will be done with Scion Image on a PC. There's a thread from about three years ago on this topic, but prices and products have probably changed since then. I will be happy to summarize any info I get for the list. Thanks a lot! Geff ********************************************* Geoffrey C. Rawling Department of Earth and Environmental Science New Mexico Tech P.O. Box 2217 Socorro, NM 87801 505-835-5952 grawling@nmt.edu ********************************************* ------------------------------ Date: Fri, 28 Aug 1998 09:39:30 +0100 From: Stephan Sous To: nih-image@io.ece.drexel.edu Subject: Re: Pausing a Macro Message-ID: <35E66CC2.1932@dv.kp.dlr.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Mr. Thomas, I am writing a macro based on the macro 'Open Files From List ....' (Input/Output-Macro, comes with NIH-Image): cut----------------------------------------------------------------- var i: integer; ListName, ImageName,spath,pa: string; function GetName(ListName: string; i: integer): string; {Returns the the ith line from a text file that has been read into a one line image named 'ListName'.} var loc, ch: integer; name: string; begin SelectWindow(ListName); loc := -1; for i := 2 to i do repeat loc := loc + 1; ch := GetPixel(loc, 0) until ch < 32; {return or linefeed} name := ''; repeat loc := loc + 1; ch := GetPixel(loc, 0); if ch >= 32 then name := concat(name, chr(ch)); until ch < 32; GetName := name; end; Macro 'Start /<'; {Opens a series of files from a list stored in a text file.} var path, FileType: string; FileSize: integer; begin ListName := 'file-list.txt'; spath:=GetPath('window'); path := concat(GetPath('window'), ListName); GetFileInfo(path, FileType, FileSize); if FileSize < 0 then begin PutMessage('The file "', ListName, '" could not be found in the same folder as images.'); exit; end; SetImport('8-bit'); SetCustom(FileSize, 1, 0); Import(path); i:=1; ImageName := GetName(ListName, i); if ImageName = '' then begin SelectWindow(ListName); close; exit; end; pa:=concat(spath,ImageName); open(pa); ShowMessage(i); SetForegroundColor(255); SelectTool('freehand'); end; Macro '(-' begin end; Macro 'Open [F1]'; begin i:=i+1; ImageName := GetName(ListName, i); if ImageName = '' then begin SelectWindow(ListName); close; exit; end; pa:=concat(spath,ImageName); open(pa); ShowMessage(i'\'pa); SetForegroundColor(255); SelectTool('freehand'); end; Macro 'Close [F2]'; begin SetSaveAs('TIFF'); pa:=concat(spath,ImageName,'Z'); SaveAs( pa); Dispose; end; cut-------------------------------------------------------------------- I hope that I understand your question right. 1. Write a text-file named 'file-list.txt'. Put in the name of your images: Image1.tif Image2.tif . . ImageN.tif 2. The macro the text-file and the images must be in the same folder. 3. Start the start-macro. At the end of this macro you can adapt parts of your own macro. 4. Start the open-macro. Here you can adapt your own macro. 5. Start the Close-macro to save the modified images (*.tifz). I hope this macro will help you. Stephan -------------------------------- End of nih-image-d Digest V98 Issue #46 *************************************** From nih-image-request@io.ece.drexel.edu Fri Aug 28 07:54 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA09860; Fri, 28 Aug 1998 07:54:13 -0400 (EDT) Resent-Date: Fri, 28 Aug 1998 07:54:13 -0400 (EDT) From: "j.gregory" Sender: ort056@abdn.ac.uk To: nih-image@io.ece.drexel.edu Message-ID: Date: Fri, 28 Aug 1998 12:39:21 +0100 (BST) Delivery-Receipt-To: "j.gregory" Priority: NORMAL X-Mailer: Simeon for Windows Version 4.0.9 X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"iFiNU1.0.Vs1.7Jfvr"@io> Resent-From: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/262 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 574 Is there a way to import masks, or tiffs with saved masks into Scion / Nih-Image from other applications such as Adobe Photoshop or Photostyler? I know it is possible to use masks / ROI's in Scion / NIH, but drawing them is tricky & clumsy & I find it easier & more accurate to use the magnetic lasso tool to select the areas I want to measure. Also are there any ways to change the cursor style from the crosshair as I find an arrow easier to use when selecting a region of the image Thanks in advance, Jenny Gregory ---------------------- j.gregory@abdn.ac.uk From nih-image-request@io.ece.drexel.edu Fri Aug 28 12:22 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA29051; Fri, 28 Aug 1998 12:20:43 -0400 (EDT) Resent-Date: Fri, 28 Aug 1998 12:20:43 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Fri, 28 Aug 1998 11:07:37 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Re: Pausing a macro to draw a freehand ROI Resent-Message-ID: <"DMTPC3.0.8t6.INjvr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/263 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1835 >Is there a way to pause in the middle of a macro, draw a freehand ROI, then >continue the macro? At present, I exit the macro, draw, then start the >macro again at the beginning; this leads to clumsy programming. > >Example: a stack of 5 images. I want to outline a cell, measure,select the >next slice, outline the slightly differently bordered cell, measure, select >the next slice, etc. >(At present, my macro F2 PutMessages "outline a cell, then hit F3", and >then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit >F3, etc.) Here is a macro to do it. incorporate it as a routine or in the body of your macro. macro 'draw' var origx,oldx,origy,oldy,x,y:integer; begin WaitForTrigger; getMouse(oldx,oldy); origx:=oldx; origy:=oldy; While button do begin getMouse(x,y); moveto(oldx,oldy); LineTo(x,y); oldx:=x; oldy:=y; end; LineTo(origx,origy); end; -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. From nih-image-request@io.ece.drexel.edu Fri Aug 28 16:51 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA14545; Fri, 28 Aug 1998 16:51:17 -0400 (EDT) Resent-Date: Fri, 28 Aug 1998 16:51:17 -0400 (EDT) Message-ID: <35E75D48.3A0D@pro.via-rs.com.br> Date: Fri, 28 Aug 1998 17:45:45 -0800 From: Luthero Martins Reply-To: luthero@pro.via-rs.com.br X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Q: Video or digital camera? References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"vgFjK2.0.7L3.SLnvr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/264 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 757 You can use a video camera Sony 3CCD and digital frame grabber MiroDC20, and software Adobe Premiere. Jan Kreft wrote: > > Dear all, > > we intend to buy some hardware to capture images from a phase contrast > microscope. We can't spend more than $5000 and would rather less. We have > a framegrabber anyway. Does anybody have experience with using both > digital cameras and video cameras and could comment on which method gives > the best image quality? The highest resolution? > > Many thanks, > > Jan. > > Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036 > School of Pure and Applied Biology Fax +44 1222 874305 > Cardiff University E-mail Kreft@cardiff.ac.uk > PO Box 915, Cardiff CF1 3TL, UK From nih-image-request@io.ece.drexel.edu Sat Aug 29 02:34 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA26241; Sat, 29 Aug 1998 02:34:24 -0400 (EDT) Resent-Date: Sat, 29 Aug 1998 02:34:24 -0400 (EDT) From: SolamereTG@aol.com Message-ID: > Date: Sat, 29 Aug 1998 02:23:52 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: control macro for a Sony U-matic? Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 78 Resent-Message-ID: <"SCn23.0.P96.Wwvvr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/265 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 195 Does anyone know where I could find an NIH macro that controls a Sony VO-9600 U-matic VCR recorder over the serial port. Off/on/play/record would be enough. Thanks in advance George A. Peeters From nih-image-d-request@io.ece.drexel.edu Sat Aug 29 02:38 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA26653; Sat, 29 Aug 1998 02:38:21 -0400 (EDT) Date: Sat, 29 Aug 1998 02:38:21 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808290638.CAA26653@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #47 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/47 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 5064 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 47 Today's Topics: Unidentified subject! [ "j.gregory" ] Re: Pausing a macro to draw a freeha [ Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Is there a way to import masks, or tiffs with saved masks into Scion / Nih-Image from other applications such as Adobe Photoshop or Photostyler? I know it is possible to use masks / ROI's in Scion / NIH, but drawing them is tricky & clumsy & I find it easier & more accurate to use the magnetic lasso tool to select the areas I want to measure. Also are there any ways to change the cursor style from the crosshair as I find an arrow easier to use when selecting a region of the image Thanks in advance, Jenny Gregory ---------------------- j.gregory@abdn.ac.uk ------------------------------ Date: Fri, 28 Aug 1998 11:07:37 -0500 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Re: Pausing a macro to draw a freehand ROI Message-Id: Content-Type: text/plain; charset="us-ascii" >Is there a way to pause in the middle of a macro, draw a freehand ROI, then >continue the macro? At present, I exit the macro, draw, then start the >macro again at the beginning; this leads to clumsy programming. > >Example: a stack of 5 images. I want to outline a cell, measure,select the >next slice, outline the slightly differently bordered cell, measure, select >the next slice, etc. >(At present, my macro F2 PutMessages "outline a cell, then hit F3", and >then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit >F3, etc.) Here is a macro to do it. incorporate it as a routine or in the body of your macro. macro 'draw' var origx,oldx,origy,oldy,x,y:integer; begin WaitForTrigger; getMouse(oldx,oldy); origx:=oldx; origy:=oldy; While button do begin getMouse(x,y); moveto(oldx,oldy); LineTo(x,y); oldx:=x; oldy:=y; end; LineTo(origx,origy); end; -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. ------------------------------ Date: Fri, 28 Aug 1998 17:45:45 -0800 From: Luthero Martins To: nih-image@io.ece.drexel.edu Subject: Re: Q: Video or digital camera? Message-ID: <35E75D48.3A0D@pro.via-rs.com.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit You can use a video camera Sony 3CCD and digital frame grabber MiroDC20, and software Adobe Premiere. Jan Kreft wrote: > > Dear all, > > we intend to buy some hardware to capture images from a phase contrast > microscope. We can't spend more than $5000 and would rather less. We have > a framegrabber anyway. Does anybody have experience with using both > digital cameras and video cameras and could comment on which method gives > the best image quality? The highest resolution? > > Many thanks, > > Jan. > > Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036 > School of Pure and Applied Biology Fax +44 1222 874305 > Cardiff University E-mail Kreft@cardiff.ac.uk > PO Box 915, Cardiff CF1 3TL, UK ------------------------------ Date: Sat, 29 Aug 1998 02:23:52 EDT From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: control macro for a Sony U-matic? Message-ID: > Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Does anyone know where I could find an NIH macro that controls a Sony VO-9600 U-matic VCR recorder over the serial port. Off/on/play/record would be enough. Thanks in advance George A. Peeters -------------------------------- End of nih-image-d Digest V98 Issue #47 *************************************** From nih-image-request@io.ece.drexel.edu Sat Aug 29 18:01 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id SAA10532; Sat, 29 Aug 1998 18:01:20 -0400 (EDT) Resent-Date: Sat, 29 Aug 1998 18:01:20 -0400 (EDT) Date: Sat, 29 Aug 1998 17:51:19 -0400 (EDT) From: Sushant Agarwal X-Sender: sushant@ds5500 To: nih-image@io.ece.drexel.edu Subject: Gray scale microscopy- suggestions? In-Reply-To: <199808290638.CAA26703@io.ECE.Drexel.EDU> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"SErKQ2.0.LK2.zV7wr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/266 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 780 Hello Folks, I am planning to purchase a digital image aquisition and analysis system which I can use with my microscope. Rightnow I have come across Scion Corporations' Gray scale Microscopy System Pr-GMS300 CCIR, which appears adequate for my purpose and seems to have reasonable price also. Does anyone of you have any experience with this particular system? I would really appreciate your input on this subject. I need this system to analyze micron size particles and thier agglomerates. Analysis part will include size measurement, particle counting etc. thanks a lot, hope to hear from you, Sushant Agarwal (sushant@ds5500.cemr.wvu.edu) Graduate Research Assistant Room # 453, P. O. Box 6102 Chemical Engineering Department West Virginia University, Morgantown, WV 26506 From nih-image-d-request@io.ece.drexel.edu Mon Aug 31 06:13 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA19909; Mon, 31 Aug 1998 06:13:56 -0400 (EDT) Date: Mon, 31 Aug 1998 06:13:56 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199808311013.GAA19909@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #48 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/48 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1402 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 48 Today's Topics: Gray scale microscopy- suggestions? [ Sushant Agarwal To: nih-image@io.ece.drexel.edu Subject: Gray scale microscopy- suggestions? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Folks, I am planning to purchase a digital image aquisition and analysis system which I can use with my microscope. Rightnow I have come across Scion Corporations' Gray scale Microscopy System Pr-GMS300 CCIR, which appears adequate for my purpose and seems to have reasonable price also. Does anyone of you have any experience with this particular system? I would really appreciate your input on this subject. I need this system to analyze micron size particles and thier agglomerates. Analysis part will include size measurement, particle counting etc. thanks a lot, hope to hear from you, Sushant Agarwal (sushant@ds5500.cemr.wvu.edu) Graduate Research Assistant Room # 453, P. O. Box 6102 Chemical Engineering Department West Virginia University, Morgantown, WV 26506 -------------------------------- End of nih-image-d Digest V98 Issue #48 *************************************** From nih-image-request@io.ece.drexel.edu Mon Aug 31 08:33 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA02975; Mon, 31 Aug 1998 08:33:24 -0400 (EDT) Resent-Date: Mon, 31 Aug 1998 08:33:24 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 31 Aug 1998 08:20:41 -0400 To: hmthomas@med.cornell.edu (Henry M. Thomas) From: Laird Bloom Subject: Re: Pausing a macro to draw a freehand ROI Cc: nih-image@io.ece.drexel.edu Resent-Message-ID: <"ZNeWD.0.mH.ZGfwr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/267 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 7517 Henry, I have used a fairly simple solution to this problem--although it may be clumsy programming--in several macros. Essentially, I write the macro in a way that expects there to be an open image file at the start, and then after doing the measurement procedures, closes or saves the current image and opens the next one. I also set up the macro so I can start it with a single keystroke (using [x] in the macro title, where x is a single key). That way it's fairly straightforward to draw your ROI and press a key, then have the computer do measurements and open your next slice for you. I often do this in conjunction with two other macros, one to set initial parameters (type of measurements, name of file for saving results, etc.) and open the first image, the other to analyze the data in the results file after the individual images have been measured. Below is an example we use for capturing live video images and measuring the areas of a number of freehand ROIs from each of a number of images, then saving each area in a file. In this case, the "Measure Area[M]" macro is used multiple times for multiple ROIs in a single image, and then theTimes 'New view of current sample [v]' macro gets rid of the current image and has the computer acquire a new one, using the GetImageToMeasure procedure. Like the old VW ads: it's ugly, but it gets you there. Good luck. Laird Bloom MIT Center for Cancer Research Times{ We use Scion Image 1.62, essentially the same as NIH Image 1.61. You may need to modify the StartCapturing and StopCapturing commands if the "measure areas on scope" macro, depending on the source of your input. Excerpt from lab protocol book precedes the macro code. "Measure areas on scope" macro It is sometimes convenient to measure areas on many parts of a sample without having to save each image and reopen it. To do this and save the areas as a set of numbers suitable for import into Excel, load the "Measure areas on scope" macro file. Data are saved as a single column of numbers for each sample, which can be copied and pasted into a single column in Excel. To start, be sure to close the video camera window. Then type P or pull down the "Set up measurement parameters" macro. It will ask you whether you want to save each image before and after labeling areas, and then it will ask you for the name of your first sample and begin showing live video images. When you have found the image you want, click the mouse button or press the shift, option, or control keys. (You may have to hold the key or mouse button down for a fraction of a second or push it a second time.) Then select a drawing tool, draw around an area you wish to measure, and press the M key when you're ready. The area of each region in pixels (this can be changed to mm, etc from the pulldown menus) will show up in a text file on the right of the screen and is saved after each entry. Be careful if you modify this file while adding data to it (e.g., if the font is too large to let you see all your data); if the text is still highlighted when you measure your next area, all of the highlighted data will be deleted (based on sad but true experience). Keep drawing and pressing M until you're done with that image. Then press V (or pull down "New view of this sample" macro), get your next image, and continue. To score another sample (and save the counts in a new file), press S or pull down "Score next sample" macro. You can open this file in Excel, or copy and paste as a single column into a single Excel file for all of you data (more convenient).} {"Measure areas on scope" macro file follows: modified area measurement macro--use while measuring areas while at microscope. Saves data for each sample in a separate file as a column of numbers; import into Excel for analysis. } var {Global variables} n,d,nLines,j,total,TotalArea:integer; mean:real; SaveMod,nSave,nSample,SampleName,ImageName:string; procedure GetImageToMeasure; begin StartCapturing; Repeat Wait(.1); Until Button or KeyDown('shift') or KeyDown('option') or KeyDown('control'); StopCapturing; SetPicName(nSample,' Image'); SelectWindow(nSample,' Image'); if nSave='Yes' then Save; end procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetBackgroundColor(1); SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('With Background'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nSample); If j=1 then writeln (nSample); SetFont('Times'); SetFontSize(12); Writeln(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set parameters for area measurements [P]'; var width,height:integer; begin nSave:=GetString('Save each image as a 1.2 MB file?','Yes'); SaveMod:=GetString('Save each image with areas marked?','Yes'); nSample:=GetString('name of first sample'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; macro 'New view of current sample [v]'; begin SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); DisposeAll; GetImageToMeasure; end; macro 'New Sample [S]'; begin If j=0 then j:=1; SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); Dispose; SelectWindow(nSample); mean:=total/j; writeln('Mean ='); write(mean); save; dispose; nSample:=GetString('Name of next sample:'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; >Is there a way to pause in the middle of a macro, draw a freehand ROI, then >continue the macro? At present, I exit the macro, draw, then start the >macro again at the beginning; this leads to clumsy programming. > >Example: a stack of 5 images. I want to outline a cell, measure,select the >next slice, outline the slightly differently bordered cell, measure, select >the next slice, etc. >(At present, my macro F2 PutMessages "outline a cell, then hit F3", and >then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit >F3, etc.) >Thanks in advance, Harry > >Henry M. Thomas, III MD (Harry) >Professor of Clinical Medicine, Pulmonary and Critical Care Division >Department of Medicine, Cornell Univ. Medical School >Director, Pulmonary Research, Burke Rehabilitation Hospital >785 Mamaroneck Ave. White Plains, NY 10605 >(914) 597-2141 From nih-image-request@io.ece.drexel.edu Mon Aug 31 08:52 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA04954; Mon, 31 Aug 1998 08:52:02 -0400 (EDT) Resent-Date: Mon, 31 Aug 1998 08:52:02 -0400 (EDT) Message-Id: <3.0.5.32.19980831153838.007c9da0@mail.biu.ac.il> X-Sender: goldst@mail.biu.ac.il X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Mon, 31 Aug 1998 15:38:38 +0300 To: nih-image@io.ece.drexel.edu From: "Dr. Ron Goldstein" Subject: integration of dim fluorescent signals Mime-Version: 1.0 Resent-Message-ID: <"n22iW3.0.Bu.9cfwr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/268 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1399 Hi, I have been having trouble figuring out how to use the integration function of the Averaging menu in Image. I am aquiring dim fluorescence images, and do not have on chip integration, or a mathematical grabber (I'm using the Scion LG-3). I do not think that I want the program to automatically scale the sum of the multiple frames linearly to 0-255 as it does by default. In Image Pro, integration is intuitive, one sets how many frames are to be captured, and what number to divided the integrated result by. For example, if I want an image that "holds the shutter open" twice as long, I would tell the program to capture 8 frames, and divide the resulting values by four. The resulting image gives a brighter signal, and with some playing with the contrast, the increased background can be reduced (or subtracted using an image of an empty area of the specimen). In Image, to do the same thing it seems that one must use the "Fix Scale" dialog, is that correct? How would one obtain the "holding the camera shutter open" that I described before using this method? Thanks, -Ron -------------------------------------------------------- Dr. Ron Goldstein email goldst@mail.biu.ac.il Dept. Life Sciences Tel. 972-3-531-8216 Bar-Ilan Univ FAX 972-3-535-1824 52900 Ramat-Gan, ISRAEL http://www.biu.ac.il/NAT/ls/goldstein.html From nih-image-request@io.ece.drexel.edu Mon Aug 31 10:32 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA14150; Mon, 31 Aug 1998 10:32:36 -0400 (EDT) Resent-Date: Mon, 31 Aug 1998 10:32:36 -0400 (EDT) Message-Id: <3.0.4.32.19980831101943.00b41388@130.91.91.1> X-Sender: lewis@130.91.91.1 X-Mailer: QUALCOMM Windows Eudora Light Plus Version 3.0.4 (32) with Spelling Checker Date: Mon, 31 Aug 1998 10:19:43 -0400 To: nih-image@io.ece.drexel.edu From: "Linda J. Lewis" Subject: writing macros Cc: bldallap@vet.upenn.edu Mime-Version: 1.0 Resent-Message-ID: <"cPO3Q3.0.cz2.Yygwr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/269 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1979 Hello, I have been asked to write a macro for some clinicians here at our vet hospital. I am unfamiliar with NIH Image (the person who was supposed to do this is no longer here). I have had Pascal and the language doesn't look too bad but I'm not sure exactly how much detail I need to go into for the user interface. This is what they are looking to accomplish: For each slide: For i=1:? captures per slide: (the whole slide isn't visible at once) Measure the perimeter (let's call it p(i)) Measure the bone value (let's call it b(i)) Measure the amt near growth plate (if any) (let's call it g(i)) Calculate the amount of no bone formation (p(i) - b(i)) (let's call it n(i)) Save the image onto a disk Sum up measurements for all the captures per slide: For i=1:? psum=psum + p(i) bsum=bsum + b(i) gsum=gsum + g(i) nsum=nsum + n(i) Calculate the % bone formation, let's call it f: f = bsum/psum Calculate the % no bone formation near growth plate (let's call it ng): ng = gsum/nsum After all the slides, export the data to an excel file. Writing macros to do the calculations doesn't seem to be difficult. Do I have to write a user interface so that they can signify what measurements to use (ie. they make a mistake and measure the perimeter again) and to signal when each slide is finished? All the macros I've seen don't appear to do this. If you can give me any insight, I'd appreciate it. And of course, we need this asap. Thanks in advance. ljl ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Linda J. Lewis New Bolton Center On-Site Support For help at NBC: call ext. HELP send email to help@vet.upenn.edu or browse http://www.vet.upenn.edu/help New Bolton Center University of Pennsylvania, School of Veterinary Medicine 382 W. Street Road Kennett Square, PA 19348-1692 610-444-5800 x2482 fax 610-444-4724 email: lewis@vet.upenn.edu From nih-image-request@io.ece.drexel.edu Mon Aug 31 12:31 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA23182; Mon, 31 Aug 1998 12:31:55 -0400 (EDT) Resent-Date: Mon, 31 Aug 1998 12:31:55 -0400 (EDT) Message-Id: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> X-Sender: billb@neuro.duke.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Mon, 31 Aug 1998 12:16:48 -0400 To: nih-image@io.ece.drexel.edu From: Bill Bosking Subject: Code Warrior Pro 3 Mime-Version: 1.0 Resent-Message-ID: <"vrSWL2.0.jN5.soiwr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/270 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 991 Wayne/others: Currently, I am using CodeWarrior Academic Pro 11 for the Macintosh to compile Image 1.62b4 source code. I looked on the Image home page and found there was a version 1.62b20 for Code Warrior Pro 2. I recently bought Code Warrior Pro 3 which I installed on a Windows 95 machine. I was wondering if there was any version of the Image source code that would compile using Code Warrior Pro 3 (or if there isn't one now if there might be one in the near future). In addition, since Code Warrior Pro 3 allows you to compile projects for multiple targets, will it ever be possible to obtain source code that I could use with Code Warrior Pro 3 to compile a version of Image to run on a Windows machine? Sorry for being greedy, but a version of the source code that would allow me to compile an extended version of Image for a Windows machine would be of great value to me (and I assume to others as well). Bill Bosking billb@neuro.duke.edu 919-684-8510 phone 919-684-4431 FAX From nih-image-request@io.ece.drexel.edu Tue Sep 1 00:30 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id AAA13619; Tue, 1 Sep 1998 00:30:06 -0400 (EDT) Resent-Date: Tue, 1 Sep 1998 00:30:06 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: goldst@mail.biu.ac.il, nih-image@io.ece.drexel.edu Date: Tue, 1 Sep 1998 14:23:13 GMT+1000 Subject: Re: integration of dim fluorescent signals Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <761767A26AC@rna.bio.mq.edu.au> Resent-Message-ID: <"ZnGVR.0.453.gOtwr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/271 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 3542 >Date: Mon, 31 Aug 1998 15:38:38 +0300 >To: nih-image@io.ece.drexel.edu >From: "Dr. Ron Goldstein" >Subject: integration of dim fluorescent signals > >I have been having trouble figuring out how to use the integration function >of the Averaging menu in Image. I am aquiring dim fluorescence images, and >do not have on chip integration, or a mathematical grabber (I'm using the >Scion LG-3). I do not think that I want the program to automatically scale >the sum of the multiple frames linearly to 0-255 as it does by default. > >In Image Pro, integration is intuitive, one sets how many frames are to be >captured, and what number to divided the integrated result by. For example, >if I want an image that "holds the shutter open" twice as long, I would >tell the program to capture 8 frames, and divide the resulting values by >four. The resulting image gives a brighter signal, and with some playing >with the contrast, the increased background can be reduced (or subtracted >using an image of an empty area of the specimen). > >In Image, to do the same thing it seems that one must use the "Fix Scale" >dialog, is that correct? How would one obtain the "holding the camera >shutter open" that I described before using this method? > >Thanks, > >-Ron >-------------------------------------------------------- >Dr. Ron Goldstein email goldst@mail.biu.ac.il >Dept. Life Sciences Tel. 972-3-531-8216 >Bar-Ilan Univ FAX 972-3-535-1824 >52900 Ramat-Gan, ISRAEL >http://www.biu.ac.il/NAT/ls/goldstein.html > If you captured n images with the integration box checked, you would also see min=, max=,and timing information recorded in the "Info" window. These give the range of the actual (integrated) sum of pixel values as stored in the intermediate temporary real image which would then be scaled to set max=254, min=1 (not 255,0). Using "Fix Scale" your own offset and scale values are used. For n=8, the maximum accumulated pixel value would be 256n = 2048 so "Fix Scale",0,1024 would achieve your requested result. In practice you would probably find a non-zero minimum (which you can read off the Info window. (Re)Entry of the values min,min+1024 would then result in better contrast. Better still, inspect the histogram of the captured integrated image to see where the "real" max/min are ie the range of interest excluding backround, outliers or highlights. It is then practical (if not always straight forward) to set min/max values to maximising useful contrast in converting from the internal real value image to the 8 bit result. You can test this at the macro level by imageing print on paper ("black" on "white") with integration checked. With video controls gain/offset set correctly (or regardless) and "Fix Scale" not checked, the histogram should range 1-254 (0,255 vacant). ShowHistogram should then enable you to see the histogram pixel range which corresponds to the "white" paper. Select a ROI which excludes text (ie white paper only) and capture again. The Info window will report the min/max of the integrated ROI ie paper only. Feeding these values back into a "Fix Scale" integration will give you a high contrast image of the "white" paper (with the print saturated black and effectively ignored in this contrast range). Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Tue Sep 1 00:32 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id AAA13915; Tue, 1 Sep 1998 00:32:35 -0400 (EDT) Date: Tue, 1 Sep 1998 00:32:35 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809010432.AAA13915@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #49 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/49 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 17535 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 49 Today's Topics: Re: Pausing a macro to draw a freeha [ Laird Bloom ] integration of dim fluorescent signa [ "Dr. Ron Goldstein" ] Re: integration of dim fluorescent s [ GJOSS@rna.bio.mq.edu.au ] ------------------------------ Date: Mon, 31 Aug 1998 08:20:41 -0400 From: Laird Bloom To: hmthomas@med.cornell.edu (Henry M. Thomas) Cc: nih-image@io.ece.drexel.edu Subject: Re: Pausing a macro to draw a freehand ROI Message-Id: Content-Type: text/enriched; charset="us-ascii" Henry, I have used a fairly simple solution to this problem--although it may be clumsy programming--in several macros. Essentially, I write the macro in a way that expects there to be an open image file at the start, and then after doing the measurement procedures, closes or saves the current image and opens the next one. I also set up the macro so I can start it with a single keystroke (using [x] in the macro title, where x is a single key). That way it's fairly straightforward to draw your ROI and press a key, then have the computer do measurements and open your next slice for you. I often do this in conjunction with two other macros, one to set initial parameters (type of measurements, name of file for saving results, etc.) and open the first image, the other to analyze the data in the results file after the individual images have been measured. Below is an example we use for capturing live video images and measuring the areas of a number of freehand ROIs from each of a number of images, then saving each area in a file. In this case, the "Measure Area[M]" macro is used multiple times for multiple ROIs in a single image, and then theTimes 'New view of current sample [v]' macro gets rid of the current image and has the computer acquire a new one, using the GetImageToMeasure procedure. Like the old VW ads: it's ugly, but it gets you there. Good luck. Laird Bloom MIT Center for Cancer Research Times{ We use Scion Image 1.62, essentially the same as NIH Image 1.61. You may need to modify the StartCapturing and StopCapturing commands if the "measure areas on scope" macro, depending on the source of your input. Excerpt from lab protocol book precedes the macro code. "Measure areas on scope" macro It is sometimes convenient to measure areas on many parts of a sample without having to save each image and reopen it. To do this and save the areas as a set of numbers suitable for import into Excel, load the "Measure areas on scope" macro file. Data are saved as a single column of numbers for each sample, which can be copied and pasted into a single column in Excel. To start, be sure to close the video camera window. Then type P or pull down the "Set up measurement parameters" macro. It will ask you whether you want to save each image before and after labeling areas, and then it will ask you for the name of your first sample and begin showing live video images. When you have found the image you want, click the mouse button or press the shift, option, or control keys. (You may have to hold the key or mouse button down for a fraction of a second or push it a second time.) Then select a drawing tool, draw around an area you wish to measure, and press the M key when you're ready. The area of each region in pixels (this can be changed to mm, etc from the pulldown menus) will show up in a text file on the right of the screen and is saved after each entry. Be careful if you modify this file while adding data to it (e.g., if the font is too large to let you see all your data); if the text is still highlighted when you measure your next area, all of the highlighted data will be deleted (based on sad but true experience). Keep drawing and pressing M until you're done with that image. Then press V (or pull down "New view of this sample" macro), get your next image, and continue. To score another sample (and save the counts in a new file), press S or pull down "Score next sample" macro. You can open this file in Excel, or copy and paste as a single column into a single Excel file for all of you data (more convenient).} {"Measure areas on scope" macro file follows: modified area measurement macro--use while measuring areas while at microscope. Saves data for each sample in a separate file as a column of numbers; import into Excel for analysis. } var {Global variables} n,d,nLines,j,total,TotalArea:integer; mean:real; SaveMod,nSave,nSample,SampleName,ImageName:string; procedure GetImageToMeasure; begin StartCapturing; Repeat Wait(.1); Until Button or KeyDown('shift') or KeyDown('option') or KeyDown('control'); StopCapturing; SetPicName(nSample,' Image'); SelectWindow(nSample,' Image'); if nSave='Yes' then Save; end procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetBackgroundColor(1); SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('With Background'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nSample); If j=1 then writeln (nSample); SetFont('Times'); SetFontSize(12); Writeln(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set parameters for area measurements [P]'; var width,height:integer; begin nSave:=GetString('Save each image as a 1.2 MB file?','Yes'); SaveMod:=GetString('Save each image with areas marked?','Yes'); nSample:=GetString('name of first sample'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; macro 'New view of current sample [v]'; begin SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); DisposeAll; GetImageToMeasure; end; macro 'New Sample [S]'; begin If j=0 then j:=1; SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); Dispose; SelectWindow(nSample); mean:=total/j; writeln('Mean ='); write(mean); save; dispose; nSample:=GetString('Name of next sample:'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; >Is there a way to pause in the middle of a macro, draw a freehand ROI, then >continue the macro? At present, I exit the macro, draw, then start the >macro again at the beginning; this leads to clumsy programming. > >Example: a stack of 5 images. I want to outline a cell, measure,select the >next slice, outline the slightly differently bordered cell, measure, select >the next slice, etc. >(At present, my macro F2 PutMessages "outline a cell, then hit F3", and >then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit >F3, etc.) >Thanks in advance, Harry > >Henry M. Thomas, III MD (Harry) >Professor of Clinical Medicine, Pulmonary and Critical Care Division >Department of Medicine, Cornell Univ. Medical School >Director, Pulmonary Research, Burke Rehabilitation Hospital >785 Mamaroneck Ave. White Plains, NY 10605 >(914) 597-2141 ------------------------------ Date: Mon, 31 Aug 1998 15:38:38 +0300 From: "Dr. Ron Goldstein" To: nih-image@io.ece.drexel.edu Subject: integration of dim fluorescent signals Message-Id: <3.0.5.32.19980831153838.007c9da0@mail.biu.ac.il> Content-Type: text/plain; charset="us-ascii" Hi, I have been having trouble figuring out how to use the integration function of the Averaging menu in Image. I am aquiring dim fluorescence images, and do not have on chip integration, or a mathematical grabber (I'm using the Scion LG-3). I do not think that I want the program to automatically scale the sum of the multiple frames linearly to 0-255 as it does by default. In Image Pro, integration is intuitive, one sets how many frames are to be captured, and what number to divided the integrated result by. For example, if I want an image that "holds the shutter open" twice as long, I would tell the program to capture 8 frames, and divide the resulting values by four. The resulting image gives a brighter signal, and with some playing with the contrast, the increased background can be reduced (or subtracted using an image of an empty area of the specimen). In Image, to do the same thing it seems that one must use the "Fix Scale" dialog, is that correct? How would one obtain the "holding the camera shutter open" that I described before using this method? Thanks, -Ron -------------------------------------------------------- Dr. Ron Goldstein email goldst@mail.biu.ac.il Dept. Life Sciences Tel. 972-3-531-8216 Bar-Ilan Univ FAX 972-3-535-1824 52900 Ramat-Gan, ISRAEL http://www.biu.ac.il/NAT/ls/goldstein.html ------------------------------ Date: Mon, 31 Aug 1998 10:19:43 -0400 From: "Linda J. Lewis" To: nih-image@io.ece.drexel.edu Cc: bldallap@vet.upenn.edu Subject: writing macros Message-Id: <3.0.4.32.19980831101943.00b41388@130.91.91.1> Content-Type: text/plain; charset="us-ascii" Hello, I have been asked to write a macro for some clinicians here at our vet hospital. I am unfamiliar with NIH Image (the person who was supposed to do this is no longer here). I have had Pascal and the language doesn't look too bad but I'm not sure exactly how much detail I need to go into for the user interface. This is what they are looking to accomplish: For each slide: For i=1:? captures per slide: (the whole slide isn't visible at once) Measure the perimeter (let's call it p(i)) Measure the bone value (let's call it b(i)) Measure the amt near growth plate (if any) (let's call it g(i)) Calculate the amount of no bone formation (p(i) - b(i)) (let's call it n(i)) Save the image onto a disk Sum up measurements for all the captures per slide: For i=1:? psum=psum + p(i) bsum=bsum + b(i) gsum=gsum + g(i) nsum=nsum + n(i) Calculate the % bone formation, let's call it f: f = bsum/psum Calculate the % no bone formation near growth plate (let's call it ng): ng = gsum/nsum After all the slides, export the data to an excel file. Writing macros to do the calculations doesn't seem to be difficult. Do I have to write a user interface so that they can signify what measurements to use (ie. they make a mistake and measure the perimeter again) and to signal when each slide is finished? All the macros I've seen don't appear to do this. If you can give me any insight, I'd appreciate it. And of course, we need this asap. Thanks in advance. ljl ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Linda J. Lewis New Bolton Center On-Site Support For help at NBC: call ext. HELP send email to help@vet.upenn.edu or browse http://www.vet.upenn.edu/help New Bolton Center University of Pennsylvania, School of Veterinary Medicine 382 W. Street Road Kennett Square, PA 19348-1692 610-444-5800 x2482 fax 610-444-4724 email: lewis@vet.upenn.edu ------------------------------ Date: Mon, 31 Aug 1998 12:16:48 -0400 From: Bill Bosking To: nih-image@io.ece.drexel.edu Subject: Code Warrior Pro 3 Message-Id: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Content-Type: text/plain; charset="us-ascii" Wayne/others: Currently, I am using CodeWarrior Academic Pro 11 for the Macintosh to compile Image 1.62b4 source code. I looked on the Image home page and found there was a version 1.62b20 for Code Warrior Pro 2. I recently bought Code Warrior Pro 3 which I installed on a Windows 95 machine. I was wondering if there was any version of the Image source code that would compile using Code Warrior Pro 3 (or if there isn't one now if there might be one in the near future). In addition, since Code Warrior Pro 3 allows you to compile projects for multiple targets, will it ever be possible to obtain source code that I could use with Code Warrior Pro 3 to compile a version of Image to run on a Windows machine? Sorry for being greedy, but a version of the source code that would allow me to compile an extended version of Image for a Windows machine would be of great value to me (and I assume to others as well). Bill Bosking billb@neuro.duke.edu 919-684-8510 phone 919-684-4431 FAX ------------------------------ Date: Tue, 1 Sep 1998 14:23:13 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: goldst@mail.biu.ac.il, nih-image@io.ece.drexel.edu Subject: Re: integration of dim fluorescent signals Message-ID: <761767A26AC@rna.bio.mq.edu.au> >Date: Mon, 31 Aug 1998 15:38:38 +0300 >To: nih-image@io.ece.drexel.edu >From: "Dr. Ron Goldstein" >Subject: integration of dim fluorescent signals > >I have been having trouble figuring out how to use the integration function >of the Averaging menu in Image. I am aquiring dim fluorescence images, and >do not have on chip integration, or a mathematical grabber (I'm using the >Scion LG-3). I do not think that I want the program to automatically scale >the sum of the multiple frames linearly to 0-255 as it does by default. > >In Image Pro, integration is intuitive, one sets how many frames are to be >captured, and what number to divided the integrated result by. For example, >if I want an image that "holds the shutter open" twice as long, I would >tell the program to capture 8 frames, and divide the resulting values by >four. The resulting image gives a brighter signal, and with some playing >with the contrast, the increased background can be reduced (or subtracted >using an image of an empty area of the specimen). > >In Image, to do the same thing it seems that one must use the "Fix Scale" >dialog, is that correct? How would one obtain the "holding the camera >shutter open" that I described before using this method? > >Thanks, > >-Ron >-------------------------------------------------------- >Dr. Ron Goldstein email goldst@mail.biu.ac.il >Dept. Life Sciences Tel. 972-3-531-8216 >Bar-Ilan Univ FAX 972-3-535-1824 >52900 Ramat-Gan, ISRAEL >http://www.biu.ac.il/NAT/ls/goldstein.html > If you captured n images with the integration box checked, you would also see min=, max=,and timing information recorded in the "Info" window. These give the range of the actual (integrated) sum of pixel values as stored in the intermediate temporary real image which would then be scaled to set max=254, min=1 (not 255,0). Using "Fix Scale" your own offset and scale values are used. For n=8, the maximum accumulated pixel value would be 256n = 2048 so "Fix Scale",0,1024 would achieve your requested result. In practice you would probably find a non-zero minimum (which you can read off the Info window. (Re)Entry of the values min,min+1024 would then result in better contrast. Better still, inspect the histogram of the captured integrated image to see where the "real" max/min are ie the range of interest excluding backround, outliers or highlights. It is then practical (if not always straight forward) to set min/max values to maximising useful contrast in converting from the internal real value image to the 8 bit result. You can test this at the macro level by imageing print on paper ("black" on "white") with integration checked. With video controls gain/offset set correctly (or regardless) and "Fix Scale" not checked, the histogram should range 1-254 (0,255 vacant). ShowHistogram should then enable you to see the histogram pixel range which corresponds to the "white" paper. Select a ROI which excludes text (ie white paper only) and capture again. The Info window will report the min/max of the integrated ROI ie paper only. Feeding these values back into a "Fix Scale" integration will give you a high contrast image of the "white" paper (with the print saturated black and effectively ignored in this contrast range). Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #49 *************************************** From nih-image-request@io.ece.drexel.edu Tue Sep 1 11:57 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA06472; Tue, 1 Sep 1998 11:56:52 -0400 (EDT) Resent-Date: Tue, 1 Sep 1998 11:56:52 -0400 (EDT) Message-Id: In-Reply-To: <3.0.4.32.19980831101943.00b41388@130.91.91.1> Mime-Version: 1.0 Date: Tue, 1 Sep 1998 10:06:10 -0500 To: "Linda J. Lewis" From: Laird Bloom Subject: Re: writing macros Cc: nih-image@io.ece.drexel.edu Resent-Message-ID: <"u3JVY2.0.Zk6.Iy_wr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/272 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 4025 Hi Linda, I've written a few sets of macros to record data into text files while the user is scoring slides. The general structure that works for me is to have individual macros that can be run by a single keystroke (by including [x] in the macro name, where x is any key), each of which instructs the computer to make a single measurement, write it to a data file, increment a counter, and return to the image. I also have a macro for setting parameters (sample names, name of results files, etc.) and opening the initial image, and a second macro that calculates averages,etc. for the data file when the slide is completely scored. It's fairly simple to teach people to use macros written this way; they just have to remember which keys to press to score which parameters. The user can outline areas on the image and choose not to measure them if they make a mistake. (I'm not sure there's an easy way to undo mistakes). As for recording data, writing each data point for a single parameter as a single column of numbers works nicely for import into Excel (just select all, copy, and paste into Excel, no reformatting needed). If you're scoring multiple parameters, I would suggest setting up multiple data files. The transition to Excel is somewhat cumbersome, since you have to copy and paste each file separately, but there's no editing needed once you get there. Alternately, you can write your data to a single text file and open the whole thing in Excel, deleting extra cells as needed. An alternative might be to record data in the two rUser arrays and then write a procedure to write each value (or just the averages) to a text file; unfortunately, there are only two arrays available. You'll find code for one set of macros written like this, for measuring outlined areas, in the same nih-image-d Digest V98 #42 set in which your inquiry appeared; see my message about pausing macros in that set, or contact me directly for the code. Laird Bloom MIT Center for Cancer Research >Hello, >I have been asked to write a macro for some clinicians here at our vet >hospital. I am unfamiliar with NIH Image (the person who was supposed to >do this is no longer here). I have had Pascal and the language doesn't >look too bad but I'm not sure exactly how much detail I need to go into for >the user interface. This is what they are looking to accomplish: >For each slide: > For i=1:? captures per slide: (the whole slide isn't visible at once) > Measure the perimeter (let's call it p(i)) > Measure the bone value (let's call it b(i)) > Measure the amt near growth plate (if any) (let's call it g(i)) > Calculate the amount of no bone formation (p(i) - b(i)) (let's call >it n(i)) > Save the image onto a disk > Sum up measurements for all the captures per slide: For i=1:? > psum=psum + p(i) > bsum=bsum + b(i) > gsum=gsum + g(i) > nsum=nsum + n(i) > Calculate the % bone formation, let's call it f: f = bsum/psum > Calculate the % no bone formation near growth plate (let's call it ng): >ng = gsum/nsum >After all the slides, export the data to an excel file. > >Writing macros to do the calculations doesn't seem to be difficult. Do I >have to write a user interface so that they can signify what measurements >to use (ie. they make a mistake and measure the perimeter again) and to >signal when each slide is finished? All the macros I've seen don't appear >to do this. If you can give me any insight, I'd appreciate it. And of >course, we need this asap. Thanks in advance. ljl >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Linda J. Lewis >New Bolton Center On-Site Support >For help at NBC: call ext. HELP > send email to help@vet.upenn.edu > or browse http://www.vet.upenn.edu/help > >New Bolton Center >University of Pennsylvania, School of Veterinary Medicine >382 W. Street Road >Kennett Square, PA 19348-1692 >610-444-5800 x2482 >fax 610-444-4724 >email: lewis@vet.upenn.edu From nih-image-request@io.ece.drexel.edu Tue Sep 1 12:10 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA07813; Tue, 1 Sep 1998 12:10:36 -0400 (EDT) Resent-Date: Tue, 1 Sep 1998 12:10:36 -0400 (EDT) X-Sender: toberysz@pop.service.ohio-state.edu Message-Id: Mime-Version: 1.0 Date: Tue, 1 Sep 1998 11:01:53 -0500 To: nih-image@io.ece.drexel.edu From: oberyszyn.1@osu.edu (Tatiana Oberyszyn) Subject: Mac G3 Resent-Message-ID: <"nTVCG1.0.UT.jo0xr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/273 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 363 As and NIH Image neophyte I have a very basic question. Has anyone used NIH image on a PowerMac G3? The computer has a VCR like video in port. We have a Sony CCD camera on a Nikon microscope which was hooked up to a Windows based computer. Hopefully I'll be able to, once I find the necessary hardware, hook into the video in port on the Mac. Thanks Tania From nih-image-request@io.ece.drexel.edu Tue Sep 1 12:20 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA08777; Tue, 1 Sep 1998 12:20:27 -0400 (EDT) Resent-Date: Tue, 1 Sep 1998 12:20:27 -0400 (EDT) Message-ID: <35EC1A1E.35C4FBF9@netmatters.co.uk> Date: Tue, 01 Sep 1998 16:00:32 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: GetTime Command References: <761767A26AC@rna.bio.mq.edu.au> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"e28SM3.0.Lh.Ez0xr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/274 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 529 Dear all, I'm having a lot of trouble with what should be an extremely easy task. I can not get the command GetTime(year, month, day, hour, minute, second, dayofweek); to work at all. NIH Image, Object Image and Image SXM all return an unidentified identifier "GetTime" error message. Any one have the solution? many thanks in advance, Jeremy *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html From nih-image-request@io.ece.drexel.edu Tue Sep 1 12:37 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA10116; Tue, 1 Sep 1998 12:37:05 -0400 (EDT) Resent-Date: Tue, 1 Sep 1998 12:37:05 -0400 (EDT) Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9F6B@cheetah.uits.iupui.edu> From: "Kirk, Todd Jason" To: nih-image@io.ece.drexel.edu Subject: Image capture to a stack Date: Tue, 1 Sep 1998 10:42:44 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"tC2B22.0.QH1.2O1xr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/275 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 503 Hey, I'm just starting out with the Scion version of NIH Image and have a question about capturing images to a stack. I can capture an Image but how do I add it to the stack? I have made a new stack, when I try to add the new capture, it just adds a white slice in the new stack. Also, how would I save pictures with an incrementing counter for the name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried saveas('slice'+slicenumber), but it wants only a string. Thanks ...... Todd From nih-image-request@io.ece.drexel.edu Tue Sep 1 13:28 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA14894; Tue, 1 Sep 1998 13:27:57 -0400 (EDT) Resent-Date: Tue, 1 Sep 1998 13:27:57 -0400 (EDT) Message-Id: In-Reply-To: <35EC1A1E.35C4FBF9@netmatters.co.uk> References: <761767A26AC@rna.bio.mq.edu.au> Mime-Version: 1.0 Date: Tue, 1 Sep 1998 12:55:44 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: GetTime Command Resent-Message-ID: <"6d_N02.0.Sm2.HN2xr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/276 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 648 >Dear all, > >I'm having a lot of trouble with what should be an extremely easy task. I >can not >get the command > >GetTime(year, month, day, hour, minute, second, dayofweek); > >to work at all. NIH Image, Object Image and Image SXM all return an >unidentified >identifier "GetTime" error message. Any one have the solution? Here's an exmple of how to use GetTime: macro 'GetTime Test'; var year,month,day,hour,minute,second,DayOfWeek:integer; begin GetTime(year,month,day,hour,minute,second,DayOfWeek); PutMessage(year:1,'/',month:1,'/',day:1, ' ',hour:1,':'minute:1,':',second:1); end; Output: 1998/9/1 12:52:21 -wayne From nih-image-request@io.ece.drexel.edu Tue Sep 1 13:50 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA17086; Tue, 1 Sep 1998 13:47:32 -0400 (EDT) <9D916278299FD111A7E100805FA7C2BA4B9F6B@cheetah.uits.iupui.edu> Resent-Date: Tue, 1 Sep 1998 13:47:32 -0400 (EDT) Message-Id: In-Reply-To: <9D916278299FD111A7E100805FA7C2BA4B9F6B@cheetah.uits.iupui.edu> Mime-Version: 1.0 Date: Tue, 1 Sep 1998 13:18:43 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Image capture to a stack Resent-Message-ID: <"-qzR02.0.lJ3.oi2xr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/277 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 754 >Hey, > I'm just starting out with the Scion version of NIH Image and have >a question about capturing images to a stack. > >I can capture an Image but how do I add it to the stack? I have made a >new stack, when I try to add the new capture, it just adds a white slice >in the new stack. The "Capture Frames" command captures images and adds them to a stack. All the "Add Slice" command does is add a blank slice to the stack. You need to Copy and Paste to put an image into that slice. >Also, how would I save pictures with an incrementing counter for the >name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried >saveas('slice'+slicenumber), but it wants only a string. This should work: SaveAs('slice', slicenumber:3); -wayne From nih-image-request@io.ece.drexel.edu Tue Sep 1 14:01 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA18420; Tue, 1 Sep 1998 14:01:28 -0400 (EDT) Resent-Date: Tue, 1 Sep 1998 14:01:28 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Tue, 01 Sep 1998 12:26:44 -0500 From: "STEPHEN MOORMAN" To: nih-image@io.ece.drexel.edu Subject: G3 Video Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id NAA15050 Resent-Message-ID: <"2yDbo3.0.Mh3.0y2xr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/279 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 265 I have yet to be able to get NIH Image to capture video from the builtin video port on my G3. All the other Video capture programs I use work just fine except for NIH Image. I use my 8600/300 for video capture through NIH Image instead of my G3 because of this. From nih-image-request@io.ece.drexel.edu Tue Sep 1 14:04 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA18705; Tue, 1 Sep 1998 14:03:58 -0400 (EDT) Resent-Date: Tue, 1 Sep 1998 14:03:58 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Tue, 1 Sep 1998 13:33:09 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Mac G3 Resent-Message-ID: <"60Ok72.0.ud3.Gw2xr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/278 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 584 >As and NIH Image neophyte I have a very basic question. Has anyone used >NIH image on a PowerMac G3? The computer has a VCR like video in port. We >have a Sony CCD camera on a Nikon microscope which was hooked up to a >Windows based computer. Hopefully I'll be able to, once I find the >necessary hardware, hook into the video in port on the Mac. Thanks > >Tania NIH Image's Start Capturing command does not work with the PowerMac G3's built-in digitizer. You can, however, use the Plug-in Digitizer available from ftp://codon.nih.gov/pub/nih-image/plug-ins/ -wayne From nih-image-request@io.ece.drexel.edu Tue Sep 1 14:12 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA19588; Tue, 1 Sep 1998 14:12:10 -0400 (EDT) Resent-Date: Tue, 1 Sep 1998 14:12:10 -0400 (EDT) Message-Id: In-Reply-To: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Mime-Version: 1.0 Date: Tue, 1 Sep 1998 13:43:31 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Code Warrior Pro 3 Resent-Message-ID: <"qM7_w2.0.Rv3._33xr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/280 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1170 >Wayne/others: > >Currently, I am using CodeWarrior Academic Pro 11 for the Macintosh to >compile Image 1.62b4 source code. I looked on the Image home page and found >there was a version 1.62b20 for Code Warrior Pro 2. I recently bought Code >Warrior Pro 3 which I installed on a Windows 95 machine. I was wondering if >there was any version of the Image source code that would compile using >Code Warrior Pro 3 (or if there isn't one now if there might be one in the >near future). In addition, since Code Warrior Pro 3 allows you to compile >projects for multiple targets, will it ever be possible to obtain source >code that I could use with Code Warrior Pro 3 to compile a version of Image >to run on a Windows machine? Sorry for being greedy, but a version of the >source code that would allow me to compile an extended version of Image for >a Windows machine would be of great value to me (and I assume to others as >well). You should be able to compile the 1.62b20 source with CodeWarrior Pro 3. To compile and run it on a Windows machine, however, would require writing Windows equivalents for the hundreds of Mac toolbox routines used by NIH Image. -wayne From nih-image-request@io.ece.drexel.edu Tue Sep 1 15:53 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA27561; Tue, 1 Sep 1998 15:53:20 -0400 (EDT) <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Resent-Date: Tue, 1 Sep 1998 15:53:20 -0400 (EDT) X-Authentication-Warning: mail.bio.uva.nl: Host gold.bio.uva.nl [145.18.160.48] claimed to be [145.18.160.48] Message-Id: In-Reply-To: References: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Mime-Version: 1.0 Date: Tue, 1 Sep 1998 21:36:18 +0200 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: Code Warrior Pro 3 Resent-Message-ID: <"ZL2th3.0.YI6.Dl4xr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/281 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 657 I had problems with NIH Image and CodeWorrior 3: in the 68k project, the 'StringOf' function did not work, with the effect that many strings showed garbage or nothing. This became visible in the file and edit menu, the info window and so on. If I remember right, this also applied to the original NIH Image version. I sent the source code to the technical staff of Metroworks, they were 'puzzled' and could reproduce the error, but not in a simple example. Meanwhile, I tried the newest updates (a few days ago) but the error remained. At this moment, I still use CodeWarrior 2. Has any one successfully compiled NIH Image/68k with CW3? Norbert Vischer From nih-image-d-request@io.ece.drexel.edu Wed Sep 2 05:03 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA10592; Wed, 2 Sep 1998 05:03:22 -0400 (EDT) Date: Wed, 2 Sep 1998 05:03:22 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809020903.FAA10592@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #50 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/50 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 15619 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 50 Today's Topics: Re: writing macros [ Laird Bloom ] Mac G3 [ oberyszyn.1@osu.edu (Tatiana Oberys ] GetTime Command [ Jeremy Brown ] Re: Image capture to a stack [ Wayne Rasband ] Re: Mac G3 [ Wayne Rasband ] G3 Video [ "STEPHEN MOORMAN" ] Re: Code Warrior Pro 3 [ Norbert Vischer To: "Linda J. Lewis" Cc: nih-image@io.ece.drexel.edu Subject: Re: writing macros Message-Id: Content-Type: text/plain; charset="us-ascii" Hi Linda, I've written a few sets of macros to record data into text files while the user is scoring slides. The general structure that works for me is to have individual macros that can be run by a single keystroke (by including [x] in the macro name, where x is any key), each of which instructs the computer to make a single measurement, write it to a data file, increment a counter, and return to the image. I also have a macro for setting parameters (sample names, name of results files, etc.) and opening the initial image, and a second macro that calculates averages,etc. for the data file when the slide is completely scored. It's fairly simple to teach people to use macros written this way; they just have to remember which keys to press to score which parameters. The user can outline areas on the image and choose not to measure them if they make a mistake. (I'm not sure there's an easy way to undo mistakes). As for recording data, writing each data point for a single parameter as a single column of numbers works nicely for import into Excel (just select all, copy, and paste into Excel, no reformatting needed). If you're scoring multiple parameters, I would suggest setting up multiple data files. The transition to Excel is somewhat cumbersome, since you have to copy and paste each file separately, but there's no editing needed once you get there. Alternately, you can write your data to a single text file and open the whole thing in Excel, deleting extra cells as needed. An alternative might be to record data in the two rUser arrays and then write a procedure to write each value (or just the averages) to a text file; unfortunately, there are only two arrays available. You'll find code for one set of macros written like this, for measuring outlined areas, in the same nih-image-d Digest V98 #42 set in which your inquiry appeared; see my message about pausing macros in that set, or contact me directly for the code. Laird Bloom MIT Center for Cancer Research >Hello, >I have been asked to write a macro for some clinicians here at our vet >hospital. I am unfamiliar with NIH Image (the person who was supposed to >do this is no longer here). I have had Pascal and the language doesn't >look too bad but I'm not sure exactly how much detail I need to go into for >the user interface. This is what they are looking to accomplish: >For each slide: > For i=1:? captures per slide: (the whole slide isn't visible at once) > Measure the perimeter (let's call it p(i)) > Measure the bone value (let's call it b(i)) > Measure the amt near growth plate (if any) (let's call it g(i)) > Calculate the amount of no bone formation (p(i) - b(i)) (let's call >it n(i)) > Save the image onto a disk > Sum up measurements for all the captures per slide: For i=1:? > psum=psum + p(i) > bsum=bsum + b(i) > gsum=gsum + g(i) > nsum=nsum + n(i) > Calculate the % bone formation, let's call it f: f = bsum/psum > Calculate the % no bone formation near growth plate (let's call it ng): >ng = gsum/nsum >After all the slides, export the data to an excel file. > >Writing macros to do the calculations doesn't seem to be difficult. Do I >have to write a user interface so that they can signify what measurements >to use (ie. they make a mistake and measure the perimeter again) and to >signal when each slide is finished? All the macros I've seen don't appear >to do this. If you can give me any insight, I'd appreciate it. And of >course, we need this asap. Thanks in advance. ljl >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Linda J. Lewis >New Bolton Center On-Site Support >For help at NBC: call ext. HELP > send email to help@vet.upenn.edu > or browse http://www.vet.upenn.edu/help > >New Bolton Center >University of Pennsylvania, School of Veterinary Medicine >382 W. Street Road >Kennett Square, PA 19348-1692 >610-444-5800 x2482 >fax 610-444-4724 >email: lewis@vet.upenn.edu ------------------------------ Date: Tue, 1 Sep 1998 11:01:53 -0500 From: oberyszyn.1@osu.edu (Tatiana Oberyszyn) To: nih-image@io.ece.drexel.edu Subject: Mac G3 Message-Id: Content-Type: text/plain; charset="us-ascii" As and NIH Image neophyte I have a very basic question. Has anyone used NIH image on a PowerMac G3? The computer has a VCR like video in port. We have a Sony CCD camera on a Nikon microscope which was hooked up to a Windows based computer. Hopefully I'll be able to, once I find the necessary hardware, hook into the video in port on the Mac. Thanks Tania ------------------------------ Date: Tue, 01 Sep 1998 16:00:32 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: GetTime Command Message-ID: <35EC1A1E.35C4FBF9@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear all, I'm having a lot of trouble with what should be an extremely easy task. I can not get the command GetTime(year, month, day, hour, minute, second, dayofweek); to work at all. NIH Image, Object Image and Image SXM all return an unidentified identifier "GetTime" error message. Any one have the solution? many thanks in advance, Jeremy *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html ------------------------------ Date: Tue, 1 Sep 1998 10:42:44 -0500 From: "Kirk, Todd Jason" To: nih-image@io.ece.drexel.edu Subject: Image capture to a stack Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9F6B@cheetah.uits.iupui.edu> Content-Type: text/plain Hey, I'm just starting out with the Scion version of NIH Image and have a question about capturing images to a stack. I can capture an Image but how do I add it to the stack? I have made a new stack, when I try to add the new capture, it just adds a white slice in the new stack. Also, how would I save pictures with an incrementing counter for the name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried saveas('slice'+slicenumber), but it wants only a string. Thanks ...... Todd ------------------------------ Date: Tue, 1 Sep 1998 12:55:44 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: GetTime Command Message-Id: Content-Type: text/plain; charset="us-ascii" >Dear all, > >I'm having a lot of trouble with what should be an extremely easy task. I >can not >get the command > >GetTime(year, month, day, hour, minute, second, dayofweek); > >to work at all. NIH Image, Object Image and Image SXM all return an >unidentified >identifier "GetTime" error message. Any one have the solution? Here's an exmple of how to use GetTime: macro 'GetTime Test'; var year,month,day,hour,minute,second,DayOfWeek:integer; begin GetTime(year,month,day,hour,minute,second,DayOfWeek); PutMessage(year:1,'/',month:1,'/',day:1, ' ',hour:1,':'minute:1,':',second:1); end; Output: 1998/9/1 12:52:21 -wayne ------------------------------ Date: Tue, 1 Sep 1998 13:18:43 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Image capture to a stack Message-Id: Content-Type: text/plain; charset="us-ascii" >Hey, > I'm just starting out with the Scion version of NIH Image and have >a question about capturing images to a stack. > >I can capture an Image but how do I add it to the stack? I have made a >new stack, when I try to add the new capture, it just adds a white slice >in the new stack. The "Capture Frames" command captures images and adds them to a stack. All the "Add Slice" command does is add a blank slice to the stack. You need to Copy and Paste to put an image into that slice. >Also, how would I save pictures with an incrementing counter for the >name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried >saveas('slice'+slicenumber), but it wants only a string. This should work: SaveAs('slice', slicenumber:3); -wayne ------------------------------ Date: Tue, 1 Sep 1998 13:33:09 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Mac G3 Message-Id: Content-Type: text/plain; charset="us-ascii" >As and NIH Image neophyte I have a very basic question. Has anyone used >NIH image on a PowerMac G3? The computer has a VCR like video in port. We >have a Sony CCD camera on a Nikon microscope which was hooked up to a >Windows based computer. Hopefully I'll be able to, once I find the >necessary hardware, hook into the video in port on the Mac. Thanks > >Tania NIH Image's Start Capturing command does not work with the PowerMac G3's built-in digitizer. You can, however, use the Plug-in Digitizer available from ftp://codon.nih.gov/pub/nih-image/plug-ins/ -wayne ------------------------------ Date: Tue, 01 Sep 1998 12:26:44 -0500 From: "STEPHEN MOORMAN" To: nih-image@io.ece.drexel.edu Subject: G3 Video Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit I have yet to be able to get NIH Image to capture video from the builtin video port on my G3. All the other Video capture programs I use work just fine except for NIH Image. I use my 8600/300 for video capture through NIH Image instead of my G3 because of this. ------------------------------ Date: Tue, 1 Sep 1998 13:43:31 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Code Warrior Pro 3 Message-Id: Content-Type: text/plain; charset="us-ascii" >Wayne/others: > >Currently, I am using CodeWarrior Academic Pro 11 for the Macintosh to >compile Image 1.62b4 source code. I looked on the Image home page and found >there was a version 1.62b20 for Code Warrior Pro 2. I recently bought Code >Warrior Pro 3 which I installed on a Windows 95 machine. I was wondering if >there was any version of the Image source code that would compile using >Code Warrior Pro 3 (or if there isn't one now if there might be one in the >near future). In addition, since Code Warrior Pro 3 allows you to compile >projects for multiple targets, will it ever be possible to obtain source >code that I could use with Code Warrior Pro 3 to compile a version of Image >to run on a Windows machine? Sorry for being greedy, but a version of the >source code that would allow me to compile an extended version of Image for >a Windows machine would be of great value to me (and I assume to others as >well). You should be able to compile the 1.62b20 source with CodeWarrior Pro 3. To compile and run it on a Windows machine, however, would require writing Windows equivalents for the hundreds of Mac toolbox routines used by NIH Image. -wayne ------------------------------ Date: Tue, 1 Sep 1998 21:36:18 +0200 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: Code Warrior Pro 3 Message-Id: Content-Type: text/plain; charset="us-ascii" I had problems with NIH Image and CodeWorrior 3: in the 68k project, the 'StringOf' function did not work, with the effect that many strings showed garbage or nothing. This became visible in the file and edit menu, the info window and so on. If I remember right, this also applied to the original NIH Image version. I sent the source code to the technical staff of Metroworks, they were 'puzzled' and could reproduce the error, but not in a simple example. Meanwhile, I tried the newest updates (a few days ago) but the error remained. At this moment, I still use CodeWarrior 2. Has any one successfully compiled NIH Image/68k with CW3? Norbert Vischer ------------------------------ Date: Wed, 2 Sep 1998 10:51:01 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: Image capture to a stack Message-Id: Content-Type: text/plain; charset="us-ascii" > >I can capture an Image but how do I add it to the stack? I have made a >new stack, when I try to add the new capture, it just adds a white slice >in the new stack. > AddSlice only creates a new blank slice. You need to copy your captured image and then paste it into the new slice. You can make a macro do it: var CameraImage, StackedImages: integer; FinishedFirstSlice: boolean; procedure Initialize; var w,h: integer; begin Capture; GetPicSize(w,h); CameraImage:= PidNumber; SetNewSize(w,h); MakeNewStack('captured images'); StackedImages:= PidNumber; end; macro 'capture image to stack'; begin if not FinishedFirstSlice then Initialize; Capture; ChoosePic(CameraImage); SelectAll; Copy; ChoosePic(StackedImages); if FinishedFirstSlice then AddSlice; Paste; FinishedFirstSlice:= true; end; This macro is not tested and might not work but you get the idea. >Also, how would I save pictures with an incrementing counter for the >name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried >saveas('slice'+slicenumber), but it wants only a string. > Use saveas('slice',slicenumber:2,'.tif') for a sequence slice01.tif etc. The syntax of using a + operator in strings works only in Turbo Pascal. In NIH image you can use concat() to merge a series of strings, or insert them directly in commands that expects a single string parameter. Hope this helps. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ -------------------------------- End of nih-image-d Digest V98 Issue #50 *************************************** From nih-image-request@io.ece.drexel.edu Wed Sep 2 05:05 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA10897; Wed, 2 Sep 1998 05:05:14 -0400 (EDT) <9D916278299FD111A7E100805FA7C2BA4B9F6B@cheetah.uits.iupui.edu> Resent-Date: Wed, 2 Sep 1998 05:05:14 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: In-Reply-To: <9D916278299FD111A7E100805FA7C2BA4B9F6B@cheetah.uits.iupui.edu> Mime-Version: 1.0 Date: Wed, 2 Sep 1998 10:51:01 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Re: Image capture to a stack Resent-Message-ID: <"nxLD1.0.n72.DPGxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/282 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1880 > >I can capture an Image but how do I add it to the stack? I have made a >new stack, when I try to add the new capture, it just adds a white slice >in the new stack. > AddSlice only creates a new blank slice. You need to copy your captured image and then paste it into the new slice. You can make a macro do it: var CameraImage, StackedImages: integer; FinishedFirstSlice: boolean; procedure Initialize; var w,h: integer; begin Capture; GetPicSize(w,h); CameraImage:= PidNumber; SetNewSize(w,h); MakeNewStack('captured images'); StackedImages:= PidNumber; end; macro 'capture image to stack'; begin if not FinishedFirstSlice then Initialize; Capture; ChoosePic(CameraImage); SelectAll; Copy; ChoosePic(StackedImages); if FinishedFirstSlice then AddSlice; Paste; FinishedFirstSlice:= true; end; This macro is not tested and might not work but you get the idea. >Also, how would I save pictures with an incrementing counter for the >name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried >saveas('slice'+slicenumber), but it wants only a string. > Use saveas('slice',slicenumber:2,'.tif') for a sequence slice01.tif etc. The syntax of using a + operator in strings works only in Turbo Pascal. In NIH image you can use concat() to merge a series of strings, or insert them directly in commands that expects a single string parameter. Hope this helps. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Wed Sep 2 05:15 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA12073; Wed, 2 Sep 1998 05:15:12 -0400 (EDT) <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Resent-Date: Wed, 2 Sep 1998 05:15:12 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: In-Reply-To: References: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Mime-Version: 1.0 Date: Wed, 2 Sep 1998 11:02:33 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Re: Code Warrior Pro 3 Resent-Message-ID: <"hEeSg2.0.FT2._ZGxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/283 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1978 >I had problems with NIH Image and CodeWorrior 3: in the 68k project, the >'StringOf' function did not work, with the effect that many strings showed >garbage or nothing. This became visible in the file and edit menu, the info >window and so on. If I remember right, this also applied to the original >NIH Image version. I sent the source code to the technical staff of >Metroworks, they were 'puzzled' and could reproduce the error, but not in a >simple example. Meanwhile, I tried the newest updates (a few days ago) but >the error remained. >At this moment, I still use CodeWarrior 2. >Has any one successfully compiled NIH Image/68k with CW3? > >Norbert Vischer Strange compiler bugs may appear when the size of allocated data structures gets too large, especially in the 68k version. Try experimenting with the compiler options like far calls etc. I planned to upgrade to CW Pro 3 this week, but since there appears to be a problem I will not upgrade permanently but install it on a Zip or similar. I will let you know if I find out about this. Fortunately, CodeWarrior compiler bugs are very rare. BTW, I was successfully able to make a multiple target NIH image project file with CW Pro 2. You can then create a PPC, 68k and FAT binary from the same project. This will ensure that your source files and libraries are consistent across the different targets. I once spent a whole day searching for a bug that was caused by including an out-of-date library file in the 68k project file. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Wed Sep 2 12:38 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA10454; Wed, 2 Sep 1998 12:37:52 -0400 (EDT) Resent-Date: Wed, 2 Sep 1998 12:37:52 -0400 (EDT) Message-ID: <35ED7FC3.D43@cisea.it> Date: Wed, 02 Sep 1998 18:26:27 +0100 From: domenico di girolamo X-Mailer: Mozilla 2.02 (Macintosh; I; 68K) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: NIH Image and MAC OS X References: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"GsuL93.0.Yj1.p2Nxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/284 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 294 hello, the Apple CEO presented the new OS called MAC OS X, with new interesting features (multithreating, protected memory, fast I/O, etc); To get fully advantage from these features the application must be or become Carbon (a clean set of MAC API) compliant. How about NIH Image? TIA -dom From nih-image-request@io.ece.drexel.edu Wed Sep 2 13:11 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA25267; Wed, 2 Sep 1998 13:11:29 -0400 (EDT) Resent-Date: Wed, 2 Sep 1998 13:11:29 -0400 (EDT) Message-ID: <69B43248FE73D11197BB00A0C99AB067891E@jvcserver.vanguardweb.org> From: "Mehmet Dondurur, Ph. D." To: "'nih-image@biomed.drexel.edu'" Subject: 12 bit 8 bit conversion Date: Wed, 2 Sep 1998 12:50:57 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"Gz2rS2.0.Up5.WaNxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/285 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 374 Hi, I have 12 bit images and I am having trouble to opne them in NIH and others. Is ther anyway to convert images from 12 bit 8 bit in NIH or other softwares?. or Is ther any other way to diplay and edit these 12 bit images in any software? Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-Univ. of Michigan Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 From nih-image-d-request@io.ece.drexel.edu Thu Sep 3 06:14 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA23013; Thu, 3 Sep 1998 06:14:11 -0400 (EDT) Date: Thu, 3 Sep 1998 06:14:11 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809031014.GAA23013@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #51 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/51 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4020 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 51 Today's Topics: Re: Code Warrior Pro 3 [ Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: Code Warrior Pro 3 Message-Id: Content-Type: text/plain; charset="us-ascii" >I had problems with NIH Image and CodeWorrior 3: in the 68k project, the >'StringOf' function did not work, with the effect that many strings showed >garbage or nothing. This became visible in the file and edit menu, the info >window and so on. If I remember right, this also applied to the original >NIH Image version. I sent the source code to the technical staff of >Metroworks, they were 'puzzled' and could reproduce the error, but not in a >simple example. Meanwhile, I tried the newest updates (a few days ago) but >the error remained. >At this moment, I still use CodeWarrior 2. >Has any one successfully compiled NIH Image/68k with CW3? > >Norbert Vischer Strange compiler bugs may appear when the size of allocated data structures gets too large, especially in the 68k version. Try experimenting with the compiler options like far calls etc. I planned to upgrade to CW Pro 3 this week, but since there appears to be a problem I will not upgrade permanently but install it on a Zip or similar. I will let you know if I find out about this. Fortunately, CodeWarrior compiler bugs are very rare. BTW, I was successfully able to make a multiple target NIH image project file with CW Pro 2. You can then create a PPC, 68k and FAT binary from the same project. This will ensure that your source files and libraries are consistent across the different targets. I once spent a whole day searching for a bug that was caused by including an out-of-date library file in the 68k project file. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Wed, 02 Sep 1998 18:26:27 +0100 From: domenico di girolamo To: nih-image@io.ece.drexel.edu Subject: NIH Image and MAC OS X Message-ID: <35ED7FC3.D43@cisea.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hello, the Apple CEO presented the new OS called MAC OS X, with new interesting features (multithreating, protected memory, fast I/O, etc); To get fully advantage from these features the application must be or become Carbon (a clean set of MAC API) compliant. How about NIH Image? TIA -dom ------------------------------ Date: Wed, 2 Sep 1998 12:50:57 -0400 From: "Mehmet Dondurur, Ph. D." To: "'nih-image@biomed.drexel.edu'" Subject: 12 bit 8 bit conversion Message-ID: <69B43248FE73D11197BB00A0C99AB067891E@jvcserver.vanguardweb.org> Content-Type: text/plain Hi, I have 12 bit images and I am having trouble to opne them in NIH and others. Is ther anyway to convert images from 12 bit 8 bit in NIH or other softwares?. or Is ther any other way to diplay and edit these 12 bit images in any software? Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-Univ. of Michigan Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 -------------------------------- End of nih-image-d Digest V98 Issue #51 *************************************** From nih-image-request@io.ece.drexel.edu Thu Sep 3 09:32 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA11090; Thu, 3 Sep 1998 09:31:54 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 09:31:54 -0400 (EDT) Date: Thu, 3 Sep 1998 09:21:26 -0400 (EDT) From: Xuanliang Dong Reply-To: Xuanliang Dong To: nih-image@io.ece.drexel.edu Subject: Video Digitizer error-2208 Message-Id: Mime-Version: 1.0 Resent-Message-ID: <"DNDXm1.0.oL2.CSfxr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/286 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 510 Dear All: I want to use NIH image to capture image from Digital Camera on a Power PC(Power Mac 6500/275).When I click start capturing, there is an error message:Video Digitizer error-2208(Turning Vitual Memory off or RAM double off). I don't have an RAM double on Mac and vitual memory has been turned off. I am sure that Video card is installed on Mac since Apple Video Played can be used to obtained an image correctly. Does anyone have meet such problem? Thank you very much. Have a nice day. Neil From nih-image-request@io.ece.drexel.edu Thu Sep 3 10:02 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA13947; Thu, 3 Sep 1998 10:02:13 -0400 (EDT) <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Resent-Date: Thu, 3 Sep 1998 10:02:13 -0400 (EDT) Message-Id: In-Reply-To: <35ED7FC3.D43@cisea.it> References: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Mime-Version: 1.0 Date: Thu, 3 Sep 1998 09:59:02 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: NIH Image and MAC OS X Resent-Message-ID: <"JwI01.0.cB3.Xzfxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/287 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 576 >hello, >the Apple CEO presented the new OS called MAC OS X, with new >interesting features (multithreating, protected memory, fast I/O, >etc); >To get fully advantage from these features the application must be or >become Carbon (a clean set of MAC API) compliant. >How about NIH Image? NIH Image is not Carbon compliant but my new Image/J program at http://rsb.info.nih.gov/ij/ will be. BTW, Mac OS Runtime for Java 2.1 Early Access 2 is now available at It runs Image/J a lot better than MRJ 2.0. -wayne From nih-image-request@io.ece.drexel.edu Thu Sep 3 10:50 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA18106; Thu, 3 Sep 1998 10:50:06 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 10:50:06 -0400 (EDT) Date: Thu, 3 Sep 98 7:37:47 PDT From: Walter Wolf To: nih-image@io.ece.drexel.edu Cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu Subject: Re: NIH Image and MAC OS X In-Reply-To: Your message of Thu, 3 Sep 1998 09:59:02 -0400 Message-ID: Resent-Message-ID: <"9TUmo3.0.C84.3dgxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/288 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1059 Wayne: Last time you mentioned that the documentation for Image/J was not yet available. Is it now, and if not, when will it become available? Also, and I appologize for my ignorance, what is "Carbon compliant"? ====================================================================== | Professor Walter Wolf, Ph.D. E-Mail: wwolfw@hsc.usc.edu | | Distinguished Professor of Pharmaceutical Sciences | | Director, Pharmacokinetic Imaging Program | | Department of Pharmaceutical Sciences, School of Pharmacy | | University of Southern California Telephone: 323-442-1405 | | 1985 Zonal Ave., Los Angeles, CA 90033 Fax: 323-442-9804 | | | |Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute| | MRI at St. Vincent Medical Center Telephone: 213-484-7235 | | 2131 Third St., Los Angeles, CA 90057 Fax: 213-484-7447 | ====================================================================== From nih-image-request@io.ece.drexel.edu Thu Sep 3 12:03 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA24420; Thu, 3 Sep 1998 12:03:42 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 12:03:42 -0400 (EDT) X-Sender: cgustafs@ece.drexel.edu Message-Id: In-Reply-To: References: Your message of Thu, 3 Sep 1998 09:59:02 -0400 Mime-Version: 1.0 Date: Thu, 3 Sep 1998 11:55:34 -0400 To: nih-image@io.ece.drexel.edu From: Carl Gustafson Subject: Carbon Compliance (Was: NIH Image and MAC OS X) Resent-Message-ID: <"8WUwE.0.rh5.cihxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/289 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1432 >Also, and I appologize for my ignorance, what is "Carbon compliant"? Apple Computer went over their system software libraries (APIs, in geek speek), and weeded out a large number of routines that either were rarely used, superceded by other routines, or were just too crufty to continue to maintain and still allow for advancement of their system software. The routines that survived the cut are now known as the Carbon APIs. (And yes, there have been programmer-jokes about being carbon-based.) Anyway, a carbon-compliant program is one that doesn't call routines not in the official, honest-to-Apple, totally cool and approved Carbon APIs. Calling non-existent routines is a generally bad thing, and will usually toast the application. There is a test application that Apple has available called the carbon dater, that will check any application, and score it for compatibility, BTW. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== From nih-image-request@io.ece.drexel.edu Thu Sep 3 12:21 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA26275; Thu, 3 Sep 1998 12:21:39 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 12:21:39 -0400 (EDT) Message-Id: In-Reply-To: References: Your message of Thu, 3 Sep 1998 09:59:02 -0400 Mime-Version: 1.0 Date: Thu, 3 Sep 1998 12:17:37 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: NIH Image and MAC OS X Resent-Message-ID: <"ajEKn2.0.w96.S_hxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/291 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 432 >Wayne: > >Last time you mentioned that the documentation for Image/J was not yet >available. Is it now, and if not, when will it become available? There is some prelimimary HTML documentation for Image/J at: http://rsb.info.nih.gov/ij/ >Also, and I appologize for my ignorance, what is "Carbon compliant"? Henry Knorr has a good article about Mac OS X and Carbon at: http://www1.macintouch.com/norr006.html -wayne From nih-image-request@io.ece.drexel.edu Thu Sep 3 12:23 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA26392; Thu, 3 Sep 1998 12:23:01 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 12:23:01 -0400 (EDT) Date: Thu, 3 Sep 1998 11:10:44 -0500 (CDT) From: Doug Martin To: nih-image@io.ece.drexel.edu Subject: maximum stack and text sizes Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"4n3-b1.0.d66.jzhxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/290 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 279 Does anyone know of a way to get around the maximum stack size (1000 frames) or text clipboard size (32K), or of a version of image which as been modified to increase these limits? Thanks a million, Douglas Martin University of Texas at Austin From nih-image-request@io.ece.drexel.edu Thu Sep 3 12:51 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA28790; Thu, 3 Sep 1998 12:50:40 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 12:50:40 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Thu, 3 Sep 1998 12:44:42 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: maximum stack and text sizes Resent-Message-ID: <"npsjL3.0._m6.qOixr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/292 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 449 >Does anyone know of a way to get around the maximum stack size (1000 >frames) or text clipboard size (32K), or of a version of image which as >been modified to increase these limits? NIH Image 1.62b21 at ftp://codon.nih.gov/pub/nih-image/nih-image162b21_fat.hqx has a maximum stack size of 5000, at least on PowerMacs. There is no easy fix for the 32K text size limit since it's built into the Mac OS TextEdit toolbox routine. -wayne From nih-image-request@io.ece.drexel.edu Thu Sep 3 13:15 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA01211; Thu, 3 Sep 1998 13:15:31 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 13:15:31 -0400 (EDT) Date: Thu, 3 Sep 1998 10:06:40 -0700 (PDT) From: Stephan Anagnostaras Reply-To: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: G3 AV problems continued Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"yiB5R.0.P3.aoixr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/294 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 521 Hello, I am wondering if any progress has been made on the fact that NIH Image is not compatible with the G3 built in digitizer. It seems like a long time has gone by, and the proposed solution doesn't really work. Are there any plans to implement support for the digitizer? Thanks, Stephan ------------------------------- Stephan G. Anagnostaras, Ph.D. UCLA Dept. of Neurobiology stephan@lifesci.ucla.edu sanagnos@mediaone.net 310-822-7100 / 306-0294 ------------------------------- From nih-image-request@io.ece.drexel.edu Thu Sep 3 13:15 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA01197; Thu, 3 Sep 1998 13:15:24 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 13:15:24 -0400 (EDT) Message-ID: <35EEDACB.25D7@cisea.it> Date: Thu, 03 Sep 1998 19:07:07 +0100 From: domenico di girolamo X-Mailer: Mozilla 2.02 (Macintosh; I; 68K) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image and MAC OS X References: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"SRfYe3.0.XH7.gkixr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/293 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 149 hello, I have two further question: - it will support Scion framegrabbers? - how about the existing usermacros(i'm not a Java programmer)? TIA -dom From nih-image-request@io.ece.drexel.edu Thu Sep 3 14:03 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id OAA04916; Thu, 3 Sep 1998 14:02:54 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 14:02:54 -0400 (EDT) Mime-Version: 1.0 Message-Id: Date: Thu, 3 Sep 1998 14:04:08 -0400 To: nih-image@io.ece.drexel.edu From: Gloria Hoffman Subject: counting/cataloging Resent-Message-ID: <"6i7GR1.0.j-.WUjxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/295 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 606 This may be simple and I have missed something very obvious but....I would like to take drawings made on Adobe Illustrator or Canvas, acquired from a digital pad/camera lucida and obtain numbers of the objects I have drawn, then tally them up according to the color I have selected for those objects (perhaps 3 or four at most). Does anyone know a program (NIH image eg) that could do that after importing images from either application? Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Fax 410 706-2512 email gehoffma@umaryland.edu From nih-image-request@io.ece.drexel.edu Thu Sep 3 16:44 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA16206; Thu, 3 Sep 1998 16:43:38 -0400 (EDT) <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Resent-Date: Thu, 3 Sep 1998 16:43:38 -0400 (EDT) Message-Id: In-Reply-To: <35EEDACB.25D7@cisea.it> References: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu> Mime-Version: 1.0 Date: Thu, 3 Sep 1998 16:31:23 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: NIH Image and MAC OS X Resent-Message-ID: <"zKQSw1.0.id3.Ujlxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/296 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 371 >hello, >I have two further question: >- it will support Scion framegrabbers? >- how about the existing usermacros(i'm not a Java programmer)? >TIA >-dom I plan to add frame grabber support and a Pascal-like macro interpreter to Image.J but it may be a year or two. There is a list of planned features at: http://rsb.info.nih.gov/ij/docs/to-do-list.html -wayne From nih-image-request@io.ece.drexel.edu Thu Sep 3 17:20 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA18688; Thu, 3 Sep 1998 17:20:33 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 17:20:33 -0400 (EDT) Date: 03 Sep 98 14:10:59 -0600 From: Steven Moore Subject: Video Digitizer Error 2208, Re-visited To: "nih-image@biomed.drexel.edu" X-Mailer: QuickMail Pro 1.5.2 (Windows32) X-Priority: 3 MIME-Version: 1.0 Reply-To: Steven Moore Message-ID: <1307290659-53216033@mailhost.cipe.com> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id RAA17833 Resent-Message-ID: <"odeys1.0.oM4.UNmxr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/297 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-Ascii" Content-Length: 684 Hello, I took a tech support call from a teacher in Oregon who was attempting to use the Start Capture command on NIH Image 1.61 (and 1.62) installed on a Mac 5500 AV. He received the message Video Digitizer Error 2208, Turn Off Virtual Memory or RAM Doubler. After turning Virtual Memory off and restarting the machine, he still got the same message. I've searched the archive and found messages about this problem dating back to 1995, but no solution. Can anybody tell me how to solve this problem? Thanks. Steven D. Moore, Ph.D. Director of Evaluation Services Center for Image Processing in Education Tucson, AZ stevem@cipe.com http://www.cipe.com (800) 322-9884 ext. 125 From nih-image-request@io.ece.drexel.edu Thu Sep 3 21:57 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA08920; Thu, 3 Sep 1998 21:56:55 -0400 (EDT) Resent-Date: Thu, 3 Sep 1998 21:56:55 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: gehoffma@umaryland.edu, nih-image@io.ece.drexel.edu Date: Fri, 4 Sep 1998 11:48:12 GMT+1000 Subject: Re: counting/cataloging Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <7A6E6244344@rna.bio.mq.edu.au> Resent-Message-ID: <"q1Poh1.0.Ux1._Oqxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/298 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2102 >Date: Thu, 3 Sep 1998 14:04:08 -0400 >To: nih-image@io.ece.drexel.edu >From: Gloria Hoffman >Subject: counting/cataloging > >This may be simple and I have missed something very obvious but....I would >like to take drawings made on Adobe Illustrator or Canvas, acquired from a >digital pad/camera lucida and obtain numbers of the objects I have drawn, >then tally them up according to the color I have selected for those objects >(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that >could do that after importing images from either application? >Gloria E. Hoffman, Ph.D. >Department of Anatomy and Neurobiology >685 W Baltimore St >Baltimore MD 21201 >Phone 410 706-2438 >Fax 410 706-2512 >email gehoffma@umaryland.edu In principle, NIH-Image analyzeParticles will do this quite well. In practice, there are a few wrinkles and computer internals that need to be addressed. Adobe Illustrator files are text files containing directives, coordinates etc rather than pixelated images. You can convert Adobe Illustrator files to pixelated images in TIFF format acceptable to NIH-Image by: open Illustrator file in Photoshop, flaten (to remove layers) and convert to RGB then save as an uncompressed 8 bit TIFF image. You can then open the TIFF image in NIH-Image. As image is RGB, you will then have a 3 frame stack (Red Green Blue) and/or an indexed color representation of the image. Density sliceing; analyzeParticles; can then be applied to either(any) of these to count/measure the particles by color. How easy the color to RGB stack or indexed color is to you will depend on your understanding of color separations and the colors you used in Illustrator. Rather than go into that here, try it to see what you get. It will be much easier to understand by inspection than by an attempted pracie by email. Come back (with a sample) if you have problems. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Fri Sep 4 06:18 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA15409; Fri, 4 Sep 1998 06:18:12 -0400 (EDT) Date: Fri, 4 Sep 1998 06:18:12 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809041018.GAA15409@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #52 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/52 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 14254 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 52 Today's Topics: Video Digitizer error-2208 [ Xuanliang Dong ] Re: NIH Image and MAC OS X [ Walter Wolf ] Carbon Compliance (Was: NIH Image an [ Carl Gustafson ] Re: maximum stack and text sizes [ Wayne Rasband ] Re: NIH Image and MAC OS X [ domenico di girolamo ] Video Digitizer Error 2208, Re-visit [ Steven Moore ] Re: counting/cataloging [ GJOSS@rna.bio.mq.edu.au ] ------------------------------ Date: Thu, 3 Sep 1998 09:21:26 -0400 (EDT) From: Xuanliang Dong To: nih-image@io.ece.drexel.edu Subject: Video Digitizer error-2208 Message-Id: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All: I want to use NIH image to capture image from Digital Camera on a Power PC(Power Mac 6500/275).When I click start capturing, there is an error message:Video Digitizer error-2208(Turning Vitual Memory off or RAM double off). I don't have an RAM double on Mac and vitual memory has been turned off. I am sure that Video card is installed on Mac since Apple Video Played can be used to obtained an image correctly. Does anyone have meet such problem? Thank you very much. Have a nice day. Neil ------------------------------ Date: Thu, 3 Sep 1998 09:59:02 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image and MAC OS X Message-Id: Content-Type: text/plain; charset="us-ascii" >hello, >the Apple CEO presented the new OS called MAC OS X, with new >interesting features (multithreating, protected memory, fast I/O, >etc); >To get fully advantage from these features the application must be or >become Carbon (a clean set of MAC API) compliant. >How about NIH Image? NIH Image is not Carbon compliant but my new Image/J program at http://rsb.info.nih.gov/ij/ will be. BTW, Mac OS Runtime for Java 2.1 Early Access 2 is now available at It runs Image/J a lot better than MRJ 2.0. -wayne ------------------------------ Date: Thu, 3 Sep 98 7:37:47 PDT From: Walter Wolf To: nih-image@io.ece.drexel.edu Cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu Subject: Re: NIH Image and MAC OS X Message-ID: Wayne: Last time you mentioned that the documentation for Image/J was not yet available. Is it now, and if not, when will it become available? Also, and I appologize for my ignorance, what is "Carbon compliant"? ====================================================================== | Professor Walter Wolf, Ph.D. E-Mail: wwolfw@hsc.usc.edu | | Distinguished Professor of Pharmaceutical Sciences | | Director, Pharmacokinetic Imaging Program | | Department of Pharmaceutical Sciences, School of Pharmacy | | University of Southern California Telephone: 323-442-1405 | | 1985 Zonal Ave., Los Angeles, CA 90033 Fax: 323-442-9804 | | | |Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute| | MRI at St. Vincent Medical Center Telephone: 213-484-7235 | | 2131 Third St., Los Angeles, CA 90057 Fax: 213-484-7447 | ====================================================================== ------------------------------ Date: Thu, 3 Sep 1998 11:55:34 -0400 From: Carl Gustafson To: nih-image@io.ece.drexel.edu Subject: Carbon Compliance (Was: NIH Image and MAC OS X) Message-Id: Content-Type: text/plain; charset="us-ascii" >Also, and I appologize for my ignorance, what is "Carbon compliant"? Apple Computer went over their system software libraries (APIs, in geek speek), and weeded out a large number of routines that either were rarely used, superceded by other routines, or were just too crufty to continue to maintain and still allow for advancement of their system software. The routines that survived the cut are now known as the Carbon APIs. (And yes, there have been programmer-jokes about being carbon-based.) Anyway, a carbon-compliant program is one that doesn't call routines not in the official, honest-to-Apple, totally cool and approved Carbon APIs. Calling non-existent routines is a generally bad thing, and will usually toast the application. There is a test application that Apple has available called the carbon dater, that will check any application, and score it for compatibility, BTW. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== ------------------------------ Date: Thu, 3 Sep 1998 11:10:44 -0500 (CDT) From: Doug Martin To: nih-image@io.ece.drexel.edu Subject: maximum stack and text sizes Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know of a way to get around the maximum stack size (1000 frames) or text clipboard size (32K), or of a version of image which as been modified to increase these limits? Thanks a million, Douglas Martin University of Texas at Austin ------------------------------ Date: Thu, 3 Sep 1998 12:17:37 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image and MAC OS X Message-Id: Content-Type: text/plain; charset="us-ascii" >Wayne: > >Last time you mentioned that the documentation for Image/J was not yet >available. Is it now, and if not, when will it become available? There is some prelimimary HTML documentation for Image/J at: http://rsb.info.nih.gov/ij/ >Also, and I appologize for my ignorance, what is "Carbon compliant"? Henry Knorr has a good article about Mac OS X and Carbon at: http://www1.macintouch.com/norr006.html -wayne ------------------------------ Date: Thu, 3 Sep 1998 12:44:42 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: maximum stack and text sizes Message-Id: Content-Type: text/plain; charset="us-ascii" >Does anyone know of a way to get around the maximum stack size (1000 >frames) or text clipboard size (32K), or of a version of image which as >been modified to increase these limits? NIH Image 1.62b21 at ftp://codon.nih.gov/pub/nih-image/nih-image162b21_fat.hqx has a maximum stack size of 5000, at least on PowerMacs. There is no easy fix for the 32K text size limit since it's built into the Mac OS TextEdit toolbox routine. -wayne ------------------------------ Date: Thu, 03 Sep 1998 19:07:07 +0100 From: domenico di girolamo To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image and MAC OS X Message-ID: <35EEDACB.25D7@cisea.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hello, I have two further question: - it will support Scion framegrabbers? - how about the existing usermacros(i'm not a Java programmer)? TIA -dom ------------------------------ Date: Thu, 3 Sep 1998 10:06:40 -0700 (PDT) From: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: G3 AV problems continued Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am wondering if any progress has been made on the fact that NIH Image is not compatible with the G3 built in digitizer. It seems like a long time has gone by, and the proposed solution doesn't really work. Are there any plans to implement support for the digitizer? Thanks, Stephan ------------------------------- Stephan G. Anagnostaras, Ph.D. UCLA Dept. of Neurobiology stephan@lifesci.ucla.edu sanagnos@mediaone.net 310-822-7100 / 306-0294 ------------------------------- ------------------------------ Date: Thu, 3 Sep 1998 14:04:08 -0400 From: Gloria Hoffman To: nih-image@io.ece.drexel.edu Subject: counting/cataloging Message-Id: Content-Type: text/plain; charset="us-ascii" This may be simple and I have missed something very obvious but....I would like to take drawings made on Adobe Illustrator or Canvas, acquired from a digital pad/camera lucida and obtain numbers of the objects I have drawn, then tally them up according to the color I have selected for those objects (perhaps 3 or four at most). Does anyone know a program (NIH image eg) that could do that after importing images from either application? Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Fax 410 706-2512 email gehoffma@umaryland.edu ------------------------------ Date: Thu, 3 Sep 1998 16:31:23 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image and MAC OS X Message-Id: Content-Type: text/plain; charset="us-ascii" >hello, >I have two further question: >- it will support Scion framegrabbers? >- how about the existing usermacros(i'm not a Java programmer)? >TIA >-dom I plan to add frame grabber support and a Pascal-like macro interpreter to Image.J but it may be a year or two. There is a list of planned features at: http://rsb.info.nih.gov/ij/docs/to-do-list.html -wayne ------------------------------ Date: 03 Sep 98 14:10:59 -0600 From: Steven Moore To: "nih-image@biomed.drexel.edu" Subject: Video Digitizer Error 2208, Re-visited Message-ID: <1307290659-53216033@mailhost.cipe.com> Content-Type: text/plain; charset="US-Ascii" Content-Transfer-Encoding: 8bit Hello, I took a tech support call from a teacher in Oregon who was attempting to use the Start Capture command on NIH Image 1.61 (and 1.62) installed on a Mac 5500 AV. He received the message Video Digitizer Error 2208, Turn Off Virtual Memory or RAM Doubler. After turning Virtual Memory off and restarting the machine, he still got the same message. I've searched the archive and found messages about this problem dating back to 1995, but no solution. Can anybody tell me how to solve this problem? Thanks. Steven D. Moore, Ph.D. Director of Evaluation Services Center for Image Processing in Education Tucson, AZ stevem@cipe.com http://www.cipe.com (800) 322-9884 ext. 125 ------------------------------ Date: Fri, 4 Sep 1998 11:48:12 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: gehoffma@umaryland.edu, nih-image@io.ece.drexel.edu Subject: Re: counting/cataloging Message-ID: <7A6E6244344@rna.bio.mq.edu.au> >Date: Thu, 3 Sep 1998 14:04:08 -0400 >To: nih-image@io.ece.drexel.edu >From: Gloria Hoffman >Subject: counting/cataloging > >This may be simple and I have missed something very obvious but....I would >like to take drawings made on Adobe Illustrator or Canvas, acquired from a >digital pad/camera lucida and obtain numbers of the objects I have drawn, >then tally them up according to the color I have selected for those objects >(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that >could do that after importing images from either application? >Gloria E. Hoffman, Ph.D. >Department of Anatomy and Neurobiology >685 W Baltimore St >Baltimore MD 21201 >Phone 410 706-2438 >Fax 410 706-2512 >email gehoffma@umaryland.edu In principle, NIH-Image analyzeParticles will do this quite well. In practice, there are a few wrinkles and computer internals that need to be addressed. Adobe Illustrator files are text files containing directives, coordinates etc rather than pixelated images. You can convert Adobe Illustrator files to pixelated images in TIFF format acceptable to NIH-Image by: open Illustrator file in Photoshop, flaten (to remove layers) and convert to RGB then save as an uncompressed 8 bit TIFF image. You can then open the TIFF image in NIH-Image. As image is RGB, you will then have a 3 frame stack (Red Green Blue) and/or an indexed color representation of the image. Density sliceing; analyzeParticles; can then be applied to either(any) of these to count/measure the particles by color. How easy the color to RGB stack or indexed color is to you will depend on your understanding of color separations and the colors you used in Illustrator. Rather than go into that here, try it to see what you get. It will be much easier to understand by inspection than by an attempted pracie by email. Come back (with a sample) if you have problems. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #52 *************************************** From nih-image-request@io.ece.drexel.edu Fri Sep 4 07:56 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA22916; Fri, 4 Sep 1998 07:56:42 -0400 (EDT) Resent-Date: Fri, 4 Sep 1998 07:56:42 -0400 (EDT) X-Sender: zacchetti.daniele@mail.hsr.it Message-Id: Mime-Version: 1.0 Date: Fri, 4 Sep 1998 13:51:50 +0200 To: nih-image@io.ece.drexel.edu From: Daniele Zacchetti Subject: NIH Image and Hamamatsu camera Resent-Message-ID: <"35j-z3.0.vJ5.h9zxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/299 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 577 Dear All, I'm just on the way to setup a videoimaging with a Hamamatsu Orca camera and I would like to use NIH Image (or Image/J) for acquisition and analysis. I have two main (and probably naive) questions: -which frame grabber should I need? Is there a plug-in to control the camera? -can NIH Image handle the acquisition of 12/14/16 bit images from the camera? TIA Daniele Dr. Daniele Zacchetti, PhD Cellular Neurophysiology Unit Dibit, San Raffaele Inst. via Olgettina 58 20132 Milano, Italy Phone: +39-02-2643-4812 Fax:+39-02-2643-4813 e-mail: zacchetti.daniele@hsr.it From nih-image-request@io.ece.drexel.edu Fri Sep 4 08:12 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA24273; Fri, 4 Sep 1998 08:11:57 -0400 (EDT) Resent-Date: Fri, 4 Sep 1998 08:11:57 -0400 (EDT) X-Sender: zacchetti.daniele@mail.hsr.it Message-Id: Mime-Version: 1.0 Date: Fri, 4 Sep 1998 14:10:50 +0200 To: NIH Image mailing list From: Daniele Zacchetti Resent-Message-ID: <"vH1lJ.0.Xj5.RRzxr"@io> Resent-From: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/300 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 25 egrep grabber latest/* From nih-image-request@io.ece.drexel.edu Fri Sep 4 08:48 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA27365; Fri, 4 Sep 1998 08:48:37 -0400 (EDT) Resent-Date: Fri, 4 Sep 1998 08:48:37 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Fri, 4 Sep 1998 08:40:50 -0400 To: nih-image@io.ece.drexel.edu From: Marc Steed Subject: Stereology Resent-Message-ID: <"tdUrh1.0.ZP6.Rxzxr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/301 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 226 List Members: Has anyone conducted stereological analyses with IMAGE? Marc A. Steed, M.S. Department of Psychology University of Cincinnati P.O. Box 210376 Cincinnati, OH 45221-0376 513-556-1615 (lab) 513-556-1904 (fax) From nih-image-request@io.ece.drexel.edu Fri Sep 4 10:58 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA07531; Fri, 4 Sep 1998 10:58:33 -0400 (EDT) Resent-Date: Fri, 4 Sep 1998 10:58:33 -0400 (EDT) From: "Herbert M. Geller" To: nih-image@io.ece.drexel.edu Subject: Metamorph to NIH Image In-Reply-To: Message-ID: Date: Fri, 4 Sep 1998 10:51:57 -0400 (Eastern Daylight Time) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1.5 Build (43) X-Authentication: none MIME-Version: 1.0 Resent-Message-ID: <"FkAq03.0.NX1.Eo_xr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/302 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 496 Has anyone taken a Metamorph stack of images and imported them into NIH Image as a stack? My colleague has captured a series of images on Metamorph which I would like to analyze. ---------------------------------------------------------- Herbert M. Geller, Ph.D. Professor Department of Pharmacology voice - 732-235-4084 Robert Wood Johnson Medical School fax - 732-235-4073 Piscataway, New Jersey 08854 Internet - geller@umdnj.edu www: http//www2.umdnj.edu/~geller/lab/ From nih-image-request@io.ece.drexel.edu Fri Sep 4 15:07 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA24489; Fri, 4 Sep 1998 15:06:12 -0400 (EDT) Resent-Date: Fri, 4 Sep 1998 15:06:12 -0400 (EDT) Message-ID: <35F044F1.D1BB624B@netmatters.co.uk> Date: Fri, 04 Sep 1998 19:52:20 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Metamorph to NIH Image References: Content-Transfer-Encoding: 8bit Resent-Message-ID: <"LizRr3.0.fj5.rP3yr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/303 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1111 I've seen it done Metamorph (PC) to NIH Image (Mac). It was pretty strait forward, it should just open like any other PIC or TIFF stack. Scion Image b2 (PC) did not work managing to misalign all the images through the stack or simply crashed when trying to open the file. I would hope that an £8000 package like Metamorph would come with all the features of NIH anyway. Apparently not. Jeremy Herbert M. Geller wrote: > Has anyone taken a Metamorph stack of images and imported > them into NIH Image as a stack? My colleague has captured > a series of images on Metamorph which I would like to > analyze. > > ---------------------------------------------------------- > Herbert M. Geller, Ph.D. > Professor > Department of Pharmacology voice - 732-235-4084 > Robert Wood Johnson Medical School fax - 732-235-4073 > Piscataway, New Jersey 08854 Internet - geller@umdnj.edu > www: http//www2.umdnj.edu/~geller/lab/ *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html From nih-image-request@io.ece.drexel.edu Fri Sep 4 15:35 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA26522; Fri, 4 Sep 1998 15:34:46 -0400 (EDT) Resent-Date: Fri, 4 Sep 1998 15:34:46 -0400 (EDT) Date: Fri, 04 Sep 1998 15:19:31 -0500 (EST) From: Glenn Holm Subject: Re: counting/cataloging In-reply-to: Your message dated "Thu, 03 Sep 1998 14:04:08 -0400" To: nih-image@io.ece.drexel.edu Message-id: <01J1EW20MTIC8WXUEO@wccf.mit.edu> Organization: Mass. Inst. Tech. - Whitaker College MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"5jZv22.0.kF6.Fu3yr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/304 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1159 Macromedia FreeHand has find and replace by fill/stroke color attribute and tells you how many drawing objects of a particular color it finds. Perhaps Illustrator and/or Canvas also has that feature. >This may be simple and I have missed something very obvious but....I would >like to take drawings made on Adobe Illustrator or Canvas, acquired from a >digital pad/camera lucida and obtain numbers of the objects I have drawn, >then tally them up according to the color I have selected for those objects >(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that >could do that after importing images from either application? >Gloria E. Hoffman, Ph.D. >Department of Anatomy and Neurobiology >685 W Baltimore St >Baltimore MD 21201 >Phone 410 706-2438 >Fax 410 706-2512 >email gehoffma@umaryland.edu ------------------------------------------------------------------ |Glenn Holm | |Graybiel Lab (617)253-5780;fax (617)253-1599 | |M.I.T Dept. of Brain + Cog. Sci. Cambridge, MA 02139 | ------------------------------------------------------------------ From nih-image-d-request@io.ece.drexel.edu Sat Sep 5 06:09 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA01865; Sat, 5 Sep 1998 06:09:42 -0400 (EDT) Date: Sat, 5 Sep 1998 06:09:42 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809051009.GAA01865@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #53 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/53 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6118 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 53 Today's Topics: NIH Image and Hamamatsu camera [ Daniele Zacchetti ] Metamorph to NIH Image [ "Herbert M. Geller" ] ------------------------------ Date: Fri, 4 Sep 1998 13:51:50 +0200 From: Daniele Zacchetti To: nih-image@io.ece.drexel.edu Subject: NIH Image and Hamamatsu camera Message-Id: Content-Type: text/plain; charset="us-ascii" Dear All, I'm just on the way to setup a videoimaging with a Hamamatsu Orca camera and I would like to use NIH Image (or Image/J) for acquisition and analysis. I have two main (and probably naive) questions: -which frame grabber should I need? Is there a plug-in to control the camera? -can NIH Image handle the acquisition of 12/14/16 bit images from the camera? TIA Daniele Dr. Daniele Zacchetti, PhD Cellular Neurophysiology Unit Dibit, San Raffaele Inst. via Olgettina 58 20132 Milano, Italy Phone: +39-02-2643-4812 Fax:+39-02-2643-4813 e-mail: zacchetti.daniele@hsr.it ------------------------------ Date: Fri, 4 Sep 1998 14:10:50 +0200 From: Daniele Zacchetti To: NIH Image mailing list Subject: Unidentified subject! Message-Id: Content-Type: text/plain; charset="us-ascii" egrep grabber latest/* ------------------------------ Date: Fri, 4 Sep 1998 08:40:50 -0400 From: Marc Steed To: nih-image@io.ece.drexel.edu Subject: Stereology Message-Id: Content-Type: text/plain; charset="us-ascii" List Members: Has anyone conducted stereological analyses with IMAGE? Marc A. Steed, M.S. Department of Psychology University of Cincinnati P.O. Box 210376 Cincinnati, OH 45221-0376 513-556-1615 (lab) 513-556-1904 (fax) ------------------------------ Date: Fri, 4 Sep 1998 10:51:57 -0400 (Eastern Daylight Time) From: "Herbert M. Geller" To: nih-image@io.ece.drexel.edu Subject: Metamorph to NIH Image Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Has anyone taken a Metamorph stack of images and imported them into NIH Image as a stack? My colleague has captured a series of images on Metamorph which I would like to analyze. ---------------------------------------------------------- Herbert M. Geller, Ph.D. Professor Department of Pharmacology voice - 732-235-4084 Robert Wood Johnson Medical School fax - 732-235-4073 Piscataway, New Jersey 08854 Internet - geller@umdnj.edu www: http//www2.umdnj.edu/~geller/lab/ ------------------------------ Date: Fri, 04 Sep 1998 19:52:20 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: Metamorph to NIH Image Message-ID: <35F044F1.D1BB624B@netmatters.co.uk> Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 8bit I've seen it done Metamorph (PC) to NIH Image (Mac). It was pretty strait forward, it should just open like any other PIC or TIFF stack. Scion Image b2 (PC) did not work managing to misalign all the images through the stack or simply crashed when trying to open the file. I would hope that an £8000 package like Metamorph would come with all the features of NIH anyway. Apparently not. Jeremy Herbert M. Geller wrote: > Has anyone taken a Metamorph stack of images and imported > them into NIH Image as a stack? My colleague has captured > a series of images on Metamorph which I would like to > analyze. > > ---------------------------------------------------------- > Herbert M. Geller, Ph.D. > Professor > Department of Pharmacology voice - 732-235-4084 > Robert Wood Johnson Medical School fax - 732-235-4073 > Piscataway, New Jersey 08854 Internet - geller@umdnj.edu > www: http//www2.umdnj.edu/~geller/lab/ *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html ------------------------------ Date: Fri, 04 Sep 1998 15:19:31 -0500 (EST) From: Glenn Holm To: nih-image@io.ece.drexel.edu Subject: Re: counting/cataloging Message-id: <01J1EW20MTIC8WXUEO@wccf.mit.edu> Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Macromedia FreeHand has find and replace by fill/stroke color attribute and tells you how many drawing objects of a particular color it finds. Perhaps Illustrator and/or Canvas also has that feature. >This may be simple and I have missed something very obvious but....I would >like to take drawings made on Adobe Illustrator or Canvas, acquired from a >digital pad/camera lucida and obtain numbers of the objects I have drawn, >then tally them up according to the color I have selected for those objects >(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that >could do that after importing images from either application? >Gloria E. Hoffman, Ph.D. >Department of Anatomy and Neurobiology >685 W Baltimore St >Baltimore MD 21201 >Phone 410 706-2438 >Fax 410 706-2512 >email gehoffma@umaryland.edu ------------------------------------------------------------------ |Glenn Holm | |Graybiel Lab (617)253-5780;fax (617)253-1599 | |M.I.T Dept. of Brain + Cog. Sci. Cambridge, MA 02139 | ------------------------------------------------------------------ -------------------------------- End of nih-image-d Digest V98 Issue #53 *************************************** From nih-image-request@io.ece.drexel.edu Sat Sep 5 07:40 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA09800; Sat, 5 Sep 1998 07:39:55 -0400 (EDT) Resent-Date: Sat, 5 Sep 1998 07:39:55 -0400 (EDT) Message-ID: <35F120F8.FCACA4D5@virginia.edu> Date: Sat, 05 Sep 1998 07:31:04 -0400 From: Lance Davidson X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Metamorph to NIH Image References: <199809051008.GAA01644@io.ECE.Drexel.EDU> Resent-Message-ID: <"b5lyk.0.8A2.n3Iyr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/305 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="------------BC7C11B71928C9E56283692C" Content-Length: 3036 --------------BC7C11B71928C9E56283692C Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Here are two different ways you can transfer stacks from Metamorph to NIH-Image: 1. In Metamorph - save stack as a sequentially numbered series of single frame tiff files. 2. In NIH-Image - open all those files and use "windows to stack". Or 1. In Metamorph - use "save as" a Biorad MRC-600 stack to produce a stack of images that have the same format as a Biorad confocal stack. 2. In NIH-Image - Use the "I/O macros" and open the stack as a Biorad MRC-500 file. These are just two ways to do this and I'm sure others here can think of several other ways to do this. However, the quaint idea of just opening the metamorph stack file as a tiff will not work. Metamorph hides alot of other information in their file format (it is proprietary). The Biorad format is not proprietary. There is almost no such thing as "standard" tiff. The format specifications (tiff 5.0 last time I looked) allow for so much variability that special features such as multi-image or 16 bit files are almost never supported outside of their native program. As others have commented here in the past, the only truely portable format is the single image tiff format. Good luck transferring, Lance ----------------------------- Lance Davidson Research Associate (postdoc) Department of Biology University of Virginia Charlottesville, VA 22903 804-243-2596 --------------BC7C11B71928C9E56283692C Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Here are two different ways you can transfer stacks from Metamorph to NIH-Image:

1. In Metamorph - save stack as a sequentially numbered series of single frame tiff files.
2. In NIH-Image - open all those files and use "windows to stack".

Or

1. In Metamorph - use "save as" a Biorad MRC-600 stack to produce a stack of images that have the same format as a Biorad confocal stack.
2. In NIH-Image - Use the "I/O macros" and open the stack as a Biorad MRC-500 file.

These are just two ways to do this and I'm sure others here can think of several other ways to do this. However, the quaint idea of just opening the metamorph stack file as a tiff will not work. Metamorph hides alot of other information in their file format (it is proprietary). The Biorad format is not proprietary. There is almost no such thing as "standard" tiff. The format specifications (tiff 5.0 last time I looked) allow for so much variability that special features such as multi-image or 16 bit files are almost never supported outside of their native program.

As others have commented here in the past, the only truely portable format is the single image tiff format.

Good luck transferring,

Lance

-----------------------------
Lance Davidson
Research Associate (postdoc)
Department of Biology
University of Virginia
Charlottesville, VA 22903
804-243-2596 --------------BC7C11B71928C9E56283692C-- From nih-image-d-request@io.ece.drexel.edu Sun Sep 6 06:18 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA07208; Sun, 6 Sep 1998 06:18:55 -0400 (EDT) Date: Sun, 6 Sep 1998 06:18:55 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809061018.GAA07208@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #54 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/54 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3658 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 54 Today's Topics: Re: Metamorph to NIH Image [ Lance Davidson ] ------------------------------ Date: Sat, 05 Sep 1998 07:31:04 -0400 From: Lance Davidson To: nih-image@io.ece.drexel.edu Subject: Re: Metamorph to NIH Image Message-ID: <35F120F8.FCACA4D5@virginia.edu> Content-Type: multipart/alternative; boundary="------------BC7C11B71928C9E56283692C" --------------BC7C11B71928C9E56283692C Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Here are two different ways you can transfer stacks from Metamorph to NIH-Image: 1. In Metamorph - save stack as a sequentially numbered series of single frame tiff files. 2. In NIH-Image - open all those files and use "windows to stack". Or 1. In Metamorph - use "save as" a Biorad MRC-600 stack to produce a stack of images that have the same format as a Biorad confocal stack. 2. In NIH-Image - Use the "I/O macros" and open the stack as a Biorad MRC-500 file. These are just two ways to do this and I'm sure others here can think of several other ways to do this. However, the quaint idea of just opening the metamorph stack file as a tiff will not work. Metamorph hides alot of other information in their file format (it is proprietary). The Biorad format is not proprietary. There is almost no such thing as "standard" tiff. The format specifications (tiff 5.0 last time I looked) allow for so much variability that special features such as multi-image or 16 bit files are almost never supported outside of their native program. As others have commented here in the past, the only truely portable format is the single image tiff format. Good luck transferring, Lance ----------------------------- Lance Davidson Research Associate (postdoc) Department of Biology University of Virginia Charlottesville, VA 22903 804-243-2596 --------------BC7C11B71928C9E56283692C Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Here are two different ways you can transfer stacks from Metamorph to NIH-Image:

1. In Metamorph - save stack as a sequentially numbered series of single frame tiff files.
2. In NIH-Image - open all those files and use "windows to stack".

Or

1. In Metamorph - use "save as" a Biorad MRC-600 stack to produce a stack of images that have the same format as a Biorad confocal stack.
2. In NIH-Image - Use the "I/O macros" and open the stack as a Biorad MRC-500 file.

These are just two ways to do this and I'm sure others here can think of several other ways to do this. However, the quaint idea of just opening the metamorph stack file as a tiff will not work. Metamorph hides alot of other information in their file format (it is proprietary). The Biorad format is not proprietary. There is almost no such thing as "standard" tiff. The format specifications (tiff 5.0 last time I looked) allow for so much variability that special features such as multi-image or 16 bit files are almost never supported outside of their native program.

As others have commented here in the past, the only truely portable format is the single image tiff format.

Good luck transferring,

Lance

-----------------------------
Lance Davidson
Research Associate (postdoc)
Department of Biology
University of Virginia
Charlottesville, VA 22903
804-243-2596 --------------BC7C11B71928C9E56283692C-- -------------------------------- End of nih-image-d Digest V98 Issue #54 *************************************** From nih-image-request@io.ece.drexel.edu Sun Sep 6 12:16 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA09665; Sun, 6 Sep 1998 12:15:50 -0400 (EDT) Resent-Date: Sun, 6 Sep 1998 12:15:50 -0400 (EDT) Message-ID: <009001bdd9af$71afe920$0f0a13c0@oemcomputer> From: "Joan Main" To: "scion image" Subject: Fw: scion image histogram plots Date: Sun, 6 Sep 1998 09:00:16 -0700 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Resent-Message-ID: <"8Soye2.0.I22.DBhyr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/306 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 1105 -----Original Message----- From: Joan Main To: joan.main@gte.net Date: Wednesday, September 02, 1998 3:46 PM Subject: scion image histogram plots > Hi, > I have a very urgent question regarding measurements: > > 1. Histograms from ROI's, retangle is the only tool available for > histograms? > 2. Can you label the plot with the intensities? > > 3. I can not savew the Histogram, can only print from screen print? > > 4. URGENT: I can't find definition or macro for what is being > calculated for the intergrated density. > > > 5. I have just finished a series of measurements on 6 animals, the > data doesn't make sense....is there a way I can measure the MODAL not > the mean of the pixel intensities within an ROI? > > Please let me know if Beta 3 version is ready for download...I know > you notified me that Beta 3 fixed the image problem I had reported... > > Thank you for your prompt help > Joan Main > Joan.Main@gte.net or jmain @ acuson.com > > > From nih-image-request@io.ece.drexel.edu Sun Sep 6 12:16 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA09676; Sun, 6 Sep 1998 12:15:53 -0400 (EDT) Resent-Date: Sun, 6 Sep 1998 12:15:53 -0400 (EDT) Message-ID: <009501bdd9af$b3c0c0a0$0f0a13c0@oemcomputer> From: "Joan Main" To: "scion image" Subject: Fw: subscribe: scion image histogram plots Date: Sun, 6 Sep 1998 09:02:07 -0700 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Resent-Message-ID: <"JFmWV.0.062.yChyr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/307 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 1335 -----Original Message----- From: Joan Main To: scion image Date: Sunday, September 06, 1998 9:00 AM Subject: Fw: scion image histogram plots > >-----Original Message----- >From: Joan Main >To: joan.main@gte.net >Date: Wednesday, September 02, 1998 3:46 PM >Subject: scion image histogram plots > > >> Hi, >> I have a very urgent question regarding measurements: >> >> 1. Histograms from ROI's, retangle is the only tool available for >> histograms? >> 2. Can you label the plot with the intensities? >> >> 3. I can not savew the Histogram, can only print from screen print? >> >> 4. URGENT: I can't find definition or macro for what is being >> calculated for the intergrated density. >> >> >> 5. I have just finished a series of measurements on 6 animals, the >> data doesn't make sense....is there a way I can measure the MODAL not >> the mean of the pixel intensities within an ROI? >> >> Please let me know if Beta 3 version is ready for download...I know >> you notified me that Beta 3 fixed the image problem I had reported... >> >> Thank you for your prompt help >> Joan Main >> Joan.Main@gte.net or jmain @ acuson.com >> >> >> > From nih-image-request@io.ece.drexel.edu Mon Sep 7 05:43 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA11372; Mon, 7 Sep 1998 05:43:46 -0400 (EDT) Resent-Date: Mon, 7 Sep 1998 05:43:46 -0400 (EDT) From: "j.gregory" Sender: ort056@abdn.ac.uk To: nih-image@io.ece.drexel.edu Subject: Re: Fw: subscribe: scion image histogram plots Message-ID: Date: Mon, 7 Sep 1998 10:40:11 +0100 (BST) Delivery-Receipt-To: "j.gregory" Priority: NORMAL X-Mailer: Simeon for Windows Version 4.0.9 X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"FQ9CB.0.eQ2.6Vwyr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/308 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 572 > > > >> Hi, > >> I have a very urgent question regarding measurements: > >> > >> 3. I can not savew the Histogram, can only print from screen > print? > >> > > >> Thank you for your prompt help > >> Joan Main I can help you with this one, Whilst the histogram window is selected, choose File/Export from the menu bar. This saves the histogram values as a text file (Change the extension to .txt) you can then open them up somewhere else such as Excel & do whatever you want with them. Jenny ---------------------- j.gregory@abdn.ac.uk From nih-image-d-request@io.ece.drexel.edu Mon Sep 7 05:49 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA12221; Mon, 7 Sep 1998 05:49:37 -0400 (EDT) Date: Mon, 7 Sep 1998 05:49:37 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809070949.FAA12221@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #55 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/55 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4441 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 55 Today's Topics: Fw: scion image histogram plots [ "Joan Main" ] Fw: subscribe: scion image histogram [ "Joan Main" ] Re: Fw: subscribe: scion image histo [ "j.gregory" ] ------------------------------ Date: Sun, 6 Sep 1998 09:00:16 -0700 From: "Joan Main" To: "scion image" Subject: Fw: scion image histogram plots Message-ID: <009001bdd9af$71afe920$0f0a13c0@oemcomputer> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit -----Original Message----- From: Joan Main To: joan.main@gte.net Date: Wednesday, September 02, 1998 3:46 PM Subject: scion image histogram plots > Hi, > I have a very urgent question regarding measurements: > > 1. Histograms from ROI's, retangle is the only tool available for > histograms? > 2. Can you label the plot with the intensities? > > 3. I can not savew the Histogram, can only print from screen print? > > 4. URGENT: I can't find definition or macro for what is being > calculated for the intergrated density. > > > 5. I have just finished a series of measurements on 6 animals, the > data doesn't make sense....is there a way I can measure the MODAL not > the mean of the pixel intensities within an ROI? > > Please let me know if Beta 3 version is ready for download...I know > you notified me that Beta 3 fixed the image problem I had reported... > > Thank you for your prompt help > Joan Main > Joan.Main@gte.net or jmain @ acuson.com > > > ------------------------------ Date: Sun, 6 Sep 1998 09:02:07 -0700 From: "Joan Main" To: "scion image" Subject: Fw: subscribe: scion image histogram plots Message-ID: <009501bdd9af$b3c0c0a0$0f0a13c0@oemcomputer> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit -----Original Message----- From: Joan Main To: scion image Date: Sunday, September 06, 1998 9:00 AM Subject: Fw: scion image histogram plots > >-----Original Message----- >From: Joan Main >To: joan.main@gte.net >Date: Wednesday, September 02, 1998 3:46 PM >Subject: scion image histogram plots > > >> Hi, >> I have a very urgent question regarding measurements: >> >> 1. Histograms from ROI's, retangle is the only tool available for >> histograms? >> 2. Can you label the plot with the intensities? >> >> 3. I can not savew the Histogram, can only print from screen print? >> >> 4. URGENT: I can't find definition or macro for what is being >> calculated for the intergrated density. >> >> >> 5. I have just finished a series of measurements on 6 animals, the >> data doesn't make sense....is there a way I can measure the MODAL not >> the mean of the pixel intensities within an ROI? >> >> Please let me know if Beta 3 version is ready for download...I know >> you notified me that Beta 3 fixed the image problem I had reported... >> >> Thank you for your prompt help >> Joan Main >> Joan.Main@gte.net or jmain @ acuson.com >> >> >> > ------------------------------ Date: Mon, 7 Sep 1998 10:40:11 +0100 (BST) From: "j.gregory" To: nih-image@io.ece.drexel.edu Subject: Re: Fw: subscribe: scion image histogram plots Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > > > >> Hi, > >> I have a very urgent question regarding measurements: > >> > >> 3. I can not savew the Histogram, can only print from screen > print? > >> > > >> Thank you for your prompt help > >> Joan Main I can help you with this one, Whilst the histogram window is selected, choose File/Export from the menu bar. This saves the histogram values as a text file (Change the extension to .txt) you can then open them up somewhere else such as Excel & do whatever you want with them. Jenny ---------------------- j.gregory@abdn.ac.uk -------------------------------- End of nih-image-d Digest V98 Issue #55 *************************************** From nih-image-request@io.ece.drexel.edu Mon Sep 7 11:39 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA13256; Mon, 7 Sep 1998 11:38:25 -0400 (EDT) Resent-Date: Mon, 7 Sep 1998 11:38:25 -0400 (EDT) X-Sender: cesc@cucafera Message-Id: Mime-Version: 1.0 Date: Mon, 7 Sep 1998 17:27:30 +0200 To: nih-image@io.ece.drexel.edu From: Francesc Peters Subject: image analysis setup Resent-Message-ID: <"JcXPf.0.Kw2.5i_yr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/309 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1206 Hi all, Our biological oceanography dept. wants a brand new microscopy/image analysis setup, especially for epifluorescence microscopy (natural bacterial and algal samples, stained with a variety of fluorochromes), but also wants to have the flexibility to have phase contrast. They have about $100000. I figure that about $40000-$50000 can go to the microscope. They asked me about cameras and image analysis systems. I am not used to such big bugs, so can somebody give me advice on expensive cameras (cooled, 3CCD, etc.) and image analysis systems (based on Silicon Graphics workstations perhaps?), and what are their advantages, enhancements, etc, over less expensive systems. I'd appreciate each and every advice and suggestion. I need to give my input to the dept by *yesterday*. Thanks a lot to evrybody. cesc. ****************************************************************** PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!! Francesc Peters FAX: 34-93-221-7340 Institut de Ciencies del Mar (CSIC) Phone: 34-93-221-6416 (Ext. 255) Passeig Joan de Borbo s/n cesc@icm.csic.es E-08039 Barcelona, Catalunya Spain From nih-image-d-request@io.ece.drexel.edu Tue Sep 8 06:15 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA05477; Tue, 8 Sep 1998 06:15:06 -0400 (EDT) Date: Tue, 8 Sep 1998 06:15:06 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809081015.GAA05477@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #56 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/56 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1798 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 56 Today's Topics: image analysis setup [ Francesc Peters To: nih-image@io.ece.drexel.edu Subject: image analysis setup Message-Id: Content-Type: text/plain; charset="us-ascii" Hi all, Our biological oceanography dept. wants a brand new microscopy/image analysis setup, especially for epifluorescence microscopy (natural bacterial and algal samples, stained with a variety of fluorochromes), but also wants to have the flexibility to have phase contrast. They have about $100000. I figure that about $40000-$50000 can go to the microscope. They asked me about cameras and image analysis systems. I am not used to such big bugs, so can somebody give me advice on expensive cameras (cooled, 3CCD, etc.) and image analysis systems (based on Silicon Graphics workstations perhaps?), and what are their advantages, enhancements, etc, over less expensive systems. I'd appreciate each and every advice and suggestion. I need to give my input to the dept by *yesterday*. Thanks a lot to evrybody. cesc. ****************************************************************** PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!! Francesc Peters FAX: 34-93-221-7340 Institut de Ciencies del Mar (CSIC) Phone: 34-93-221-6416 (Ext. 255) Passeig Joan de Borbo s/n cesc@icm.csic.es E-08039 Barcelona, Catalunya Spain -------------------------------- End of nih-image-d Digest V98 Issue #56 *************************************** From nih-image-request@io.ece.drexel.edu Tue Sep 8 08:17 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA16025; Tue, 8 Sep 1998 08:17:19 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 08:17:19 -0400 (EDT) Message-ID: <35F56595.2C3A@pro.via-rs.com.br> Date: Tue, 08 Sep 1998 09:12:53 -0800 From: Luthero Martins Reply-To: luthero@pro.via-rs.com.br X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: question References: <199809041007.GAA14507@io.ECE.Drexel.EDU> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"13h-y1.0.Oc3.-rHzr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/310 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 676 Group! I'm an ophthalmologist in Brazil. We are working with NIH's applications on Ophthalmology, specially with Glaucom, where we study the optic disk and the Retinal Nerve Fiber Layer. We see the variation of this images according of the luminosity's variation. The equipment that give us this image is a Canon Non-Mydriatic Retinal Camera. But the threshold of variations when we apply the OPTIONS DENSITY SLICE is very sensitive. Can we reduce this sensitivity? Or can we work with another part of NIH program? If anybody can help us, thanks. You can see this images and results on: http://www.oftalmologia-digital.com/clininih.html From nih-image-request@io.ece.drexel.edu Tue Sep 8 09:10 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA20694; Tue, 8 Sep 1998 09:10:22 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 09:10:22 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Tue, 8 Sep 1998 09:06:15 -0400 To: nih-image@io.ece.drexel.edu From: Laird Bloom Subject: Transferring ROIs to a new image Resent-Message-ID: <"nQYj23.0.cp4.-gIzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/311 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 650 Hi, I'd like to write a macro that allows me to draw a freehand ROI in an image (e.g., the outline of rhodamine-stained cells), open another image (e.g., the FITC channel image of the same cells), and count particles within the same ROI in the second image. I'd like it to be able to analyze multiple ROIs within the same image, but also to keep the data for each ROI separate. In the NIH Image archives, I saw a suggestion for copying the two images to a stack, then toggling back and forth between slices to do this analysis. Has anyone written such a macro using this or another algorithm? Thanks, Laird Bloom MIT Center for Cancer Research From nih-image-request@io.ece.drexel.edu Tue Sep 8 09:54 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA24318; Tue, 8 Sep 1998 09:53:46 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 09:53:46 -0400 (EDT) Date: Tue, 8 Sep 1998 08:35:35 -0500 (CDT) From: Doug Morris X-Sender: dmorris@phase.med.uiuc.edu To: nih-image@io.ece.drexel.edu Subject: Re: Transferring ROIs to a new image In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"7PkKF2.0.RX5.l9Jzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/312 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1294 I've written a macro set that uses these techniques for multiple ROIs in some specialized magnetic resonance imaging and spectroscopy techniques. The macros are available at the following URL: http://bmrl.med.uiuc.edu:8080/software/macsoft.html Good Luck, Doug | Doug Morris | University of Illinois | | email: dmorris@bmrl.med.uiuc.edu | Biomedical Magnetic Resonance Lab | | fax: 217-244-1330 | 2100 S. Goodwin Ave. | | voice: 217-244-0290 | Urbana Il 61801 | On Tue, 8 Sep 1998, Laird Bloom wrote: > Hi, > I'd like to write a macro that allows me to draw a freehand ROI in > an image (e.g., the outline of rhodamine-stained cells), open another image > (e.g., the FITC channel image of the same cells), and count particles > within the same ROI in the second image. I'd like it to be able to analyze > multiple ROIs within the same image, but also to keep the data for each ROI > separate. In the NIH Image archives, I saw a suggestion for copying the > two images to a stack, then toggling back and forth between slices to do > this analysis. Has anyone written such a macro using this or another > algorithm? > Thanks, > Laird Bloom > MIT Center for Cancer Research > > > From nih-image-request@io.ece.drexel.edu Tue Sep 8 10:40 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA28116; Tue, 8 Sep 1998 10:40:26 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 10:40:26 -0400 (EDT) Mime-Version: 1.0 Message-Id: In-Reply-To: Date: Tue, 8 Sep 1998 10:37:21 -0400 To: nih-image@io.ece.drexel.edu From: Gloria Hoffman Subject: image analysis setup Resent-Message-ID: <"hamSe1.0.HX6.xuJzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/313 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2198 I am working with the Photometrics Sensys camera. It is excellent for relatively low light fluorescence, and maintains pretty high resolution as well. Image analysis with a IP systems software is very friently interface to the camera and enables very easy scripting of routines. The camera with IP software runs about $28,000; there is now an attachement unit that can capture the image using a liquid crystal mechanism that will achieve color for brightfield as well. The capture of phase images is superb with that system as well. (I am a big fan of Nikon's Eclipse microscopes for the scope in that it has such wonderful light transmission for fluorescence) and your system should then run about $55,000-$60,000 for the scope with the best objectives and a variety of fluorescence cubes. Enjoy! >Hi all, > >Our biological oceanography dept. wants a brand new microscopy/image >analysis setup, especially for epifluorescence microscopy (natural >bacterial and algal samples, stained with a variety of fluorochromes), but >also wants to have the flexibility to have phase contrast. They have about >$100000. I figure that about $40000-$50000 can go to the microscope. They >asked me about cameras and image analysis systems. I am not used to such >big bugs, so can somebody give me advice on expensive cameras (cooled, >3CCD, etc.) and image analysis systems (based on Silicon Graphics >workstations perhaps?), and what are their advantages, enhancements, etc, >over less expensive systems. > >I'd appreciate each and every advice and suggestion. I need to give my >input to the dept by *yesterday*. Thanks a lot to evrybody. > >cesc. > >****************************************************************** >PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!! > >Francesc Peters FAX: 34-93-221-7340 >Institut de Ciencies del Mar (CSIC) Phone: 34-93-221-6416 (Ext. 255) >Passeig Joan de Borbo s/n cesc@icm.csic.es >E-08039 Barcelona, Catalunya >Spain Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Fax 410 706-2512 email gehoffma@umaryland.edu From nih-image-request@io.ece.drexel.edu Tue Sep 8 11:00 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA29983; Tue, 8 Sep 1998 11:00:10 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 11:00:10 -0400 (EDT) Message-Id: <199809081445.AA10130@igw.nationalsteel.com> Date: Tue, 08 Sep 1998 10:45:10 -0400 From: Sam Purdy Reply-To: spurdy@nationalsteel.com Organization: National Steel X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: image analysis setup References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"vLYa62.0.5_6._CKzr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/314 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 53 with respect to Gloria HOffmans messge, what is IP? From nih-image-request@io.ece.drexel.edu Tue Sep 8 11:00 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA00045; Tue, 8 Sep 1998 11:00:36 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 11:00:36 -0400 (EDT) Message-Id: <199809081446.AA16363@igw.nationalsteel.com> Date: Tue, 08 Sep 1998 10:45:55 -0400 From: Sam Purdy Reply-To: spurdy@nationalsteel.com Organization: National Steel X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: image analysis setup References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"Rn4EU2.0.007.8DKzr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/315 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 24 With respect to Gloria From nih-image-request@io.ece.drexel.edu Tue Sep 8 11:32 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA02760; Tue, 8 Sep 1998 11:31:46 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 11:31:46 -0400 (EDT) Mime-Version: 1.0 X-Sender: rwadkins@wwwctrc.fs.saci.org Message-Id: In-Reply-To: <199809081003.GAA04310@io.ECE.Drexel.EDU> Date: Tue, 8 Sep 1998 10:23:47 -0600 To: nih-image@io.ece.drexel.edu From: "Randy M. Wadkins" Subject: Epson Photo 700 printers Resent-Message-ID: <"QFBso.0.pL.UfKzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/316 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 801 Hi All: According to the latest MacWorld, the Epson Photo 700 printers are supposed to output images of comparable quality to the Kodak dye sub printers. Would anyone comment whether this is indeed true? Does the Epson Photo 700 or EX output "journal quality" prints, like the dye sub printers do? Thanks, --Randy ****************************************************************** "Godzilla's approach My mouth agape in horror I just bought that car" --Dwight A. Macpherson, _Godzilla_Hiaku_ Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** From nih-image-request@io.ece.drexel.edu Tue Sep 8 11:39 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA03518; Tue, 8 Sep 1998 11:39:35 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 11:39:35 -0400 (EDT) Message-Id: In-Reply-To: References: <199809081003.GAA04310@io.ECE.Drexel.EDU> Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: yip@ibme.utoronto.ca (Christopher Yip) Subject: Re: Epson Photo 700 printers Date: Tue, 8 Sep 1998 11:27:20 -0400 Resent-Message-ID: <"Ehey-1.0.VW.PnKzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/317 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1553 >Hi All: >According to the latest MacWorld, the Epson Photo 700 printers are supposed >to output images of comparable quality to the Kodak dye sub printers. >Would anyone comment whether this is indeed true? Does the Epson Photo 700 >or EX output "journal quality" prints, like the dye sub printers do? > >Thanks, >--Randy >****************************************************************** >"Godzilla's approach >My mouth agape in horror >I just bought that car" --Dwight A. Macpherson, _Godzilla_Hiaku_ > >Randy M. Wadkins, Ph.D. >Cancer Therapy & Research Center >Institute for Drug Development >14960 Omicron Drive >San Antonio, TX 78245 >phone: (210)-677-3835 >fax: (210)-677-0058 >E-mail: rwadkins@saci.org >CTRC Homepage: http://www.ccc.saci.org >****************************************************************** I just picked up an Epson Photo700 as a part of the Polaroid DMC promotion. It is in fact quite nice when printing to photo paper and it's fast - I don't know what the upgrade is to the new Photo740 (besides maybe the USB bus). TIFF images from Photoshop look really sharp (an admittedly qualitative description). Chris. Christopher M. Yip, Ph.D., P.Eng. Assistant Professor Department of Chemical Engineering and Applied Chemistry Institute of Biomedical Engineering Department of Biochemistry University of Toronto 407 Rosebrugh Building, 4 Taddle Creek Rd. Toronto, Ontario CANADA M5S 3G9 Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317; e-mail: yip@ibme.utoronto.ca WWW: http://goldie.ibme.utoronto.ca From nih-image-request@io.ece.drexel.edu Tue Sep 8 12:48 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA09402; Tue, 8 Sep 1998 12:47:44 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 12:47:44 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Tue, 8 Sep 1998 11:29:41 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Re: Transferring ROIs to a new image Resent-Message-ID: <"fnIZJ2.0.mt1.sjLzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/318 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2126 >Hi, > I'd like to write a macro that allows me to draw a freehand ROI in >an image (e.g., the outline of rhodamine-stained cells), open another image >(e.g., the FITC channel image of the same cells), and count particles >within the same ROI in the second image. I'd like it to be able to analyze >multiple ROIs within the same image, but also to keep the data for each ROI >separate. In the NIH Image archives, I saw a suggestion for copying the >two images to a stack, then toggling back and forth between slices to do >this analysis. Has anyone written such a macro using this or another >algorithm? >Thanks, >Laird Bloom >MIT Center for Cancer Research Draw each ROI (you can use the while button loop as discussed last week or so to draw while running a macro) and fill each with a different grayvalue. You can name each by incorporating a getstring command after each delineation. To analyze, make a copy of your delineations and use the density slice to isolate one of the regions. Use AND when pasting to your FITC image to restrict analysis to the ROI. Repeat for each of your delineations. To associate the ROI name with the measurement, write the results to a text window along with the ROI name. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. From nih-image-request@io.ece.drexel.edu Tue Sep 8 17:12 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA02245; Tue, 8 Sep 1998 17:11:54 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 17:11:54 -0400 (EDT) Date: Tue, 8 Sep 1998 13:57:21 -0700 (PDT) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re: stereology In-Reply-To: <199809051010.GAA01941@io.ECE.Drexel.EDU> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"h2DV83.0.U7.vePzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/319 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 16 >>Has onyone From nih-image-request@io.ece.drexel.edu Tue Sep 8 17:15 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA02632; Tue, 8 Sep 1998 17:14:50 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 17:14:50 -0400 (EDT) Date: Tue, 8 Sep 1998 14:00:51 -0700 (PDT) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re:Stereology In-Reply-To: <199809051010.GAA01941@io.ECE.Drexel.EDU> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"gEJu_2.0.EE.AiPzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/320 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 481 what sort of stereology are you going to do? There are 2 sets of stereology macros for Image. One is the 'Stereology plug-ins', the other is called 'Cavalieri3'. Both come with documentation and are available from the Image ftp site Regards, Glen Glen MacDonald Research Scientist Hearing Research Laboratories of the Virginia Merrill Bloedel Hearing Research Center Box 35-7923 University of Washington Seattle, WA 98195-7923 (206) 616-4156 glenmac@u.washington.edu From nih-image-request@io.ece.drexel.edu Tue Sep 8 19:28 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id TAA16333; Tue, 8 Sep 1998 19:28:47 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 19:28:47 -0400 (EDT) From: SolamereTG@aol.com Message-ID: <341e8951.35f5baf8@aol.com> Date: Tue, 8 Sep 1998 19:17:12 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: image analysis setup Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 16-bit for Windows sub 38 Resent-Message-ID: <"bH4Uv3.0.jf3.XiRzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/321 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1090 Less expensive systems are available: In the US the microscope should be under $30,000 (range $15,000 to $30,000) with a full compliment of obj. lens. Frame grabber $3000 or less (range $900 to 3000) digital &/or analog Computer ; G-3 Mac 300 Mhz, 17" monitor, 64 MB, 6GB HD cost under $2500 For non-moving (or fixed) visible specimens that you can illuminate without damage or bleaching I would suggest 1) High resolution on-chip integrating Peltier Cooled CCD (2 stage Peltier) is able to can integrate for minutes athough a second or two is usually enough, cost $6,500. For low light, low level illumination, living specimens sensitive to light then an intensified camera is better. cost ($16,750 to $25,000 (GEN IV intensifier, fiber optically coupled, >550 TVLs). These can also integrate on chip to permit very high magnification, sub-visual (nothing to see in the microscope ocular) imaging. Therefore under $42,000 for a low light but visible imaging system, $55,000 for high end sub-visual imaging. There are several sources. We are one. Solamere Technology Group From nih-image-request@io.ece.drexel.edu Tue Sep 8 20:47 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA24388; Tue, 8 Sep 1998 20:47:26 -0400 (EDT) Resent-Date: Tue, 8 Sep 1998 20:47:26 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: lbloom@MIT.EDU, nih-image@io.ece.drexel.edu Date: Wed, 9 Sep 1998 10:33:20 GMT+1000 Subject: Re: Transferring ROIs to a new image Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <81DAE9E2114@rna.bio.mq.edu.au> Resent-Message-ID: <"3BdSS2.0.eV5.omSzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/322 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2364 >Date: Tue, 8 Sep 1998 09:06:15 -0400 >To: nih-image@io.ece.drexel.edu >From: Laird Bloom > I'd like to write a macro that allows me to draw a freehand ROI in >an image (e.g., the outline of rhodamine-stained cells), open another image >(e.g., the FITC channel image of the same cells), and count particles >within the same ROI in the second image. I'd like it to be able to analyze >multiple ROIs within the same image, but also to keep the data for each ROI >separate. In the NIH Image archives, I saw a suggestion for copying the >two images to a stack, then toggling back and forth between slices to do >this analysis. Has anyone written such a macro using this or another >algorithm? >Thanks, >Laird Bloom >MIT Center for Cancer Research There are a number of approachs available to this including the stack method you mention, the mapping method suggested by Jonathan Nissanov, particular applications as in Doug Morris's site, etc but the simplest most useful method is often overlooked, probably because this specific application is not explicitly mentioned in the manual. The macro restoreRoi or the restore selection (analyse Menu) will restore the previously active selection to the current image (even if a compound ROI selection made using control/option keys). The trick is that the restoration takes effect on the current image even if the ROI was active on a different but previously active image regardless of whether the previous image associated with the ROI was of the same dimensions or not. It is located in the same position relative to 0,0 ie topleft. Thus a ROI established on an image (a roi can be associated with any/each open window) can be transferred from that image to another, simply by: activating the image carrying the ROI; activate the image to receive the ROI; invoke restore selection (analyse Menu) or selectPic(pid2);killRoi; selectPic(pid1);selectPic(pid2);restoreRoi;{transfers ROI from pid1 to 2} In addition, you can selectPic(pid1); SetSaveAs('Outline');saveas('aParticularROI'); selectPic(pid2);open('aParticularROI'); if you want to have a disk record of the ROI. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Wed Sep 9 00:21 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id AAA16796; Wed, 9 Sep 1998 00:21:00 -0400 (EDT) Resent-Date: Wed, 9 Sep 1998 00:21:00 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: luthero@pro.via-rs.com.br, nih-image@io.ece.drexel.edu Date: Wed, 9 Sep 1998 14:12:53 GMT+1000 Subject: Re: question (image contrast optimisation) Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <82157F20EEB@rna.bio.mq.edu.au> Resent-Message-ID: <"sJzKf3.0.dp3.80Wzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/323 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 4437 >Date: Tue, 08 Sep 1998 09:12:53 -0800 >From: Luthero Martins >Reply-To: luthero@pro.via-rs.com.br > >I'm an ophthalmologist in Brazil. We are working with NIH's >applications on Ophthalmology, specially with Glaucom, where we study >the optic disk and the Retinal Nerve Fiber Layer. > We see the variation of this images according of the >luminosity's >variation. > The equipment that give us this image is a Canon Non-Mydriatic >Retinal >Camera. But the threshold of variations when we apply the OPTIONS >DENSITY SLICE is very sensitive. > > Can we reduce this sensitivity? Or can we work with another part >of NIH >program? > > If anybody can help us, thanks. > >You can see this images and results on: >http://www.oftalmologia-digital.com/clininih.html Luthero, I expect what you are after is to get finer discrimination within the bright region of the image where you have made your selection. The following numbers may not be accurate as the images on your web site are JPEG rather than TIFF but should be adequate to make the point. You have used a color camera and apparently chosed to use the green channel image. You dodn't say whether the Canon camera was a digital camera or a video camera with a framgrabber. For a specialised application like this,I would expect that you would potentially get better results with a good monochrome camera (<$1000 US) with an appropriate color filter and a Scion framegrabber(<$1000). It is important to look at and understand the histogram. I will attach an annoted version to a direct email. The histogram spread ranges from 25 or 28 (the bright end) to 248 (the dark end) The peak centered around 238 is not image data but the spread of pixels forming a black border around the image. The image itself has a maximum pixel value of about 210. Hence your image contrast range is at best 210-25 = 185 out of the available 256 values ie 72% of available When you look at the histogram taken when density slice is active, the sliced portion of the histogram is shown in black as opposed to gray for the background. Your slice extends from 25 or 28 to 47 and is <860 pixels of the total 320x240=76800 pixels and is part of an image segment roughly 60 pixels diameter which is much brighter than the background image of the retina but only occupies about 5% of the image and on the histogram is all represented in the low outliers to the left of the double peaked histogram of the main retina. You can see that if your image histogram was spread to fit the available 256 values, then you would have much better contrast discrimination for the bright region of the retina. You should be able to arrange this by adjustment of the brightness,contrast, colour balance controls on the camera if digital or on the framegrabber. If a framegrabber, then, under NIH-Image, set a live histogram while you live capture and you adjust the gain(video control dialogue) up until the histogram is as wide as the histogram window while keeping it in the window by adjusting the offset (down will move it left in window, up will move it right towards the dark end). More extremely, as you know where your region of interest falls on the histogram you can adjust the contrast ie gain up as long as the live histogram remains reasonably stable and keeping the histogram roi within the window by adjusting offset. This will saturate the retina background to be very dark or even black ie >=255 but will maximise discrimination in the intensity range that is of interest for the density slice segmentation. Also if you make a selection that is restricted to the bright region and then use integrate, the integration processing will ensure the max/min levels in the ROI fill the histogram window. If you need to retain contrast info to see blood vessel detail of current image, the you can expand a range of 25 to 25+166= to 256 by cutting off the dark end of the histogram where 191 falls now ie an improvement of 256/166=1.5+ or over 50% or you can take two images with different contrast settings and transfer the segmented ROI from the image contrasted at the bright end to the perceptually acceptable image afterwards. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Wed Sep 9 00:23 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id AAA17221; Wed, 9 Sep 1998 00:23:45 -0400 (EDT) Date: Wed, 9 Sep 1998 00:23:45 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809090423.AAA17221@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #57 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/57 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 23108 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 57 Today's Topics: question [ Luthero Martins ] Re: Transferring ROIs to a new image [ Doug Morris To: nih-image@io.ece.drexel.edu Subject: question Message-ID: <35F56595.2C3A@pro.via-rs.com.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Group! I'm an ophthalmologist in Brazil. We are working with NIH's applications on Ophthalmology, specially with Glaucom, where we study the optic disk and the Retinal Nerve Fiber Layer. We see the variation of this images according of the luminosity's variation. The equipment that give us this image is a Canon Non-Mydriatic Retinal Camera. But the threshold of variations when we apply the OPTIONS DENSITY SLICE is very sensitive. Can we reduce this sensitivity? Or can we work with another part of NIH program? If anybody can help us, thanks. You can see this images and results on: http://www.oftalmologia-digital.com/clininih.html ------------------------------ Date: Tue, 8 Sep 1998 09:06:15 -0400 From: Laird Bloom To: nih-image@io.ece.drexel.edu Subject: Transferring ROIs to a new image Message-Id: Content-Type: text/plain; charset="us-ascii" Hi, I'd like to write a macro that allows me to draw a freehand ROI in an image (e.g., the outline of rhodamine-stained cells), open another image (e.g., the FITC channel image of the same cells), and count particles within the same ROI in the second image. I'd like it to be able to analyze multiple ROIs within the same image, but also to keep the data for each ROI separate. In the NIH Image archives, I saw a suggestion for copying the two images to a stack, then toggling back and forth between slices to do this analysis. Has anyone written such a macro using this or another algorithm? Thanks, Laird Bloom MIT Center for Cancer Research ------------------------------ Date: Tue, 8 Sep 1998 08:35:35 -0500 (CDT) From: Doug Morris To: nih-image@io.ece.drexel.edu Subject: Re: Transferring ROIs to a new image Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I've written a macro set that uses these techniques for multiple ROIs in some specialized magnetic resonance imaging and spectroscopy techniques. The macros are available at the following URL: http://bmrl.med.uiuc.edu:8080/software/macsoft.html Good Luck, Doug | Doug Morris | University of Illinois | | email: dmorris@bmrl.med.uiuc.edu | Biomedical Magnetic Resonance Lab | | fax: 217-244-1330 | 2100 S. Goodwin Ave. | | voice: 217-244-0290 | Urbana Il 61801 | On Tue, 8 Sep 1998, Laird Bloom wrote: > Hi, > I'd like to write a macro that allows me to draw a freehand ROI in > an image (e.g., the outline of rhodamine-stained cells), open another image > (e.g., the FITC channel image of the same cells), and count particles > within the same ROI in the second image. I'd like it to be able to analyze > multiple ROIs within the same image, but also to keep the data for each ROI > separate. In the NIH Image archives, I saw a suggestion for copying the > two images to a stack, then toggling back and forth between slices to do > this analysis. Has anyone written such a macro using this or another > algorithm? > Thanks, > Laird Bloom > MIT Center for Cancer Research > > > ------------------------------ Date: Tue, 8 Sep 1998 10:37:21 -0400 From: Gloria Hoffman To: nih-image@io.ece.drexel.edu Subject: image analysis setup Message-Id: Content-Type: text/plain; charset="us-ascii" I am working with the Photometrics Sensys camera. It is excellent for relatively low light fluorescence, and maintains pretty high resolution as well. Image analysis with a IP systems software is very friently interface to the camera and enables very easy scripting of routines. The camera with IP software runs about $28,000; there is now an attachement unit that can capture the image using a liquid crystal mechanism that will achieve color for brightfield as well. The capture of phase images is superb with that system as well. (I am a big fan of Nikon's Eclipse microscopes for the scope in that it has such wonderful light transmission for fluorescence) and your system should then run about $55,000-$60,000 for the scope with the best objectives and a variety of fluorescence cubes. Enjoy! >Hi all, > >Our biological oceanography dept. wants a brand new microscopy/image >analysis setup, especially for epifluorescence microscopy (natural >bacterial and algal samples, stained with a variety of fluorochromes), but >also wants to have the flexibility to have phase contrast. They have about >$100000. I figure that about $40000-$50000 can go to the microscope. They >asked me about cameras and image analysis systems. I am not used to such >big bugs, so can somebody give me advice on expensive cameras (cooled, >3CCD, etc.) and image analysis systems (based on Silicon Graphics >workstations perhaps?), and what are their advantages, enhancements, etc, >over less expensive systems. > >I'd appreciate each and every advice and suggestion. I need to give my >input to the dept by *yesterday*. Thanks a lot to evrybody. > >cesc. > >****************************************************************** >PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!! > >Francesc Peters FAX: 34-93-221-7340 >Institut de Ciencies del Mar (CSIC) Phone: 34-93-221-6416 (Ext. 255) >Passeig Joan de Borbo s/n cesc@icm.csic.es >E-08039 Barcelona, Catalunya >Spain Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Fax 410 706-2512 email gehoffma@umaryland.edu ------------------------------ Date: Tue, 08 Sep 1998 10:45:10 -0400 From: Sam Purdy To: nih-image@io.ece.drexel.edu Subject: Re: image analysis setup Message-Id: <199809081445.AA10130@igw.nationalsteel.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit with respect to Gloria HOffmans messge, what is IP? ------------------------------ Date: Tue, 08 Sep 1998 10:45:55 -0400 From: Sam Purdy To: nih-image@io.ece.drexel.edu Subject: Re: image analysis setup Message-Id: <199809081446.AA16363@igw.nationalsteel.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit With respect to Gloria ------------------------------ Date: Tue, 8 Sep 1998 10:23:47 -0600 From: "Randy M. Wadkins" To: nih-image@io.ece.drexel.edu Subject: Epson Photo 700 printers Message-Id: Content-Type: text/plain; charset="us-ascii" Hi All: According to the latest MacWorld, the Epson Photo 700 printers are supposed to output images of comparable quality to the Kodak dye sub printers. Would anyone comment whether this is indeed true? Does the Epson Photo 700 or EX output "journal quality" prints, like the dye sub printers do? Thanks, --Randy ****************************************************************** "Godzilla's approach My mouth agape in horror I just bought that car" --Dwight A. Macpherson, _Godzilla_Hiaku_ Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** ------------------------------ Date: Tue, 8 Sep 1998 11:27:20 -0400 From: yip@ibme.utoronto.ca (Christopher Yip) To: nih-image@io.ece.drexel.edu Subject: Re: Epson Photo 700 printers Message-Id: Content-Type: text/plain; charset="us-ascii" >Hi All: >According to the latest MacWorld, the Epson Photo 700 printers are supposed >to output images of comparable quality to the Kodak dye sub printers. >Would anyone comment whether this is indeed true? Does the Epson Photo 700 >or EX output "journal quality" prints, like the dye sub printers do? > >Thanks, >--Randy >****************************************************************** >"Godzilla's approach >My mouth agape in horror >I just bought that car" --Dwight A. Macpherson, _Godzilla_Hiaku_ > >Randy M. Wadkins, Ph.D. >Cancer Therapy & Research Center >Institute for Drug Development >14960 Omicron Drive >San Antonio, TX 78245 >phone: (210)-677-3835 >fax: (210)-677-0058 >E-mail: rwadkins@saci.org >CTRC Homepage: http://www.ccc.saci.org >****************************************************************** I just picked up an Epson Photo700 as a part of the Polaroid DMC promotion. It is in fact quite nice when printing to photo paper and it's fast - I don't know what the upgrade is to the new Photo740 (besides maybe the USB bus). TIFF images from Photoshop look really sharp (an admittedly qualitative description). Chris. Christopher M. Yip, Ph.D., P.Eng. Assistant Professor Department of Chemical Engineering and Applied Chemistry Institute of Biomedical Engineering Department of Biochemistry University of Toronto 407 Rosebrugh Building, 4 Taddle Creek Rd. Toronto, Ontario CANADA M5S 3G9 Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317; e-mail: yip@ibme.utoronto.ca WWW: http://goldie.ibme.utoronto.ca ------------------------------ Date: Tue, 8 Sep 1998 11:29:41 -0500 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Re: Transferring ROIs to a new image Message-Id: Content-Type: text/plain; charset="us-ascii" >Hi, > I'd like to write a macro that allows me to draw a freehand ROI in >an image (e.g., the outline of rhodamine-stained cells), open another image >(e.g., the FITC channel image of the same cells), and count particles >within the same ROI in the second image. I'd like it to be able to analyze >multiple ROIs within the same image, but also to keep the data for each ROI >separate. In the NIH Image archives, I saw a suggestion for copying the >two images to a stack, then toggling back and forth between slices to do >this analysis. Has anyone written such a macro using this or another >algorithm? >Thanks, >Laird Bloom >MIT Center for Cancer Research Draw each ROI (you can use the while button loop as discussed last week or so to draw while running a macro) and fill each with a different grayvalue. You can name each by incorporating a getstring command after each delineation. To analyze, make a copy of your delineations and use the density slice to isolate one of the regions. Use AND when pasting to your FITC image to restrict analysis to the ROI. Repeat for each of your delineations. To associate the ROI name with the measurement, write the results to a text window along with the ROI name. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. ------------------------------ Date: Tue, 8 Sep 1998 13:57:21 -0700 (PDT) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re: stereology Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII >>Has onyone ------------------------------ Date: Tue, 8 Sep 1998 14:00:51 -0700 (PDT) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re:Stereology Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII what sort of stereology are you going to do? There are 2 sets of stereology macros for Image. One is the 'Stereology plug-ins', the other is called 'Cavalieri3'. Both come with documentation and are available from the Image ftp site Regards, Glen Glen MacDonald Research Scientist Hearing Research Laboratories of the Virginia Merrill Bloedel Hearing Research Center Box 35-7923 University of Washington Seattle, WA 98195-7923 (206) 616-4156 glenmac@u.washington.edu ------------------------------ Date: Tue, 8 Sep 1998 19:17:12 EDT From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: image analysis setup Message-ID: <341e8951.35f5baf8@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Less expensive systems are available: In the US the microscope should be under $30,000 (range $15,000 to $30,000) with a full compliment of obj. lens. Frame grabber $3000 or less (range $900 to 3000) digital &/or analog Computer ; G-3 Mac 300 Mhz, 17" monitor, 64 MB, 6GB HD cost under $2500 For non-moving (or fixed) visible specimens that you can illuminate without damage or bleaching I would suggest 1) High resolution on-chip integrating Peltier Cooled CCD (2 stage Peltier) is able to can integrate for minutes athough a second or two is usually enough, cost $6,500. For low light, low level illumination, living specimens sensitive to light then an intensified camera is better. cost ($16,750 to $25,000 (GEN IV intensifier, fiber optically coupled, >550 TVLs). These can also integrate on chip to permit very high magnification, sub-visual (nothing to see in the microscope ocular) imaging. Therefore under $42,000 for a low light but visible imaging system, $55,000 for high end sub-visual imaging. There are several sources. We are one. Solamere Technology Group ------------------------------ Date: Wed, 9 Sep 1998 10:33:20 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: lbloom@MIT.EDU, nih-image@io.ece.drexel.edu Subject: Re: Transferring ROIs to a new image Message-ID: <81DAE9E2114@rna.bio.mq.edu.au> >Date: Tue, 8 Sep 1998 09:06:15 -0400 >To: nih-image@io.ece.drexel.edu >From: Laird Bloom > I'd like to write a macro that allows me to draw a freehand ROI in >an image (e.g., the outline of rhodamine-stained cells), open another image >(e.g., the FITC channel image of the same cells), and count particles >within the same ROI in the second image. I'd like it to be able to analyze >multiple ROIs within the same image, but also to keep the data for each ROI >separate. In the NIH Image archives, I saw a suggestion for copying the >two images to a stack, then toggling back and forth between slices to do >this analysis. Has anyone written such a macro using this or another >algorithm? >Thanks, >Laird Bloom >MIT Center for Cancer Research There are a number of approachs available to this including the stack method you mention, the mapping method suggested by Jonathan Nissanov, particular applications as in Doug Morris's site, etc but the simplest most useful method is often overlooked, probably because this specific application is not explicitly mentioned in the manual. The macro restoreRoi or the restore selection (analyse Menu) will restore the previously active selection to the current image (even if a compound ROI selection made using control/option keys). The trick is that the restoration takes effect on the current image even if the ROI was active on a different but previously active image regardless of whether the previous image associated with the ROI was of the same dimensions or not. It is located in the same position relative to 0,0 ie topleft. Thus a ROI established on an image (a roi can be associated with any/each open window) can be transferred from that image to another, simply by: activating the image carrying the ROI; activate the image to receive the ROI; invoke restore selection (analyse Menu) or selectPic(pid2);killRoi; selectPic(pid1);selectPic(pid2);restoreRoi;{transfers ROI from pid1 to 2} In addition, you can selectPic(pid1); SetSaveAs('Outline');saveas('aParticularROI'); selectPic(pid2);open('aParticularROI'); if you want to have a disk record of the ROI. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Wed, 9 Sep 1998 14:12:53 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: luthero@pro.via-rs.com.br, nih-image@io.ece.drexel.edu Subject: Re: question (image contrast optimisation) Message-ID: <82157F20EEB@rna.bio.mq.edu.au> >Date: Tue, 08 Sep 1998 09:12:53 -0800 >From: Luthero Martins >Reply-To: luthero@pro.via-rs.com.br > >I'm an ophthalmologist in Brazil. We are working with NIH's >applications on Ophthalmology, specially with Glaucom, where we study >the optic disk and the Retinal Nerve Fiber Layer. > We see the variation of this images according of the >luminosity's >variation. > The equipment that give us this image is a Canon Non-Mydriatic >Retinal >Camera. But the threshold of variations when we apply the OPTIONS >DENSITY SLICE is very sensitive. > > Can we reduce this sensitivity? Or can we work with another part >of NIH >program? > > If anybody can help us, thanks. > >You can see this images and results on: >http://www.oftalmologia-digital.com/clininih.html Luthero, I expect what you are after is to get finer discrimination within the bright region of the image where you have made your selection. The following numbers may not be accurate as the images on your web site are JPEG rather than TIFF but should be adequate to make the point. You have used a color camera and apparently chosed to use the green channel image. You dodn't say whether the Canon camera was a digital camera or a video camera with a framgrabber. For a specialised application like this,I would expect that you would potentially get better results with a good monochrome camera (<$1000 US) with an appropriate color filter and a Scion framegrabber(<$1000). It is important to look at and understand the histogram. I will attach an annoted version to a direct email. The histogram spread ranges from 25 or 28 (the bright end) to 248 (the dark end) The peak centered around 238 is not image data but the spread of pixels forming a black border around the image. The image itself has a maximum pixel value of about 210. Hence your image contrast range is at best 210-25 = 185 out of the available 256 values ie 72% of available When you look at the histogram taken when density slice is active, the sliced portion of the histogram is shown in black as opposed to gray for the background. Your slice extends from 25 or 28 to 47 and is <860 pixels of the total 320x240=76800 pixels and is part of an image segment roughly 60 pixels diameter which is much brighter than the background image of the retina but only occupies about 5% of the image and on the histogram is all represented in the low outliers to the left of the double peaked histogram of the main retina. You can see that if your image histogram was spread to fit the available 256 values, then you would have much better contrast discrimination for the bright region of the retina. You should be able to arrange this by adjustment of the brightness,contrast, colour balance controls on the camera if digital or on the framegrabber. If a framegrabber, then, under NIH-Image, set a live histogram while you live capture and you adjust the gain(video control dialogue) up until the histogram is as wide as the histogram window while keeping it in the window by adjusting the offset (down will move it left in window, up will move it right towards the dark end). More extremely, as you know where your region of interest falls on the histogram you can adjust the contrast ie gain up as long as the live histogram remains reasonably stable and keeping the histogram roi within the window by adjusting offset. This will saturate the retina background to be very dark or even black ie >=255 but will maximise discrimination in the intensity range that is of interest for the density slice segmentation. Also if you make a selection that is restricted to the bright region and then use integrate, the integration processing will ensure the max/min levels in the ROI fill the histogram window. If you need to retain contrast info to see blood vessel detail of current image, the you can expand a range of 25 to 25+166= to 256 by cutting off the dark end of the histogram where 191 falls now ie an improvement of 256/166=1.5+ or over 50% or you can take two images with different contrast settings and transfer the segmented ROI from the image contrasted at the bright end to the perceptually acceptable image afterwards. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #57 ***************************************