From bnhirsch@dapsas1.weizmann.ac.il Fri Oct 1 12:15:41 1993 Received: from dapsas1.weizmann.ac.il by nx1.soils.umn.edu (5.65c) id AA27457; Fri, 1 Oct 1993 03:06:36 -0500 Return-Path: Received: from [132.76.66.31] by dapsas1.weizmann.ac.il via SMTP (920110.SGI/911001.SGI) for nih-image@soils.umn.edu id AA27632; Fri, 1 Oct 93 10:06:42 +0300 Message-Id: <9310010706.AA27632@dapsas1.weizmann.ac.il> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 1 Oct 1993 10:15:41 +0200 To: nih-image@soils.umn.edu From: bnhirsch@dapsas1.weizmann.ac.il (David L. Hirschberg) Subject: Understanding the dif between integrated and mean density Forgive me if this issue has come up before. I am having trouble understanding the difference between integrated and mean density. I read the explanation in the 1.51 manual and am still a little confused. For what application is each applicable? Thank you, David =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= David L. Hirschberg bnhirsch@dapsas.weizmann.ac.il Department of Neurobiology (972) 834-2127 work Weizmann Institute of Science (972) 847-4805 home Rehovot 76100 Israel (972) 834-4131 fax From wayne@helix.nih.gov Fri Oct 1 08:55:25 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA01406; Fri, 1 Oct 1993 08:57:00 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA26710; Fri, 1 Oct 93 09:17:12 -0400 Message-Id: <9310011317.AA26710@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 1 Oct 1993 08:55:25 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: reslicing volume in another plane >Has anyone out there written macros to reslice a stack in a user specified >plane? We are currently looking at high resolution MRI datasets of the >cochlea (ie. inner ear). The problem is that each specimen is scanned >differently, however it happens to rest in the small well it's placed in. >It would be real nice if we could resection this volume in user selected >plane other than the original plane of acquisition. This would enable us >to make some critical measurements between specimens. I though I'd put >this question out there before I attempt to write any of my own macros. The are serveral macros for orthogonal reslicing of volumes in the macro file "Stacks". --wayne From brown@alsys1.aecom.yu.edu Fri Oct 1 05:36:20 1993 Received: from alsys1.aecom.yu.edu by nx1.soils.umn.edu (5.65c) id AA02335; Fri, 1 Oct 1993 10:43:30 -0500 Return-Path: Received: from [129.98.90.119] (garbo.aecom.yu.edu) by alsys1.aecom.yu.edu with SMTP id AA11361 (5.67a/IDA-1.5/AECOM-RIT for ); Fri, 1 Oct 1993 11:44:22 -0400 From: "Lucy Brown" Date: Fri, 1 Oct 93 11:36:20 CST Message-Id: <41781.brown@alsys1.aecom.yu.edu> X-Popmail-Charset: English To: nih-image@soils.umn.edu Subject: Re: Understanding the dif between integrated and mean density On Fri, 1 Oct 1993 03:16:39 -0500, David L. Hirschberg wrote: >Forgive me if this issue has come up before. I am having trouble >understanding the difference between integrated and mean density. I read >the explanation in the 1.51 manual and am still a little confused. For >what application is each applicable? > >Thank you, David > >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >David L. Hirschberg bnhirsch@dapsas.weizmann.ac.il >Department of Neurobiology (972) 834-2127 work >Weizmann Institute of Science (972) 847-4805 home >Rehovot 76100 Israel (972) 834-4131 fax Integrated optical density is the SUM of the optical density of each pixel in your box, or region of interest, with background subtracted. Mean optical density is the sum of all the pixels in your region of interest, divided by the number of pixels in your region of interest. Integrated is useful and more sensitive than mean when you're analyzing a gel, and the region of interest is a box around a band with some of the background in the box. Also, bands in gels often contain a range of optical densities that are not well characterized by a mean. Mean should be used in material where your region of interest is fairly uniform and does not contain background. Mean optical density is used to describe individual brain regions with relatively homogeneous densities in autoradiograms, for example. ----------------------------------------------------------------------- Lucy L. Brown, Ph.D. email: brown@aecom.yu.edu Department of Neurology lab : (718) 430-3632 Albert Einstein College of Medicine New York From brown@alsys1.aecom.yu.edu Fri Oct 1 05:43:26 1993 Received: from alsys1.aecom.yu.edu by nx1.soils.umn.edu (5.65c) id AA02473; Fri, 1 Oct 1993 10:50:20 -0500 Return-Path: Received: from [129.98.90.119] (garbo.aecom.yu.edu) by alsys1.aecom.yu.edu with SMTP id AA11581 (5.67a/IDA-1.5/AECOM-RIT for ); Fri, 1 Oct 1993 11:51:29 -0400 From: "Lucy Brown" Date: Fri, 1 Oct 93 11:43:26 CST Message-Id: <42208.brown@alsys1.aecom.yu.edu> X-Popmail-Charset: English To: nih-image@soils.umn.edu Subject: Automatic threshold Has anyone written a macro for automatic thresholding? Russ describes automatic thresholding using the change in area and perimeter of the binary image formed over a series of threshold-detect values (Russ,1992, The Image Procesing Handbook, pgs 258-259). ----------------------------------------------------------------------- Lucy L. Brown, Ph.D. email: brown@aecom.yu.edu Department of Neurology lab : (718) 430-3632 Albert Einstein College of Medicine New York From keatinga@med.unc.edu Fri Oct 1 08:55:23 1993 Received: from med.unc.edu (durham.med.unc.edu) by nx1.soils.umn.edu (5.65c) id AA03384; Fri, 1 Oct 1993 11:52:59 -0500 Return-Path: Received: from garner.med.unc.edu by med.unc.edu (4.1/SMI-4.0-ACB-1.0) id AA16134; Fri, 1 Oct 93 12:55:28 EDT Received: by garner.med.unc.edu (4.1/SMI-4.1) id AA16052; Fri, 1 Oct 93 12:55:24 EDT From: keatinga@med.unc.edu (Arthur Keating) Message-Id: <9310011655.AA16052@garner.med.unc.edu> Subject: Re: reslicing volume in another plane To: nih-image@soils.umn.edu Date: Fri, 1 Oct 93 12:55:23 EDT In-Reply-To: <9310011317.AA26710@zippy.nimh.nih.gov>; from "Wayne Rasband" at Oct 1, 93 9:10 am X-Mailer: ELM [version 2.3 PL11] > > >Has anyone out there written macros to reslice a stack in a user specified > >plane? We are currently looking at high resolution MRI datasets of the > >cochlea (ie. inner ear). The problem is that each specimen is scanned > >differently, however it happens to rest in the small well it's placed in. > >It would be real nice if we could resection this volume in user selected > >plane other than the original plane of acquisition. This would enable us > >to make some critical measurements between specimens. I though I'd put > >this question out there before I attempt to write any of my own macros. > > The are serveral macros for orthogonal reslicing of volumes in the macro > file "Stacks". > > --wayne > > > Yes I know. I'm talking about planes other than orthogonal ones. I want to reslice an entire volume repeatedly as is done when one makes a line selection and obtains a new section with the slice command. Any help there? From @YaleVM.YCC.Yale.Edu:Mike_Schwartz@QUICKMAIL.CIS.YALE.EDU Fri Oct 1 11:57:49 1993 Received: from YALEVM.YCC.YALE.EDU by nx1.soils.umn.edu (5.65c) id AA03422; Fri, 1 Oct 1993 11:57:49 -0500 Return-Path: <@YaleVM.YCC.Yale.Edu:Mike_Schwartz@QUICKMAIL.CIS.YALE.EDU> Message-Id: <199310011657.AA03422@nx1.soils.umn.edu> Received: from quickmail.yale.edu by YaleVM.YCC.Yale.Edu (IBM VM SMTP V2R2) with TCP; Fri, 01 Oct 93 12:57:16 EDT Date: 1 Oct 1993 13:00:05 U From: "Mike Schwartz" Subject: Image compression To: "Image List" Subject: Time:9:24 AM OFFICE MEMO Image compression Date:10/1/93 I am interested in compressing grey-scale images acquired using Image and a Perceptics Megagrabber video board. I do not have the finances to go with a hardware solution and have been looking at two comercial software packages: Kodak's Colorsqueeze 2.0 and Storm Technologies Picture Press 2.5. Picture Press has a Photoshop plug-in which would be very useful if the plug-in also works with Image. However, since I have found a least one Photoshop plug-in that does not work with Image (the NuVista+ plug-in) I would like to know if anyone has experience using Picture Press and Image. Any other comments on either of these compression programs or advice on alternatives would also be greatly appreciated. Mike Schwartz Mike Schwartz@qm.yale.edu From bright@ENH.NIST.GOV Fri Oct 1 09:53:06 1993 Received: from enh.nist.gov by nx1.soils.umn.edu (5.65c) id AA04095; Fri, 1 Oct 1993 13:03:30 -0500 Return-Path: Received: from [129.6.98.4] (dsb-mac.nist.gov) by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01H3LMOESCRK0001FN@ENH.NIST.GOV>; Fri, 1 Oct 1993 13:53:06 EDT Date: Fri, 01 Oct 1993 13:53:06 -0400 (EDT) Date-Warning: Date header was inserted by ENH.NIST.GOV From: bright@ENH.NIST.GOV Subject: variance image To: nih-image@soils.umn.edu Message-Id: <01H3LMOF6JYA0001FN@ENH.NIST.GOV> Content-Transfer-Encoding: 7BIT Hi:o) Anyone have a macro that calculates a variance image? By that I mean something similar to a smoothing (convolution with all 1's in the kernel), except the new pixel value is equal to the variance (or standard deviation) of all the pixels inside the kernel, rather than equal to the sum. Thanks --Dave ------------------------------------------------------------- David S. Bright bright@enh.nist.gov Microanalysis Research Group Chem. A113 National Institute of Standards & Technology (NIST, formerly NBS) Gaithersburg, MD 20899-0001 USA 301-975-3911 - voice, 301-216-1134 - fax From wayne@helix.nih.gov Fri Oct 1 13:41:11 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA04593; Fri, 1 Oct 1993 13:42:46 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA28059; Fri, 1 Oct 93 14:02:58 -0400 Message-Id: <9310011802.AA28059@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 1 Oct 1993 13:41:11 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Automatic threshold >Has anyone written a macro for automatic thresholding? Russ describes >automatic thresholding using the change in area and perimeter of the binary >image formed over a series of threshold-detect values (Russ,1992, The Image >Procesing Handbook, pgs 258-259). The Threshold command in NIH Image (AutoThreshold in macros) does automatic thresholding using an Iterative technique, first described by Ridler & Calvard in "PIcture Thresholding Using an Iterative Selection Method", IEEE transactions on Systems, Man and Cybernetics, August, 1978. --wayne From Doug.Erickson@m.CC.UTAH.EDU Fri Oct 1 21:47:18 1993 Received: from fcom.cc.utah.edu by nx1.soils.umn.edu (5.65c) id AA05787; Fri, 1 Oct 1993 15:45:21 -0500 Return-Path: Received: from [128.110.56.10] (emcb010x.utah.edu) by fcom.cc.utah.edu (4.1/SMI-4.0 [uucc-nhj-virtual 18AUG1991]) id AA05056; Fri, 1 Oct 93 14:44:38 MDT Message-Id: <9310012044.AA05056@fcom.cc.utah.edu> Date: Fri, 1 Oct 1993 14:47:18 +0700 To: nih-image@soils.umn.edu From: Doug.Erickson@m.CC.UTAH.EDU (Doug Erickson) X-Sender: dme8844@m.cc.utah.edu Subject: Re: reslicing volume in another plane > > >Has anyone out there written macros to reslice a stack in a user specified > > >plane? It would be real nice if we could resection this volume in user > > >selected plane other than the original plane of acquisition. > > The are serveral macros for orthogonal reslicing of volumes in the macro > > file "Stacks". > Yes I know. I'm talking about planes other than orthogonal ones. I haven't written actually written the macro, but using the "Stacks" procedure as a guide, it should be fairly simple to make progressive reslices parallel to a line selection. Use the GetRoi command to calculate the slope of the line selection. Use this information, along with a parameter for distance between the output slices, to compute dx and dy. Specify the number of slices you want to make, and use MoveRoi(dx,dy) to advance the line of sectioning in- stead of the "loc" and "max" parameters in the current macro. This should work for reslicing in any plane perpendicular to the stack images. If you want to reslice to some oblique plane (I mean one that is neither paral- lel nor perpendicular to the plane of the stack's images), you could do a kind of crummy job by using "Reslice Horizontally," with an output spacing of one pixel. Then, select the desired plane in the new stack (it might be necessary to rotate the original image before reslicing horizontally to get exactly the plane you want--this is why the quality of the end product might get pretty bad), and apply your new macro. From Doug.Erickson@m.CC.UTAH.EDU Fri Oct 1 21:55:05 1993 Received: from fcom.cc.utah.edu by nx1.soils.umn.edu (5.65c) id AA05917; Fri, 1 Oct 1993 15:53:08 -0500 Return-Path: Received: from [128.110.56.10] (emcb010x.utah.edu) by fcom.cc.utah.edu (4.1/SMI-4.0 [uucc-nhj-virtual 18AUG1991]) id AA05216; Fri, 1 Oct 93 14:52:26 MDT Message-Id: <9310012052.AA05216@fcom.cc.utah.edu> Date: Fri, 1 Oct 1993 14:55:05 +0700 To: nih-image@soils.umn.edu From: Doug.Erickson@m.CC.UTAH.EDU (Doug Erickson) X-Sender: dme8844@m.cc.utah.edu Subject: Reslice Command A week or two ago I asked about the Reslice command, which kept giving me an error saying "Selection must be within image boundary." After a little experimentation, I found that this was caused by setting the slice spacing to less than one pixel. To get around this, I set the slice spacing to one pixel, reslice, and then vertically scale the resulting image so that it has the correct aspect ratio. Is this by design or is it a bug? Doug Erickson / Mechanical Engineering 2480 MEB University of Utah Salt Lake City, Utah 84112 From brown@alsys1.aecom.yu.edu Fri Oct 1 11:43:56 1993 Received: from alsys1.aecom.yu.edu by nx1.soils.umn.edu (5.65c) id AA06619; Fri, 1 Oct 1993 16:51:15 -0500 Return-Path: Received: from [129.98.90.119] (garbo.aecom.yu.edu) by alsys1.aecom.yu.edu with SMTP id AA23026 (5.67a/IDA-1.5/AECOM-RIT for ); Fri, 1 Oct 1993 17:52:23 -0400 From: "Lucy Brown" Date: Fri, 1 Oct 93 17:43:56 CST Message-Id: <63838.brown@alsys1.aecom.yu.edu> X-Popmail-Charset: English To: nih-image@soils.umn.edu Cc: wayne@helix.nih.gov Subject: Re: Automatic threshold On Fri, 1 Oct 1993 13:56:58 -0500, Wayne Rasband wrote: > >The Threshold command in NIH Image (AutoThreshold in macros) does automatic >thresholding using an Iterative technique, first described by Ridler & >Calvard in "PIcture Thresholding Using an Iterative Selection Method", IEEE >transactions on Systems, Man and Cybernetics, August, 1978. > >--wayne Thanks! Autothreshold sounds good. But I can't find it. In what series of macros? From wayne@helix.nih.gov Fri Oct 1 16:56:59 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA06690; Fri, 1 Oct 1993 16:58:36 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA28678; Fri, 1 Oct 93 17:18:48 -0400 Message-Id: <9310012118.AA28678@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Fri, 1 Oct 1993 16:56:59 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: variance image >Hi:o) > Anyone have a macro that calculates a variance image? By that= I mean >something similar to a smoothing (convolution with all 1's in the= kernel), >except the new pixel value is equal to the variance (or standard= deviation) >of all the pixels inside the kernel, rather than equal to the sum. The macro appended to the end of this message doesn't do exactly= what you're asking for, but it's probab;y the best that can be done using= the macro language. A macro that computed the standard deviation for= every pixel instead of for every cell would be hundreds of times slower= than this one. --wayne macro 'Make Variance Image=8A'; { Divides an image into cells, replacing all pixels in each cell by= the standard deviation for that cell. You will need to enter the cell= width, cell height, and estimated maximum standard deviation. The actual= maximum standard deviation is displayed when the macro finishes. } var x,y,xinc,yinc,width,height:integer; cellwidth,cellheight,value:integer; maxstd,max:real; begin GetPicSize(width,height); xinc:=3DGetNumber('Cell Width:',16); yinc:=3DGetNumber('Cell Height:',xinc); max:=3DGetNumber('Max std dev:',50); maxstd:=3D0; y:=3D0; repeat cellheight:=3Dyinc; if (y+cellheight)>height then cellheight:=3Dheight-y; x:=3D0; repeat cellwidth:=3Dxinc; if (x+cellwidth)>width then cellwidth:=3Dwidth-x-1; MakeRoi(x,y,cellwidth,cellheight); measure; if rStdDev[rcount]>maxstd then maxstd:=3DrStdDev[rcount]; value:=3Dtrunc(rStdDev[rcount]/max*253)+1; if value>254 then value:=3D254; SetForeground(value); fill; ResetCounter; x:=3Dx+xinc; until x>width; y:=3Dy+yinc; until y>height; KillRoi; ShowMessage('max std dev=3D',maxstd:1:2); end; From vokey@hg.uleth.ca Sun Oct 3 06:40:22 1993 Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c) id AA27334; Sun, 3 Oct 1993 13:47:47 -0500 Return-Path: Received: by hg.uleth.ca (MX V3.3 VAX) id 1983; Sun, 03 Oct 1993 12:40:27 MDT Date: Sun, 03 Oct 1993 12:40:22 MDT From: vokey@hg.uleth.ca To: nih-image@soils.umn.edu Message-Id: <00973772.ED479580.1983@hg.uleth.ca> Subject: imagefft As "/pub/nih-image/nih-image_spinoffs/imagefft" is not binhexed, my system refuses to allow me to download it. Could one of you nice (by definition) image-people binhex a copy of imagefft and upload it so that I may FTP it to my Mac? TIA John R. Vokey From a337ard@diamond.sara.nl Mon Oct 4 09:13:14 1993 Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c) id AA02244; Mon, 4 Oct 1993 02:16:29 -0500 Return-Path: Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF V4.2-13 #2574) id <01H3P59FF18WB631QY@vx.cis.umn.edu>; Mon, 4 Oct 1993 02:17:47 CDT Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 4 Oct 93 8:17 MET Received: by diamond.sara.nl (5.61-AIX-1.2/1.0), id AA124204, (for nih-image@soils.umn.edu, from a337ard@diamond.sara.nl); Date: Mon, 04 Oct 1993 08:13:14 +0100 From: a337ard@diamond.sara.nl (Ard Jonker) Subject: Re: Image compression To: nih-image@soils.umn.edu Message-Id: <9310040713.AA124204@diamond.sara.nl> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT Shareware packages that do jpeg compression (PICT, TIF or alike in, JPEG out), be it not Plug In,yet cheap are JPEGView and GifConverter. As far as I know they do not do 'batch' processing, so you have to save the files one by one (by drag and drop you can open many at one time, however). So this might only be the solution if your problem is mainly a storage problem on a small harddisk. JPEGView saves custom icons(=the icon looks like the picture) and a preview as well. As far as I understood, they both require Quicktime to do the compression. Ard Jonker(a337ard@diamond.sara.nl) From set@eru.mt.luth.se Mon Oct 4 11:00:22 1993 Received: from eru.mt.luth.se by nx1.soils.umn.edu (5.65c) id AA02934; Mon, 4 Oct 1993 03:59:19 -0500 Return-Path: Received: from [130.240.1.174] (osse217.mt.luth.se) by eru.mt.luth.se with SMTP (5.65+bind 1.7+ida 1.4.2/IDA-1.2.8-NS) id AA15740; Mon, 4 Oct 1993 10:00:13 +0100 Message-Id: <199310040900.AA15740@eru.mt.luth.se> Date: Mon, 4 Oct 1993 10:00:22 +0100 To: nih-image@soils.umn.edu From: set@mt.luth.se (Sven-Erik Tiberg) Subject: 64Mb SIMM on Scion X-Content-Type: Text/Quoted-Readable nih-image@soils.umn.edu We are in for expanding on-board memory to 64MB on a Scion-LG3 PAL frame grabber. We bought high profile SIMM and could't fit them on the card. Then I asked Tod Weinberg on Scion about this, and Tod Weinberg answer are as follow: ********************************************* Dear Dr. Tiberg: There are currently two types of 16 Mb SIMM on the market. The first is called composite. It consists of 32 4 Mbit RAM chips placed on both sides of the SIMM circuit board. The composite type of SIMM is generally too large to be used on a NuBus board like the LG-3. The second type consists of 8 16 Mbit RAM chips placed on one side of the SIMM circuit board. This is the type of SIMM that will fit on the LG-3. If you already have the composite type SIMM, you may be able to use them on the LG-3 by replacing the angled SIMM sockets on the LG-3 with vertical SIMM sockets. The LG-3 is a multilayer board, but a skilled technician should be able to replace the sockets without damaging the printed circuit board. We would be happy to carry out the modification for no charge, though you would have to pay for shipping in each direction. Sincerely Tod Weinberg Scion Corporation ********************************************* I hope that this will be of any help to someone else on this list that are planning to expand the on-board memory to 64Mb. We will send our card to Scion for socket replacement, as we will not risk the multilayer PC card. ********************************************************* * * * Sven-Erik Tiberg * * Div. of energy / mashineenginnering * * Lulea University of Technology * * Lulea Sweden * * email set@eru.mt.luth.se * * Fax. S-(0)920-91047 * * Tel. S-(0)920-91218, S-(0)10-2189638 * * * ********************************************************* From wayne@helix.nih.gov Mon Oct 4 08:49:58 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA06245; Mon, 4 Oct 1993 08:51:39 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA03195; Mon, 4 Oct 93 09:12:01 -0400 Message-Id: <9310041312.AA03195@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 4 Oct 1993 08:49:58 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: imagefft >As "/pub/nih-image/nih-image_spinoffs/imagefft" is not binhexed, my system >refuses to allow me to download it. Could one of you nice (by definition) >image-people binhex a copy of imagefft and upload it so that I may FTP it to my >Mac? TIA "/pub/nih-image/nih-image_spinoffs/imagefft" is a directory containing five files. I have attached a complete listing of the NIH Image related files on Zippy. Updated versions of this listing are contained in the file "FileList.txt" in the /pub directory. --wayne /pub total 56 -rw-r--r-- 1 wayne users 19008 Sep 10 08:44 FileList.txt -rw-r--r-- 1 wayne users 0 Oct 4 08:57 ls-lR drwxr-xr-x 10 wayne users 1024 Sep 27 13:39 nih-image drwxr-xr-x 2 wayne users 1024 Apr 13 11:04 quicktime drwxr-xr-x 2 wayne users 1024 Jul 22 12:27 util ./nih-image: total 4186 -rw-r--r-- 1 wayne users 5169 Jul 26 09:50 0README.txt -rw-r--r-- 1 wayne users 13054 Sep 27 13:39 Changes.txt -rw-r--r-- 1 wayne users 919 Sep 14 16:57 MailingList.txt drwxrwxrwx 2 wayne users 1024 Sep 28 11:52 contrib drwxr-xr-x 5 wayne users 1024 Sep 22 16:14 documents drwxr-xr-x 3 wayne users 1048 Jun 24 14:18 images -rw-r--r-- 1 wayne users 519115 Sep 9 15:51 nih-image152.hqx -rw-r--r-- 1 wayne users 417032 Sep 9 15:53 nih-image152_docs.hqx -rw-r--r-- 1 wayne users 629212 Sep 9 15:55 nih-image152_source.hqx -rw-r--r-- 1 wayne users 504389 Sep 27 13:37 nih-image153b7.hqx drwxr-xr-x 4 wayne users 1024 Jun 15 12:50 nih-image_spinoffs drwxr-xr-x 2 wayne users 1024 Sep 9 12:20 plug-ins drwxr-xr-x 3 wayne users 1024 Sep 9 12:10 programs drwxr-xr-x 2 wayne users 1024 Apr 15 15:07 stacks drwxr-xr-x 2 wayne users 1024 Sep 27 13:58 user-macros ./nih-image/contrib: total 12408 -rw-r--r-- 1 wayne users 13826 Sep 2 12:55 10_Image_Icons.hqx -rw-r--r-- 1 wayne users 365469 Jun 29 10:48 Contrib_NTH.sit.hqx -rw-r--r-- 1 wayne users 356172 Jun 3 10:54 Image144Markup.sit.hqx -rw-r--r-- 1 wayne users 757065 Jun 3 10:56 Image144MarkupSource.sit.hqx -rw-r--r-- 1 wayne users 460103 Apr 20 10:10 Image149_PAL_NTSC.hqx -rw-r--r-- 1 wayne users 1323531 Apr 26 10:57 Image149_pal_ntsc.2.hqx -rw-r--r-- 1 wayne users 3355 Jul 21 15:31 ImageScion1.50b83.ReadMe.txt -rw-r--r-- 1 wayne users 480176 Jul 21 15:33 ImageScion1.50b83.sit.hqx -rw-r--r-- 1 wayne users 158351 Apr 26 12:11 ImageTimer.sit.hqx -rw-r--r-- 1 wayne users 5551 Mar 7 1993 Image_Icons.hqx -rw-r----- 1 ftp other 12009 Sep 26 22:10 PreProjection_Macros.hqx -rw-r--r-- 1 wayne users 855824 Aug 23 07:08 Quantile_Crest.sit.hqx -rw-r--r-- 1 wayne users 8273 May 24 19:59 Video_presentation_1_49.txt -rw-r--r-- 1 wayne users 3425 Aug 25 05:15 image_umx_readme -rw-r----- 1 ftp other 532248 Sep 28 11:53 nihumx152b3.sit.hqx -rw-r----- 1 ftp other 879846 Sep 28 11:51 nihumx152b3source.sit.hqx -rw-r----- 1 ftp other 11057 Sep 24 11:42 preproj_macros.hqx ./nih-image/documents: total 8566 -rw-r--r-- 1 wayne users 435152 May 3 10:19 Nih-image.001.txt -rw-r--r-- 1 wayne users 561265 Jul 23 11:02 Nih-image.002.txt -rw-r--r-- 1 wayne users 536162 Sep 7 08:35 Nih-image.txt -rw-r--r-- 1 wayne users 14390 Mar 8 1993 centris_video.txt -rw-r--r-- 1 wayne users 19669 Mar 19 1993 ftp-primer.txt -rw-r--r-- 1 wayne users 38205 Mar 25 1993 mac-ftp-sites.txt -rw-r--r-- 1 wayne users 9047 May 21 14:32 mac-image-proc.txt drwxr-xr-x 2 wayne users 1024 Sep 22 16:14 map_making_tutorial -rw-r--r-- 1 wayne users 11430 Mar 4 1993 mpw_port.txt 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USGSColorCodes.sea.hqx ../nih-image/documents/v1.50b70_source: total 2434 -rw-r--r-- 1 wayne users 74151 Jun 15 15:45 Analysis.p.txt -rw-r--r-- 1 wayne users 40978 Jun 15 15:45 Background.p.txt -rw-r--r-- 1 wayne users 33054 Jun 15 15:45 Camera.p.txt -rw-r--r-- 1 wayne users 65932 Jun 15 15:45 Edit.p.txt -rw-r--r-- 1 wayne users 8948 Jun 15 15:45 Ellipse.p.txt -rw-r--r-- 1 wayne users 89856 Jun 15 15:45 File1.p.txt -rw-r--r-- 1 wayne users 69178 Jun 15 15:45 File2.p.txt -rw-r--r-- 1 wayne users 46624 Jun 15 15:45 Functions.p.txt -rw-r--r-- 1 wayne users 37087 Jun 15 15:45 Globals.p.txt -rw-r--r-- 1 wayne users 60804 Jun 15 15:45 Graphics.p.txt -rw-r--r-- 1 wayne users 69403 Jun 15 15:45 Image.p.txt -rw-r--r-- 1 wayne users 13440 Jun 15 15:45 Image.proj.bin -rw-r--r-- 1 wayne users 53376 Jun 15 15:45 Image.rsrc.bin -rw-r--r-- 1 wayne users 43806 Jun 15 15:45 Init.p.txt -rw-r--r-- 1 wayne users 6703 Jun 15 15:45 LeastSquares.p.txt -rw-r--r-- 1 wayne users 46692 Jun 15 15:46 Lut.p.txt 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-rw-r--r-- 1 wayne users 162999 Mar 14 1992 little_girl.hqx -rw-r--r-- 1 wayne users 331392 Apr 3 1993 m51_fits.bin -rw-r--r-- 1 wayne users 183 Apr 3 1993 m51_fits.txt -rw-r--r-- 1 wayne users 60357 Mar 14 1992 metabolites.hqx -rw-r--r-- 1 wayne users 230637 Mar 14 1992 molecule.hqx -rw-r--r-- 1 wayne users 291490 Mar 14 1992 mona_lisa.hqx -rw-r--r-- 1 wayne users 98688 May 8 1992 morph.bin -rw-r--r-- 1 wayne users 61623 Mar 14 1992 mri_scan.hqx -rw-r--r-- 1 wayne users 134272 Dec 8 1992 mu_opiate_receptor.bin -rw-r--r-- 1 wayne users 12792 Mar 14 1992 pet_scan.hqx -rw-r--r-- 1 wayne users 128754 Mar 14 1992 porsche.hqx -rw-r--r-- 1 wayne users 56704 May 8 1992 rat_kidney.bin -rw-r--r-- 1 wayne users 344006 Mar 14 1992 redrock.hqx -rw-r--r-- 1 wayne users 50944 Mar 1 1993 silver_lake.bin -rw-r--r-- 1 wayne users 18168 Mar 14 1992 spots_on_wave.hqx drwxr-xr-x 2 wayne users 1024 May 22 1992 wavelet_compression ./nih-image/images/wavelet_compression: total 3270 -rwxr--r-- 1 wayne users 2488 May 22 1992 README.txt -rwxr--r-- 1 wayne users 263680 May 22 1992 lena.19_4.bin -rwxr--r-- 1 wayne users 263680 May 22 1992 lena.30.bin -rwxr--r-- 1 wayne users 263680 May 22 1992 lena.3_32.bin -rwxr--r-- 1 wayne users 263680 May 22 1992 lena.61.bin -rwxr--r-- 1 wayne users 263680 May 22 1992 lena.8_1.bin -rwxr--r-- 1 wayne users 263680 May 22 1992 lena.raw.bin ./nih-image/nih-image_spinoffs: total 8724 -rw-r--r-- 1 wayne users 690796 Apr 14 1992 color_image132.hqx -rw-r--r-- 1 wayne users 488397 Jun 15 10:27 image149vdm.hqx -rw-r--r-- 1 wayne users 619037 Jun 15 08:54 image149vdm_source.hqx -rw-r--r-- 1 wayne users 983840 Mar 26 1992 imageKSC.hqx -rw-r--r-- 1 wayne users 380488 Apr 14 13:30 image_mg144b.hqx drwxr-xr-x 2 wayne users 1024 Mar 29 1993 imagefft drwxr-xr-x 2 wayne users 1024 Mar 14 1992 imagefractal -rw-r--r-- 1 wayne users 1223201 Mar 14 1992 munichimage.hqx ./nih-image/nih-image_spinoffs/imagefft: total 5922 -rw-r--r-- 1 wayne users 835581 Mar 14 1992 ImageFFT128b6.hqx -rw-r--r-- 1 wayne users 364066 Mar 14 1992 ImageFFTExamples1.hqx -rw-r--r-- 1 wayne users 1478532 Mar 14 1992 ImageFFTExamples2.sit.hqx -rw-r--r-- 1 wayne users 275 Mar 29 1993 README.txt -rw-r--r-- 1 wayne users 305346 Mar 14 1992 Thesis.hqx ./nih-image/nih-image_spinoffs/imagefractal: total 1114 -rw-r--r-- 1 wayne users 4457 Mar 14 1992 README -rw-r--r-- 1 wayne users 199293 Mar 14 1992 imagefractal12.hqx -rw-r--r-- 1 wayne users 341331 Mar 14 1992 source.hqx ./nih-image/plug-ins: total 1296 -rw-r--r-- 1 wayne users 190897 May 20 12:35 DevelopersKit.cpt.hqx -rw-r--r-- 1 wayne users 88667 May 4 16:10 LG-3PlugIn.cpt.hqx -rw-r--r-- 1 wayne users 48130 Jun 16 15:30 MegaGrabberPlugIn.hqx -rw-r--r-- 1 wayne users 56187 Jun 16 15:31 PixelBufferPlugIn.hqx -rw-r--r-- 1 wayne users 60347 Jun 16 15:31 PixelHR24PlugIn.hqx -rw-r--r-- 1 wayne users 12935 Jul 23 16:07 TV-3PlugIn.hqx -rw-r--r-- 1 wayne users 75360 Sep 9 12:20 cmulti-filter.cpt.hqx -rw-r--r-- 1 wayne users 100294 Sep 8 08:34 expression30b.cpt.hqx ./nih-image/programs: total 5240 -rw-r--r-- 1 wayne users 732030 Oct 19 1992 gifconverter221.hqx -rw-r--r-- 1 wayne users 123361 Mar 14 1992 giffer108.hqx -rw-r--r-- 1 wayne users 815438 May 25 14:44 ip_lab_demo.cpt.hqx -rw-r--r-- 1 wayne users 647869 Apr 9 1992 labtoolbox.hqx -rw-r--r-- 1 wayne users 98670 May 13 1992 macmeasure19.hqx drwxr-xr-x 2 wayne users 1024 Jul 23 13:14 ncsa -rw-r--r-- 1 wayne users 113936 Sep 9 12:11 pics-quicktime.hqx -rw-r--r-- 1 wayne users 67879 Apr 9 1992 projectionist.hqx ./nih-image/programs/ncsa: total 11866 -rw-r--r-- 1 wayne users 604490 Oct 29 1992 Image311.hqx -rw-r--r-- 1 wayne users 3613575 Oct 29 1992 Image_docs.hqx -rw-r--r-- 1 wayne users 389606 Jul 23 12:03 Layout.Examples.sit.hqx -rw-r--r-- 1 wayne users 258772 Jul 23 12:03 Layout1.3.mac.sit.hqx -rw-r--r-- 1 wayne users 259167 Jul 23 12:03 LayoutLCsi1.3.mac.sit.hqx -rw-r--r-- 1 wayne users 2216 Jul 23 12:03 PalEdit.README -rw-r--r-- 1 wayne users 112627 Mar 14 1992 PalEdit.hqx -rw-r--r-- 1 wayne users 58994 Jul 23 12:03 PalEdit.smp.sit.hqx -rw-r--r-- 1 wayne users 135499 Jul 23 12:03 PalEdit2.0.mac.sit.hqx -rw-r--r-- 1 wayne users 229468 Jul 23 12:03 PalEdit2.0.msw.sit.hqx -rw-r--r-- 1 wayne users 298318 Jul 23 12:04 PalEdit2.0.src.sit.hqx ./nih-image/stacks: total 49398 -rw-r--r-- 1 wayne users 615040 Nov 16 1992 3D-Chromosome_Movie.bin -rw-r--r-- 1 wayne users 2115 Nov 3 1992 3D_Chromosome.txt -rw-r--r-- 1 wayne users 6688384 Apr 15 15:05 3D_Knee.cpt.bin -rw-r--r-- 1 wayne users 3849 Apr 15 15:05 3D_Knee.txt -rw-r--r-- 1 wayne users 1800832 May 1 1992 Alycia.cpt.bin -rw-r--r-- 1 wayne users 30592 May 8 1992 Bird_Movie.bin -rw-r--r-- 1 wayne users 1272576 May 7 1992 CT_Head_Movie.cpt.bin -rw-r--r-- 1 wayne users 327680 May 7 1992 FluidDynamicsMovie.bin -rw-r--r-- 1 wayne users 2541 May 7 1992 FluidDynamicsMovie.txt -rw-r--r-- 1 wayne users 432512 Feb 19 1993 GE_SPECT.cpt.bin -rw-r--r-- 1 wayne users 1173 Feb 19 1993 GE_SPECT.txt -rw-r--r-- 1 wayne users 519 May 1 1992 HerpesVirus.txt -rw-r--r-- 1 wayne users 2469632 Apr 28 1992 HerpesVirusMovie.sit.bin -rw-r--r-- 1 wayne users 2626845 Sep 4 1992 Hurricanes.sit.hqx -rw-r--r-- 1 wayne users 8136960 Jul 8 1992 MRI.Axials_1.5mm.bin -rw-r--r-- 1 wayne users 754944 May 7 1992 MRI_Axials_5mm.bin ./nih-image/user-macros: total 144 -rw-r--r-- 1 wayne users 5564 Jun 3 21:03 cavalieri_doc.txt -rw-r--r-- 1 wayne users 6666 Jun 3 21:04 cavalieri_macro.txt -rw-r--r-- 1 wayne users 13761 Jul 15 09:10 gel_macros_boris.txt -rw-r--r-- 1 wayne users 4871 Sep 3 13:51 grain_counting.txt -rw-r--r-- 1 wayne users 2350 Mar 1 1993 image_registration.txt -rw-r--r-- 1 wayne users 6351 Jun 22 09:26 mac_to_vcr.txt -rw-r--r-- 1 wayne users 10986 Mar 1 1993 marzhauser_stage.txt -rw-r--r-- 1 wayne users 10278 Sep 27 13:57 preprojection.txt -rw-r--r-- 1 wayne users 5336 Mar 1 1993 section_parameters.txt -rw-r--r-- 1 wayne users 1968 Sep 10 15:31 spots_on_sine_wave.txt ./quicktime: total 16194 -rw-r--r-- 1 wayne users 8276608 Apr 13 11:03 canyon.bin -rw-r--r-- 1 wayne users 852 Apr 13 11:03 canyon.txt ./util: total 2722 -rw-r--r-- 1 wayne users 97137 Dec 11 1992 DepthGauge254.hqx -rw-r--r-- 1 wayne users 467390 Apr 14 12:04 Disinfectant31.hqx -rw-r--r-- 1 wayne users 144640 Jan 4 1993 Fetch21.bin -rw-r--r-- 1 wayne users 196303 Jan 4 1993 Fetch21.hqx -rw-r--r-- 1 wayne users 47089 Sep 2 1992 MockWrite.hqx -rw-r--r-- 1 wayne users 66954 Jul 22 12:25 Software_FPU241.hqx -rw-r--r-- 1 wayne users 117632 Mar 14 1992 Stuffit151.bin -rw-r--r-- 1 wayne users 50986 Mar 14 1992 Switch-a-Roo.hqx -rw-r--r-- 1 wayne users 144977 May 11 1992 TiffSniff.hqx From CHARLEST@macc.wisc.edu Mon Oct 4 04:59:00 1993 Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c) id AA06895; Mon, 4 Oct 1993 09:58:30 -0500 Return-Path: Received: from VMSmail by vms2.macc.wisc.edu; Mon, 04 Oct 93 09:59 CDT Message-Id: <23100409590462@vms2.macc.wisc.edu> Date: Mon, 04 Oct 93 09:59 CDT From: Charles Thomas Subject: Re: reslicing volume in another plane To: nih-image@soils.umn.edu X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST The program SPYGLASS DICER (Spyglass Inc, P.O Box 6338, Champaign, IL 61826; 217-355-6000) will allow you to load your 3D data set, then slice planes through it from whatever orientation you wish. You can see these planes one at a time or just look at the face plane with the rest of the data set displayed. This program (in case you've never worked with it) isn't like VoxelView because you don't get to rotate the data set and see it from different sides. You can shift the orientation, but not as a smooth, 360 degree movie. What Dicer allows you to do is to reslice your data from any angle, display the surface of your entire data set and cut chunks out of it to see interior details, make movies showing a plane moving through your invisible data set showing one plane at a time, and other things. I don't believe you can output your resliced planes so that you can load them into NIH Image, for example.. but my experience with the program is limited. Hope some of this helps. From keller@micros.mrd.bldrdoc.gov Mon Oct 4 03:13:37 1993 Received: from central.bldrdoc.gov by nx1.soils.umn.edu (5.65c) id AA07046; Mon, 4 Oct 1993 10:13:11 -0500 Return-Path: Received: from arc1.mrd.bldrdoc.gov by central.bldrdoc.gov (4.1/SMI-DDN) id AA15935; Mon, 4 Oct 93 09:14:03 MDT Received: from micros.mrd.bldrdoc.gov by arc1.mrd.bldrdoc.gov (4.1/SMI-3.2) id AA00410; Mon, 4 Oct 93 09:15:35 MDT Message-Id: <9310041515.AA00410@arc1.mrd.bldrdoc.gov> Date: Mon, 4 Oct 93 09:13:37 MDT From: Bob Keller Subject: Re: grain size measurements To: nih-image@soils.umn.edu X-Mailer: LeeMail 1.2.4 >I adapted a protocol to automate cell contour tracing, which might be usefull >to you. Basically, the principle is to transform the initial image in an >"edge image" (by holding the option key down with the Trace Edges command of >Image. Then, I use a special routine (which I called Crest Pathway), which >traces the edge of one cell and makes a ROI around it. You have to click on >a starting point close to the object of interest, and the routine reiterately >steps to the darkest neighbour. When it reahces a point already in the path, >the iteration ceases and the initial "tail" is eaten. > >A version of image containing the Crest Pathway routine is available, >together with some example images, on zippy, in the contrib directory. > >The name of the file is Quantile_Crest.sit.hqx Thanks. We've tried your Crest Pathway routine. Actually, it's not exactly what we need, since Crest measures the size of a single grain, or cell, or whatever you're measuring. (I've also had trouble with it when my binary images did not have nice smooth boundaries. The line would keep going well beyond the boundary near where I started and often circle back onto itself within a very small area within another boundary itself. I did vary the size of the "detected" region as well, with no luck. Is it possible to define a threshold regime which would tell the line when to change it's course?) I'm going to write a macro to do the grain size measurement myself, using the line intercept method which is standard in metallography. The xy-Quantile routine is great! Bob Keller NIST Div. 853 Boulder, CO keller@micros.mrd.bldrdoc.gov From chung@mipgsun.mipg.upenn.edu Mon Oct 4 07:26:20 1993 Received: from NOC4.DCCS.UPENN.EDU by nx1.soils.umn.edu (5.65c) id AA07200; Mon, 4 Oct 1993 10:25:18 -0500 Return-Path: Received: from MIPGSUN.MIPG.UPENN.EDU by noc4.dccs.upenn.edu id AA12770; Mon, 4 Oct 93 11:26:24 -0400 Received: by mipgsun.mipg.upenn.edu (4.1/MIPG-1.0) id AA23865; Mon, 4 Oct 93 11:26:20 EDT Date: Mon, 4 Oct 93 11:26:20 EDT From: chung@mipgsun.mipg.upenn.edu ( Hsiao-Wen Chung 09-17-93) Message-Id: <9310041526.AA23865@mipgsun.mipg.upenn.edu> To: nih-image@soils.umn.edu Subject: IRIS Smartjet A friend of mine was asking for info about IRIS Smartjet 4012 and 3024 laser printer. Does anyone know the TELs and FAXs of some agents, stores, or companies that sell these printers? Any assistance is highly appreciated. Henry Chung University of Pennsylvania From Fredboyd@bmec.micro.umn.edu Mon Oct 4 05:30:16 1993 Received: from mail.tc.umn.edu by nx1.soils.umn.edu (5.65c) id AA07883; Mon, 4 Oct 1993 11:39:25 -0500 Return-Path: Received: from mailbox.mail.umn.edu by mail.tc.umn.edu id SMTP-0012cb0401a029022; Mon, 4 Oct 93 10:24:10 -0500 Date: Mon, 4 Oct 93 10:30:16 CDT Message-Id: <9310041530.AA11377@mailbox.mail.umn.edu> Received: from pathobiology-218.med.umn.edu by mailbox.mail.umn.edu; Mon, 4 Oct 93 10:30:16 CDT From: "Fred Boyd, Ph.D." To: nih-image@soils.umn.edu Subject: LG-3 Memory Upgrade Hi all: I have just put in 4x1Mb simms on my Lg-3 board. Image still sees the board as a 1Mb board and will only capture/integrate 2 frames at video rate. What else do I have to do? Fred Boyd, Ph.D. Assistant Professor Laboratory Medicine and Pathology Cell Biology and Neuroanatomy University of Minnesota _______________________________________________________________________________ Box 609, UMHC Phone (612) 624-8150 420 Delaware St. SE FAX (612) 626-2444 Minneapolis, MN 55455 From ruzin@nature.berkeley.edu Mon Oct 4 02:08:41 1993 Received: from nak.Berkeley.EDU by nx1.soils.umn.edu (5.65c) id AA08377; Mon, 4 Oct 1993 12:07:25 -0500 Return-Path: Received: from nature.Berkeley.EDU by nak.berkeley.edu (5.67/1.40) id AA22771; Mon, 4 Oct 93 10:08:31 -0700 Received: from [128.32.128.168] (kos5mac13.Berkeley.EDU) by nature.berkeley.edu.cnr-net (4.1/SMI-4.1) id AA07818; Mon, 4 Oct 93 10:11:10 PDT Message-Id: <9310041711.AA07818@nature.berkeley.edu.cnr-net> Date: Mon, 4 Oct 1993 10:08:41 -0800 To: nih-image@soils.umn.edu From: ruzin@nature.berkeley.edu (Steven Ruzin) Subject: Re: imagefft Where may I find the non-FPU version of Image. I'd like to run it on a LCIII. Thanks. Steve... /////////////////////////////////////////////// | Steven Ruzin | | NSF Center of Plant Developmental Biology | | Dept Plant Biology | | Univ California Berkeley | | e-mail: ruzin@nature.berkeley.edu | | phone: 510-642-6602 | /////////////////////////////////////////////// From wayne@helix.nih.gov Mon Oct 4 12:41:43 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA08828; Mon, 4 Oct 1993 12:43:23 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA04123; Mon, 4 Oct 93 13:03:47 -0400 Message-Id: <9310041703.AA04123@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 4 Oct 1993 12:41:43 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: LG-3 Memory Upgrade >Hi all: >I have just put in 4x1Mb simms on my Lg-3 board. Image still sees the board >as >a 1Mb board and will only capture/integrate 2 frames at video rate. What else >do I have to do? You shouldn't have to do anything else since NIH Image checks at startup to see how much memory the LG-3 has. Are you sure those were 1MB SIMMS you put in and not 1/4MB SIMMS? --wayne From wayne@helix.nih.gov Mon Oct 4 14:58:30 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA10349; Mon, 4 Oct 1993 15:00:11 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA04844; Mon, 4 Oct 93 15:20:34 -0400 Message-Id: <9310041920.AA04844@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 4 Oct 1993 14:58:30 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Reslice Command >A week or two ago I asked about the Reslice command, which kept giving me an >error saying "Selection must be within image boundary." After a little >experimentation, I found that this was caused by setting the slice spacing to >less than one pixel. To get around this, I set the slice spacing to one >pixel, reslice, and then vertically scale the resulting image so that it has >the >correct aspect ratio. > >Is this by design or is it a bug? This is a bug that is fixed in V1.53b8, available by FTP from zippy.nimh.nih.gov. --wayne From norm_hurst@maca.sarnoff.com Mon Oct 4 15:14:02 1993 Received: from nova (nova.sarnoff.com) by nx1.soils.umn.edu (5.65c) id AA10528; Mon, 4 Oct 1993 15:14:02 -0500 Return-Path: Received: from maca.sarnoff.com by nova (4.1/SMI-4.0) id AA21412; Mon, 4 Oct 93 16:14:41 EDT Message-Id: <9310042014.AA21412@nova> Date: 4 Oct 1993 11:55:17 U From: "Norm Hurst" Subject: Variance macro To: nurit_binenbaum@maca.sarnoff.com, scott_casavant@maca.sarnoff.com, michael_isnardi@maca.sarnoff.com, prashanth_kuchibhotla@maca.sarnoff.com, James_Matey.MAILCENTER#u#17@maca.sarnoff.com, paul_meehan@maca.sarnoff.com, "NIH Image user group" , stu_perlman@maca.sarnoff.com, catherine_tsao@maca.sarnoff.com Variance macro 10/4/93 11:24 AM >>>Anyone have a macro that calculates a variance image? I assume you want the "instantaneous" variance, the variance of a pixel in its neighborhood. var(i) = (x(i) - avg(x))^2/(N-1) where avg(x) is the average of values in a neighborhood (say 5x5) around a pixel x(i), and N is the number of pixels in the neighborhood (25). Let's disregard the /(N-1) operation for now -- it's merely a scaling operation. x(i) - avg(x) can be found by convolving with an appropriate filter. Here is the filter for the 5x5 case: -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 24 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 The squaring operation can be done with a parabolic LUT. This LUT can include the scaling operation for those who need calibrated results (modify the argument to "Square" to be other than 1.0 to scale the LUT). The macro "Find Variance [V]" is below. --------------------- { Requires the file '5x5 mean diff' to contain: -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 24 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 This is an impulse filter (all zeros with a 1 in the middle) minus a 5x5 average (5x5 1's divided by 25), then scaled so the smallest tap is 1 (i.e. times 25). } procedure Square(scale:real) { APPLIES A PARABOLIC LUT} var i,y:integer; begin for i:= 1 to 254 do begin y:= (i-127)*(i-127)*scale/64.25; if y > 255 then y:=255; RedLUT[i]:=y; GreenLUT[i]:= y; BlueLUT[i]:=y; end; UpdateLUT; ApplyLUT; end; macro 'Find Variance [V]' begin Convolve('5x5 mean diff'); {impulse minus 5x5 average} Square(1.0); {Adjust argument to scale the LUT} end; From kyzy@rice.edu Mon Oct 4 10:31:20 1993 Received: from moe.rice.edu by nx1.soils.umn.edu (5.65c) id AA10742; Mon, 4 Oct 1993 15:30:20 -0500 Return-Path: Received: from [128.42.105.7] (erinna.rice.edu) by moe.rice.edu (AA13618); Mon, 4 Oct 93 15:31:22 CDT Date: Mon, 4 Oct 93 15:31:20 CDT Message-Id: <9310042031.AA13618@moe.rice.edu> To: nih-image@soils.umn.edu From: kyzy@rice.edu Subject: Re: imagefft >Where may I find the non-FPU version of Image. I'd like to run it on a LCIII. > The non-FPU version of NIH-image 1.52 is at /pub/nih-image on zippy. But, have you considered adding the FPU chip to your LC-III ? There is a socket on the LC-III motherboard for the 68882 floating point chip. All you have to do is buy a 25 MHz 68882 chip from any of the mail-order places and pop it in its socket (fairly easy to do and safe if you follow the standard grounding procedures). Depending on where you buy it, the chip will cost from 60 to 80 dollars. I have just upgraded an LCIII with more memory and the FPU chip, and it now has Mac IIci performance on everything. ------------------------------------------------------------------------ | Kyriacos Zygourakis, Professor | Phone: (713) 527-8750 Ext. 3509 Dept. of Chemical Engineering | FAX: (713) 285-5478 Rice University | e-mail: kyzy@rice.edu Houston, Texas 77251-1892 | | ------------------------------------------------------------------------ From wayne@helix.nih.gov Mon Oct 4 17:12:49 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA11965; Mon, 4 Oct 1993 17:14:30 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA05452; Mon, 4 Oct 93 17:34:53 -0400 Message-Id: <9310042134.AA05452@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 4 Oct 1993 17:12:49 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Non-FPU version of NIH Image >Where may I find the non-FPU version of Image. I'd like to run it on a LCIII. As of today, both fpu and non-fpu versions of Image1.52 are on zippy.nimh.nih.gov. Before today, only the non-fpu version was available, although it didn't have "non-fpu" in the file name. The non-fpu version runs on all Macs with 8-bit video, including the PowerPC, and is not noticably slower than the fpu version for most functions. The fpu version is faster for a few operations, such as line profile plotting using a wide line selection. --wayne From msachs@admin.ogi.edu Mon Oct 4 09:33:37 1993 Received: from ogicse.cse.ogi.edu (cse.ogi.edu) by nx1.soils.umn.edu (5.65c) id AA12773; Mon, 4 Oct 1993 18:33:12 -0500 Return-Path: Received: by ogicse.cse.ogi.edu (/\==/\ Smail3.1.25.1 #25.4) id ; Mon, 4 Oct 93 16:34 PDT Received: from [129.95.74.59] by admin.ogi.edu.ogi.edu (4.1/SMI-4.1) id AA18240; Mon, 4 Oct 93 16:33:41 PDT Date: Mon, 4 Oct 93 16:33:37 PDT Message-Id: <9310042333.AA18240@admin.ogi.edu.ogi.edu> To: Multiple recipients of list From: msachs@admin.ogi.edu (Matthew Sachs) Subject: How to correctly use Image for densitometry? Dear Imagers, Please help a new Image user to use Image correctly. I regret that the appellation "Image user" might seem oxymoronic applied to me at present. Given a MacII CX, Microtek MSF300ZS scanner, Image 1.52, Photoshop 2.5 (and given the possibility of using a CCD for image capture, if scanner is too weak a link). We wish to examine a series of autoradiographic images of gel "bands" of different intensities and morphologies derived from experimental samples. We can follow directions in Image documentation to: Scan autoradiograms at 75 dpi. Open in Image, use 2D rolling ball to remove background. Select "Calibrate" option, select radio button "Uncalibrated OD." Use Plot Gel macro to obtain profiles of a series of gel lanes. Draw baselines to make peaks that correspond to bands of interest into 'closed' objects. Select peaks of interest with the wand tool, and use option-text tool to place the calculated area of selected peaks onto the lane profiles. The questions I have concern how to use peak areas obtained with this method to CORRECTLY determine the relative amount of material in input samples. In some cases, there is an anticipated 1.5-fold difference in the amount of material of interest in cells grown under different growth conditions (based on enzyme activity assay); in other cases, hundred-fold differences are anticipated. What does experience teach as the best, most efficient way to tackle this problem? I anticipate that loading different amounts of each sample, using different exposures, and possibly defining calibration parameters empirically using standards are all necessary, but would appreciate guidance as to what constitutes a sensible protocol to begin this process, and what controls experts feel are necessary to assure legitimate comparisons. Thank you for any advice you might have on this matter. Sincerely, Matthew Sachs Assistant Professor Department of Chemistry, Biochemistry and Molecular Biology Oregon Graduate Institute of Science and Technology Beaverton, OR From skim@signal.poly.edu Mon Oct 4 15:57:56 1993 Received: from signal.poly.edu by nx1.soils.umn.edu (5.65c) id AA13143; Mon, 4 Oct 1993 19:01:00 -0500 Return-Path: Received: by signal.poly.edu (5.65/1.34) id AA09779; Mon, 4 Oct 93 19:57:56 -0400 Date: Mon, 4 Oct 93 19:57:56 -0400 From: skim@signal.poly.edu (Seung Pil Kim) Message-Id: <9310042357.AA09779@signal.poly.edu> To: nih-image@soils.umn.edu Subject: Re: LG-3 Memory Upgrade > >I have just put in 4x1Mb simms on my Lg-3 board. Image still sees the board > >as > >a 1Mb board and will only capture/integrate 2 frames at video rate. What else > >do I have to do? > > You shouldn't have to do anything else since NIH Image checks at startup to > see how much memory the LG-3 has. Are you sure those were 1MB SIMMS you put > in and not 1/4MB SIMMS? I had a similar experience when I tried to upgrade memory 1M to 4M for my Mac/SE. I found that the resister near the memory module should be cut off. I don't remember the res. number but there is a square printed beneath it on PCB. Hope this helps. S.P. Kim From stmwang@hubcap.clemson.edu Mon Oct 4 16:56:14 1993 Received: from hubcap.clemson.edu by nx1.soils.umn.edu (5.65c) id AA13763; Mon, 4 Oct 1993 19:56:01 -0500 Return-Path: Received: by hubcap.clemson.edu; Mon, 4 Oct 93 20:56:20 -0400 From: stmwang@hubcap.clemson.edu (Sam Wang) Message-Id: <9310050056.AA00613@hubcap.clemson.edu> Subject: Re: QuickImage24 To: nih-image@soils.umn.edu Date: Mon, 4 Oct 1993 20:56:14 -0400 (EDT) In-Reply-To: <199310041855.AA09686@nx1.soils.umn.edu> from "nih-image@soils.umn.edu" at Oct 4, 93 01:55:32 pm X-Mailer: ELM [version 2.4 PL2] Content-Type: text Content-Length: 365 Does anyone use the Mass Micro QuickImage 24 frame capture board with Image? Latest ad in MacWorld is selling it for $99. It's supposed to support QuickTime. I am interested to know how well it might work on a IIcx and on a Centris 610. -- Sam Wang stmwang@hubcap.clemson.edu 803/656-3924voice 656-0204fax Art Dept., Clemson University, Clemson, SC 29634-0509 From kartenh@Sdsc.Edu Tue Oct 5 03:18:42 1993 Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA15073; Mon, 4 Oct 1993 22:17:45 -0500 Return-Path: Date: Tue, 5 Oct 93 03:18:42 GMT From: kartenh@Sdsc.Edu (Harvey Karten) Message-Id: <931005031842.204065b9@m5.sdsc.edu> Subject: RE: How to correctly use Image for densitometry? To: nih-image@soils.umn.edu X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu" X-St-Vmsmail-Cc: KARTENH re: questions by Matthew Sachs If you use a CCD to gather your images, there are several critical operations that you must attend to if you want to have any hope of accurate inter-specimen comparison. 1) Get a CCD that allows you to turn the AGC OFF. Many CCDs have an internal jumper that has to be correctly repositioned to inactivate the AGC (Automatic Gain Control). 2) Use a stabilized light source. An AC fluorescent light table is not sufficiently stable for this purpose. I have heaerd that a stabilized DC fluorescent light source may be ok, but should be recalibrated every so often. 3) When initially setting up your system with the CCD and Good quality lens, you have to adjust the gain and offset (if using a Scion LG-3) to give proper spread of values in your histogram. (See various texts in video microscopy). 4) Once you have gotten this standardized, make sure you always set it up in exactly the same way each time. It would be adviseable to have a graded image with a good 8 bit spread of values for calibration each time. Some tips for this are to always use the same r egion of the ligth table, same distance from the object, same f-stop on the lens, etc. 5) Despite all these precautions, you may still have problems, because of inherent response to bloom on the part of all video devices, even if AGC is turned off. Thus, if there is a particularly bright portion to your image, some cameras will still modify their gain even with AGC off. I don't know the reason for this, but it may have to do with electrostatic charging of the CCD. Perhaps one of our other participants can explain why this happens. Hope this is of some help. HJK From rms@acsu.buffalo.edu Mon Oct 4 19:28:50 1993 Received: from lictor.acsu.buffalo.edu by nx1.soils.umn.edu (5.65c) id AA15223; Mon, 4 Oct 1993 22:27:46 -0500 Return-Path: Received: from rms@localhost by lictor.acsu.buffalo.edu (8.5/8.5) id XAA22135; Mon, 4 Oct 1993 23:28:50 -0400 Date: Mon, 4 Oct 1993 23:28:50 -0400 From: "Robert M. Straubinger" Message-Id: <199310050328.XAA22135@lictor.acsu.buffalo.edu> To: nih-image@soils.umn.edu Subject: Ratio imaging I've imported z-series of images from an Olympus confocal into Image stacks; the stacks consist of pairs of images for each z-slice (images are taken 2 different wavelengths) in order to determine pH from a pH - sensitive probe. I'd like to create a new stack of ratio'ed images. So far, I haven't found a macro to do it. The preliminary approach I've taken is to copy one image and paste it on the other, using Paste Control to divide one image by the other. A macro to automate the above would be relatively simple, but I'd like to solicit comments (better still, macros); a number of other operations ought to be done, such as mask out background values and saturated pixels. Also, it would be nice to be able to control the scaling after divide -- either to maximize dynamic range, or to force scaling of all images to the same range. If this wheel has been invented already, I'd like to hear about it- Bob Straubinger Pharmaceutics SUNY Buffalo From mhowland@alsvid.une.edu.au Wed Oct 6 00:25:12 1993 Received: from alsvid.une.edu.au by nx1.soils.umn.edu (5.65c) id AA15853; Mon, 4 Oct 1993 23:24:13 -0500 Return-Path: Received: from [129.180.146.5] (mac146_5.nr.une.edu.au) by alsvid.une.edu.au with SMTP id AA00959 (5.65c8+/IDA-1.4.4 for ); Tue, 5 Oct 1993 14:25:12 +1000 Date: Tue, 5 Oct 1993 14:25:12 +1000 Message-Id: <199310050425.AA00959@alsvid.une.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mhowland@alsvid.une.edu.au (Mick Howland) Subject: Image & AV series Macs Can Image capture video live through the on board video controller of the AV series Mac's? _____________________________________________________________ Michael Howland, Faculty of Resource Science & Management UNE - Northern Rivers, P.O. Box 157, Lismore, NSW, Australia. Phone: +61-66-203037 Fax: +61-66-212669 E-mail: mhowland@alsvid.une.edu.au _____________________________________________________________ From herro001@maroon.tc.umn.edu Tue Oct 5 01:55:04 1993 Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c) id AA20847; Tue, 5 Oct 1993 06:53:58 -0500 Return-Path: Message-Id: <199310051153.AA20847@nx1.soils.umn.edu> Received: from rash.med.umn.edu by maroon.tc.umn.edu id SMTP-0012cb16093012531; Tue, 5 Oct 93 06:55:02 -0500 From: "Mike Herron" Reply-To: "Mike Herron" To: nih-image@soils.umn.edu Subject: Re: Non-FPU version of NIH Image Date: Tue, 5 Oct 93 06:55:04 -0500 In message <9310042134.AA05452@zippy.nimh.nih.gov> writes: > >Where may I find the non-FPU version of Image. I'd like to run it on a > LCIII. > > As of today, both fpu and non-fpu versions of Image1.52 are on > zippy.nimh.nih.gov. Before today, only the non-fpu version was available, > although it didn't have "non-fpu" in the file name. The non-fpu version > runs on all Macs with 8-bit video, including the PowerPC, and is not > noticably slower than the fpu version for most functions. The fpu version > is faster for a few operations, such as line profile plotting using a wide > line selection. > > --wayne Is this right? You/someone tested Image1.52 on a PowerPC?! ______________________________________________ / Mike Herron, U of MN, Dept. of Dermatology / / herro001@maroon.tc.umn.edu / / 612-625-8935 Box 124 UMHC, Mpls MN 55455 / ______________________________________________ From a337ard@diamond.sara.nl Tue Oct 5 14:39:38 1993 Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c) id AA21353; Tue, 5 Oct 1993 07:43:43 -0500 Return-Path: Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF V4.2-13 #2574) id <01H3QUZUDTWWB6360R@vx.cis.umn.edu>; Tue, 5 Oct 1993 07:45:18 CDT Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 5 Oct 93 13:44 MET Received: by diamond.sara.nl (5.61-AIX-1.2/1.0), id AA166740, (for nih-image@soils.umn.edu, from a337ard@diamond.sara.nl); Date: Tue, 05 Oct 1993 13:39:38 +0100 From: a337ard@diamond.sara.nl (Ard Jonker) Subject: Re: Non-FPU version of NIH Image To: nih-image@soils.umn.edu Message-Id: <9310051239.AA166740@diamond.sara.nl> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT Okay, I'll bite: Is the powerPC available yet? Where? How much? From wayne@helix.nih.gov Tue Oct 5 08:13:21 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA21707; Tue, 5 Oct 1993 08:15:03 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA07159; Tue, 5 Oct 93 08:35:29 -0400 Message-Id: <9310051235.AA07159@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Oct 1993 08:13:21 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Non-FPU version of NIH Image >Is this right? You/someone tested Image1.52 on a PowerPC?! I haven't tested Image on a PowerPC, put I don't see any reason why the non-fpu version wouldn't work. The fpu version won't work because the PowerPC emulates the 68LC040 processor(used in the Centris 610), which has no floating point instructions. --wayne From wayne@helix.nih.gov Tue Oct 5 10:02:06 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA22865; Tue, 5 Oct 1993 10:03:52 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA01364; Tue, 5 Oct 93 10:22:25 -0400 Message-Id: <9310051422.AA01364@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Oct 1993 10:02:06 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Non-FPU version of NIH Image >Okay, I'll bite: >Is the powerPC available yet? Where? How much? According to MacWeek, PowerPC Macs will be announced in March at prices starting around $2000. --wayne From dickinson%g24mac1@relay.nswc.navy.mil Tue Oct 5 09:07:55 1993 Received: from relay.nswc.navy.mil by nx1.soils.umn.edu (5.65c) id AA24464; Tue, 5 Oct 1993 12:07:05 -0500 Return-Path: Received: from [128.38.34.152] (ddickensmac.nswc.navy.mil) by relay.nswc.navy.mil (4.1/SMI-4.1) id AA14240; Tue, 5 Oct 93 13:07:55 EDT Date: Tue, 5 Oct 93 13:07:55 EDT Message-Id: <9310051707.AA14240@relay.nswc.navy.mil> From: "David Dickinson" Reply-To: "David Dickinson" To: NIH-IMAGE@SOILS.UMN.EDU Subject: Question on missing results I am measuring area, x, y, major and minor axis values. The version of NIH-Image is 1.52. The count of items measured (displayed in the box on the lower left of the screen) is 952. The highest marked item on the image is also 952. However, the number of measurements displayed in the results window only goes to 526 and the x value of 527. Printing (or copying and pasting to Excel) shows the number of measurements to be 582. The max measurements value is set to 7000. The Undo and Clipboard value is set to 1600k. This process has been repeated multiple times (also with version 1.49) and the results are consistant. Any suggestions on finding the missing values is greatly appreciated. Thanks in advance. ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: David L. Dickinson dickinson@g24mac1.nswc.navy.mil Voice: (703) 663-8691 or DSN 249-8691 FAX: (703) 663-8268 Lethality and Weapons Effectiveness Branch, G24 Naval Surface Warfare Center, Dahlgren Division Dahlgren, VA 22448 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: From keller@micros.mrd.bldrdoc.gov Tue Oct 5 05:24:31 1993 Received: from central.bldrdoc.gov by nx1.soils.umn.edu (5.65c) id AA24640; Tue, 5 Oct 1993 12:23:45 -0500 Return-Path: Received: from pascal.mrd.bldrdoc.gov by central.bldrdoc.gov (4.1/SMI-DDN) id AA04461; Tue, 5 Oct 93 11:24:47 MDT Received: from micros.mrd.bldrdoc.gov by pascal.mrd.bldrdoc.gov (4.1/SMI-3.2) id AA00275; Tue, 5 Oct 93 11:25:14 MDT Message-Id: <9310051725.AA00275@pascal.mrd.bldrdoc.gov> Date: Tue, 5 Oct 93 11:24:31 MDT From: Bob Keller Subject: voyager plug-in To: nih-image@soils.umn.edu X-Mailer: LeeMail 1.2.4 Where can I find a Voyager decompression plug-in? It's not in the plug ins directory on zippy. Bob Keller keller@micros.mrd.bldrdoc.gov From ikami@liposun.lbl.gov Tue Oct 5 03:33:29 1993 Received: from lbl.gov by nx1.soils.umn.edu (5.65c) id AA24821; Tue, 5 Oct 1993 12:39:06 -0500 Return-Path: Received: from liposun.lbl.gov by lbl.gov (4.1/1.39) id AA12778; Tue, 5 Oct 93 10:45:57 PDT Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0) id AA11768; Tue, 5 Oct 93 10:33:30 PDT Date: Tue, 5 Oct 93 10:33:29 PDT Message-Id: <9310051733.AA11768@liposun.lbl.gov> To: nih-image@soils.umn.edu From: ikami@liposun.lbl.gov (Craig Ikami) Subject: first timer We have just acquired a molecular dynamics densitometer. It produces 12 bit tiff files. We have looked at image v1.44 and would like to know if future versions of image will support 12 bit acquisition and display? thanks From bnhirsch@dapsas1.weizmann.ac.il Tue Oct 5 22:08:09 1993 Received: from dapsas1.weizmann.ac.il by nx1.soils.umn.edu (5.65c) id AA25011; Tue, 5 Oct 1993 12:59:07 -0500 Return-Path: Received: from [132.76.66.33] by dapsas1.weizmann.ac.il via SMTP (920110.SGI/911001.SGI) for nih-image@soils.umn.edu id AA19817; Tue, 5 Oct 93 19:59:10 +0300 Message-Id: <9310051659.AA19817@dapsas1.weizmann.ac.il> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Oct 1993 20:08:09 +0200 To: nih-image@soils.umn.edu From: bnhirsch@dapsas1.weizmann.ac.il (David L. Hirschberg) Subject: Fluorescent Images -Help Can someone explain how ccd cameras handle fluorescent images and how can I use NIH-Image to get the maximum resolution? I have a Quadra 950 with a Scion LV-3 frame grabber and a Burle CCD camera (we also have a Sony X-77). The camera is mounted on a Nikon inverted scope. I am currently using Image 153b8. When I capture phase images I have no problem and my images look fine under most conditions. The problem comes whe I want to capture fluorescent images. I can see the image clearly through the eye piece and the image is acceptable on the Sony monitor we have attached to the camera. Using the standard acquistition in Image gives me a black screen though. I tried the summation and integration modes and still I ended up with a black screen. If I turned on the the white light then board started to see enough to capture something. I did download and try the Scion LV-3 plug-in module and was able to get a very weak image. Should the plug-in module work better than the standard method? Also is there a way to sum images using the plug-in module? I am trying to image neurites that have been stained with either FITC or Rhodamine. The LV-3 board seems to have the most problem when I am imaging a single neurite so only a very small portion of the field is lit-up and the rest is black. The neurite can be seen clearly through the eye piece weakly on the monitor but the computor monitor is black. Even if I am imaging 100 cells in a field it seems the resolution is not great after capturing. So what can I do to capture fluorescent images? Is Rhodamine better than Fluorescein? Is there a way I can change the sensitivity of the Scion board. Is there a way to boost the video part of the voltage input the LV-3 board receives? Thanks in advance. David =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= David L. Hirschberg bnhirsch@dapsas.weizmann.ac.il Department of Neurobiology (972) 834-2127 work Weizmann Institute of Science (972) 847-4805 home Rehovot 76100 Israel (972) 834-4131 fax From wayne@helix.nih.gov Tue Oct 5 14:50:08 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA26355; Tue, 5 Oct 1993 14:51:50 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA02166; Tue, 5 Oct 93 15:10:26 -0400 Message-Id: <9310051910.AA02166@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Oct 1993 14:50:08 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Variance macro Here is a version of Norm Hurst's variance macro that has the convolution filter inline. To get inline filtering to work right, I had to add width and height arguments to the NewTextWindow command and to fix the Dispose command so it works with text windows. These fixes are in V1.53b9 on zippy.nimh.nih.gov. --wayne procedure Square(scale:real) { Applies a parabolic LUT} var i,y:integer; begin for i:= 1 to 254 do begin y:= (i-127)*(i-127)*scale/64.25; if y > 255 then y:=255; RedLUT[i]:=y; GreenLUT[i]:= y; BlueLUT[i]:=y; end; UpdateLUT; ApplyLUT; end; procedure ImpulseFilter; {This is an impulse filter (all zeros with a 1 in the middle) minus a 5x5 average (5x5 1's divided by 25), then scaled so the smallest tap is 1 (i.e. times 25).} begin RequiresVersion(1.53); NewTextWindow('5x5 mean diff',150,140); writeln('-1 -1 -1 -1 -1'); writeln('-1 -1 -1 -1 -1'); writeln('-1 -1 24 -1 -1'); writeln('-1 -1 -1 -1 -1'); writeln('-1 -1 -1 -1 -1'); Convolve(''); Dispose; end; macro 'Find Variance [V]' begin ImpulseFilter; {impulse minus 5x5 average} Square(1.0); {Adjust argument to scale the LUT} end; From wayne@helix.nih.gov Tue Oct 5 15:49:55 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA27019; Tue, 5 Oct 1993 15:51:37 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA02344; Tue, 5 Oct 93 16:10:13 -0400 Message-Id: <9310052010.AA02344@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Oct 1993 15:49:55 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Question on missing results >The count of items measured (displayed in the box on the lower left of the >screen) is 952. The highest marked item on the image is also 952. However, the >number of measurements displayed in the results window only goes to 526 and >the >x value of 527. Printing (or copying and pasting to Excel) shows the number of >measurements to be 582. > >Any suggestions on finding the missing values is greatly appreciated. >From page 82 of the manual (Program Limitations): "The maximum number of characters that can be displayed, printed, or copied to the clipboard is 32,700. There is no limit to the number of measurements that can be exported to a text file." I have updated the description of the Show Results command in the manual to make this limitation clearer. --wayne From wayne@helix.nih.gov Tue Oct 5 16:51:45 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA27716; Tue, 5 Oct 1993 16:53:27 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA02489; Tue, 5 Oct 93 17:12:03 -0400 Message-Id: <9310052112.AA02489@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Oct 1993 16:51:45 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Ratio imaging >I've imported z-series of images from an Olympus confocal into >Image stacks; the stacks consist of pairs of images for each z-slice >(images are taken 2 different wavelengths) in order to determine >pH from a pH - sensitive probe. > >I'd like to create a new stack of ratio'ed images. So far, I haven't >found a macro to do it. The preliminary approach I've taken is to >copy one image and paste it on the other, using Paste Control to >divide one image by the other. > >A macro to automate the above would be relatively simple, but I'd like >to solicit comments (better still, macros); a number of other operations >ought to be done, such as mask out background values and saturated pixels. >Also, it would be nice to be able to control the scaling after divide -- >either to maximize dynamic range, or to force scaling of all images >to the same range. I am about to add a command to the macro language that will make it a lot easier to write such a macro. It will perform arithmetic and logical operations on images, eliminating the need to use Paste Control and providing the abilty to control scaling. I'm thinking of calling it DoOp (do operation). It will look something like DoOp('Divide', pid1, pid2, pid3, scale, offset) where the first argument specifies the function to be performed and pid1,pid2 and pid3 are pic id numbers. Pixel values resulting from the operation are multiplied by the scale and then the offset is added. Here are some examples: DoOp('Add', pid1, pid2, pid3, 0.5, 0); {Compute average of two images} DoOp('Copy', pid1, 0, pid1, 0.5, 128); {Multiply by .5 and add 128} DoOp('AND', pid1, pid2, pid3, 1, 0); {Logical AND of two images} --wayne From wayne@helix.nih.gov Tue Oct 5 16:59:45 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA27755; Tue, 5 Oct 1993 17:01:27 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA02501; Tue, 5 Oct 93 17:20:04 -0400 Message-Id: <9310052120.AA02501@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Oct 1993 16:59:45 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: first timer >We have just acquired a molecular dynamics densitometer. It produces 12 bit >tiff files. We have looked at image v1.44 and would like to know if future >versions of image will support 12 bit acquisition and display? The current version of NIH Image (1.52) can import the 16-bit TIFF files created by Molecular Dynamics scanners. The image data is scaled to 8-bits, but the 16-bit to 8-bit scaling can be changed using the Rescale(aka Revert to Saved) command. --wayne From kartenh@sdsc.edu Tue Oct 5 22:55:55 1993 Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA28428; Tue, 5 Oct 1993 17:55:09 -0500 Return-Path: Message-Id: <199310052255.AA28428@nx1.soils.umn.edu> Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET; Tue, 5 Oct 93 22:55:55 GMT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: kartenh@Sdsc.Edu Subject: Re: Fluorescent Images -Help Date: Tue, 5 Oct 93 22:55:55 GMT David H. Writes: >David L. Hirschberg bnhirsch@dapsas.weizmann.ac.il >Department of Neurobiology (972) 834-2127 work >Weizmann Institute of Science (972) 847-4805 home >So what can I do to capture fluorescent images? Is Rhodamine better than >Fluorescein? Is there a way I can change the sensitivity of the Scion >board. Is there a way to boost the video part of the voltage input the >LV-3 board receives? > > > >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= The image you see on your monitor may not reflect the actual values in the output signal. This most commonly happens when people "adjust" the brightness and contrast settings on the monitor. Modification of those settings may provide an image enhancement on the monitor display, but do not reflect the value that are coming out of the camera and going to the frame grabber. The use of those controls does not reflect the actual spread of values that are coming out of the camera. Ideally, you should use a running histogram when grabbing an image, then adjust the gain and offset to give a full spread of the 8 bits of your frame grabber. This is always a bit arbitrary with a fluorescent image, since most fluorescent images don't actually have that broad a point spread. Your eye is amazingly sensitive to low light levels. You may have to go to an image intensifier to get fluorescent images. If you are working on an inverted microscope (which I suspect if you are watching outgrowing neurites), you should be aware that the folded light path severely reduces the image brightness stil further, again emphasizing the need for an intensifier plate. regards, Harvey K. a.k.a. Reb Hillel of Del Mar Harvey J. Karten, M.D. Dept. of Neurosciences Univ.California San Diego La Jolla, CA 92093-0608 EMail: Kartenh@sdsc.edu Phone: (619)-534-4938 FAX: (619)-534-6602 From a337ard@diamond.sara.nl Wed Oct 6 09:01:21 1993 Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c) id AA03708; Wed, 6 Oct 1993 03:05:59 -0500 Return-Path: Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF V4.2-13 #2574) id <01H3RZKU2CMOB6397Y@vx.cis.umn.edu>; Wed, 6 Oct 1993 03:07:33 CDT Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 6 Oct 93 9:07 MET Received: by diamond.sara.nl (5.61-AIX-1.2/1.0), id AA156795, (for nih-image@soils.umn.edu, from a337ard); Date: Wed, 06 Oct 1993 08:01:21 +0100 From: a337ard@diamond.sara.nl (Ard Jonker) Subject: Re: Fluorescent Images -Help To: nih-image@soils.umn.edu Message-Id: <9310060701.AA156795@diamond.sara.nl> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT On the questionn of invisibility of fluorescent images: Regarding the Sony XC77 (CE) I can say that the image you see is likeley visible because you look at a video signal. That has been corrected for the pedestal of the camera (a floor in the camera signal ) that is caused by dark current. If you were to digitize the signal of the Sony in 127 levels, (As I do) the pedestal or dark current is 24. If you would digitize with 256 levels (NIH Image) I presume the dark current is 48. So to optimally visualize the image, grab it, subtract integer (48) from the image and do an equalization. (or make a histogram and see in which area of greylevels the interesting part is; if it ranges from a to b, then subtract a from the image and multiply by 255/(b-a), which is a strech of the area a..b over the LUT.) if this too does not work, you have another problem BTW, you could add the images of subsequent grabs, after subtracting 48 from each image. The 'official' way to do dark current correction is to grab an image with obscured camera, and subtract this image from each fluorescent image. I have found it to be satisfactory to subtract a constant (24 im n my case) because the variation in the Sony camera is very limited (as opposed to the Photometrics camera we use; pixelwise-percentage variation is bigger) ard (a337ard@diamond.sara.nl) From ptr@GRECO2.POLYTECHNIQUE.FR Wed Oct 6 12:49:28 1993 Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c) id AA05261; Wed, 6 Oct 1993 05:52:09 -0500 Return-Path: Received: from polytechnique.polytechnique.fr by chenas.inria.fr (5.65c8d/92.02.29) via Fnet-EUnet id AA07917; Wed, 6 Oct 1993 11:53:04 +0100 (MET) Received: by polytechnique.polytechnique.fr (5.65c/SMI-4.1.3) id AA14169; Wed, 6 Oct 1993 12:00:52 +0100 Received: from [129.104.27.245] by greco2.noname (4.1/SMI-4.1) id AA00446; Wed, 6 Oct 93 11:49:29 +0100 Date: Wed, 6 Oct 93 11:49:28 +0100 Message-Id: <9310061049.AA00446@greco2.noname> To: nih-image@soils.umn.edu From: ptr@GRECO2.POLYTECHNIQUE.FR (Peter Goedtkindt) Subject: Restore selection & Plot bug? Hallo, When making a profile plot using the Profile plot tool, then switching to a next image to do the same operation, using the Restore selection menu command (or cmd-4), I get inconsistent results. The selection is drawn where it should be, but the values are nonsense. When using a rectangular selection, I don't get this problem, and it is also much faster. Rectangular selections have a big disadvantage that the direction in which the plot is scanned depends on the relative width and hight. How can I choose between a vertical or a horizontal profile plot, independant of the aspect ratio of the selection? When I have my profile plot, I want to measure the FWHM of the peak. Has anybody written a Macro that allows this? Thanks, Peter Goedtkindt Universite Paris-Sud Laboratoire de Spectroscopie Atomique et Ionique X-ray Laser group bat350 Centre D'Orsay F-91405 Orsay Cedex. France Fax.:++33.1.69.41.94.60 - Tel 69.41.77.10 ------ And ------ Ecole Polytechnique, Laboratoire d'Utilisation de Lasers Intenses tel. 69.33.48.95 ----------------------------------------------------------------- From V.A.Moss@vme.glasgow.ac.uk Wed Oct 6 06:52:16 1993 Received: from hillhead.cent.gla.ac.uk by nx1.soils.umn.edu (5.65c) id AA06983; Wed, 6 Oct 1993 06:52:16 -0500 Return-Path: Received: from vme.glasgow.ac.uk by jess.glasgow.ac.uk via JANET with NIFTP (PP) id <24065-0@jess.glasgow.ac.uk>; Wed, 6 Oct 1993 12:53:14 +0100 Date: Wed, 6 Oct 93 12:51:18 BST From: V.A.Moss@vme.glasgow.ac.uk Subject: Re: Your last message... To: nih-image@soils.umn.edu Message-Id: <_6_Oct_93_12:51:18_A101DA@UK.AC.GLA.VME> In-Reply-To: Your message <9309291242.AA17983@u1.uibk.ac.at> Dear Dietmar, Thanks for your email about my last message being deleted. I too have deleted lots of messages, so I am not sure which was my last message. Any way it was not important. What it may have been was:- I am putting in a few new changes to MacStereology (moving/zooming and s shrinking in dialog boxes) and will send you a new version as soon as tested (in a few days I hope). Alignment of sections can be done manually in Align dialog of MacStereology, but it may be possible to do an automatc alignment based on the centre of gravity of objects on adjacent layers. Regards Vic Moss From pekr@research.novo.dk Wed Oct 6 14:34:22 1993 Received: from danpost.uni-c.dk by nx1.soils.umn.edu (5.65c) id AA07390; Wed, 6 Oct 1993 07:33:24 -0500 Return-Path: Received: from nngate.novo.dk (xpsrv1.novo.dk [129.142.229.2]) by danpost.uni-c.dk (8.6.beta.10/8.6.beta.10) with SMTP id NAA19383 for ; Wed, 6 Oct 1993 13:34:23 +0100 Received: by nngate.novo.dk (5.65/DEC-Ultrix/4.3A) id AA11275; Wed, 6 Oct 1993 13:34:23 +0100 Date: Wed, 6 Oct 1993 13:34:22 +0100 Message-Id: <9310061234.AA11275@nngate.novo.dk> From: pekr@research.novo.dk (Peter Kristensen) To: Internet::nih-image@soils.umn.edu Subject: Flat bed scanners The NIH-IMAGE manual notes that the LaCie Silver scanner works well with the program. Does anyone have the adress & fax number of the company selling that ? Other suggestions for flat-bed scanners working well with NIH IMAGE ? sincerely Peter Kristensen Pathology & Histochemistry Pharmaceuticals Division Novo Nordisk A/S Denmark From eric_s@BIOTEK.MCB.UCONN.EDU Wed Oct 6 04:40:10 1993 Received: from BIOTEK (biotek.mcb.uconn.edu) by nx1.soils.umn.edu (5.65c) id AA07551; Wed, 6 Oct 1993 07:40:52 -0500 Return-Path: Message-Id: <199310061240.AA07551@nx1.soils.umn.edu> Date: Wed, 6 Oct 1993 08:40:10 -0400 From: eric_s@BIOTEK.MCB.UCONN.EDU To: nih-image@soils.umn.edu Subject: looking for Dr. V. A. Moss X-Vms-To: SMTP%"nih-image@soils.umn.edu" Sorry to take up air space for this. I couple of weeks ago Dr. Moss expressed interest in a volume rendering program I have written. All my messages to him have bounced back - address unknown. Dr Moss, if you are still interested, I'd be happy to have you look at the program. Please mail me directly, and hopefully I will be able to return mail to you. Thanks, Eric From wayne@helix.nih.gov Wed Oct 6 08:22:55 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA08224; Wed, 6 Oct 1993 08:24:39 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA03210; Wed, 6 Oct 93 08:43:18 -0400 Message-Id: <9310061243.AA03210@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 6 Oct 1993 08:22:55 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Flat bed scanners >The NIH-IMAGE manual notes that the LaCie Silver scanner works well with the >program. Does anyone have the adress & fax number of the company selling that ? La Cie, Ltd. 8700 SW Creekside Place Beaverton, OR 97005 800-999-1179 503-520-9000 Fax: 503-520-9100 From rudolfo@hoh.mbl.edu Wed Oct 6 06:24:48 1993 Received: from AQUA.WHOI.EDU by nx1.soils.umn.edu (5.65c) id AA08921; Wed, 6 Oct 1993 09:26:33 -0500 Return-Path: Received: by aqua.whoi.edu (5.57/Ultrix3.0-C) id AA07209; Wed, 6 Oct 93 10:27:33 -0400 Received: from [128.128.172.47] by hoh.mbl.edu. (4.1/SMI-4.1) id AA03121; Wed, 6 Oct 93 10:24:49 EDT Date: Wed, 6 Oct 93 10:24:48 EDT Message-Id: <9310061424.AA03121@hoh.mbl.edu.> To: nih-image@soils.umn.edu From: rudolfo@hoh.mbl.edu (Rudolf Oldenbourg) X-Sender: rudolfo@hoh.mbl.edu Subject: Re: Ratio imaging >I'm thinking of calling it DoOp >(do operation). It will look something like > > DoOp('Divide', pid1, pid2, pid3, scale, offset) > >where the first argument specifies the function to be performed and >pid1,pid2 and pid3 are pic id numbers. Pixel values resulting from the >operation are multiplied by the scale and then the offset is added. > >--wayne This will be a very useful macro command. In our application of NIH-Image, we need to do successive image arithmetic operations between slices of a given stack, storing the result in a new slice. We (i.e. Guang Mei) have modified the source code of NIH-Image to do our specific calculations with the speed of compiled image arithmetic. With that experience, I'd like to suggest three features for the above new macro command: 1) For the pid #, allow the use of slices in a stack. 2) Provide for storing the scaling factor and offset value as part of the result image. By way of explanation, the original result values from image arithmetic operations are usually lost, after scaling for display purposes and because of the restriction of 8 bit data in an image array. By storing the scale factor and offset value with the result image, however, one is able to reproduce the original values. This is often very useful for quantitative image analysis. The recalculated result values will have 8 bit precision only; however, in most cases this is not a problem, since the intensity data have only 8 bit pecision to begin with. We store the scaling values in the first two pixels of the result image, using an encoding scheme which is useful in our particular application. May be there is a better way of storing those values permanently with the image. 3) May be you can allow for several successive arithmetic operations in one command, bypassing the (time and memory consuming) need to store intermidiate results. >From the desk of Rudolf Oldenbourg oldenbourg@mbl.edu Tel:(508)548-3705 ext 426 Program of Architectural Dynamics in Living Cells Marine Biological Laboratory, Woods Hole, MA 02543-1031 From wayne@helix.nih.gov Wed Oct 6 10:10:53 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA09501; Wed, 6 Oct 1993 10:12:37 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA03499; Wed, 6 Oct 93 10:31:16 -0400 Message-Id: <9310061431.AA03499@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 6 Oct 1993 10:10:53 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Restore selection & Plot bug? >When making a profile plot using the Profile plot tool, then switching to a >next image to do the same operation, using the Restore selection menu >command (or cmd-4), I get inconsistent results. The selection is drawn >where it should be, but the values are nonsense. This bug is fixed in version 1.53b10, which is available by anonymous ftp from zippy.nimh.nih.gov. >When using a rectangular selection, I don't get this problem, and it is >also much faster. Rectangular selections have a big disadvantage that the >direction in which the plot is scanned depends on the relative width and >hight. How can I choose between a vertical or a horizontal profile plot, >independant of the aspect ratio of the selection? You can force the Plot Profile command to do a horizontal plots by holding the Option key down. It will only do a vertical plots, however, when the selection is taller than it is wide and the option key is not held down. --wayne From CHARLEST@macc.wisc.edu Wed Oct 6 05:22:00 1993 Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c) id AA09661; Wed, 6 Oct 1993 10:21:57 -0500 Return-Path: Received: from VMSmail by vms2.macc.wisc.edu; Wed, 06 Oct 93 10:22 CDT Message-Id: <23100610223675@vms2.macc.wisc.edu> Date: Wed, 06 Oct 93 10:22 CDT From: Charles Thomas Subject: Re: Question on missing results To: nih-image@soils.umn.edu X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST Lethality and Weapons Effectiveness Branch? Sheesh. I bet things get done when people see THAT letterhead. :) And I thought we got good service from Pizza Pit when they heard the order was for "Dr. _______". :) From CHARLEST@macc.wisc.edu Wed Oct 6 05:31:00 1993 Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c) id AA09701; Wed, 6 Oct 1993 10:32:34 -0500 Return-Path: Received: from VMSmail by vms2.macc.wisc.edu; Wed, 06 Oct 93 10:31 CDT Message-Id: <23100610313481@vms2.macc.wisc.edu> Date: Wed, 06 Oct 93 10:31 CDT From: Charles Thomas Subject: Re: Restore selection & Plot bug? To: nih-image@soils.umn.edu X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST Just an aside... I had good luck exporting the plot values as a text file and loading them into DeltaGraph. From there, you can manipulate your curves and quantify them at will. From dickinson%g24mac1@relay.nswc.navy.mil Wed Oct 6 07:46:40 1993 Received: from relay.nswc.navy.mil by nx1.soils.umn.edu (5.65c) id AA09893; Wed, 6 Oct 1993 10:45:45 -0500 Return-Path: Received: from [128.38.34.152] (ddickensmac.nswc.navy.mil) by relay.nswc.navy.mil (4.1/SMI-4.1) id AA25586; Wed, 6 Oct 93 11:46:40 EDT Date: Wed, 6 Oct 93 11:46:40 EDT Message-Id: <9310061546.AA25586@relay.nswc.navy.mil> From: "David Dickinson" Reply-To: "David Dickinson" To: nih-image@soils.umn.edu Subject: Re: Question on missing results In message <9310052010.AA02344@zippy.nimh.nih.gov> writes: > >From page 82 of the manual (Program Limitations): > > "The maximum number of characters that can be displayed, printed, or > copied to the clipboard is 32,700. There is no limit to the number of > measurements that can be exported to a text file." > > I have updated the description of the Show Results command in the manual to > make this limitation clearer. > > --wayne > > When I click on Export I see a sub-menu "About Export Plug-ins ...". This tells me the plug-ins need to be a Plug-in folder. Where do I find the plug-in to export measurements to a tab-delimited text file compatible with Excel? I can't find info on this in V1.52 of the manual and none of the titles on the server at NIH seem to match up. Thanks for your help. ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: David L. Dickinson dickinson@g24mac1.nswc.navy.mil Voice: (703) 663-8691 or DSN 249-8691 FAX: (703) 663-8268 Lethality and Weapons Effectiveness Branch, G24 Naval Surface Warfare Center, Dahlgren Division Dahlgren, VA 22448 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: From kartenh@sdsc.edu Wed Oct 6 17:52:36 1993 Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA11635; Wed, 6 Oct 1993 12:51:43 -0500 Return-Path: Message-Id: <199310061751.AA11635@nx1.soils.umn.edu> Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET; Wed, 6 Oct 93 17:52:36 GMT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: kartenh@Sdsc.Edu Subject: Re: Your last message... Date: Wed, 6 Oct 93 17:52:36 GMT Re: >I am putting in a few new changes to MacStereology (moving/zooming and s >shrinking in dialog boxes) and will send you a new version as soon as tested >(in a few days I hope). > >Alignment of sections can be done manually in Align dialog of MacStereology, >but it may be possible to do an automatc alignment based on the centre of >gravity of objects on adjacent layers. > >Regards >Vic Moss What is MacStereology? How does it interact with NIH-Image? thnaks, Harvey Karten Harvey J. Karten, M.D. Dept. of Neurosciences Univ.California San Diego La Jolla, CA 92093-0608 EMail: Kartenh@sdsc.edu Phone: (619)-534-4938 FAX: (619)-534-6602 From vokey@hg.uleth.ca Wed Oct 6 06:07:48 1993 Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c) id AA11721; Wed, 6 Oct 1993 13:04:41 -0500 Return-Path: Received: by hg.uleth.ca (MX V3.3 VAX) id 13563; Wed, 06 Oct 1993 12:08:21 MDT Date: Wed, 06 Oct 1993 12:07:48 MDT From: vokey@hg.uleth.ca To: nih-image@soils.umn.edu Message-Id: <009739C9.DF9988E0.13563@hg.uleth.ca> Subject: Dithering It is said (in the manual) that Image "uses the Floyd-Stenberg error diffusion algorithm" to dither images. Could someone please provide an explanation of this algorithm? TIA John R. Vokey From herro001@maroon.tc.umn.edu Wed Oct 6 08:14:22 1993 Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c) id AA11950; Wed, 6 Oct 1993 13:13:18 -0500 Return-Path: Message-Id: <199310061813.AA11950@nx1.soils.umn.edu> Received: from rash.med.umn.edu by maroon.tc.umn.edu id SMTP-0012cb30a9c023125; Wed, 6 Oct 93 13:12:47 -0500 From: "Mike Herron" Reply-To: "Mike Herron" To: nih-image@soils.umn.edu Subject: Re: Ratio imaging Date: Wed, 6 Oct 93 13:14:22 -0500 I would like to second Rudolf's suggestions. Operations on a stack and storing the scaling factor and offset value as part of the resulting image's header (?) would be a real improvement. In message <9310061424.AA03121@hoh.mbl.edu.> writes: > >I'm thinking of calling it DoOp > >(do operation). It will look something like > > > > DoOp('Divide', pid1, pid2, pid3, scale, offset) > > > >where the first argument specifies the function to be performed and > >pid1,pid2 and pid3 are pic id numbers. Pixel values resulting from the > >operation are multiplied by the scale and then the offset is added. > > > >--wayne > > This will be a very useful macro command. In our application of NIH-Image, > we need to do successive image arithmetic operations between slices of a > given stack, storing the result in a new slice. We (i.e. Guang Mei) have > modified the source code of NIH-Image to do our specific calculations with > the speed of compiled image arithmetic. With that experience, I'd like to > suggest three features for the above new macro command: > > 1) For the pid #, allow the use of slices in a stack. > > 2) Provide for storing the scaling factor and offset value as part of the > result image. > By way of explanation, the original result values from image arithmetic > operations are usually lost, after scaling for display purposes and because > of the restriction of 8 bit data in an image array. By storing the scale > factor and offset value with the result image, however, one is able to > reproduce the original values. This is often very useful for quantitative > image analysis. The recalculated result values will have 8 bit precision > only; however, in most cases this is not a problem, since the intensity > data have only 8 bit pecision to begin with. We store the scaling values > in the first two pixels of the result image, using an encoding scheme which > is useful in our particular application. May be there is a better way of > storing those values permanently with the image. > > 3) May be you can allow for several successive arithmetic operations in one > command, bypassing the (time and memory consuming) need to store > intermidiate results. > > >From the desk of > > Rudolf Oldenbourg oldenbourg@mbl.edu Tel:(508)548-3705 ext 426 > Program of Architectural Dynamics in Living Cells > Marine Biological Laboratory, Woods Hole, MA 02543-1031 > > ______________________________________________ / Mike Herron, U of MN, Dept. of Dermatology / / herro001@maroon.tc.umn.edu / / 612-625-8935 Box 124 UMHC, Mpls MN 55455 / ______________________________________________ From wayne@helix.nih.gov Wed Oct 6 13:24:17 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA12168; Wed, 6 Oct 1993 13:26:03 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA03881; Wed, 6 Oct 93 13:44:42 -0400 Message-Id: <9310061744.AA03881@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 6 Oct 1993 13:24:17 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Question on missing results >When I click on Export I see a sub-menu "About Export Plug-ins ...". This >tells >me the plug-ins need to be a Plug-in folder. Where do I find the plug-in to >export measurements to a tab-delimited text file compatible with Excel? I >can't >find info on this in V1.52 of the manual and none of the titles on the server >at >NIH seem to match up. NIH Image has two Export commands in the file menu, use the first one to export measurements to a text file and the second to use Photoshop compatible export plug-ins. --wayne From a337ard@diamond.sara.nl Thu Oct 7 08:59:09 1993 Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c) id AA20448; Thu, 7 Oct 1993 02:02:24 -0500 Return-Path: Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF V4.2-13 #2574) id <01H3TBN468LCB7AMAA@vx.cis.umn.edu>; Thu, 7 Oct 1993 02:03:47 CDT Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 7 Oct 93 8:03 MET Received: by diamond.sara.nl (5.61-AIX-1.2/1.0), id AA173479, (for nih-image@soils.umn.edu, from a337ard@diamond.sara.nl); Date: Thu, 07 Oct 1993 07:59:09 +0100 From: a337ard@diamond.sara.nl (Ard Jonker) Subject: Re: Dithering To: nih-image@soils.umn.edu Message-Id: <9310070659.AA173479@diamond.sara.nl> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT Without going into the detail of the floyd-Steinberg, it comes down to reducing the number of colors (greylevels) by using the available grey levels and by propagating the error that has been made to adjacent (right, left) pixels. The most well known examples are the 'dotty' black and white images on bw macs, that still 'look like' having shades. Once you have seen it, you will recognize it. (so, try it on a picture). ard (a337ard@diamond.sara.nl) From D.A.Davies@bham.ac.uk Thu Oct 7 10:38:39 1993 Received: from bham.ac.uk by nx1.soils.umn.edu (5.65c) id AA22057; Thu, 7 Oct 1993 04:41:07 -0500 Return-Path: Received: from sun1.bham.ac.uk by bham.ac.uk with SMTP (PP) id <03434-0@bham.ac.uk>; Thu, 7 Oct 1993 10:38:46 +0100 Received: from [147.188.64.23] (med138.bham.ac.uk) by sun1.bham.ac.uk (5.0/SMI-SVR4) id AA02095; Thu, 7 Oct 93 10:39:43 BST Message-Id: <9310070939.AA02095@sun1.bham.ac.uk> X-Sender: daviesda@sun1.bham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 7 Oct 1993 10:38:39 +0000 To: nih-image@soils.umn.edu From: D.A.Davies@bham.ac.uk (David Davies) Subject: Re: Flatbed Scanners and Image Content-Length: 1046 In response to the request for flatbed scanners that work well with Image, we use the MirrorScan 600 Plus, an excellent 24bit 600dpi scanner. This scanner works well with Image via the supplied PhotoShop plug-in to grab images directly into Image. Incidentely, for those interested in grabbing frames from video (from a microscope for example) we also grab images directly into Image using the PhotoShop plug-in that came with our Radius VideoVision video grabber. Implementing the PhotoShop plug-in extension to Image was one of the most useful improvements to Image in our opinion. We use Image a lot in our Department and just couldn't do our work without it! David Davies Tel No - +44-(0)-21-414-6898 Physiology Department Fax - +44-(0)-21-414-6924 The Medical School Janet - D.A.Davies@UK.AC.BHAM University of Birminghan Internet - D.A.Davies@BHAM.AC.UK Edgbaston, Birmingham Talk - david@med138.bham.ac.uk B15 2TT URL - http://med152.bham.ac.uk/davies.html From wayne@helix.nih.gov Thu Oct 7 08:30:17 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA25976; Thu, 7 Oct 1993 08:32:05 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA04757; Thu, 7 Oct 93 08:50:45 -0400 Message-Id: <9310071250.AA04757@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 7 Oct 1993 08:30:17 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: QuickImage24 >Does anyone use the Mass Micro QuickImage 24 frame capture board >with Image? Latest ad in MacWorld is selling it for $99. It's >supposed to support QuickTime. I am interested to know how well >it might work on a IIcx and on a Centris 610. I believe the QuickImage frame grabber is a full size NuBus card, if so, it won't fit in the Centris 610 since it only accepts 7 inch cards. --wayne From ikami@liposun.lbl.gov Thu Oct 7 03:01:42 1993 Received: from lbl.gov by nx1.soils.umn.edu (5.65c) id AA28415; Thu, 7 Oct 1993 12:06:33 -0500 Return-Path: Received: from liposun.lbl.gov by lbl.gov (4.1/1.39) id AA07264; Thu, 7 Oct 93 10:14:15 PDT Received: from [131.243.32.28] (b1-lipo5.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0) id AA12335; Thu, 7 Oct 93 10:01:43 PDT Date: Thu, 7 Oct 93 10:01:42 PDT Message-Id: <9310071701.AA12335@liposun.lbl.gov> To: nih-image@soils.umn.edu From: ikami@liposun.lbl.gov (Craig Ikami) Subject: Re: first timer >>We have just acquired a molecular dynamics densitometer. It produces 12 bit >>tiff files. We have looked at image v1.44 and would like to know if future >>versions of image will support 12 bit acquisition and display? > >The current version of NIH Image (1.52) can import the 16-bit TIFF files >created by Molecular Dynamics scanners. The image data is scaled to 8-bits, >but the 16-bit to 8-bit scaling can be changed using the Rescale(aka Revert >to Saved) command. > Thanks for the response .... Does this mean it will read our 12 bit tiff files and convert to 8 bit? If so can we ever have a LUT deeper than 256 ? From vokey@hg.uleth.ca Thu Oct 7 07:23:33 1993 Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c) id AA29554; Thu, 7 Oct 1993 14:19:40 -0500 Return-Path: Received: by hg.uleth.ca (MX V3.3 VAX) id 17900; Thu, 07 Oct 1993 13:23:48 MDT Date: Thu, 07 Oct 1993 13:23:33 MDT From: vokey@hg.uleth.ca To: nih-image@soils.umn.edu Message-Id: <00973A9D.9ED8E4C0.17900@hg.uleth.ca> Subject: Re: Dithering Thank you, Ard, for the introduction to the Floyd-Steinberg dithering technique. Does anyone have a summary (or psuedocode) of the error propogation algorithm itself? I am working on a system that has to move unpredictably between grey-scale and B&W, and I want to automatically apply the dither whenever a switch to B&W is detected (the grey-scale image will always be held in an off-screen pixel-map, only its projection to the screen will be adjusted). TIA John R. Vokey From vokey@hg.uleth.ca Thu Oct 7 07:33:57 1993 Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c) id AA29681; Thu, 7 Oct 1993 14:29:45 -0500 Return-Path: Received: by hg.uleth.ca (MX V3.3 VAX) id 17951; Thu, 07 Oct 1993 13:33:59 MDT Date: Thu, 07 Oct 1993 13:33:57 MDT From: vokey@hg.uleth.ca To: nih-image@soils.umn.edu Message-Id: <00973A9F.12A62B00.17951@hg.uleth.ca> Subject: FFT Is there any way with either ImageFFT or ImageVDM to access directly or save as text the actual results of the FFT? As far as I can acertain, only the power spectrum (in optical -- centred -- form) can be saved, and then only as a (spatial) image. Presumably, the complete FFT(x) = a + ib is stored in a buffer internally and used to produce the observed power spectrum. Any ideas? TIA. John R. Vokey From wayne@helix.nih.gov Thu Oct 7 14:51:24 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA29949; Thu, 7 Oct 1993 14:53:10 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA05594; Thu, 7 Oct 93 15:11:53 -0400 Message-Id: <9310071911.AA05594@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 7 Oct 1993 14:51:24 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Dithering >Thank you, Ard, for the introduction to the Floyd-Steinberg dithering >technique. Does anyone have a summary (or psuedocode) of the error propogation >algorithm itself? I am working on a system that has to move unpredictably >between grey-scale and B&W, and I want to automatically apply the dither >whenever a switch to B&W is detected (the grey-scale image will always be held >in an off-screen pixel-map, only its projection to the screen will be >adjusted). TIA Why not look at the real code that NIH Image uses? It's part of the routine "Filter" in the source file Functions.p. The algorithm is described in the paper "An Adaptive Algorithm for Spatial Greyscale" by Robert Floyd and Louis Steinberg, in Proceeding of the S.I.D, Vol.17/2, Second Quarter 1976. --wayne From PHILSON@macc.wisc.edu Thu Oct 7 10:00:00 1993 Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c) id AA00121; Thu, 7 Oct 1993 15:00:17 -0500 Return-Path: Received: from VMSmail by vms2.macc.wisc.edu; Thu, 07 Oct 93 15:00 CDT Message-Id: <23100715005034@vms2.macc.wisc.edu> Date: Thu, 07 Oct 93 15:00 CDT From: Pierre Hilson Subject: angles To: NIH-IMAGE@soils.umn.edu X-Vms-To: IN%"nih-image@nx1.soils.umn.edu",PHILSON As a new user, I have basic questions. I work with Image version 1.50b75. I am measuring the orientation of root growth. Is there a way to measure angles directionally... by that I mean from 0 to 360 degrees (or -180 to +180) along the whole circle. As it is set up, the program will give the same value if a segment ends at a given angle with respect to the horizontal above its starting point or below it. Is it normal, can it be changed and how? Thank you for your help. Pierre Hilson Genetics University of Wisconsin EMail: philson@macc.wisc.edu From vokey@hg.uleth.ca Thu Oct 7 08:09:30 1993 Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c) id AA00217; Thu, 7 Oct 1993 15:05:38 -0500 Return-Path: Received: by hg.uleth.ca (MX V3.3 VAX) id 18107; Thu, 07 Oct 1993 14:09:47 MDT Date: Thu, 07 Oct 1993 14:09:30 MDT From: vokey@hg.uleth.ca To: nih-image@soils.umn.edu Message-Id: <00973AA4.0A1365C0.18107@hg.uleth.ca> Subject: Re: Dithering Wayne said: --> Why not look at the real code that NIH Image uses? It's part of the routine "Filter" in the source file Functions.p. The algorithm is described in the paper "An Adaptive Algorithm for Spatial Greyscale" by Robert Floyd and Louis Steinberg, in Proceeding of the S.I.D, Vol.17/2, Second Quarter 1976. <-- Now, why didn't I think of that? I completely forgot that the source code was available! Thanks Wayne, for this advice AND Image. John R. Vokey From wayne@helix.nih.gov Thu Oct 7 15:59:19 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA00649; Thu, 7 Oct 1993 16:01:06 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA05709; Thu, 7 Oct 93 16:19:49 -0400 Message-Id: <9310072019.AA05709@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 7 Oct 1993 15:59:19 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: angles >I work with Image version 1.50b75. I am measuring the orientation >of root growth. Is there a way to measure angles directionally... by >that I mean from 0 to 360 degrees (or -180 to +180) along the whole >circle. As it is set up, the program will give the same value if a >segment ends at a given angle with respect to the horizontal above >its starting point or below it. Is it normal, can it be changed and >how? How would Image know what direction a particle is pointing? A particle pointing straight up and a particle pointing straight down will both have a measured angles of 90 degrees since Image has no way of knowing that the two particles point in opposite directions. There is a test image in the images directory on zippy.nimh.nih.gov called angles.hqx that is helpful in understanding how Image measure angles. --wayne From ptr@GRECO2.POLYTECHNIQUE.FR Fri Oct 8 12:05:51 1993 Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c) id AA04436; Fri, 8 Oct 1993 05:08:33 -0500 Return-Path: Received: from polytechnique.polytechnique.fr by chenas.inria.fr (5.65c8d/92.02.29) via Fnet-EUnet id AA20717; Fri, 8 Oct 1993 11:09:28 +0100 (MET) Received: by polytechnique.polytechnique.fr (5.65c/SMI-4.1.3) id AA06803; Fri, 8 Oct 1993 11:17:18 +0100 Received: from [129.104.27.245] by greco2.noname (4.1/SMI-4.1) id AA03791; Fri, 8 Oct 93 11:05:51 +0100 Date: Fri, 8 Oct 93 11:05:51 +0100 Message-Id: <9310081005.AA03791@greco2.noname> To: nih-image@soils.umn.edu From: ptr@GRECO2.POLYTECHNIQUE.FR (Peter Goedtkindt) Subject: Remove density calibration command? Hallo, I think the subject explains the question. The only way I found to remove the calibration was to copy the whole image, close all images (or select an uncalibrated image) open a new image and paste. I haven't found any macro command that allows me to uncalibrate more directly, sorry if I missed it. ptr. Peter Goedtkindt Universite Paris-Sud Laboratoire de Spectroscopie Atomique et Ionique X-ray Laser group bat350 Centre D'Orsay F-91405 Orsay Cedex. France Fax.:++33.1.69.41.94.60 - Tel 69.41.77.10 ------ And ------ Ecole Polytechnique, Laboratoire d'Utilisation de Lasers Intenses tel. 69.33.48.95 ----------------------------------------------------------------- From esb107@cent1.lancs.ac.uk Fri Oct 8 12:53:01 1993 Received: from cent1.lancs.ac.uk by nx1.soils.umn.edu (5.65c) id AA04705; Fri, 8 Oct 1993 05:52:06 -0500 Return-Path: From: "Mr R Herd" Message-Id: <14293.9310081053@cent1.lancs.ac.uk> Received: by cent1.lancs.ac.uk; Fri, 8 Oct 93 11:53:11 +0100 Subject: line plots->data To: nih-image@soils.umn.edu Date: Fri, 8 Oct 1993 11:53:01 +0100 (BST) In-Reply-To: <15085.9310080930@cent1.lancs.ac.uk> from "nih-image@soils.umn.edu" at Oct 8, 93 04:30:35 am X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 493 Hi, I've been trying to digitise topographic maps and recover coordinate data using the "line plots->data" macros. As it is they order the data by X or by Y. Consequently the data cannot be used to replot, for example a contour line. Is there any easy way to modify the macro so it measures X-Y points along the line, rather than along the X or Y direction? Many thanks Richard Herd Volcanology Group Dept. of Environmental Sciences Lancaster University Bailrigg Lancaster LA1 4YQ England From @cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be Fri Oct 8 13:07:43 1993 Received: from cc1.kuleuven.ac.be by nx1.soils.umn.edu (5.65c) id AA04802; Fri, 8 Oct 1993 06:07:49 -0500 Return-Path: <@cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be> Received: from rc1.vub.ac.be by cc1.kuleuven.ac.be (IBM VM SMTP V2R2) with TCP; Fri, 08 Oct 93 12:07:56 +0100 Received: from dec5.ulb.ac.be (dbmdec5) by rc1.vub.ac.be (4.1/RC1-930922) id AA22887; Fri, 8 Oct 93 12:09:03 +0100 Received: by dec5.ulb.ac.be (5.65/ULB.920908) id AA00433; Fri, 8 Oct 1993 12:07:44 +0100 From: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN) Message-Id: <9310081107.AA00433@dec5.ulb.ac.be> Subject: Re: grain size measurements To: nih-image@soils.umn.edu Date: Fri, 8 Oct 1993 12:07:43 +0100 (WET DST) Cc: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN) In-Reply-To: <9310041515.AA00410@arc1.mrd.bldrdoc.gov> from "Bob Keller" at Oct 4, 93 10:20:58 am X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 1686 > Thanks. We've tried your Crest Pathway routine. Actually, it's not exactly > what we need, since Crest measures the size of a single grain, or cell, or > whatever you're measuring. (I've also had trouble with it when my binary > images did not have nice smooth boundaries. The line would keep going well > beyond the boundary near where I started and often circle back onto itself > within a very small area within another boundary itself. I did vary the size > of the "detected" region as well, with no luck. Is it possible to define a > threshold regime which would tell the line when to change it's course?) I'm > going to write a macro to do the grain size measurement myself, using the line > intercept method which is standard in metallography. > > Bob Keller > NIST Div. 853 > Boulder, CO > keller@micros.mrd.bldrdoc.gov In order to avoid small back circling, you could try to increase the averaging distance. However this will reduce the resolution (the crest will not very well follow strong curves). Another parameter to fiddle around with is the maximal angle: if you chose 1, the crest will rotate of max 45 degrees at each step. You are not the first user to suggest a threshold in this routine.It seems a useful update, but I am not very sure about the best way to do it. What would you precisely mean by "threshold regime" ? Would you prefer a threshold on the absolute grey value or for the difference between neighbour points (one could choose to stop when the crest abruptly steps down) ? You could maybe contact Sven-Erik Tiberg (set@eru.mt.luth.se), who is adaptating a threshold to the routine. Jacques van Helden jvanheld@ulb.ac.be From wayne@helix.nih.gov Fri Oct 8 08:16:26 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA06932; Fri, 8 Oct 1993 08:18:14 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA06354; Fri, 8 Oct 93 08:37:00 -0400 Message-Id: <9310081237.AA06354@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Oct 1993 08:16:26 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Remove density calibration command? >Hallo, I think the subject explains the question. >The only way I found to remove the calibration was to copy the whole image, >close all images (or select an uncalibrated image) open a new image and >paste. >I haven't found any macro command that allows me to uncalibrate more >directly, sorry if I missed it. Check "Remove Calibration" in the Calibrate dialog box and click OK. --wayne From wayne@helix.nih.gov Fri Oct 8 08:30:32 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA07088; Fri, 8 Oct 1993 08:32:21 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA06378; Fri, 8 Oct 93 08:51:06 -0400 Message-Id: <9310081251.AA06378@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Oct 1993 08:30:32 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: line plots->data >Hi, >I've been trying to digitise topographic maps and recover coordinate data >using the "line plots->data" macros. As it is they order the data by X or by >Y. >Consequently the data cannot be used to replot, for example a contour line. >Is there any easy way to modify the macro so it measures X-Y points along the >line, rather than along the X or Y direction? One way to do this would be to use the wand tool to trace the contour line, the Measure command to record the coordinates, and then Export the coordinates to a text file. You can use a graphing program such as KaleidaGraph to replot the data. --wayne From smithj@acad.winthrop.edu Fri Oct 8 07:56:17 1993 Received: from acad ([192.203.180.3]) by nx1.soils.umn.edu (5.65c) id AA08091; Fri, 8 Oct 1993 11:01:14 -0500 Return-Path: Message-Id: <199310081601.AA08091@nx1.soils.umn.edu> Date: Fri, 8 Oct 1993 11:56:17 -0400 From: smithj@acad.winthrop.edu To: nih-image@soils.umn.edu Subject: Re: QuickImage24 X-Vms-To: SMTP%"nih-image@soils.umn.edu" Yes. I just bought one, and have it in a IIcx w/ RS-170 monochrome camera. I can't say about quick-time support, but the two defects I've seen thus far are that it only assigns about 24 (29?) grey levels (a rather extreme version of Wayne's comment "favors odd pixel values"); though the histogram is otherwise o.k. and that the plug-in doesn't work with Image (Image reports that there is insufficient video memory). I'm leaving for the coast with my invertebrate class in 2 hours, so more on this Tuesday. It is a full-size Nu-bus card, by the way. >Does anyone use the Mass Micro QuickImage 24 frame capture board >with Image? Latest ad in MacWorld is selling it for $99. It's >supposed to support QuickTime. I am interested to know how well >it might work on a IIcx and on a Centris 610. I believe the QuickImage frame grabber is a full size NuBus card, if so, it won't fit in the Centris 610 since it only accepts 7 inch cards. --JSIII From gmei@hoh.mbl.edu Fri Oct 8 08:08:00 1993 Received: from AQUA.WHOI.EDU by nx1.soils.umn.edu (5.65c) id AA08183; Fri, 8 Oct 1993 11:10:03 -0500 Return-Path: Received: by aqua.whoi.edu (5.57/Ultrix3.0-C) id AA25567; Fri, 8 Oct 93 12:10:50 -0400 Received: from [128.128.172.219] (SMAC19.MBL.EDU) by hoh.mbl.edu. (4.1/SMI-4.1) id AA04934; Fri, 8 Oct 93 12:08:02 EDT Date: Fri, 8 Oct 93 12:08:00 EDT Message-Id: <9310081608.AA04934@hoh.mbl.edu.> To: nih-image@soils.umn.edu From: gmei@hoh.mbl.edu (Guang Mei) Subject: Too many constants in enumerated type Hi, I have a question about "constants in enumerated type". When I tried to add something like "Myadd1C, Myadd2C, ... MyaddnC" (n is an integer) to CommandType = (InvertLUTC, UserCodeC, .... PidNumC, SortPaletteC, Myadd1C, Myadd2C, ... MyaddnC) in Globals.p (NIH Image 1.52), I always got compile error "Too many constants in enumerated type" when n is larger than some certain integer. Is there a limit of number of constants (identifiers?) in this parenthesis? I am using THINK Pascal 4.0.2. Thanks for the help. ------------- Guang Mei gmei@hoh.mbl.edu Tel:(508)548-3705 ext 374 Program of Architectural Dynamics in Living Cells Marine Biological Laboratory, Woods Hole, MA 02543-1031 From wayne@helix.nih.gov Fri Oct 8 15:36:34 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA01558; Fri, 8 Oct 1993 15:37:37 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA07231; Fri, 8 Oct 93 15:57:09 -0400 Message-Id: <9310081957.AA07231@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Oct 1993 15:36:34 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Too many constants in enumerated type >Hi, > >I have a question about "constants in enumerated type". When I tried to add >something like "Myadd1C, Myadd2C, ... MyaddnC" (n is an integer) to > >CommandType = (InvertLUTC, UserCodeC, .... PidNumC, SortPaletteC, Myadd1C, >Myadd2C, ... MyaddnC) > >in Globals.p (NIH Image 1.52), I always got compile error "Too many >constants in enumerated type" when n is larger than some certain integer. >Is there a limit of number of constants (identifiers?) in this parenthesis? >I am using THINK Pascal 4.0.2. There seems to be a limit of 256 or so constants in enumerated types. I ran into this problem when I tried to add a new command to the macro language today. The short term work-around I used was to recycle some obsolete commands. The long range solution will be to break CommandType into two parts: commands and functions.There are 10 obsolete commands starting at symbol table entry 165(SetArea, SetMean, etc.) and 0ne(SetMinMax) at 185. --wayne From glenmac@u.washington.edu Fri Oct 8 15:01:41 1993 Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c) id AA05061; Sat, 9 Oct 1993 00:14:14 -0500 Return-Path: Received: by carson.u.washington.edu (5.65/UW-NDC Revision: 2.29 ) id AA05061; Fri, 8 Oct 93 22:15:59 -0700 X-Sender: glenmac@carson.u.washington.edu Date: Fri, 8 Oct 1993 22:01:41 -0700 (PDT) From: Glen Macdonald Subject: Re: Saving results in Excel file To: nih-image@soils.umn.edu Cc: Multiple recipients of list In-Reply-To: <9310061744.AA03881@zippy.nimh.nih.gov> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=us-ascii The results are now being saved as tab delimited text files. Would it be posstible to add the ability to save them as Excel text files, as in the pas, as an option? It doesn't bother me, but our lab's many intermittant users of Image get confused having to open their files through Excel rather than double clicking on the file itself. While I'm asking, how about more user labelled arrays (the manual doen't mention rMinor and rMajor labels anymore, although they still work), or the ability to rearrange the order of the arrays in the Measurements so that data can be better grouped and named for custom applications. Thanks much. Glen MacDonald Hearing Development Laboratories University of Washington RL-30 Seattle, WA 98195 From glenmac@u.washington.edu Fri Oct 8 15:22:19 1993 Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c) id AA05205; Sat, 9 Oct 1993 00:30:58 -0500 Return-Path: Received: by carson.u.washington.edu (5.65/UW-NDC Revision: 2.29 ) id AA06488; Fri, 8 Oct 93 22:32:42 -0700 X-Sender: glenmac@carson.u.washington.edu Date: Fri, 8 Oct 1993 22:22:19 -0700 (PDT) From: Glen Macdonald Subject: Re: angles To: nih-image@soils.umn.edu Cc: Multiple recipients of list In-Reply-To: <23100715005034@vms2.macc.wisc.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=us-ascii One way is to write a macro that compares x1,y1 to x2,y2 in order to determine which quadrant your angle is in. this inequality check then determines whether your angles are positive or negative. I will send you a macro that does this. I was measuring the angle of auditory hair cell stereocilia bundles, which are random in newly differenctiated cells and then rotate during matureation to a mature position angle. This needed angles 0-180 positive and negative. Glen MacDonald Hearing Development Laboratories University of Washington RL-30 Seattle, WA 98195 On Thu, 7 Oct 1993, Pierre Hilson wrote: > > > > As a new user, I have basic questions. > > I work with Image version 1.50b75. I am measuring the orientation > of root growth. Is there a way to measure angles directionally... by > that I mean from 0 to 360 degrees (or -180 to +180) along the whole > circle. As it is set up, the program will give the same value if a > segment ends at a given angle with respect to the horizontal above > its starting point or below it. Is it normal, can it be changed and > how? > > Thank you for your help. > > Pierre Hilson > Genetics > University of Wisconsin > EMail: philson@macc.wisc.edu > From mt1ntg@fencer.cis.dsto.gov.au Mon Oct 11 19:46:28 1993 Received: from fencer.cis.dsto.gov.au by nx1.soils.umn.edu (5.65c) id AA19279; Sun, 10 Oct 1993 18:44:49 -0500 Return-Path: Message-Id: <199310102344.AA19279@nx1.soils.umn.edu> Received: from [160.64.14.216] by fencer.cis.dsto.gov.au with SMTP; Mon, 11 Oct 1993 9:57:19 +1000 (EST) Date: Mon, 11 Oct 1993 09:46:28 +1000 To: nih-image@soils.umn.edu From: NoelGoldsmith (Noel Goldsmith) Subject: Re: Too many constants in enumerated type >Hi, > >I have a question about "constants in enumerated type". When I tried to add >something like "Myadd1C, Myadd2C, ... MyaddnC" (n is an integer) to > >CommandType = (InvertLUTC, UserCodeC, .... PidNumC, SortPaletteC, Myadd1C, >Myadd2C, ... MyaddnC) > >in Globals.p (NIH Image 1.52), I always got compile error "Too many >constants in enumerated type" when n is larger than some certain integer. >Is there a limit of number of constants (identifiers?) in this parenthesis? >I am using THINK Pascal 4.0.2. > >Thanks for the help. > >------------- >Guang Mei gmei@hoh.mbl.edu Tel:(508)548-3705 ext 374 >Program of Architectural Dynamics in Living Cells >Marine Biological Laboratory, Woods Hole, MA 02543-1031 Guang, Think Pascal has a limit of 256 constants for each enumerated type. This problem has hit me too. When you have a program like NIH-Image which is added to by many, such things are bound to occur. Who would have thought that 256 commands in the macro interpreter would not have been enough? I see Wayne has suggested the use of some no-longer used commands.A list of macro commands could be set up, but if you look a the source code, it is really the list you need. What would be nice would be a list of ACTIVE macro-commands for each new version of NIH-Image. I understood that the use of the UMX extensions somehow would overcome this problem, I think the use of this facility requires that your code all lives in the user unit. I am about to try using the latest version for my code additions, and will report to the list, (this may take a few weeks as I have a full plate). regards Noel. Noel T Goldsmith DSTO Aeronautical Research Laboratory 506 Lorimer Street Port Melbourne Vic 3207 Australia From kehrer@informatik.uni-ulm.de Mon Oct 11 11:57:39 1993 Received: from julia.informatik.uni-ulm.de by nx1.soils.umn.edu (5.65c) id AA21977; Mon, 11 Oct 1993 04:56:04 -0500 Return-Path: Received: from fonzo (kehrer.informatik.uni-ulm.de) by julia.informatik.uni-ulm.de (4.1/UniUlm-info-1.1r) id AA03113; Mon, 11 Oct 93 10:57:40 +0100 Date: Mon, 11 Oct 93 10:57:39 +0100 Message-Id: <9310110957.AA03113@julia.informatik.uni-ulm.de> From: Juergen Kehrer To: nih-image@soils.umn.edu Subject: Raleigh equalisazion? Hi, does anybody know something about the "Raleigh equalization". It+s something like the "histogram equalization" use in Nih-image, but I need more information about the differences and the usage of this equalization. Thanks for the help. =============================================================== Juergen Kehrer University of Ulm/Germany Dept of Distributed Systems Internet: kehrer@informatik.uni-ulm.de =============================================================== From csebeny@goodyear.com Mon Oct 11 11:05:32 1993 Received: from goodyear.com (goodyear.goodyear.com) by nx1.soils.umn.edu (5.65c) id AA27404; Mon, 11 Oct 1993 15:02:42 -0500 Return-Path: Received: from rdsrv2 (rdsrv2.goodyear.com) by goodyear.com (4.1/SMI-4.1) id AA14583; Mon, 11 Oct 93 16:04:27 EDT Received: from rds012 by rdsrv2 (4.1/SMI-4.1) id AA10000; Mon, 11 Oct 93 16:04:49 EDT Received: from rds323 ([163.243.12.66]) by rds012 (4.1/SMI-4.1) id AA24258; Mon, 11 Oct 93 16:04:08 EDT X-Mailer: InterCon TCP/Connect II 1.1 Message-Id: <9310111605.AA32995@rds323> Date: Mon, 11 Oct 1993 16:05:32 -0500 From: Carl Sebeny To: nih-image@soils.umn.edu Cc: csebeny@goodyear.com Subject: Macro for Particle Centroid & Moment of Inertia Does anyone have a macro to calulate particle centroid coordinates and moment of inertia of particles about their centroid? ----------------------------------------------------------- Joel Lazeration rdealer1@goodyear.com Goodyear Tire From mmoberg%smhi.dnet.smhi.se@lurch.smhi.se Tue Oct 12 08:42:23 1993 Received: from palantir.p.tvt.se by nx1.soils.umn.edu (5.65c) id AA00866; Tue, 12 Oct 1993 01:40:42 -0500 Return-Path: Received: from gatekeeper.smhi.se by palantir.p.tvt.se with smtp (Smail3.1.28.1 #2) id m0omdUV-000AD9C; Tue, 12 Oct 93 07:45 WET Received: by gatekeeper.smhi.se (5.65/DEC-Ultrix/4.3) id AA01022; Tue, 12 Oct 1993 07:42:53 +0100 Received: by lurch.smhi.se (5.65/DEC-Ultrix/4.3) id AA17554; Tue, 12 Oct 1993 07:42:24 +0100 Date: Tue, 12 Oct 1993 07:42:23 +0100 Message-Id: <9310120642.AA17554@lurch.smhi.se> From: mmoberg%smhi.dnet.smhi.se@lurch.smhi.se (mmoberg@smhi.se) To: "nih-image@soils.umn.edu"%LURCH.dnet.smhi.se@lurch.smhi.se Cc: mmoberg@lurch.smhi.se Subject: Beginner's LUT-question Could someone give me a hint on how to create a pseudo-color LUT for NIH-Image given that a specified DN will have a specified color in R, G and B. Thanks! /mmoberg@smhi.se From wayne@helix.nih.gov Tue Oct 12 09:01:46 1993 Received: from zippy.nimh.nih.gov ([128.231.98.32]) by nx1.soils.umn.edu (5.65c) id AA04401; Tue, 12 Oct 1993 09:04:53 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA10238; Tue, 12 Oct 93 09:22:41 -0400 Message-Id: <9310121322.AA10238@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Tue, 12 Oct 1993 09:01:46 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Beginner's LUT-question >Could someone give me a hint on how to create a pseudo-color LUT= for NIH-Image=20 >given that a specified DN will have a specified color in R, G and= B. One way to do this is to write a macro that assigns RGB colors to= specified gray values. Here is an example macro that allows you to specify= a gray value and the RGB color you want that value to be displayed in. Not= that this macro modifies only one of the 256 LUT entries. Also note that= LUT entries 0 and 256 can not be modified. They are always mapped to= white and black respectively.=20 To run this macro, Copy it to the Clipboard, Open a new text window= in Image, Paste, Load Macros, and then select 'Change One LUT Entry=8A'= from the Special menu. --wayne macro 'Change One LUT Entry=8A'; var dn:integer; begin dn:=3DGetNumber('Gray Value(1-254):',128); RedLut[dn]:=3DGetNumber('Red(0-255):',255); GreenLut[dn]:=3DGetNumber('Green(0-255):',0); BlueLut[dn]:=3DGetNumber('Blue(0-255):',0); UpdateLUT; end; From ptr@GRECO2.POLYTECHNIQUE.FR Tue Oct 12 17:57:11 1993 Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c) id AA05105; Tue, 12 Oct 1993 10:59:39 -0500 Return-Path: Received: from polytechnique.polytechnique.fr by chenas.inria.fr (5.65c8d/92.02.29) via Fnet-EUnet id AA20380; Tue, 12 Oct 1993 17:00:53 +0100 (MET) Received: by polytechnique.polytechnique.fr (5.65c/SMI-4.1.3) id AA07074; Tue, 12 Oct 1993 17:08:45 +0100 Received: from [129.104.27.245] by greco2.noname (4.1/SMI-4.1) id AA05665; Tue, 12 Oct 93 16:57:12 +0100 Date: Tue, 12 Oct 93 16:57:11 +0100 Message-Id: <9310121557.AA05665@greco2.noname> To: nih-image@soils.umn.edu From: ptr@GRECO2.POLYTECHNIQUE.FR (Peter Goedtkindt) Subject: Re: Remove density calibration command? >>Hallo, I think the subject explains the question. >>The only way I found to remove the calibration was to copy the whole image, >>close all images (or select an uncalibrated image) open a new image and >>paste. >>I haven't found any macro command that allows me to uncalibrate more >>directly, sorry if I missed it. > >Check "Remove Calibration" in the Calibrate dialog box and click OK. > >--wayne Yes, I know how to do this manually, but how to do this in a macro call? peter From wayne@helix.nih.gov Tue Oct 12 12:06:07 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA05734; Tue, 12 Oct 1993 12:07:18 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA10752; Tue, 12 Oct 93 12:27:03 -0400 Message-Id: <9310121627.AA10752@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 12 Oct 1993 12:06:07 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Saving results in Excel file >The results are now being saved as tab delimited text files. Would it be >posstible to add the ability to save them as Excel text files, as in the >pas, as an option? It doesn't bother me, but our lab's many intermittant >users of Image get confused having to open their files through Excel >rather than double clicking on the file itself. The latest 1.53 beta on zippy.nimh.nih.gov allows you to specify (in Preferences) the four character creator code Image uses for exported text files. This code determines which application is launched when you double-click on an exported text file (e.g., measurements, profile plot data, XY coordinates). Use 'Imag' for Image, 'XCEL' for Excel and 'QKPT' for KaleidaGraph. >While I'm asking, how about more user labelled arrays (the manual doen't >mention rMinor and rMajor labels anymore, although they still work), or >the ability to rearrange the order of the arrays in the Measurements so >that data can be better grouped and named for custom applications. I am considering ways to allow more results data types, including more user arrays. --wayne From wayne@helix.nih.gov Tue Oct 12 12:10:37 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA05758; Tue, 12 Oct 1993 12:11:47 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA10764; Tue, 12 Oct 93 12:31:33 -0400 Message-Id: <9310121631.AA10764@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 12 Oct 1993 12:10:37 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Remove density calibration command? >>>Hallo, I think the subject explains the question. >>>The only way I found to remove the calibration was to copy the whole image, >>>close all images (or select an uncalibrated image) open a new image and >>>paste. >>>I haven't found any macro command that allows me to uncalibrate more >>>directly, sorry if I missed it. >> >>Check "Remove Calibration" in the Calibrate dialog box and click OK. >> >>--wayne > >Yes, I know how to do this manually, but how to do this in a macro call? > Sorry, I didn't read you original message very carefully. The only other way I know of to disable density calibration from within a macro is to open an uncalibrated image and use the PropagateDensity maco command. --wayne From huff@MCCLB0.MED.NYU.EDU Tue Oct 12 09:59:45 1993 Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c) id AA06705; Tue, 12 Oct 1993 13:57:12 -0500 Return-Path: Received: from DialupEudora (ANNEX1.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU (PMDF V4.2-14 #2884) id <01H4126HTPSW001375@MCCLB0.MED.NYU.EDU>; Tue, 12 Oct 1993 14:58:41 EDT Date: Tue, 12 Oct 1993 14:59:45 -0500 From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff) Subject: RE: Too many constants in enumerated type To: nih-image@soils.umn.edu Message-Id: <01H4126IOIZM001375@MCCLB0.MED.NYU.EDU> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT Noel T Goldsmith writes >I understood that the use of the UMX extensions somehow would overcome this >problem, I think the use of this facility requires that your code all lives >in the user unit. I am about to try using the latest version for my code >additions, and will report to the list, (this may take a few weeks as I >have a full plate). The UMX facility requires that each pascal programmer create his own new .p file where the new macro commands go. This permits integration of code from a number of people with minimal disruption. The procedure is easy and clearly described in UMacroDef.p in the UMX source code. UMSample.p is a sample user macro module which you duplicate and modify. The reason the "too many constants" problem is solved by UMX is because a new token type was created for user macro tokens, and a new enumerated type. This allows for up to 256 user macro commands or functions. -- Edward J. Huff huff@mcclb0.med.nyu.edu (212)998-8465 Keck Laboratory for Biomolecular Imaging NYU Chemistry Department, 31 Washington Place, New York NY 10003 From sarmienu@rnisd0.DNET.roche.com Wed Oct 13 03:29:33 1993 Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c) id AA12348; Wed, 13 Oct 1993 06:27:57 -0500 Return-Path: Received: by gatekeeper.roche.com (5.65/fma-120691); id AA15905; Wed, 13 Oct 93 07:29:34 -0400 Received: by mailgate.roche.com (5.65/fma-120691); id AA17847; Wed, 13 Oct 93 07:23:14 -0400 From: sarmienu@rnisd0.DNET.roche.com Message-Id: <9310131123.AA17847@mailgate.roche.com> Received: from rnisd0.enet; by inet.enet; Wed, 13 Oct 93 07:29:33 EDT Date: Wed, 13 Oct 93 07:29:33 EDT To: nih-image@soils.umn.edu Apparently-To: nih-image@soils.umn.edu Subject: NIH-Image References Here is an update in the list of references which quote image. I guess I am now committed to update the list periodically. Please continue to send me new references, as they become available, to my address (see below),. If any of you notice an error, please let me know. Thank you to all contributors. Juan I. Sarmiento Department of Toxicology and Pathology Hoffmann-La Roche, INC. 340 Kingsland street Nutley, NJ 07110 (201) 235 3907 Sarmienu@RNISD0.DNET.ROCHE.COM P.S. Wayne, thanks for the address for Thomas M. Marschner. --------------------------------------------------------------------------- References for NIH-Image 1. Bouabid, R., E.A. Nater, and P. Barak. 1992. Measurement of particle and pore size distribution in a lamellar B horizon by fluorescence microscopy and image analysis. Geoderma 53 (3/4):309-328. 2. Magunda, M.K. 1992. Influence of some physico- chemical properties on soil strength, stability of crusts and soil erosion. Ph.D. Dissertation. 3. Bouabid, R. 1992. Soil solution chemistry, mineral weathering, and pedogenesis in sandy outwash soils of east-central Minnesota. Ph.D. Dissertation. 4. Dyck, RH and Cynader, MS (1993) Histochemical localization of synaptic zinc in the developing kitten visual cortex. Journal of Comparative Neurology, 329, 53-67. 5. Dyck, RH and Cynader MS (1993) An interdigitated columnar mosaic of cytochrome oxidase, zinc, and neurotransmitter-related molecules in cat and monkey visual cortex. Proceedings of the National Academy of Science, USA, 90, 9066-9069. 6. Dyck, RH and Cynader MS (1993) Autoradiographic localization of serotonin receptor subtypes in cat visual cortex: regional, laminar, and columnar distributions during postnatal development. Journal of Neuroscience, 13, 4316-4338. 7. Biophys. J. 60:629-641 (1991) 8. Gough, A.H. and Taylor, D. L. (1993) Journal of Cell Biology, 121:5:1095-1107. 9. T. K. Teague, L.L. Munn, K. Zygourakis and B.W. McIntyre "Analysis of Lymphocyte Activation and Proliferation by Video Microscopy and Digital Imaging," Cytometry, in press (1993). 10. L.L. Munn, M.W. Glacken, B.W. McIntyre and K. Zygourakis "Analysis of Lymphocyte Aggregation Using Digital Image Analysis," J. Immunol. Methods, in press (1993). 11. Hammer, R.P., Pires,W.S., Markou, A. and Koob, G.F.: Withdrawal following cocaine self- administration decreases regional metabolism in critical brain reward regions, Synapse, 14: 73-80, 1993. 12. Hammer, R.P., Margulies, J.E., Lynn, A.B. and Brady, L.S.: Chronic fluoxetine treatment up- regulates dopamine receptors in the mesolimbic forebrain of the rat, Depression, 1: 82-87, 1993. 13. Hammer, R.P., Bogic, L. and Handa, R.J.: Estrogenic regulation of proenkephalin mRNA expression in the ventromedial hypothalamus of the adult male rat, Molecular Brain Research, 19: 129- 134, 1993. 14. Chin DJ; Straubinger RM; Acton S; Nathke I; Brodsky FM; 100kDa polypeptides in peripheral clathrin-coated vesicles are required for receptor- mediated endocytosis. Proc. Natl. Acad. Sci. 86: 9289-93, 1989 15. Chin DJ; Green G; Zon G; Szoka FC; Straubinger RM; Rapid nuclear accumulation of injected oligodeoxyribonucleotides. New Biologist 2: 1091- 1100, 1990. 16. Xuan-Hui Guo, Edward J. Huff and David C. Schwartz. Sizing of Large DNA Molecules by Hook Formation in a Loose Matrix. Journal of Biomolecular Structure & Dynamics, Volume 11, Issue 1 (1993) pp 1-10 17. Science, "Ordered Restriction Maps of Saccharomyces Cerevisiae Chromosomes Constructed by Optical Mapping," David C. Schwartz, Xiaojun Li, Luis I. Hernandez, Satyadarshan P. Ramnarain, Edward J. Huff, Yu-Ker Wang. 18. Vivino MA, Chintalagiri S, Trus BL, Datiles M, "Development of a Scheimpflug Slit Lamp Camera System for Quantitative Densitometric Analysis", Eye, Vol 7, number 6 19. Adam DR, Kempner KM, Vivino MA, Tucker EE, Jones M, "Measurement of Flow Velocity in a Phantom by Corrected Doppler Color Mapping Technique, using Transverse Cross-Sectional Imaging", Computers in Cardiology 1993, in press 20. Short Term Water Heat storage : Studies of Velocity and Temerature Fields and their Importance for sizing of the Storage. Lulea Univ. of Technology. Lulea Sweden. 1993:131D 21. Roger Hermansson. An experimental and numerical investigation of phenomena that affect the degree of therminal stratification. Lulea Univ. of Technology. Lulea Sweden. 1993:127D 22. Velocoimetry ( PIV) in process Metallurgy for Steal mills. Gabriella Trandell : Modelling of tundish alloying for small lot production. Lulea Univ. of Technology. Lulea Sweden. 1992:100E 23. D. S. Bright, "Software Tools for examination of microanalytical images", pp. 73-78 in MICROBEAM ANALYSIS 1990, SAN FRANCISCO Press, CA. 24. Bright, D.S., Steel, E.B. and Newbury, D.E. (1991), "Visibility of Objects in Noisy Images as a Function of Contrast, Noise Level, and Object Size", Microbeam Analysis 1991: 185-188. 25. Neuron 11:237-251 (1993). 26. Richardson ML, Gillespy TG 3rd. An inexpensive computer-based digital imaging teaching file. Am J Roentgenology 1993;160:1299-1301. 27. Richardson ML. Using a personal computer to create anatomic drawings for publication. Am J Roentgenology 1993, in press. 28. Robert Parry, et. al., Computer-Aided Cell Colony Counting, BioTechniques, Vol. 10, No 6, 1991, pages 772- 774. 29. Ricardo Correa-Rotter, et. al., Loading and Transfer Control for Northern Hybridization, BioTechniques, Vol. 12, No 2, 1992, pages 154-158. 30. Thomas Ford-Holevinski et al., Microcomputer-based Three-dimensional Reconstruction of in situ Hybridization Autoradiographs, Journal of Chemical Neuroanatomy, Vol 4, 1991, pages 373-385. 31. Raymond O'Neill et al., Use of Image Analysis to Quantitate Changes in Form of Mitochondrial DNA After X-irradiation, Applied and Theoretical Electrophoresis, 1989-1, pages 163-167. 32. DeVoogd, T.J., Krebs, J.R., Healy, S.D. & Purvis, A. "Relations between song repertoire size and the volume of brain nuclei related to song: comparative evolutionary analyses amongst oscine birds." In press, Proc. Roy. Soc Lon. B. 33. Garlow, S.J., Morilak, D.A., Dean, R.R., Roth, B.L. and Ciaranello, R.D. (1993) Production and characterization of a specific 5-HT2 receptor antibody. Brain Research, 615: 113-120. 34. F. D'Amelio, N.G. Daunton. Effects of spaceflight in the adductor longus muscle of rats flown in the Soviet biosatellite COSMOS 2044. A study employing neural cell adhesion molecule (N-CAM) immunocytochemistry and conventional morphological techniques (light and electron microscopy). J. Neuropath. Exp. Neurol. 51(4):415-431, 1992. 35 Ester Hill, Emily Holton. J. Orthopedic Research. 1993 36. Reiss, A.L., et. al., "Neuroantomy of Fragile X Syndrome: the Posterior Fossa, Annals of Neurology, Vol. 29, No. 1, January 1991. 37. Lieberman, D.E., et. al., "Computer Image Enhancement and Analysis of Cementum Increments as Applied to Teeth of Gazella gazella", Journal of Archaeological Science, in press (1989). 38. Chiang, P.K., et. al., "Activation of Collagen IV Expression in F9 Teratocarcinoma Cells by 3-Deazaadenosine Analogs", Journal of Biological Chemistry, Vol. 267, No. 7, March 1992. 39. Correa-Rotter, R., et. al., "Loading and Transfer Control for Northern Hybridization", BioTechniques, Vol. 12, No. 2 (1992). 40. Masters, D.B., et. al., "High Sensitivity Quantification of RNA from Gels and Autoradiograms with Affordable Optical Scanning", BioComputing, Vol. 12, No. 6 (1992). 41. Gwon, A.E., et. al., "Lens Regeneration in Juvenile and Adult Rabbits Measured by Image Analysis", Investigative Ophthalmology & Visual Science, Vol. 33, No. 7, June 1992. 42. Plotorak, M., et. al., "L1 Substrate Enhances Outgrowth of Tyrosine Hydroxylase-Immunoreactive Neurites in Mesencephalic Cell Culture", Experimental Neurology 117, 176-184 (1992). From glenmac@u.washington.edu Wed Oct 13 01:11:12 1993 Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c) id AA15133; Wed, 13 Oct 1993 10:15:42 -0500 Return-Path: Received: by carson.u.washington.edu (5.65/UW-NDC Revision: 2.29 ) id AA22317; Wed, 13 Oct 93 08:12:38 -0700 X-Sender: glenmac@carson.u.washington.edu Date: Wed, 13 Oct 1993 08:11:12 -0700 (PDT) From: Glen Macdonald Subject: Re: Saving results in Excel file To: nih-image@soils.umn.edu Cc: Multiple recipients of list In-Reply-To: <9310121627.AA10752@zippy.nimh.nih.gov> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=us-ascii On Tue, 12 Oct 1993, Wayne Rasband wrote: > > The latest 1.53 beta on zippy.nimh.nih.gov allows you to specify (in > Preferences) the four character creator code Image uses for exported text > files. This code determines which application is launched when you > double-click on an exported text file (e.g., measurements, profile plot > data, XY coordinates). Use 'Imag' for Image, 'XCEL' for Excel and 'QKPT' > for KaleidaGraph. Thank you, thank you, thank you, thank you, thank you, thank you. > - Glen> > > From ikami@liposun.lbl.gov Wed Oct 13 10:01:20 1993 Received: from lbl.gov by nx1.soils.umn.edu (5.65c) id AA19611; Wed, 13 Oct 1993 19:05:41 -0500 Return-Path: Received: from liposun.lbl.gov by lbl.gov (4.1/1.39) id AA10082; Wed, 13 Oct 93 17:14:07 PDT Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0) id AA13458; Wed, 13 Oct 93 17:01:21 PDT Date: Wed, 13 Oct 93 17:01:20 PDT Message-Id: <9310140001.AA13458@liposun.lbl.gov> To: nih-image@soils.umn.edu From: ikami@liposun.lbl.gov (Craig Ikami) Subject: wand tool area Is it possible to get the area outlined by the wand tool? From a337ard@diamond.sara.nl Thu Oct 14 09:18:39 1993 Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c) id AA21977; Thu, 14 Oct 1993 02:21:03 -0500 Return-Path: Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF V4.2-13 #2574) id <01H434DMCXF4B7BAF8@vx.cis.umn.edu>; Thu, 14 Oct 1993 02:23:14 CDT Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 14 Oct 93 8:23 MET Received: by diamond.sara.nl (5.65/1.37) id AA29776; Thu, 14 Oct 93 08:18:39 +0100 Date: Thu, 14 Oct 1993 08:18:39 +0100 From: a337ard@diamond.sara.nl (Ard Jonker) Subject: Re: NIH-Image References To: nih-image@soils.umn.edu Message-Id: <9310140718.AA29776@diamond.sara.nl> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT It is very neat of you to maintain a reference list of NIH-image and to offer to keep it up to date. It would, for convenience, be even more helpful if the same file would begin with a short notice on the way Wayne prefers being quoted. (I have a paper submitted, which was just before the item came up, and now I may comply with Wayne's wishes when re-submiting) ard From sarmienu@rnisd0.DNET.roche.com Thu Oct 14 04:18:08 1993 Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c) id AA24782; Thu, 14 Oct 1993 07:16:34 -0500 Return-Path: Received: by gatekeeper.roche.com (5.65/fma-120691); id AA22093; Thu, 14 Oct 93 08:18:08 -0400 Received: by mailgate.roche.com (5.65/fma-120691); id AA25712; Thu, 14 Oct 93 08:16:48 -0400 From: sarmienu@rnisd0.DNET.roche.com Message-Id: <9310141216.AA25712@mailgate.roche.com> Received: from rnisd0.enet; by inet.enet; Thu, 14 Oct 93 08:18:08 EDT Date: Thu, 14 Oct 93 08:18:08 EDT To: nih-image@soils.umn.edu Apparently-To: nih-image@soils.umn.edu Subject: How to cite NIH-Image: Concensus? Is there a general consensus in using the following quote when mentioning image in the materials and methods section of a manuscript?"... analysis performed in a Macintosh [model] computer using the public domain NIH-Image (written by Wayne Rasband and available via Internet by anonymous ftp from zippy.nimh.nih.gov or from Library 9 of the MacApp forum on CompuServe)". Shouldn't Image be available for a more general audience, say via floppy disk from the National Library of Medicine? I remember when I first try to get Image, not having access to E-mail, Internet and never having used Compuserve, it took me several months to figure out how to get it. Finally somebody handed me a diskette with an old version of Image. I think the program should be more easy to obtain. Particularly since it is becoming so popular among scientist. Also, I agree with Michael J. Herron that "to appear in a medline search the words "NIH Image" must appear in either the abstract or the Keywords index...", Therefore, all people publishing manuscripts using NIH-Image should include the name of the program in the abstract whenever possible. Suggestions and comments to my address below, please Juan I. Sarmiento Department of Toxicology and Pathology Hoffmann-La Roche, INC. 340 Kingsland street Nutley, NJ 07110 (201) 235 3907 Sarmienu@RNISD0.DNET.ROCHE.COM From mvivino@helix.nih.gov Thu Oct 14 04:34:20 1993 Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c) id AA24923; Thu, 14 Oct 1993 07:32:44 -0500 Return-Path: Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0)) id AA19807; Thu, 14 Oct 93 08:34:20 -0400 Date: Thu, 14 Oct 93 08:34:20 -0400 Message-Id: <9310141234.AA19807@helix.nih.gov> X-Sender: mvivino@128.231.2.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mvivino@helix.nih.gov (Mark Vivino) Subject: Re: wand tool area >Is it possible to get the area outlined by the wand tool? Use the Measure command from the analyze menu. Be sure Area is checked under Options... in the analyze menu Mark Vivino NIH/DCRT mvivino@helix.nih.gov From wayne@helix.nih.gov Thu Oct 14 08:43:07 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA25472; Thu, 14 Oct 1993 08:44:21 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA13508; Thu, 14 Oct 93 09:04:13 -0400 Message-Id: <9310141304.AA13508@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 14 Oct 1993 08:43:07 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: How to cite NIH-Image: Concensus? >Is there a general consensus in using the following quote when mentioning image >in the materials and methods section of a manuscript?"... analysis performed in >a Macintosh [model] computer using the public domain NIH-Image (written by >Wayne >Rasband and available via Internet by anonymous ftp from zippy.nimh.nih.gov or >from Library 9 of the MacApp forum on CompuServe)". Looks good to me except I would use "NIH Image" instead of NIH-Image. >Shouldn't Image be available for a more general audience, say via floppy disk >from the National Library of Medicine? I remember when I first try to get >Image, >not having access to E-mail, Internet and never having used Compuserve, it took >me several months to figure out how to get it. Finally somebody handed me a >diskette with an old version of Image. I think the program should be more easy >to obtain. Particularly since it is becoming so popular among scientist. NIH Image is available on a floppy disk from the National Technical Information Service (NTIS) for $100. Their phone number is 703-487-4650. Use order number PB93-504868. --wayne From waheeschen@dow.com Thu Oct 14 06:12:10 1993 Received: from na1.dow.com (na2.dow.com) by nx1.soils.umn.edu (5.65c) id AA25718; Thu, 14 Oct 1993 09:10:52 -0500 Return-Path: Received: by na1.dow.com id AA04159 (InterLock SMTP Gateway 1.1 for nih-image@soils.umn.edu); Thu, 14 Oct 1993 08:58:20 -0500 Message-Id: <199310141358.AA04159@na1.dow.com> Date: Thu, 14 Oct 1993 10:12:10 -0400 From: waheeschen@dow.com (Bill Heeschen (517)636-4005 PMRC/ASL) To: nih-image@soils.umn.edu Subject: re: How to cite NIH Image X-Vms-To: SMTP%"nih-image@soils.umn.edu" Folks: My two cents worth regarding citation of NIH Image. The nature of NIH Image is interesting - it is extremely useful, widely used and well supported, yet it is not a commercial product. I suggest that we treat it with the respect normally accorded commercial software or even more respect. 8-) How about calling it NIH Image, not NIH-Image? This is how it is written in the manual except that Image is italicized and I can't figure out how to get italics into E-mail. Also, I suggest we treat "NIH Image" as a trademark. I have modified Juan Sarmiento's citation to reflect my concerns and to address the non-electronic distribution issue: "...using the public domain NIH Image image analysis software (written by Wayne Rasband at the U.S. National Institutes of Health and available electronically via Internet by anonymous ftp from zippy.nimh.nih.gov or from Library 9 of the MacApp forum on CompuServe and on floppy disk from NTIS, 5285 Port Royal Rd., Springfield, VA 22161, part number PB93-504868)." As for an alternate, non-electronic source, the $100 NTIS option listed in Appendix I of the manual seems reasonable to me and would be money well spent. Once "hooked" with the disk version from NTIS, new users without internet or CompuServe would find that the money investment (modem, account, long distance) to download from CompuServe still makes NIH Image the best deal around. With no money coming in to Wayne to support physical distribution, the current method of distribution (FTP, CompuServe,etc.) is quite reasonable in that it allows widespread, rapid response with extremely low time overhead. Any physical distribution system results in a huge relative increase in time (disk duplication, mailing) and money (wages, media) for software that is being improved at a rate of about once/week. If it can be done cheaper by the National Library of Medicine than NTIS, that would be OK, but for now the NTIS option looks reasonable. By the way, thanks to Juan for compiling the citation list! Bill ========================== Bill Heeschen / Analytical Sciences - Materials Characterization 1897-D Building / The Dow Chemical Company Midland, MI 48667 U.S.A. phone: (517)636-4005 fax: (517)636-5453 Email: waheeschen@dow.com ========================== From m_palchuk@ACAD.FANDM.EDU Thu Oct 14 07:43:52 1993 Received: from Acad.FandM.EDU by nx1.soils.umn.edu (5.65c) id AA26420; Thu, 14 Oct 1993 10:43:09 -0500 Return-Path: Received: from [155.68.24.16] (Matvey.FandM.edu) by ACAD.FANDM.EDU (PMDF V4.2-11 #3427) id <01H43NXODMJK00BFXN@ACAD.FANDM.EDU>; Thu, 14 Oct 1993 11:43:52 EDT Date: Thu, 14 Oct 1993 11:43:52 -0400 From: m_palchuk@ACAD.FANDM.EDU (Matvey Palchuk) Subject: System configuration To: NIH-IMAGE@SOILS.UMN.EDU Message-Id: <01H43NXP3CGY00BFXN@ACAD.FANDM.EDU> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7BIT I am a new subscriber to the list and would like to first say a few words about myself. I am a senior in Franklin & Marshall College, Lancaster, PA majoring in Biology. I am also a Macintosh software troubleshooter. That's enough... Recently our Bio department decided to try to implement image analysis system based on a Mac and using NIH Image. Neither me nor anyone in the department has enough knowledge about third-parties hardware and software necessary for image acquisition and subsequent manipulation. I would like to know if there is a document somewhere describing possible configuration of equipment and software supported by NIH Image. If there is no such thing, I think it would be a good idea to compile a list of configuration used by everybody reading this message and make it available to everyone who wishes to start from ground zero as a reference source. I would be happy to compile all the responses I receive and post the summary to the list. If you think it's a good idea, please answer the following questions and feel free to add or delete anything: 1. Purpose of use. Kind of research or educational process. 2. Method of data acquisition. Hardware (like cameras etc.). 3. Computer. Model. Configuration (RAM, HD, add-ons, etc.). 4. Software used except NIH Image. 5. If you were creating your system today, how would you respond to questions 2-4? Your reply is greatly appreciated. Please send your messages directly to me at the address m_palchuk@fandm.edu and not to the list. I will post summary. -- ------------------------------------------------------------------------------ Matvey Palchuk '94 Computing Services Manager CISCS, Franklin & Marshall College Internet: m_palchuk@fandm.edu ------------------------------------------------------------------------------ From gmei@hoh.mbl.edu Thu Oct 14 08:17:55 1993 Received: from AQUA.WHOI.EDU by nx1.soils.umn.edu (5.65c) id AA26929; Thu, 14 Oct 1993 11:19:21 -0500 Return-Path: Received: by aqua.whoi.edu (5.57/Ultrix3.0-C) id AA08886; Thu, 14 Oct 93 12:20:56 -0400 Received: from [128.128.172.215] (SMAC15.MBL.EDU) by hoh.mbl.edu. (4.1/SMI-4.1) id AA26716; Thu, 14 Oct 93 12:17:57 EDT Date: Thu, 14 Oct 93 12:17:55 EDT Message-Id: <9310141617.AA26716@hoh.mbl.edu.> To: nih-image@soils.umn.edu From: gmei@hoh.mbl.edu (Guang Mei) Subject: Convert HSV to 8-bit color image Hi: Does anyone have code (or information about) to convert a stack of HSV images (Hue, Saturation, Value, 8-bit resolution each) to an 8-bit color image. We like to include this function into our version of NIH Image 1.52 (either in macro or in User.p). ------------- Guang Mei gmei@hoh.mbl.edu Tel:(508)548-3705 ext 374 Program of Architectural Dynamics in Living Cells Marine Biological Laboratory, Woods Hole, MA 02543 From jamiel@sybase.com Thu Oct 14 01:56:05 1993 Received: from halon.sybase.com by nx1.soils.umn.edu (5.65c) id AA27310; Thu, 14 Oct 1993 11:52:05 -0500 Return-Path: Received: from sybase.com (sybgate.sybase.com) by halon.sybase.com (5.0/SMI-SVR4/SybFW4.0) id AA27903; Thu, 14 Oct 93 09:55:09 PDT Received: from ralph.sybgate.sybase.com by sybase.com (4.1/SMI-4.1/SybH3.2) id AA01923; Thu, 14 Oct 93 09:53:36 PDT Received: from [130.214.134.8] by ralph.sybgate.sybase.com (4.1/SMI-4.1/SybEC3.1) id AA11499; Thu, 14 Oct 93 09:53:34 PDT Message-Id: <9310141653.AA11499@ralph.sybgate.sybase.com> X-Sender: jamiel@ralph.sybase.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 14 Oct 1993 09:56:05 -0800 To: nih-image@soils.umn.edu From: jamiel@sybase.com (Healthier, More Manageable Hair) Subject: To the person needing quicktime recorder... Content-Length: 624 Hi- I apologize for the bandwidth, but I lost the enote from the person who described the plight of having bought a frame grabber card for research and finding that the software didn't support grabbing multiple frames. I wrote and said that I had the apple recorder, and then couldn't find it. In the mean time, I replied and said sorry, and wither lost or deleted the original note. Well, I found it, and can send it to you. Write me if (1) this makes enough sense for you to figure it out and (2) if you still need it. Again, sorry to everyone else. jamie jamiel@sybase.com "Static- It's all just static"- Bryna Bank From CMSABEL@minna.acc.iit.edu Thu Oct 14 07:34:03 1993 Received: from harpo.acc.iit.edu by nx1.soils.umn.edu (5.65c) id AA27611; Thu, 14 Oct 1993 12:33:01 -0500 Return-Path: Received: from minna.acc.iit.edu by minna.acc.iit.edu (PMDF V4.2-12 #3556) id <01H43PI8JDU88ZG910@minna.acc.iit.edu>; Thu, 14 Oct 1993 12:34:03 CDT Date: Thu, 14 Oct 1993 12:34:03 -0500 (CDT) From: CMSABEL@minna.acc.iit.edu Subject: grain counting macros To: nih-image@soils.umn.edu Message-Id: <01H43PI8KGF68ZG910@minna.acc.iit.edu> X-Vms-To: IN%"nih-image@soils.umn.edu." Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Hi. I'm a new member of 'the list' and don't know if this has been covered yet. Has anyone tried the grain-counting macros that Karl Beykirch put up for anonymous ftp transfer? I've been trying them, and having some difficulty. In particular, when using the 'Count Grains in Area (F7) macro, it is graying out my entire selection and counting it as -one- grain. Perhaps I am not calibrating the area/grain properly. I am not macro-literate (yet), so any info that you can offer is appreciated. Marc cmsabel@minna.acc.iit.edu From ikami@liposun.lbl.gov Thu Oct 14 04:01:47 1993 Received: from lbl.gov by nx1.soils.umn.edu (5.65c) id AA27961; Thu, 14 Oct 1993 13:06:10 -0500 Return-Path: Received: from liposun.lbl.gov by lbl.gov (4.1/1.39) id AA18503; Thu, 14 Oct 93 11:14:35 PDT Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0) id AA03509; Thu, 14 Oct 93 11:01:48 PDT Date: Thu, 14 Oct 93 11:01:47 PDT Message-Id: <9310141801.AA03509@liposun.lbl.gov> To: nih-image@soils.umn.edu From: ikami@liposun.lbl.gov (Craig Ikami) Subject: Re: wand tool area >>Is it possible to get the area outlined by the wand tool? > >Use the Measure command from the analyze menu. Be sure Area is checked >under Options... in the analyze menu > > >Mark Vivino >NIH/DCRT >mvivino@helix.nih.gov Sorry for all these beginner questions. I am running image 1.52 on an LC III. I have checked the area under options in the analyze menu and the area numbers i am getting don't seem to make much sense to me. From ikami@liposun.lbl.gov Thu Oct 14 04:08:51 1993 Received: from lbl.gov by nx1.soils.umn.edu (5.65c) id AA27999; Thu, 14 Oct 1993 13:13:15 -0500 Return-Path: Received: from liposun.lbl.gov by lbl.gov (4.1/1.39) id AA18573; Thu, 14 Oct 93 11:21:40 PDT Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0) id AA03932; Thu, 14 Oct 93 11:08:53 PDT Date: Thu, 14 Oct 93 11:08:51 PDT Message-Id: <9310141808.AA03932@liposun.lbl.gov> To: nih-image@soils.umn.edu From: ikami@liposun.lbl.gov (Craig Ikami) Subject: Re: wand tool area Just a thank-you note for responding to all these first timer questions. We really like the package. Is there anyone in the San Francisco/Berkeley/Lawrence Laboratory area who would mind demo'ing his/her NIH image setup? Thanks again in advance From BUSCH@zodiac.rutgers.edu Thu Oct 14 09:41:43 1993 Received: from PISCES.rutgers.edu by nx1.soils.umn.edu (5.65c) id AA28125; Thu, 14 Oct 1993 13:21:37 -0500 Return-Path: Received: from zodiac.rutgers.edu by zodiac.rutgers.edu (PMDF V4.2-11 #3450) id <01H43RB763HC9YF118@zodiac.rutgers.edu>; Thu, 14 Oct 1993 13:41:43 EDT Date: Thu, 14 Oct 1993 13:41:43 -0400 (EDT) From: BUSCH@zodiac.rutgers.edu Subject: To: nih-image@soils.umn.edu Message-Id: <01H43RB7IYG29YF118@zodiac.rutgers.edu> X-Envelope-To: nih-image@soils.umn.edu X-Vms-To: IN%"nih-image@soils.umn.edu" Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Subscribers: Every now and then, I poke my head into a local laboratory which is working with NIH_Image and a Macintosh, (and I might say, some very nice imaging equipment), to capture and analyse images of neurons. This particular laboratory is interested in things like the size and shape of the cell soma, neurite lengths, number of branches, ... the usual. After listening in on a few conversations recently, it appeared to me that an interesting problem has arisen: How can you tell, from an image, how long a neurite is? This particular question rests in a subclass of the more general problem: Where are the edges of an object? Let me expand on the general problem. In the presence of background noise, what defines the edges of an object, particularly when the pixel intensity defining the object is only modestly above the background. The detection problem is not easy to solve, and many heuristic methods have been employed. In the case of neurite detection, an additional problem arises; the characteristics of the neurites are the data used in determining the effects of various substrates, etc. on sprouting, extension, and in general cell and neurite viability. It is critical therefore that an objective, consistent method be used in determining where the neurites are, and where they are not (sic). I wish to propose a partial answer to this problem. Recently I attended a seminar given at the New York Academy of Sciences on wavelets. I have been working with wavelets on the solution of the near infra-red tomography problem, and was particularly interested in the contents of the seminar. It struck me that embodied in the material presented was the "answer" to the neurite detection problem, and to the more general edge detection problem. The image may be represented as a set of wavelets, the coefficients of which represent all the 'information' contained in the image. It turns out that particular properties of these coefficients, which I will not go into here, reveal the location of discontinuities in the original image, (i.e. where the edges are). Some work has been done on automating the process, but there is still work to be done. I have taken a brief look at the algorithm, and it may be suited to a Mac Quadra class machine and therefore should be able to be implemented as a macro under NIH-image. It appears to me that the problem of neurite and edge detection in the biological sciences must be made rigorous! Therefore it seems sensible to pursue a path in this direction. Any interested parties may contact me directly: Nathan A. Busch Department of Chemical Engineering Rutgers University Piscataway, NJ (908) 932-5511 busch@zodiac.rutgers.edu Nathan. From Doug.Erickson@m.CC.UTAH.EDU Thu Oct 14 05:33:25 1993 Received: from fcom.cc.utah.edu by nx1.soils.umn.edu (5.65c) id AA28175; Thu, 14 Oct 1993 13:30:57 -0500 Return-Path: Received: from [128.110.56.17] (emcb017x.utah.edu) by fcom.cc.utah.edu (4.1/SMI-4.0 [uucc-nhj-virtual 18AUG1991]) id AA21155; Thu, 14 Oct 93 12:30:40 MDT Message-Id: <9310141830.AA21155@fcom.cc.utah.edu> Date: Thu, 14 Oct 1993 12:33:25 -0700 To: nih-image@soils.umn.edu From: Doug.Erickson@m.CC.UTAH.EDU (Doug Erickson) X-Sender: dme8844@u.cc.utah.edu Subject: HERESY! An Image-like program for the PC? I am hope I don't incur the wrath and ridicule of you all--I love my Mac and Image has been an _invaluable_ tool for the project I am currently working on. There are times, however, when all I have handy is a PC. Does anyone know of a public domain program that has capabilities similar to Image? If you can help, please let me know where and how I can get a copy. Also, if you have looked for the same thing recently and know that nothing can compare to Image and that I am wasting my time, I'd like to know that too. Thanks, Doug Erickson U of Utah Dept. of Bioengineering Doug.Erickson@m.cc.utah.edu From jladwig@soils.umn.edu Thu Oct 14 08:59:14 1993 Received: from saturn.soils.umn.edu by nx1.soils.umn.edu (5.65c) id AA28504; Thu, 14 Oct 1993 13:59:09 -0500 Return-Path: Received: by saturn.soils.umn.edu (4.1) id AA12047; Thu, 14 Oct 93 13:59:14 CDT Date: Thu, 14 Oct 93 13:59:14 CDT From: "John Ladwig" Message-Id: <9310141859.AA12047@saturn.soils.umn.edu> To: nih-image@soils.umn.edu Subject: NIH-Image Message Archives [was: grain counting macros] In-Reply-To: CMSABEL@minna.acc.iit.edu's message <01H43PI8KGF68ZG910@minna.acc.iit.edu> of 14 October 1993 References: <01H43PI8KGF68ZG910@minna.acc.iit.edu> >>>>> On Thu, 14 Oct 1993 12:36:13 -0500, CMSABEL@minna.acc.iit.edu said: CMSABEL> I'm a new member of 'the list' and don't know if this has CMSABEL> been covered yet. Has anyone tried the grain-counting CMSABEL> macros that Karl Beykirch put up for anonymous ftp CMSABEL> transfer? As a reminder, all past message from the NIH-Image mailing list are archived, and available via email, FTP, and gopher. >From the welcome message (which probably no one reads, anyhow) sent at subscription time: ======================================================================== Contributions sent to this list are automatically archived. You can obtain a list of the available archive files by sending an "INDEX NIH-IMAGE" command to LISTPROC@SOILS.UMN.EDU. These files can then be retrieved by means of a "GET NIH-IMAGE filename" command. MESSAGE ARCHIVE ACCESS ====================== 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 Archives to search the archived messagesd for keywords, or 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: ftp.soils.umn.edu:pub/info/email-lists/Nih-image* Please note that it is presently possible for anybody to determine that you are signed up to the list through the use of the "REVIEW" command, which returns the network address and name of all the subscribers. More information on Listprocessor commands can be found in the Help document, which you can retrieve by sending a "HELP" command to LISTPROC@SOILS.UMN.EDU. From mvivino@helix.nih.gov Thu Oct 14 12:03:08 1993 Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c) id AA29091; Thu, 14 Oct 1993 15:01:36 -0500 Return-Path: Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0)) id AA12002; Thu, 14 Oct 93 16:03:08 -0400 Date: Thu, 14 Oct 93 16:03:08 -0400 Message-Id: <9310142003.AA12002@helix.nih.gov> X-Sender: mvivino@128.231.2.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mvivino@helix.nih.gov (Mark Vivino) Subject: Re: wand tool area >Sorry for all these beginner questions. >I am running image 1.52 on an LC III. I have checked the area under options >in the analyze menu and the area numbers i am getting don't seem to make >much sense to me. If you want units other than pixels you must scale the image into some unit like mm or cm with the set scale command. Draw a line of aknown length on the image with the line tool, then say set scale. Set scale is below options... Otherwise you can remove any scale that is on the image by checking pixels in the set scale. Mark Vivino NIH/DCRT mvivino@helix.nih.gov From bright@ENH.NIST.GOV Thu Oct 14 13:41:59 1993 Received: from enh.nist.gov by nx1.soils.umn.edu (5.65c) id AA00144; Thu, 14 Oct 1993 16:41:08 -0500 Return-Path: Received: from [129.6.98.4] (dsb-mac.nist.gov) by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01H440GKVC74001HYX@ENH.NIST.GOV>; Thu, 14 Oct 1993 17:41:59 EDT Date: Thu, 14 Oct 1993 17:41:59 -0400 (EDT) Date-Warning: Date header was inserted by ENH.NIST.GOV From: bright@ENH.NIST.GOV Subject: Re: HERESY! An Image-like program for the PC? To: nih-image@soils.umn.edu Message-Id: <01H440GOJYIE001HYX@ENH.NIST.GOV> Content-Transfer-Encoding: 7BIT >I am hope I don't incur the wrath and ridicule of you all--I love my Mac and >Image has been an _invaluable_ tool for the project I am currently working on. >There are times, however, when all I have handy is a PC. Does anyone know >of a public domain program that has capabilities similar to Image? > >If you can help, please let me know where and how I can get a copy. Also, if >you have looked for the same thing recently and know that nothing can compare >to Image and that I am wasting my time, I'd like to know that too. > >Thanks, > >Doug Erickson >U of Utah Dept. of Bioengineering >Doug.Erickson@m.cc.utah.edu Try the National Center for Supercomputing.. PC show or something like that: FTP host: ftp.ncsa.uiuc.edu Questions: softdev@ncsa.uiuc.edu :8o) Dave ------------------------------------------------------------- David S. Bright bright@enh.nist.gov Microanalysis Research Group Chem. A113 National Institute of Standards & Technology (NIST, formerly NBS) Gaithersburg, MD 20899-0001 USA 301-975-3911 - voice, 301-216-1134 - fax From ikami@liposun.lbl.gov Thu Oct 14 08:18:25 1993 Received: from lbl.gov by nx1.soils.umn.edu (5.65c) id AA00560; Thu, 14 Oct 1993 17:22:50 -0500 Return-Path: Received: from liposun.lbl.gov by lbl.gov (4.1/1.39) id AA21455; Thu, 14 Oct 93 15:31:16 PDT Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0) id AA08449; Thu, 14 Oct 93 15:18:27 PDT Date: Thu, 14 Oct 93 15:18:25 PDT Message-Id: <9310142218.AA08449@liposun.lbl.gov> To: nih-image@soils.umn.edu From: ikami@liposun.lbl.gov (Craig Ikami) Subject: Re: wand tool area >>Sorry for all these beginner questions. >>I am running image 1.52 on an LC III. I have checked the area under options >>in the analyze menu and the area numbers i am getting don't seem to make >>much sense to me. > >If you want units other than pixels you must scale the image into some unit >like mm or cm with the set scale command. Draw a line of aknown length on >the image with the line tool, then say set scale. Set scale is below >options... > > Otherwise you can remove any scale that is on the image by checking pixels >in the set scale. > > >Mark Vivino >NIH/DCRT >mvivino@helix.nih.gov The measure option is setup on pixels. This is what i get for the wand measurments. (These are round HDL particles under em). area mean x y 1 1.00 100.00 134.50 253.50 2 1.00 100.00 218.50 209.50 3 3.00 100.33 331.86 172.83 4 2.00 100.00 370.43 219.55 5 0.00 0.00 245.90 330.08 area 2 is slightly larger than area 1 area 3 is twice the size of area 1 area 4 is about the same size as area 1 area 5 is about the same size as area 1 The areas seem to be correct when i use the rectangle, ellipse or free hand. Is there something i am supposed to set for the wand? The outline looks correct. Is there a volume measurement? That is can i circle an area and get some kind of density/area integration without any averaging? thanks again in advance From ikami@liposun.lbl.gov Thu Oct 14 10:29:27 1993 Received: from lbl.gov by nx1.soils.umn.edu (5.65c) id AA01609; Thu, 14 Oct 1993 19:33:52 -0500 Return-Path: Received: from liposun.lbl.gov by lbl.gov (4.1/1.39) id AA22951; Thu, 14 Oct 93 17:42:18 PDT Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0) id AA10134; Thu, 14 Oct 93 17:29:29 PDT Date: Thu, 14 Oct 93 17:29:27 PDT Message-Id: <9310150029.AA10134@liposun.lbl.gov> To: nih-image@soils.umn.edu From: ikami@liposun.lbl.gov (Craig Ikami) Subject: Re: wand tool area >>Is it possible to get the area outlined by the wand tool? > >Use the Measure command from the analyze menu. Be sure Area is checked >under Options... in the analyze menu > > >Mark Vivino >NIH/DCRT >mvivino@helix.nih.gov ok .. i have some answers. I am reading 12 bit TIFF from Molecular Dynamics. I turns out that if i use some "diddled" version of NIH image from Molecular Dynamics, then everything seems ok. If i use the NIH version , the images look ok but do not seem to computer ok. This is trial by fire for a first timer. From @UWAVM.U.WASHINGTON.EDU:tom@peptide.chem.washington.edu Thu Oct 14 13:59:59 1993 Received: from uwavm.u.washington.edu by nx1.soils.umn.edu (5.65c) id AA03304; Thu, 14 Oct 1993 22:58:53 -0500 Return-Path: <@UWAVM.U.WASHINGTON.EDU:tom@peptide.chem.washington.edu> Received: from peptide.chem.washington.edu by UWAVM.U.WASHINGTON.EDU (IBM VM SMTP V2R1) with TCP; Thu, 14 Oct 93 20:59:55 PDT Received: by peptide.chem.washington.edu (920330.SGI/911001.SGI) for @uwavm.u.washington.edu:nih-image@soils.umn.edu id AA22741; Thu, 14 Oct 93 20:59:59 -0700 Date: Thu, 14 Oct 93 20:59:59 -0700 From: tom@peptide.chem.washington.edu (Tom Marschner) Message-Id: <9310150359.AA22741@peptide.chem.washington.edu> To: nih-image@soils.umn.edu Subject: Re: wand tool area From nih-image@soils.umn.edu Thu Oct 14 16:02:25 1993 Received: from mail.tc.umn.edu by peptide.chem.washington.edu via SMTP (920330.SGI/911001.SGI) for tom id AA22176; Thu, 14 Oct 93 16:02:25 -0700 Received: from nx1.soils.umn.edu by mail.tc.umn.edu id SMTP-0012cbdd366016168; Thu, 14 Oct 93 17:32:07 -0500 Received: from (localhost) by nx1.soils.umn.edu (5.65c) id AA00634; Thu, 14 Oct 1993 17:29:56 -0500 Date: Thu, 14 Oct 1993 17:29:56 -0500 Message-Id: <9310142218.AA08449@liposun.lbl.gov> Errors-To: owner-nih-image@soils.umn.edu Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu Precedence: bulk From: ikami%liposun.lbl.gov@relay.tc.umn.edu (Craig Ikami) To: Multiple recipients of list Subject: Re: wand tool area X-Listprocessor-Version: 6.0 -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List >>Sorry for all these beginner questions. >>I am running image 1.52 on an LC III. I have checked the area under options >>in the analyze menu and the area numbers i am getting don't seem to make >>much sense to me. > >If you want units other than pixels you must scale the image into some unit >like mm or cm with the set scale command. Draw a line of aknown length on >the image with the line tool, then say set scale. Set scale is below >options... > > Otherwise you can remove any scale that is on the image by checking pixels >in the set scale. > > >Mark Vivino >NIH/DCRT >mvivino@helix.nih.gov The measure option is setup on pixels. This is what i get for the wand measurments. (These are round HDL particles under em). area mean x y 1 1.00 100.00 134.50 253.50 2 1.00 100.00 218.50 209.50 3 3.00 100.33 331.86 172.83 4 2.00 100.00 370.43 219.55 5 0.00 0.00 245.90 330.08 area 2 is slightly larger than area 1 area 3 is twice the size of area 1 area 4 is about the same size as area 1 area 5 is about the same size as area 1 The areas seem to be correct when i use the rectangle, ellipse or free hand. Is there something i am supposed to set for the wand? The outline looks correct. Is there a volume measurement? That is can i circle an area and get some kind of density/area integration without any averaging? thanks again in advance From @UWAVM.U.WASHINGTON.EDU:tom@peptide.chem.washington.edu Thu Oct 14 14:15:27 1993 Received: from uwavm.u.washington.edu by nx1.soils.umn.edu (5.65c) id AA03442; Thu, 14 Oct 1993 23:14:20 -0500 Return-Path: <@UWAVM.U.WASHINGTON.EDU:tom@peptide.chem.washington.edu> Received: from peptide.chem.washington.edu by UWAVM.U.WASHINGTON.EDU (IBM VM SMTP V2R1) with TCP; Thu, 14 Oct 93 21:15:22 PDT Received: by peptide.chem.washington.edu (920330.SGI/911001.SGI) for @uwavm.u.washington.edu:nih-image@soils.umn.edu id AA22793; Thu, 14 Oct 93 21:15:27 -0700 Date: Thu, 14 Oct 93 21:15:27 -0700 From: tom@peptide.chem.washington.edu (Tom Marschner) Message-Id: <9310150415.AA22793@peptide.chem.washington.edu> To: nih-image@soils.umn.edu >>Sorry for all these beginner questions. >>I am running image 1.52 on an LC III. I have checked the area under options >>in the analyze menu and the area numbers i am getting don't seem to make >>much sense to me. > >If you want units other than pixels you must scale the image into some unit >like mm or cm with the set scale command. Draw a line of aknown length on >the image with the line tool, then say set scale. Set scale is below >options... > > Otherwise you can remove any scale that is on the image by checking pixels >in the set scale. > > >Mark Vivino >NIH/DCRT >mvivino@helix.nih.gov Is density slicing or thresholding turned on? If either is turned on the measurement is carried out on only the selected pixels. Tom Marschner tom@peptide.chem.washington.edu From ptr@GRECO2.POLYTECHNIQUE.FR Fri Oct 15 13:09:15 1993 Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c) id AA05892; Fri, 15 Oct 1993 06:11:38 -0500 Return-Path: Received: from polytechnique.polytechnique.fr by chenas.inria.fr (5.65c8d/92.02.29) via Fnet-EUnet id AA09323; Fri, 15 Oct 1993 12:13:01 +0100 (MET) Received: by polytechnique.polytechnique.fr (5.65c/SMI-4.1.3) id AA29312; Fri, 15 Oct 1993 12:20:54 +0100 Received: from [129.104.27.245] by greco2.noname (4.1/SMI-4.1) id AA10522; Fri, 15 Oct 93 12:09:15 +0100 Date: Fri, 15 Oct 93 12:09:15 +0100 Message-Id: <9310151109.AA10522@greco2.noname> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: ptr@GRECO2.POLYTECHNIQUE.FR (Peter Goedtkindt) Subject: Re: NIH-Image Message Archives [was: grain counting macros] >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 Archives > I'm having difficulties using gopher: he's telling me at manny occasions that he "cannot resolve host name...". I also get a lot of system errors using TurboGopher. (Sys 7.1, MacTCP 1.1.1) I've added all the adresses of the mac-ftp-list to my hosts file in the system folder, and this improved some connections. Can someone help me out here? We have a domain name server on the campus, but I have sometimes problems getting to sites of which I only know the name and not the IP number. This is why I keep a long list on my mac. Is there a limit on the size of the Hosts file? Is MacTCP 2.02 better in some way? Can someone send it to me so I can try it out. Peter Goedtkindt Universite Paris-Sud Laboratoire de Spectroscopie Atomique et Ionique X-ray Laser group bat350 Centre D'Orsay F-91405 Orsay Cedex. France Fax.:++33.1.69.41.94.60 - Tel 69.41.77.10 ------ And ------ Ecole Polytechnique, Laboratoire d'Utilisation de Lasers Intenses tel. 69.33.48.95 ----------------------------------------------------------------- From mvivino@helix.nih.gov Fri Oct 15 04:56:51 1993 Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c) id AA08333; Fri, 15 Oct 1993 07:55:16 -0500 Return-Path: Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0)) id AA02969; Fri, 15 Oct 93 08:56:51 -0400 Date: Fri, 15 Oct 93 08:56:51 -0400 Message-Id: <9310151256.AA02969@helix.nih.gov> X-Sender: mvivino@128.231.2.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mvivino@helix.nih.gov (Mark Vivino) Subject: Re: modified software by molecular dynamics, Was: wand tool area >ok .. i have some answers. I am reading 12 bit TIFF from Molecular >Dynamics. I turns out that if i use some "diddled" version of NIH image >from Molecular Dynamics, then everything seems ok. If i use the NIH version >, the images look ok but do not seem to computer ok. I know that NIH Image does measurements just fine. I can't say how many hundreds of times i have done them and often tested the software and it is correct. I can't say anything on software which molecular dynamics modified. Mark Vivino NIH/DCRT mvivino@helix.nih.gov From sarmienu@rnisd0.DNET.roche.com Fri Oct 15 09:32:37 1993 Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c) id AA10453; Fri, 15 Oct 1993 12:31:05 -0500 Return-Path: Received: by gatekeeper.roche.com (5.65/fma-120691); id AA00221; Fri, 15 Oct 93 13:32:38 -0400 Received: by mailgate.roche.com (5.65/fma-120691); id AA06359; Fri, 15 Oct 93 13:27:15 -0400 From: sarmienu@rnisd0.DNET.roche.com Message-Id: <9310151727.AA06359@mailgate.roche.com> Received: from rnisd0.enet; by inet.enet; Fri, 15 Oct 93 13:32:37 EDT Date: Fri, 15 Oct 93 13:32:37 EDT To: nih-image@soils.umn.edu Apparently-To: nih-image@soils.umn.edu Subject: More on FDA approval Everybody on the list knows that I have been confronted with the problem of validation of the NIH Image program for FDA approval. Because of Image rapid increased popularity in the scientific community, it is a matter of time before Image becomes widely used in Industry. I have been an advocate of the use of NIH Image in the drug industry, particularly in the use of the program in toxicologic pathology for morphometric use. The program is severely limited in that it must be FDA approved before it can be used for some studies. This is in response to an E-mail message by Dr. Thomas M. Marschner (see below), that may be of use to some of the members of this list. I would like to receive separate replies to my address from those of you who have an interest in validating the system. >Dear [Dr. Sarmiento] >I received you e-mail regarding validation of NIH Image. We have not >yet validated the program itself--only the particular measurements >we are concerned with (area and perimeter). What this means is that we have >calibrated the system using rulers, and compared the results with >"standards" of known area and perimeter. We are just now starting to >think about validation of such things as backups, etc. We are >probably a bit naive about this since we currently do not yet have >any approved drugs (we are still in the development phase). Any insight >or recommendations you might have are welcome. One question I have >is why your computer people think that validation of a public domain >program is more difficult that validation of any other program. It's not >like Microsoft is going to validate Excel for the few users that may >be using it for GMP data analysis. Thanks in advance for any suggestions >you can make. I will keep you informed of any progress we make in >validating the software. > >Sincerely, > >Thomas M. Marschner, Ph.D. >Senior Scientist >ProCyte Corporation >tom@peptide.chem.washington.edu > Dear Dr. Marschner: Thank you for replying to my message. I have been frustrated and disappointed regarding the use of NIH Image for GLP (good laboratory practice) studies because recently, FDA (food and drug administration) has put many restrictions on computer software lately. Widely used commercial software such as EXCEL, for example, do not require validation, as there are actually millions of users to confirm that the application works as advertised. Programs with a limited number of users (e.g. NIH Image), require verification of every decision routine in the code. Sometimes, vendors are able to provide the code and the warranty that the verification of the routines have taken place. There are two parts to this verification process: 1) Black box verification, in which the original data is compared to the processed data, to confirm that the computer has done its job, without errors. 2) The White box verification which involves the verification of each "if..." decision of the code by a computer expert of programmer. Documents verifying that both tests have been performed are send to FDA. The way I understand it is that the white box testing does not have to be made for every routine in the program. Further, the code must be supplied with the application for validation to FDA. Even though the code for NIH Image is available, there are some problems inherited of a public domain program: The support to the program depends on one individual, Wayne Rasband. If something were to happen to Wayne, physically or say he'd just give up, the program will be not validatable, as there is not the support of an commercial institution behind the program. Wayne has said in the past that he has no intention of going commercial, which is just fine for must people that cannot afford >$3000 worth of commercial image analysis software. Due to the fact that this great program is the result of the generosity of Wayne, preclude us from asking him to perform time consuming white or black box test that would only limit the time he has available to upgrade NIH Image, the way he has been doing for the last few years. Ironically, those upgrades are a problem with the FDA because if the upgrade is major, a new set of validation documents would have to be prepared. Possibly the best solution, perhaps not the cheapest is to take advantage of the availability of the NIH Image code and have an in house computer programmer validate the program and perhaps customize it to the needs of your operation. However, the upgrades that Wayne performs regularly are actually quite valuable, I for one would hate to loose that feature. A validation test kit that I prepared containing multiple tests of the morphometric features of NIH Image must be used every time a new project is started and every time a new version of NIH Image is obtained. We here have gotten an error of less than 1% from test to test. Another solution to the problem is to acquired a commercially available spin-off version of NIH Image. Vic Moss in this list suggests: " There is a program Prism View based on Image, but including many new features. This was developed by John Russ (NC State Univ) and his son Christian. For details I suggest you contact John Russ at russ@edu.ncsu.mte.mat". Unfortunately, all messages that I have sent to that address have bounced. Another program such as IP Lab may be an alternatively. They are planning to or have made the software compatible with Scion's LG- 3 frame grabber, which is the preferred card for NIH Image. I personally, prefer NIH Image. It is much more easy to use, since it has the tool bar, it is more intuitive and thus easy to teach to technicians and other pathologists in this department. You can call Paul Kumpe at signal analytics (703) 281 3277. Finally, just today, I received the following note from Wayne: >I just found out that MedVision, one of the Mac imaging programs listed in >Appended D of the NIH Image manual, has FDA 510K approval for clinical use. >They just moved to Maine, so the phone number in the manual is incorrect. > >--wayne > >MedVision >Evergreen Technologies >Castine, Maine >207-326-8300, fax:207-326-8333 >evergreen@applelink.apple.com" Thank you Wayne... Any comments or suggestions will be appreciated Juan I. Sarmiento Department of Toxicology and Pathology Hoffmann-La Roche, INC. 340 Kingsland street Nutley, NJ 07110 (201) 235 3907 Sarmienu@RNISD0.DNET.ROCHE.COM The opinions expressed here are solely my own, for which I am solely responsible and do not reflect those of Hoffmann-La Roche Inc. From jcrum%sunstroke@sdsu.edu Fri Oct 15 08:21:38 1993 Received: from sdsu.edu by nx1.soils.umn.edu (5.65c) id AA12668; Fri, 15 Oct 1993 17:22:23 -0500 Return-Path: Received: from sunstroke.sdsu.edu by sdsu.edu; id AA06393 sendmail 5.64/SDSU-GW-1.11 via SMTP Fri, 15 Oct 93 15:21:40 -0700 Received: from .sdsu.edu (lif_sci_n4-mac6.sdsu.edu) by sunstroke.SDSU.EDU (4.1/SDSU-GENERIC.3) id AA00771; Fri, 15 Oct 93 15:21:38 PDT Date: Fri, 15 Oct 93 15:21:38 PDT From: jcrum%sunstroke@sdsu.edu (John Crum) Message-Id: <9310152221.AA00771@sunstroke.SDSU.EDU> Subject: Image capture on SEM To: nih-image@soils.umn.edu X-Mailer: SDSUMail [Version 1.9 beta] X-Type: TEXT NIH Image Users: Is anyone out there using NIH Image and a Macintosh to capture images from a scanning electron microscope? If so, what is the resolution (i.e. image size) that you are getting? What hardware (i.e. image capture board and Mac) are you using? What does it cost? The reason I ask is that our EM facility is in the market for a new SEM. A nice feature we have now on our SEM is image capture, using a part of a Princeton Gamma Tech EDS system. The core of that system, though, is a Sun 3/60, which doesn't really work well and will need a costly upgrade. We can capture images of 512 pixels and 1024 pixels sqaure. New software (on top of hardware upgrade) will capture 2kX2k images. So, the ultimate question is: should we adapt the system we have now to a new SEM, or buy a new Mac/Image based system? Any advice is greatly appreciated. jc From ZALUZEC@anlemc.msd.anl.gov Fri Oct 15 13:34:47 1993 Received: from anlemc.msd.anl.gov by nx1.soils.umn.edu (5.65c) id AA13074; Fri, 15 Oct 1993 18:33:07 -0500 Return-Path: Date: Fri, 15 Oct 1993 18:34:47 -0500 (CDT) From: "Nestor J. Zaluzec (708)-252-5075, -4964" To: nih-image@soils.umn.edu Cc: ZALUZEC@anlemc.msd.anl.gov Message-Id: <931015183447.20201a62@anlemc.msd.anl.gov> Subject: Image capture on SEM's There is a good commerical product which will drive your SEM scanning system and capture images directly into Photoshop using plug-ins (don't know if the plug-ins will work using NIH Image) Contact Scott Davilla at "GO4pi@appleline.apple.com" or call 919-489-1757, Fax: 919-489-1487. This is not TV rate acquistion but slow scan control of your SEM giving you the highest quality digitized SEM pictures (up to 4K x 4K) I've seen on-line. I plan on buying one for my lab when I scrap up the $$. Ball park cost of the hardware boards is about $7K, assuming you already have the Mac, Display, SEM, and Photoshop. Nestor Zaluzec ANL EMCenter From GARRISSJ@ctrvax.Vanderbilt.Edu Tue Oct 15 15:31:08 1993 Received: from ctrvx1.Vanderbilt.Edu by nx1.soils.umn.edu (5.65c) id AA13816; Fri, 15 Oct 1993 20:29:39 -0500 Return-Path: Received: from ctrvax.Vanderbilt.Edu by ctrvax.Vanderbilt.Edu (PMDF #3899 ) id <01H45K9TMHU88WYXDY@ctrvax.Vanderbilt.Edu>; Fri, 15 Oct 1993 20:31:08 CDT Date: 15 Oct 1993 20:31:08 -0500 (CDT) From: GARRISSJ@ctrvax.Vanderbilt.Edu Subject: Message to Unknown Beginner on List (10/15/93) To: nih-image@soils.umn.edu Message-Id: <01H45K9TMHUA8WYXDY@ctrvax.Vanderbilt.Edu> X-Vms-To: IN%"nih-image@soils.umn.edu" Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT A beginning user of Image wrote about needing general info. about setting up a sytem for image analysis. I'm sorry, but I lost your msg., but you are in precisely the same position as I am. I need to set up a lab for scanning gels and film in biology and can't decide which hardware (cameras, scanners, frame grabbers, etc) to use, which software (besides Image) and how to link the whole system together so it works. Our lab has Centris 650's with 8 mb of RAM. I understand that a high-res monochrome camera is preferable to color. Image supports particular frame-grabbers and scanners (that much can be seen from the Image Manual). It's scary thinking about buying components, though and not being sure if the system will work! One stumbling block seems to be the difficulty in digitizing ethidium bromide gels, because UV light while viewing the gel, not regular visible light. Apparently cameras have a hard time picking up the image because of low-light conditions. Sorry to ramble on. This is the system we are thinking of putting together: Cohu monochrome camera Scion frame-grabber Image software with export to Adobe Photoshop & MS Word A dual-purpose illuminator (UV & visible) Centris 650 computer Oh, and the purpose of the lab is for students to run gels, clean them up (on screen) and print out the results for their lab notebooks. The lab set-up is not intended for research purposes. Please comment, anyone. Thanks. ------------------------------------------------------------------------- Steve Garrison Internet username: GARRISSJ@CTRVAX.VANDERBILT.EDU Vanderbilt University Dept. of Molecular Biology or.... Learning Technology Center 615-322-4942 Vanderbilt University 322-8070 ------------------------------------------------------------------------- From rms@acsu.buffalo.edu Fri Oct 15 17:39:23 1993 Received: from autarch.acsu.buffalo.edu by nx1.soils.umn.edu (5.65c) id AA13954; Fri, 15 Oct 1993 20:37:49 -0500 Return-Path: Received: from rms@localhost by autarch.acsu.buffalo.edu (8.5/8.5) id VAA19083; Fri, 15 Oct 1993 21:39:23 -0400 Date: Fri, 15 Oct 1993 21:39:23 -0400 From: "Robert M. Straubinger" Message-Id: <199310160139.VAA19083@autarch.acsu.buffalo.edu> To: nih-image@soils.umn.edu Subject: Re: More on FDA approval Juan I. Sarmiento writes: [deleted discussion of FDA and validation of NIH Image] We're interested in this topic as well, as (if the gods smile) we may need to do particle sizing for pre-IND purposes. One point brought up: > Possibly the best solution, perhaps not the cheapest is to take > advantage of the availability of the NIH Image code and have an in > house computer programmer validate the program and perhaps > customize it to the needs of your operation. However, the upgrades > that Wayne performs regularly are actually quite valuable, I for one > would hate to loose that feature. And these frequent updates likewise may also be a major source of trouble, since changes thought to be inconsequential might be made without documentation, perhaps. In your experience, is it possible that if (say) major-release versions of the program were 'frozen' in object-library format, then only new routines would have to be validated? >A validation test kit that I prepared >containing multiple tests of the morphometric features of NIH >Image must be used every time a new project is started and every >time a new version of NIH Image is obtained. We here have gotten >an error of less than 1% from test to test. If there is general interest, do you think the 'black box' data could be posted or otherwise made available? Perhaps it would be relatively painless to assemble a database for black-box qualification of the program. We recently have had trouble repeating measurements done with a script developed for a version somewhere around 1.43, so this question of qualifying new versions of NIH Image is an important one even outside the context of FDA approval. If it turns out there is too little interest to keep this discussion going in the mailing list, and it goes off-line, please keep in mind that we're interested in how things develop, for the above reasons. Bob Straubinger Pharmaceutics SUNY/Buffalo From kartenh@Sdsc.Edu Sat Oct 16 20:51:36 1993 Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA21711; Sat, 16 Oct 1993 15:50:12 -0500 Return-Path: Date: Sat, 16 Oct 93 20:51:36 GMT From: kartenh@Sdsc.Edu (Harvey Karten) Message-Id: <931016205136.204079d8@m5.sdsc.edu> Subject: RE: Message to Unknown Beginner on List (10/15/93) To: nih-image@soils.umn.edu X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu" X-St-Vmsmail-Cc: KARTENH I have both a Cohu and a Sony/Dage camera. The Cohu is somewhat more sensitive to lower light levels, but is of poorer image quality. It has had to be recalilbrated recalibrated on several occasions, and gives a crummy image when the calibration deteriorates. The Sony/Dage gives an excellent image, has not deteriorated in image quality over the past several years, and has proven an excellent general workhorse. (I am referring to the B&W- monochrome camera). If you do decide to go for a color camera, you should consider the three chip Sony or the 3 chip Panasonic. The one chip color camera from Sony gives a decent image, but if you attempt to use it as a monochrome camera, the results are not satisfactory, when compared to a true monochrome (having to do with the way a single chip color CCD is manufactured). If you use is as a color camera you will be very disappointed. The image will not be as crisp as that with a 3 chip configuration. H. Karten From @CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu Sat Oct 16 17:05:00 1993 Received: from cunyvm.cuny.edu by nx1.soils.umn.edu (5.65c) id AA23846; Sat, 16 Oct 1993 22:11:04 -0500 Return-Path: <@CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu> Received: from darban.cc.usm.edu by CUNYVM.CUNY.EDU (IBM VM SMTP V2R2) with TCP; Sat, 16 Oct 93 23:11:41 EDT Received: by darban.cc.usm.edu (5.57/Ultrix3.0-C) id AA15680; Sat, 16 Oct 93 22:11:36 -0500 Date: Sat, 16 Oct 93 22:05 CDT From: GLEN SHEARER To: nih-image@soils.umn.edu Really-To: nih-image@soils.umn.edu Subject: hand scanners Message-Id: <931016.22072692.038073@USM.CP6> Any recommendations for hand held scanners that work with Image? Glen Shearer From H.Patel@southampton.ac.uk Mon Oct 18 06:21:11 1993 Received: from sun2.nsfnet-relay.ac.uk by nx1.soils.umn.edu (5.65c) id AA07369; Mon, 18 Oct 1993 06:21:11 -0500 Return-Path: Via: uk.ac.southampton; Mon, 18 Oct 1993 12:14:38 +0100 From: "H.Patel" Message-Id: <2894.9310181106@mail.soton.ac.uk> Date: Mon, 18 Oct 93 12:06:14 BST To: nih-image@soils.umn.edu Subject: Re: Another Beginner's Question In-Reply-To: <9310120642.AA17554@lurch.smhi.se>; from "mmoberg@smhi.se" at Oct 12, 93 1:42 am X-Mailer: ELM [version 2.3 PL11] More really basic questions yet again. I'm trying to use Image for the first time and in a lab where no one has any working knowledge of it at all. So 2 questions? 1 I have used ftp to get the image program. What is the difference between the fpu and non-fpu programs? 2 Is there anyone in the United Kingdom using Image for densitometry. (or anyone coming anywhere near Southampton who could talk me through it ?) H.Patel, Clinical Neurological Sciences, Southampton General Hospital, Southampton, SO9 4XY, U.K. From herro001@maroon.tc.umn.edu Mon Oct 18 01:46:30 1993 Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c) id AA07505; Mon, 18 Oct 1993 06:44:58 -0500 Return-Path: Message-Id: <199310181144.AA07505@nx1.soils.umn.edu> Received: from dialup-slip-1-27.gw.umn.edu by maroon.tc.umn.edu id SMTP-0012cc2820f026686; Mon, 18 Oct 93 06:46:26 -0500 From: "Mike Herron" Reply-To: "Mike Herron" To: nih-image@soils.umn.edu Subject: Re: Another Beginner's Question Date: Mon, 18 Oct 93 06:46:30 -0500 The fpu version is for Macs _WITH_ an fpu (an fpu does floating point calculcations _much_ faster and speeds up a few of the NIH Image functions). Any Mac with a true 68040 already has an fpu built in (it is part of the 68040 chip) A mac with a 68030 (IIsi,LC III, Color Classic, et. al.) may or may not have an fpu (you can easily install one for about $80) The densitometry thing is so simple I doubt you will need help! There is a macro for scanning gels in the macro folder that does this on electrophoresis gels, and there is a pretty good explanation of the whole thing in the manual too. The only slightly confusing aspect is which measurement to use. There was a good post on this point recently could someone repost it? In message <2894.9310181106@mail.soton.ac.uk> writes: > > > More really basic questions yet again. > > I'm trying to use Image for the first time and in a lab where no one has any > working knowledge of it at all. > > So 2 questions? > > 1 I have used ftp to get the image program. What is the difference between > the > fpu and non-fpu programs? > > 2 Is there anyone in the United Kingdom using Image for densitometry. (or > anyone coming anywhere near Southampton who could talk me through it ?) > > H.Patel, > Clinical Neurological Sciences, > Southampton General Hospital, > Southampton, > SO9 4XY, > U.K. > _____________________________________________________________ / Michael J. Herron University of MN, Dept. of Dermatology / / herro001@staff.tc.umn.edu / _____________________________________________________________ From smithj@acad.winthrop.edu Mon Oct 18 05:17:09 1993 Received: from acad ([192.203.180.3]) by nx1.soils.umn.edu (5.65c) id AA08163; Mon, 18 Oct 1993 08:18:05 -0500 Return-Path: Message-Id: <199310181318.AA08163@nx1.soils.umn.edu> Date: Mon, 18 Oct 1993 09:17:09 -0400 From: smithj@acad.winthrop.edu To: nih-image@soils.umn.edu Subject: Video for TEM? X-Vms-To: SMTP%"nih-image@soils.umn.edu" Hi, I'm interested in hooking a video camera to my TEM (JEOL 100B): 1)To demonstrate procedures such as filament saturation and 'scope alignment when teaching my EM class, and 2) To capture "quickie" EM prints to a video printer for students in my cell bio and vertebrate histology classes. I'm looking for about 640x480 pixels and 8 bits, and would like something that covers about the same area at each magnification as the film camera. I know about Gatan's systems, and I've been told "look at the Fullam system before you buy it". Is there anything else out there that I should know about? Have any of you used either the Gatan system or the Fullam system, and how satisfied are you with it? Any help/feedback would be appreciated. TIA Julian Smith III (smithj@winthrop.edu) From Scott.Wurcer@analog.com Mon Oct 18 06:30:11 1993 Received: from nic.near.net by nx1.soils.umn.edu (5.65c) id AA08924; Mon, 18 Oct 1993 09:29:27 -0500 Return-Path: Received: from [137.71.23.11] by nic.near.net id aa12160; 18 Oct 93 10:30 EDT Received: from nwd2sun1.analog.com ([137.71.22.41]) by adi.analog.com Received: from titania.adsdesign.analog.com by nwd2sun1.analog.com (4.1/SMI-4.1) Message-Id: <9310181429.AA11453@nwd2sun1.analog.com> Received: from hermia.adsdesign.analog.com by titania.adsdesign.analog.com Date: Mon, 18 Oct 93 10:30:11 EDT From: Scott Wurcer To: nih-image@soils.umn.edu Subject: Plug-Ins I just finished my first plug-in. It translates packed 12-bit data from a Lynxx CCD camera into 8-bit. I noticed that in Image the window does not show the file name, even though Photoshop does. Does 1.53 fix this? BTW I agree with a previous poster that adding plug-ins is a great addition to Image, at least it allows me to keep working in C. From wayne@helix.nih.gov Mon Oct 18 10:37:02 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA09694; Mon, 18 Oct 1993 10:38:26 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA18852; Mon, 18 Oct 93 10:58:30 -0400 Message-Id: <9310181458.AA18852@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 18 Oct 1993 10:37:02 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Plug-Ins >I just finished my first plug-in. It translates packed 12-bit data from a Lynxx >CCD camera into 8-bit. I noticed that in Image the window does not show the >file name, even though Photoshop does. Does 1.53 fix this? BTW I agree with >a previous poster that adding plug-ins is a great addition to Image, at least >it allows me to keep working in C. Do you plan to make this plug-in available to other NIH Image users? It would be helpful to others trying to write file import plug-ins to have a source code example to look at. The acquistion file name bug will be fixed in the next 1.53 beta (1.53b17 or later), which I will upload to Zippy by the end of the week. I'm adding on a nifty new command called "Image Math" that does image arithmetic and allows you to specify the gain and offset values used to convert the result back to 8-bits. The dialog box uses pop-up menus for specifying the two source images and the operation to be performed. --wayne From sarmienu@rnisd0.DNET.roche.com Mon Oct 18 08:23:26 1993 Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c) id AA10242; Mon, 18 Oct 1993 11:21:58 -0500 Return-Path: Received: by gatekeeper.roche.com (5.65/fma-120691); id AA12670; Mon, 18 Oct 93 12:23:27 -0400 Received: by mailgate.roche.com (5.65/fma-120691); id AA24906; Mon, 18 Oct 93 12:16:48 -0400 From: sarmienu@rnisd0.DNET.roche.com Message-Id: <9310181616.AA24906@mailgate.roche.com> Received: from rnisd0.enet; by inet.enet; Mon, 18 Oct 93 12:23:26 EDT Date: Mon, 18 Oct 93 12:23:26 EDT To: nih-image@soils.umn.edu Apparently-To: nih-image@soils.umn.edu Subject: Updated, Sorted reference list Use the following quote when mentioning image in the materials and methods section of a manuscript"... analysis performed in a Macintosh [model] computer using the public domain NIH Image software program (written by Wayne Rasband at the U.S. National Institutes of Health and available electronically via Internet by anonymous ftp from zippy.nimh.nih.gov or from Library 9 of the MacApp forum on CompuServe and on floppy disk from NTIS, 5285 Port Royal Rd.,Springfield, VA 22161, part number PB93-504868). To appear in a medline search the words "NIH Image" must appear in either the abstract or the Keywords index. Therefore, all people publishing manuscripts using NIH Image should include the name of the program in the abstract whenever possible. Here is an update in the list of references which quote image. I have volunteered to update the list periodically. Please continue to send me new references, as they become available, to my address (see below),. If any of you notice an error, please let me know. Thank you to all contributors. Suggestions and comments to my address below, please Juan I. Sarmiento Department of Toxicology and Pathology Hoffmann-La Roche, INC. 340 Kingsland street Nutley, NJ 07110 (201) 235 3907 Sarmienu@RNISD0.DNET.ROCHE.COM --------------------------------------------------------------------------- References for NIH-Image Adam DR, Kempner KM, Vivino MA, Tucker EE, Jones M, "Measurement of Flow Velocity in a Phantom by Corrected Doppler Color Mapping Technique, using Transverse Cross-Sectional Imaging", Computers in Cardiology 1993, in press Bouabid, R., E.A. Nater, and P. Barak. 1992. Measurement of particle and pore size distribution in a lamellar B horizon by fluorescence microscopy and image analysis. Geoderma 53 (3/4):309-328. Brenneman & collaborators. Nature, March, 1993 (Title has something to do with VIP) Bright, D. S. Software Tools for examination of microanalytical images. pp. 73-78 in MICROBEAM ANALYSIS 1990, SAN FRANCISCO Press, CA. Bright, D.S., Steel, E.B. and Newbury, D.E. (1991), "Visibility of Objects in Noisy Images as a Function of Contrast, Noise Level, and Object Size", Microbeam Analysis 1991: 185-188. Chiang, P.K., et. al., "Activation of Collagen IV Expression in F9 Teratocarcinoma Cells by 3-Deazaadenosine Analogs", Journal of Biological Chemistry, Vol. 267, No. 7, March 1992. Chien, CB; DE Rosenthal, WA Harris, and CE Holt, (1993) "Navigational errors made by growth cones without filopodia in the embryonic Xenopus brain." Neuron 11:237-251. Chin DJ; Green G; Zon G; Szoka FC; Straubinger RM; Rapid nuclear accumulation of injected oligodeoxyribonucleotides. New Biologist 2: 1091- 1100, 1990. Chin DJ; Straubinger RM; Acton S; Nathke I; Brodsky FM; 100kDa polypeptides in peripheral clathrin-coated vesicles are required for receptor- mediated endocytosis. Proc. Natl. Acad. Sci. 86: 9289-93, 1989 Correa-Rotter, R., et. al., "Loading and Transfer Control for Northern Hybridization", BioTechniques, Vol. 12, No. 2 (1992). Correa-Rotter, Ricardo et. al., Loading and Transfer Control for Northern Hybridization, BioTechniques, Vol. 12, No 2, 1992, pages 154-158. D'Amelio, F. and N.G. Daunton. Effects of spaceflight in the adductor longus muscle of rats flown in the Soviet biosatellite COSMOS 2044. A study employing neural cell adhesion molecule (N-CAM) immunocytochemistry and conventional morphological techniques (light and electron microscopy). J. Neuropath. Exp. Neurol. 51(4):415-431, 1992. DeVoogd, T.J., Krebs, J.R., Healy, S.D. & Purvis, A. "Relations between song repertoire size and the volume of brain nuclei related to song: comparative evolutionary analyses amongst oscine birds." In press, Proc. Roy. Soc Lon. B. Dyck, RH and Cynader MS (1993) An interdigitated columnar mosaic of cytochrome oxidase, zinc, and neurotransmitter-related molecules in cat and monkey visual cortex. Proceedings of the National Academy of Science, USA, 90, 9066-9069. Dyck, RH and Cynader MS (1993) Autoradiographic localization of serotonin receptor subtypes in cat visual cortex: regional, laminar, and columnar distributions during postnatal development. Journal of Neuroscience, 13, 4316-4338. Biophys. J. 60:629-641 (1991) Dyck, RH and Cynader, MS (1993) Histochemical localization of synaptic zinc in the developing kitten visual cortex. Journal of Comparative Neurology, 329, 53-67. Ford-Holevinski, Thomas et al., Microcomputer-based Three-dimensional Reconstruction of in situ Hybridization Autoradiographs, Journal of Chemical Neuroanatomy, Vol 4, 1991, pages 373-385. Garlow, S.J., Morilak, D.A., Dean, R.R., Roth, B.L. and Ciaranello, R.D. (1993) Production and characterization of a specific 5-HT2 receptor antibody. Brain Research, 615: 113-120. Gough, A.H. and Taylor, D. L. (1993) Journal of Cell Biology, 121:5:1095-1107. T. K. Teague, L.L. Munn, K. Zygourakis and B.W. McIntyre "Analysis of Lymphocyte Activation and Proliferation by Video Microscopy and Digital Imaging," Cytometry, in press (1993). Gwon, A.E., et. al., "Lens Regeneration in Juvenile and Adult Rabbits Measured by Image Analysis", Investigative Ophthalmology & Visual Science, Vol. 33, No. 7, June 1992. Hammer, R.P., Bogic, L. and Handa, R.J.: Estrogenic regulation of proenkephalin mRNA expression in the ventromedial hypothalamus of the adult male rat, Molecular Brain Research, 19: 129- 134, 1993. Hammer, R.P., Margulies, J.E., Lynn, A.B. and Brady, L.S.: Chronic fluoxetine treatment up- regulates dopamine receptors in the mesolimbic forebrain of the rat, Depression, 1: 82-87, 1993. Hammer, R.P., Pires,W.S., Markou, A. and Koob, G.F.: Withdrawal following cocaine self- administration decreases regional metabolism in critical brain reward regions, Synapse, 14: 73-80, 1993. Herd, R.A. & Pinkerton, H. 1993. Bubble coalescence in magmas. Lunar and Planetary Science Conference. XXIV(2). p.641-642. W. Rasband. NIH Image: An image processing software package for the Macintosh II. Available free of charge from Wayne Rasband, NIH, Bldg. 36, Rm. 2A03, Bethesda, MD 20892", ref. 3 in Hermansson, Roger . An experimental and numerical investigation of phenomena that affect the degree of therminal stratification. Lulea Univ. of Technology. Lulea Sweden. 1993:127D Hill, Ester; Emily Holton. J. Orthopedic Research. 1993 Lieberman, D.E., et. al., "Computer Image Enhancement and Analysis of Cementum Increments as Applied to Teeth of Gazella gazella", Journal of Archaeological Science, in press (1989). Lulea University. Short Term Water Heat storage : Studies of Velocity and Temperature Fields and their Importance for sizing of the Storage. Lulea Univ. of Technology. Lulea Sweden. 1993:131D Magunda, M.K. 1992. Influence of some physico- chemical properties on soil strength, stability of crusts and soil erosion. Ph.D. Dissertation. Bouabid, R. 1992. Soil solution chemistry, mineral weathering, and pedogenesis in sandy outwash soils of east-central Minnesota. Ph.D. Dissertation. Mansfield, John F. & Douglas C. Crawford. Thickness Measurement in the Analytical Electron Microscope by Macintosh-based analysis of two-beam convergent beam patterns. IN: Proc. XIIth Int. Cong. for EM (1990) p504-505. Mansfield, John F. Visit Thaveeprungsriporn & Gary S. Was. Design And Construction Of An Electron Back-Scattering Pattern Camera For The Environmental Scanning Electron Microscope. Scanning 15 (1993) pIII36-III37 Masters, D.B., et. al., "High Sensitivity Quantification of RNA from Gels and Autoradiograms with Affordable Optical Scanning", BioComputing, Vol. 12, No. 6 (1992). Meiners, S., Marone, M., Rittenhouse, J.L, Geller, H.M. Basic FGF upregulates tenascin in cultured astrocytes. Dev. Biol., 1993, in press. Munn, L.L. M.W. Glacken, B.W. McIntyre and K. Zygourakis "Analysis of Lymphocyte Aggregation Using Digital Image Analysis," J. Immunol. Methods, in press (1993). O'Neill, R. et al., Use of Image Analysis to Quantitate Changes in Form of Mitochondrial DNA After X-irradiation, Applied and Theoretical Electrophoresis, 1989-1, pages 163-167. Parry, Robert et. al., Computer-Aided Cell Colony Counting, BioTechniques, Vol. 10, No 6, 1991, pages 772- 774. Plotorak, M., et. al., "L1 Substrate Enhances Outgrowth of Tyrosine Hydroxylase-Immunoreactive Neurites in Mesencephalic Cell Culture", Experimental Neurology 117, 176-184 (1992). Reiss, A.L., et. al., "Neuroantomy of Fragile X Syndrome: the Posterior Fossa, Annals of Neurology, Vol. 29, No. 1, January 1991. Richardson ML, Gillespy TG 3rd. An inexpensive computer-based digital imaging teaching file. Am J Roentgenology 1993;160:1299-1301. Richardson ML. Using a personal computer to create anatomic drawings for publication. Am J Roentgenology 1993, in press. Schwartz, David C., Xiaojun Li, Luis I. Hernandez, Satyadarshan P. Ramnarain, Edward J. Huff, Yu-Ker Wang. Ordered Restriction Maps of Saccharomyces Cerevisiae Chromosomes Constructed by Optical Mapping. Science 262:110 (1993) Velocoimetry ( PIV) in process Metallurgy for Steal mills. Gabriella Trandell : Modelling of tundish alloying for small lot production. Lulea Univ. of Technology. Lulea Sweden. 1992:100E Vivino MA, Chintalagiri S, Trus BL, Datiles M, "Development of a Scheimpflug Slit Lamp Camera System for Quantitative Densitometric Analysis", Eye, Vol 7, number 6 Xuan-Hui Guo, Edward J. Huff and David C. Schwartz. Sizing of Large DNA Molecules by Hook Formation in a Loose Matrix. Journal of Biomolecular Structure & Dynamics, Volume 11, Issue 1 (1993) pp 1-10 From mk@nwu.edu Mon Oct 18 06:03:27 1993 Received: from merle.acns.nwu.edu by nx1.soils.umn.edu (5.65c) id AA10569; Mon, 18 Oct 1993 12:02:02 -0500 Return-Path: Received: from aragorn27.acns.nwu.edu by merle.acns.nwu.edu with SMTP (1.36.108.4.1.1/16.2) id AA10831; Mon, 18 Oct 93 12:03:29 -0500 Message-Id: <9310181703.AA10831@merle.acns.nwu.edu> X-Sender: mkhokha@merle.acns.nwu.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 18 Oct 1993 12:03:27 -0600 To: nih-image@soils.umn.edu From: mk@nwu.edu (M. Khokha) Subject: Data Output Hello Everyone, I was wondering if anyone had any thoughts about output of image files to generate figures to submit for application. I have created and analyzed a large number of image files and finally gotten some interesting results that I would now like to publish. I would also like to create a figure for the paper that shows some of the images that I generated. The problem is how do I turn my image file into something on paper that I can send to a journal? Unfortunately the journal that I would like to submit to does not accept electronic submissions. >From what I know there are a couple of ways to do this: A film recorder to create a slide and then turn that into a print. A dye sublimation printer Service bureaus that will accept electronic images and then make prints The problem with theses methods is that they require either multiple steps so that they take a long time making experimentation on what looks the best rather impossible or too expensive. I was wondering what other people do. Thanks, Mustafa Khokha (mk@nwu.edu) Markey Program in Developmental Biology T239 Northwestern University Medical School 303 E. Chicago Ave Tel:(312) 503-5232 Chicago IL 60611-3008 FAX:(312) 908-5253 U.S.A. From @CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu Mon Oct 18 07:09:00 1993 Received: from cunyvm.cuny.edu by nx1.soils.umn.edu (5.65c) id AA10708; Mon, 18 Oct 1993 12:12:48 -0500 Return-Path: <@CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu> Received: from darban.cc.usm.edu by CUNYVM.CUNY.EDU (IBM VM SMTP V2R2) with TCP; Mon, 18 Oct 93 13:13:19 EDT Received: by darban.cc.usm.edu (5.57/Ultrix3.0-C) id AA17487; Mon, 18 Oct 93 12:13:07 -0500 Date: Mon, 18 Oct 93 12:09 CDT From: GLEN SHEARER To: nih-image@soils.umn.edu Really-To: soillist Subject: sequence reader Message-Id: <931018.12104548.039175@USM.CP6> Has anyone tried to write a macro to read DNA sequence films with Image? It seems that the potential is there in terms of image manipulations. Glen Shearer From mvivino@helix.nih.gov Mon Oct 18 10:32:05 1993 Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c) id AA11472; Mon, 18 Oct 1993 13:30:35 -0500 Return-Path: Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0)) id AA07631; Mon, 18 Oct 93 14:32:05 -0400 Date: Mon, 18 Oct 93 14:32:05 -0400 Message-Id: <9310181832.AA07631@helix.nih.gov> X-Sender: mvivino@128.231.2.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mvivino@helix.nih.gov (Mark Vivino) Subject: Re: sequence reader >Has anyone tried to write a macro to read DNA sequence films >with Image? It seems that the potential is there in terms of >image manipulations. In case anyone has an interest in this, I was given a snipet of 'c' code several years ago that could read in raw data files from an Applied Biosystems sequencer. I never bothered to try and port it to NIH Image, but if someone has the kind of signal processing interest let me know and I'll see if I can dig it out. Warning though, I doubt it is as nicely flowing and elegantly programmed as wayne rasband's code. Mark Vivino NIH/DCRT mvivino@helix.nih.gov From djm@cidmv1.wustl.edu Mon Oct 18 09:10:47 1993 Received: from wugate.wustl.edu by nx1.soils.umn.edu (5.65c) id AA11940; Mon, 18 Oct 1993 14:11:27 -0500 Return-Path: Received: by wugate.wustl.edu (5.67a+/WUSTL-0.3) with DECnet id AA16153; Mon, 18 Oct 1993 14:10:48 -0500 Date: Mon, 18 Oct 1993 14:10:47 -0500 Message-Id: <199310181910.AA16153@wugate.wustl.edu> From: djm@cidmv1.wustl.edu (D.J. Meyer) To: "nih-image@soils.umn.edu"@WUGATE.wustl.edu Subject: Removing Blur though Deconvolution Hi, can anyone give me an explanation of how this works? thank dj meyer From jcrum%sunstroke@sdsu.edu Mon Oct 18 05:20:14 1993 Received: from sdsu.edu by nx1.soils.umn.edu (5.65c) id AA12077; Mon, 18 Oct 1993 14:21:38 -0500 Return-Path: Received: from sunstroke.sdsu.edu by sdsu.edu; id AA15810 sendmail 5.64/SDSU-GW-1.11 via SMTP Mon, 18 Oct 93 12:20:16 -0700 Received: from .sdsu.edu (lif_sci_n4-mac5.sdsu.edu) by sunstroke.SDSU.EDU (4.1/SDSU-GENERIC.3) id AA07528; Mon, 18 Oct 93 12:20:14 PDT Date: Mon, 18 Oct 93 12:20:14 PDT From: jcrum%sunstroke@sdsu.edu (John Crum) Message-Id: <9310181920.AA07528@sunstroke.SDSU.EDU> Subject: Re Data Output To: nih-image@soils.umn.edu X-Mailer: SDSUMail [Version 1.9 beta] X-Type: TEXT Mustafa Khokha: If you don't have the hardware (or time), go with the service bureau. The one we use here in San Diego uses a Linotronic L300 to output to film or paper. The costs are farily reasonable. For an 8.5 X 11 on RC paper the costs is $6.00 for 1200dpi and $7.50 for 2400dpi. Multiple copies of the same file run at the same time are 1/2 price. We have printed grayscale images from SuperPaint at both the medium and high resolution and saw little difference- 1200dpi is probably the limit of resolution for SuperPaint. If you use them, you must ask them what file formats and what media formats they support. If your files are big (larger than 1.4MB), use a SyQuest drive, as most of the service bureaus have them. Also, many service bureaus also like PostScript files, instead of applications files because they can print a PS file from any application whereas they have to have the application to print a file of that applications format. For instance, they probably don't have NIH Image, so you would have to save the file in another application (that they have) or convert your files to PostScript. They might also take PICT or TIFF files, too, but check with them first. If you have any more question, please feel free to write. John Crum San Diego State University From bbug1@cc.swarthmore.edu Mon Oct 18 12:06:35 1993 Received: from oak.cc.swarthmore.edu by nx1.soils.umn.edu (5.65c) id AA12550; Mon, 18 Oct 1993 15:05:15 -0500 Return-Path: Received: from [130.58.70.120] (mac05.martin2.swarthmore.edu [130.58.70.120]) by oak.cc.swarthmore.edu (8.6.2/8.6.2) with SMTP id QAA10064 for ; Mon, 18 Oct 1993 16:06:35 -0400 Date: Mon, 18 Oct 1993 16:06:35 -0400 Message-Id: <199310182006.QAA10064@oak.cc.swarthmore.edu> X-Mailer: Eudora/Swarthmore 1.3b116 To: nih-image@soils.umn.edu From: Bill Bug Subject: Re: Removing Blur though Deconvolution >Hi, >can anyone give me an explanation of how this works? >thank >dj meyer Two references that cleared the haze for me: 1) Castelman, K.R.(1979) Digital image processing. Prentice-Hall,Inc., Englewood Cliffs, NY, 429pp. * THE general reference on digital imaging techniques; most of the subsequent work in this field has derived from algorithms outlined in this book 2) Monck, J.R., Oberhauser,A.F., Keating, T.J., Fernandez, J.M. (1992) Thin-section ratiometric Ca+2 images obtained by optical sectioning of fura-2 loaded mast cells * This is an extremely well illustrated example of some of the less computationally-intense methods for applying digital deconvolution. They compare and evaluate several methods, testing them on model and real data sets. Good luck!! Cheers, Bill Bug ************************* * Bill Bug * * Dept. of Biology * * Swarthmore College * ************************* From John_Mansfield@mse.engin.umich.edu Mon Oct 18 16:11:54 1993 Received: from mse.engin.umich.edu by nx1.soils.umn.edu (5.65c) id AA13205; Mon, 18 Oct 1993 16:11:54 -0500 Return-Path: Message-Id: <199310182111.AA13205@nx1.soils.umn.edu> Date: 18 Oct 1993 17:06:32 U From: "John Mansfield" Subject: Re: Data Output To: nih-image@soils.umn.edu Reply to: RE>Data Output The Kodak Dye Sublimation Printer Model ColorEase PS 300 should do the job for you very nicely, Around $7000 university price. From V112LNKD@ubvms.cc.buffalo.edu Mon Oct 18 15:27:15 1993 Received: from ubvmsc.cc.buffalo.edu by nx1.soils.umn.edu (5.65c) id AA14553; Mon, 18 Oct 1993 18:53:53 -0500 Return-Path: Received: from ubvms.cc.buffalo.edu by ubvms.cc.buffalo.edu (PMDF V4.2-13 #3449) id <01H49PA6Q1CK8WXM1U@ubvms.cc.buffalo.edu>; Mon, 18 Oct 1993 19:27:15 EDT Date: Mon, 18 Oct 1993 19:27:15 -0400 (EDT) From: V112LNKD@ubvms.cc.buffalo.edu Subject: scale to fit window To: nih-image@soils.umn.edu Message-Id: <01H49PA6Q1CM8WXM1U@ubvms.cc.buffalo.edu> Organization: University at Buffalo X-Vms-To: IN%"nih-image@soils.umn.edu" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT hi, I'm trying to use the scale to fit window function to resize two electrophor etic gels (so that they may appear the same size, for analysis)...So, i open the two images and use the scaling function to get both the same size. But, how ca n you keep the new scale of the image...thanks for any advice.....Mark From @CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu Tue Oct 19 03:06:00 1993 Received: from cunyvm.cuny.edu by nx1.soils.umn.edu (5.65c) id AA20511; Tue, 19 Oct 1993 08:12:05 -0500 Return-Path: <@CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu> Received: from darban.cc.usm.edu by CUNYVM.CUNY.EDU (IBM VM SMTP V2R2) with TCP; Tue, 19 Oct 93 09:12:36 EDT Received: by darban.cc.usm.edu (5.57/Ultrix3.0-C) id AA20241; Tue, 19 Oct 93 08:12:26 -0500 Date: Tue, 19 Oct 93 08:06 CDT From: GLEN SHEARER To: nih-image@soils.umn.edu Really-To: soillist Subject: VideoSpigot Message-Id: <931019.08085112.040077@USM.CP6> Has anyone tried the video capture card called VideoSpigot. I hear that the Mac LC card is only about $300. If this would work well we could probably afford a board and camera. Thanks for any info. Glen Shearer From wayne@helix.nih.gov Tue Oct 19 09:11:09 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA21127; Tue, 19 Oct 1993 09:12:51 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA28087; Tue, 19 Oct 93 09:32:41 -0400 Message-Id: <9310191332.AA28087@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 19 Oct 1993 09:11:09 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: scale to fit window >hi, I'm trying to use the scale to fit window function to resize two >electrophor >etic gels (so that they may appear the same size, for analysis)...So, i open >the > two images and use the scaling function to get both the same size. But, how >ca >n you keep the new scale of the image...thanks for any advice.....Mark The Scale and Rotate command would probably work better in this situation. You should avoid the "Nearest Neighbor" option when reducing images since it is known to alter the mean gray value. --wayne From wayne@helix.nih.gov Tue Oct 19 09:36:14 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA21429; Tue, 19 Oct 1993 09:37:37 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA28673; Tue, 19 Oct 93 09:57:46 -0400 Message-Id: <9310191357.AA28673@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 19 Oct 1993 09:36:14 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: VideoSpigot >Has anyone tried the video capture card called VideoSpigot. I hear >that the Mac LC card is only about $300. If this would work well >we could probably afford a board and camera. Thanks for any info. I tried a Video Spigot card. The quality of captured 640x480 grayscale images is greatly inferior to what you get with either the DT QuickCapture or the Scion LG-3. The Video Spigot was designed for making 160x120 color QuickTime movies, and should work well for that purpose. NIH Image does not directly support the Video Spigot, but you can use the conversion utility in the programs directory on zippy.nimh.nih.gov to convert QuickTime movies into the PICS format that NIH can read. --wayne From ruzin@nature.berkeley.edu Mon Oct 18 23:55:34 1993 Received: from nak.Berkeley.EDU by nx1.soils.umn.edu (5.65c) id AA21617; Tue, 19 Oct 1993 09:53:18 -0500 Return-Path: Received: from nature.Berkeley.EDU by nak.berkeley.edu (5.67/1.40) id AA20499; Tue, 19 Oct 93 07:54:42 -0700 Received: from [128.32.128.177] (kos5mac22.Berkeley.EDU) by nature.berkeley.edu.cnr-net (4.1/SMI-4.1) id AA14233; Tue, 19 Oct 93 07:57:44 PDT Message-Id: <9310191457.AA14233@nature.berkeley.edu.cnr-net> Date: Tue, 19 Oct 1993 07:55:34 -0800 To: nih-image@soils.umn.edu From: ruzin@nature.berkeley.edu (Steven Ruzin) Subject: Re: wand tool area >Just a thank-you note for responding to all these first timer questions. We >really like the package. Is there anyone in the San >Francisco/Berkeley/Lawrence Laboratory area who would mind demo'ing his/her >NIH image setup? > > Thanks again in advance I don't know if anyone has responded (I've been out f town) but give me a call/msg and we can set something up. I have Macs, framers, NIH Image, a confocal scope... you might like to see. Steve... ______________________________________________ | Steven Ruzin | | NSF Center of Plant Developmental Biology | | Dept Plant Biology | | Univ California Berkeley | | e-mail: ruzin@nature.berkeley.edu | | phone: 510-642-6602 | |_____________________________________________| From @CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu Tue Oct 19 05:05:00 1993 Received: from cunyvm.cuny.edu by nx1.soils.umn.edu (5.65c) id AA21869; Tue, 19 Oct 1993 10:10:41 -0500 Return-Path: <@CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu> Received: from darban.cc.usm.edu by CUNYVM.CUNY.EDU (IBM VM SMTP V2R2) with TCP; Tue, 19 Oct 93 11:11:11 EDT Received: by darban.cc.usm.edu (5.57/Ultrix3.0-C) id AA20597; Tue, 19 Oct 93 10:11:02 -0500 Date: Tue, 19 Oct 93 10:05 CDT From: GLEN SHEARER To: nih-image@soils.umn.edu Really-To: nih-image@soils.umn.edu Subject: Re: sequence reader References: Re: sequence reader Message-Id: <931019.10080148.040376@USM.CP6> In-Reply-To: <9310181832.AA07631@helix.nih.gov> Thanks for the info Mark. What I had in mind was to scan an autoradiogram of a sequencing gel with a flat-bed or hand scanner and then use Image on the TIFF file to have the program read the GATC sequence by doing some type of density plot of each lane. If I was about 5X more clever and had 10X more time, I might give it a try myself. Glen Glen Shearer From sarmienu@rnisd0.DNET.roche.com Tue Oct 19 07:21:50 1993 Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c) id AA22003; Tue, 19 Oct 1993 10:20:28 -0500 Return-Path: Received: by gatekeeper.roche.com (5.65/fma-120691); id AA18574; Tue, 19 Oct 93 11:21:50 -0400 Received: by mailgate.roche.com (5.65/fma-120691); id AA02122; Tue, 19 Oct 93 11:19:21 -0400 From: sarmienu@rnisd0.DNET.roche.com Message-Id: <9310191519.AA02122@mailgate.roche.com> Received: from rnisd0.enet; by inet.enet; Tue, 19 Oct 93 11:21:50 EDT Date: Tue, 19 Oct 93 11:21:50 EDT To: nih-image@soils.umn.edu Apparently-To: nih-image@soils.umn.edu Subject: RE:Data Output This is the second time I post this message, since I did not got it back as a posted message from the list. It seems to have failed to get through. I have just recently finished shopping for a dye sublimation printer for output of images obtained with NIH Image and the Scion card. Images are publication quality. Often I do further processing in Photoshop, like adding arrows, or magnification bars. Perhaps Wayne could comment on the use of Photoshop to reintegrate RGB images from Image into a 24 bit color obtained from NIH Image. You can also make black and white pictures that can be printed on a continuous tone in the dye sublimation printer. If you have Photoshop, a color monitor, and Quark Express, you could reduce* a 640 x 480 image to 8.3 cm wide in Photoshop, mounted in QuarkXPress with other similar images and then send the compressed files to a mail printer service. Although they cannot guarantee that the printout will look the way you want, I think that your color images in Photoshop are pretty good predictors of what the image will look like. *When you reduce the image in Photoshop, your 72 dpi image becomes close to 200 dpi which in a continuous tone hard copy looks crisp and clear, without jaggies. Juan I. Sarmiento Department of Toxicology and Pathology Hoffmann-La Roche, INC. 340 Kingsland street Nutley, NJ 07110 (201) 235 3907 Sarmienu@RNISD0.DNET.ROCHE.COM From sarmienu@rnisd0.DNET.roche.com Tue Oct 19 07:26:03 1993 Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c) id AA22016; Tue, 19 Oct 1993 10:24:36 -0500 Return-Path: Received: by gatekeeper.roche.com (5.65/fma-120691); id AA18591; Tue, 19 Oct 93 11:26:04 -0400 Received: by mailgate.roche.com (5.65/fma-120691); id AA02168; Tue, 19 Oct 93 11:22:07 -0400 From: sarmienu@rnisd0.DNET.roche.com Message-Id: <9310191522.AA02168@mailgate.roche.com> Received: from rnisd0.enet; by inet.enet; Tue, 19 Oct 93 11:26:03 EDT Date: Tue, 19 Oct 93 11:26:03 EDT To: nih-image@soils.umn.edu Apparently-To: nih-image@soils.umn.edu Subject: sequence reader This is the second time I post this message, since I did not got it back as a posted message from the list. It seems to have failed to get through. >Has anyone tried to write a macro to read DNA sequence films >with Image? It seems that the potential is there in terms of >image manipulations. > >Glen Shearer > You mean using a flat bed scanner to capture the image of the gel radiograph? 3 years ago I tried to use ScanAnalysis to do this with my wife's (Dr. Ulla Sarmiento) sequencing radiographs using the 4 bit Apple Scanner. It just could not be done, even at 300 dpi. Perhaps better scanners and better software would allow that now. My approach was to locate the peaks of each band in each lane. according to the distance migrated data could be sorted. The problem was that at 1 end the bands were too close together, and at the other they curved to one side, and the program required a rectangular ROI. Perhaps with NIH Image you can get around that by using the polygonal selection tool. With high resolution scanners (e.g. 600-1200 dpi), you might get around the problem of cramped bands. Back in those days the troubles were so many that there was no time savings using this system in comparison to manual and visual reading. Juan I. Sarmiento Department of Toxicology and Pathology Hoffmann-La Roche, INC. 340 Kingsland street Nutley, NJ 07110 (201) 235 3907 Sarmienu@RNISD0.DNET.ROCHE.COM P.S. The sorting of band distances could be easily done in Microsoft Excel. A macro could probably be written for that! From tg3@u.washington.edu Tue Oct 19 01:02:49 1993 Received: from stein1.u.washington.edu (stein.u.washington.edu) by nx1.soils.umn.edu (5.65c) id AA22332; Tue, 19 Oct 1993 11:01:19 -0500 Return-Path: Received: from [128.95.15.54] by stein1.u.washington.edu (5.65/UW-NDC Revision: 2.29 ) id AA14334; Tue, 19 Oct 93 09:02:49 -0700 Date: Tue, 19 Oct 93 09:02:49 -0800 From: Thurman Gillespy III To: nih-image@soils.umn.edu Subject: Re: Data Output Message-Id: In-Reply-To: Your message <9310181703.AA10831@merle.acns.nwu.edu> of Mon, 18 Oct 1993 12:21:44 -0500 Content-Type: TEXT/plain; charset=US-ASCII > Hello Everyone, > > I was wondering if anyone had any thoughts about output > of image files to generate figures to submit for > application. I have created and analyzed a ... I regularly submit dye sub prints for publication, using Image as the image display/image processing software. The results are excellent. Usually, I print the output as a postscript file, which I submit to the medical photography folks. Its expensive, ~$10 print, but by far the best way to go that I've encountered. Thurman Gillespy III, MD tg3@u.washington.edu Department of Radiology University of Washington From wsryu@phoenix.Princeton.EDU Tue Oct 19 07:56:43 1993 Received: from Princeton.EDU by nx1.soils.umn.edu (5.65c) id AA22452; Tue, 19 Oct 1993 11:13:55 -0500 Return-Path: Received: from ponyexpress.Princeton.EDU by Princeton.EDU (5.65b/2.99/princeton) id AA27639; Tue, 19 Oct 93 11:56:45 -0400 Received: from phoenix.Princeton.EDU by ponyexpress.princeton.edu (5.65c/1.113/newPE) id AA13649; Tue, 19 Oct 1993 11:56:44 -0400 From: William Sungho Ryu Received: by phoenix.Princeton.EDU (5.65c/Phoenix_Cluster_Client) id AA22471; Tue, 19 Oct 1993 11:56:43 -0400 Date: Tue, 19 Oct 1993 11:56:43 -0400 Message-Id: <199310191556.AA22471@phoenix.Princeton.EDU> To: nih-image@soils.umn.edu Subject: 660av Screen Capture. I am thinking about purchasing a 660av to use NIH Image and was wondering about the quality of screen capture. What file type is it? What is the frame rate for a 640x400 capture? Is the 660av a poorman's viable alternative to a frame grabber card? William Ryu Princeton University From CHARLEST@macc.wisc.edu Tue Oct 19 07:00:00 1993 Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c) id AA22777; Tue, 19 Oct 1993 11:59:08 -0500 Return-Path: Received: from VMSmail by vms2.macc.wisc.edu; Tue, 19 Oct 93 12:00 CDT Message-Id: <23101912001195@vms2.macc.wisc.edu> Date: Tue, 19 Oct 93 12:00 CDT From: Charles Thomas Subject: Re: wand tool area To: nih-image@soils.umn.edu X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST Unless you've calibrated your units differently, the area will be in square pixels. From sarmienu@rnisd0.DNET.roche.com Tue Oct 19 09:42:09 1993 Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c) id AA23092; Tue, 19 Oct 1993 12:40:44 -0500 Return-Path: Received: by gatekeeper.roche.com (5.65/fma-120691); id AA19424; Tue, 19 Oct 93 13:42:10 -0400 Received: by mailgate.roche.com (5.65/fma-120691); id AA03253; Tue, 19 Oct 93 13:41:05 -0400 From: sarmienu@rnisd0.DNET.roche.com Message-Id: <9310191741.AA03253@mailgate.roche.com> Received: from rnisd0.enet; by inet.enet; Tue, 19 Oct 93 13:42:09 EDT Date: Tue, 19 Oct 93 13:42:09 EDT To: nih-image@soils.umn.edu Apparently-To: nih-image@soils.umn.edu Subject: More on sequencing gels Actually, I don't know if this will work with your system. The assumption is that each band has a different xy center in the image: 1. Set the x-y center in the options dialogue box under the analyze menu. 2. Select the area of interest with the polygonal tool. Make sure you select the A, C, G, and T lanes. 3. Threshold the image to select bands by their grey level. 4. Select Analyze particles from the analyze menu. 5. Show results and option copy. 6. Go to EXCEL and paste. 7. Sort the table by the X values. 8. Create a new column and enter the appropriate base (ACGT) according to the approximate vertical center of the location of the corresponding lane. 9. Sort the table by the y values. Your sequence should be organized properly. Play with it until you get the desired results. You may be able to create macros in NIH-Image and EXCEL to accomplish this. Juan I. Sarmiento Department of Toxicology and Pathology Hoffmann-La Roche, INC. 340 Kingsland street Nutley, NJ 07110 (201) 235 3907 Sarmienu@RNISD0.DNET.ROCHE.COM From bbug1@cc.swarthmore.edu Tue Oct 19 10:39:00 1993 Received: from oak.cc.swarthmore.edu by nx1.soils.umn.edu (5.65c) id AA23473; Tue, 19 Oct 1993 13:37:34 -0500 Return-Path: Received: from [130.58.70.116] (mac01.martin2.swarthmore.edu [130.58.70.116]) by oak.cc.swarthmore.edu (8.6.2/8.6.2) with SMTP id OAA15177 for ; Tue, 19 Oct 1993 14:39:00 -0400 Date: Tue, 19 Oct 1993 14:39:00 -0400 Message-Id: <199310191839.OAA15177@oak.cc.swarthmore.edu> X-Mailer: Eudora/Swarthmore 1.3b116 To: nih-image@soils.umn.edu From: Bill Bug Subject: Re: Removing Blur though Deconvolution Hello All, Here's a correction to my reference list on deconvolution techniques as applied in visible light microscopy. I've also added a more complete set of individual examples of digital reconstruction in biological microscopy. I'm not an authority in this field, but these are the works that helped to inform me on the topic. 1) Castelman, K.R.(1979) Digital image processing. Prentice-Hall,Inc., Englewood Cliffs, NY, 429pp. * THE general reference on digital imaging techniques; most of the subsequent work in this field has derived from algorithms outlined in this book 2) Monck, J.R., Oberhauser,A.F., Keating, T.J., Fernandez, J.M. (1992) Thin-section ratiometric Ca+2 images obtained by optical sectioning of fura-2 loaded mast cells. J. Cell Biology, v116:3, p745-759. * This is an extremely well illustrated example of some of the less computationally-intense methods for applying digital deconvolution. They compare and evaluate the "nearest-neighbor" and "no-neighbor" methods, testing them on model and real data sets. 3) Waybill, M.M., Yelamarty, R.V., Zhang,Y., Scaduto, R.C.,Jr., LaNoue, K.F., Hsu,C.-J., Smith,B.C., Tillotson,D.L., Yu,F.T.S., and Cheung,J.Y. (1991) Nuclear calcium gradients in cultured rat hepatocytes. Am. J. Physiol. v261(Endo. Metab. 24), pE49-E57. * They evaluate the effectiveness of the "nearest-neighbor" method for improving the spatial resolution and quantitative accuracy of fura-2 images in isolated hepatocytes and on model data. 4) Agard, D.A., and Sedat, J.W. (1983) Three-dimensional architecture of a polytene nucleus. Nature, v302, p676-681. 5) Carrington, W.A., Fogarty, K.E., and Fay, F.S. (1990) 3D fluorescence imaging of single cells using image restoration. In: Nonivasive techniques in cell biology, J.K. Foskett and S. Grinstein, eds., (Wiley-Liss, New York), p53-72. * 4 & 5 present methods for applying more extensive, computationally- demanding deconvolution techniques that utilize all the photon data from a axial stack >20 images. Both papers cite prior works which give a more detailed derivation of the mathematical techniques involved. Each set of authors also has a chapter in Handbook of Biological Confocal Microscopy (J.B. Pawley,ed., Plenum Press, New York, 1990) which describes their unique approach to digital reconstruction in fluorescent microscopy I hope these references are of some use to people. I came to them through a rather circuitous route but have found them all to be invaluable to the digital fluorescent imaging we are doing in the lab. Good luck!! Cheers, Bill Bug ************************* * Bill Bug * * Dept. of Biology * * Swarthmore College * ************************* From wayne@helix.nih.gov Tue Oct 19 13:46:51 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA23555; Tue, 19 Oct 1993 13:48:15 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA02758; Tue, 19 Oct 93 14:08:25 -0400 Message-Id: <9310191808.AA02758@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 19 Oct 1993 13:46:51 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: 660av Screen Capture. >I am thinking about purchasing a 660av to use NIH Image and was wondering >about the quality of screen capture. > >What file type is it? The image capture application that comes with the AV Macs creates QuickTime movies. >What is the frame rate for a 640x400 capture? It is probably no more than 5-10 frames per second and would depend if you are capturing to RAM or disk. >Is the 660av a poorman's viable alternative to a frame grabber card? Like the Video Spigot, it's a good if you wan't to hook up a camcorder to your Mac and make a color QuickTime movie. (The AV Macs use the same chip set as the Video Spigot.) You can convert the QuickTime movie into PICS format to get it into NIH Image. --wayne From kartenh@sdsc.edu Tue Oct 19 19:12:37 1993 Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA23739; Tue, 19 Oct 1993 14:11:20 -0500 Return-Path: Message-Id: <199310191911.AA23739@nx1.soils.umn.edu> Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET; Tue, 19 Oct 93 19:12:37 GMT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: kartenh@Sdsc.Edu Subject: Re: 660av Screen Capture. Date: Tue, 19 Oct 93 19:12:37 GMT >>I am thinking about purchasing a 660av to use NIH Image and was wondering >>about the quality of screen capture. >> >>Is the 660av a poorman's viable alternative to a frame grabber card? > >Like the Video Spigot, it's a good if you wan't to hook up a camcorder to >your Mac and make a color QuickTime movie. (The AV Macs use the same chip >set as the Video Spigot.) You can convert the QuickTime movie into PICS >format to get it into NIH Image. > >--wayne Does anyone know the actual performance specs of the 660av/840av on a monochrome image from a decent video camera? Linear resolution, contrast range, etc. Harvey Karten Harvey J. Karten, M.D. Dept. of Neurosciences Univ.California San Diego La Jolla, CA 92093-0608 EMail: Kartenh@sdsc.edu Phone: (619)-534-4938 FAX: (619)-534-6602 From keller@micros.mrd.bldrdoc.gov Tue Oct 19 09:54:21 1993 Received: from central.bldrdoc.gov by nx1.soils.umn.edu (5.65c) id AA24750; Tue, 19 Oct 1993 16:53:11 -0500 Return-Path: Received: from pascal.mrd.bldrdoc.gov by central.bldrdoc.gov (4.1/SMI-DDN) id AA23311; Tue, 19 Oct 93 15:54:35 MDT Received: from micros.mrd.bldrdoc.gov by pascal.mrd.bldrdoc.gov (4.1/SMI-3.2) id AA00422; Tue, 19 Oct 93 15:55:09 MDT Message-Id: <9310192155.AA00422@pascal.mrd.bldrdoc.gov> Date: Tue, 19 Oct 93 15:54:21 MDT From: Bob Keller Subject: IPLab Spectrum To: nih-image@soils.umn.edu X-Mailer: LeeMail 1.2.4 Has anyone tried using IPLab Spectrum, by Signal Analytics Corp? If so, how does it compare with NIH Image? One difference is that the former can work with greater than 256 grey levels, but otherwise it appears quite similar, based on the demo version. Bob Keller NIST Boulder From glenmac@u.washington.edu Tue Oct 19 08:44:15 1993 Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c) id AA25122; Tue, 19 Oct 1993 17:54:25 -0500 Return-Path: Received: by carson.u.washington.edu (5.65/UW-NDC Revision: 2.29 ) id AA21169; Tue, 19 Oct 93 15:55:46 -0700 X-Sender: glenmac@carson.u.washington.edu Date: Tue, 19 Oct 1993 15:44:15 -0700 (PDT) From: Glen Macdonald Subject: Re: Data Output To: nih-image@soils.umn.edu Cc: Multiple recipients of list In-Reply-To: <9310181703.AA10831@merle.acns.nwu.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=us-ascii i've used the L300 Linotronic with 640x480 SEM images. They(the campus print shop) will take PICT or TIFF, but only if created with Photoshop. The grey scale range and brightness from an Image file probably needs to be adjusted with photoshop, anyway. 1200 dpi was cheaper than 2400 and gave a comparable image. Printing at half or quarter size greatly improves the resolution and saves money, whereas a full size image suffered from the jaggies. From scudder@cpac.washington.edu Tue Oct 19 18:46:12 1993 Received: from bailey.cpac.washington.edu by nx1.soils.umn.edu (5.65c) id AA28031; Wed, 20 Oct 1993 03:50:10 -0500 Return-Path: Received: by bailey.cpac.washington.edu (5.65/UW-NDC Revision: 2.4 ) id AA01821; Wed, 20 Oct 93 01:50:46 -0700 Date: Wed, 20 Oct 1993 01:46:12 -0700 (PDT) From: Kurt Scudder Subject: Re: VideoSpigot To: nih-image@soils.umn.edu In-Reply-To: <9310191357.AA28673@zippy.nimh.nih.gov> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 19 Oct 1993, Wayne Rasband wrote: > >Has anyone tried the video capture card called VideoSpigot. I hear > >that the Mac LC card is only about $300. If this would work well > >we could probably afford a board and camera. Thanks for any info. > > I tried a Video Spigot card. The quality of captured 640x480 grayscale > images is greatly inferior to what you get with either the DT QuickCapture > or the Scion LG-3. The Video Spigot was designed for making 160x120 color > QuickTime movies, and should work well for that purpose. NIH Image does not > directly support the Video Spigot, but you can use the conversion utility > in the programs directory on zippy.nimh.nih.gov to convert QuickTime movies > into the PICS format that NIH can read. > > --wayne > > This is the first I have been aware that QuickTime movies could be brought into NIH-Image. I don't have any plans to do this, but it raises a simple question: Does Image automatically make 8-bit data out of what I assume is higher-than-8-bit (i.e., color) images? If so, is the LUT the same for every image in the movie? Kurt Scudder Dept. of Chemistry University of Washington scudder@u.washington.edu From Carl.Gustafson@cbis.ece.drexel.edu Wed Oct 20 04:39:22 1993 Received: from cbis.ece.drexel.edu by nx1.soils.umn.edu (5.65c) id AA29078; Wed, 20 Oct 1993 07:49:40 -0500 Return-Path: Received: from n1-5-228-ece-ipc.ece.drexel.edu by cbis.ECE.Drexel.EDU (5.67/1.34) id AA14963; Wed, 20 Oct 93 08:39:22 EDT Date: Wed, 20 Oct 93 08:39:22 EDT Message-Id: <9310201239.AA14963@cbis.ECE.Drexel.EDU> To: nih-image@soils.umn.edu From: Carl.Gustafson@cbis.ece.drexel.edu (Carl Gustafson) X-Sender: cgustafs@CoE.Drexel.EDU Subject: Re: Too many constants in enumerated type > >There seems to be a limit of 256 or so constants in enumerated types. I ran >into this problem when I tried to add a new command to the macro language >today. The short term work-around I used was to recycle some obsolete >commands. The long range solution will be to break CommandType into two >parts: commands and functions.There are 10 obsolete commands starting at >symbol table entry 165(SetArea, SetMean, etc.) and 0ne(SetMinMax) at 185. > >--wayne The really good solution would be to dump Think Pascal and use something like MPW. (Ducking and running) Carl Gustafson =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Your message here Philadelphia, Pennsylvania | I only speak for myself =============================================================================== From wayne@helix.nih.gov Wed Oct 20 08:29:02 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA29449; Wed, 20 Oct 1993 08:30:29 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA08900; Wed, 20 Oct 93 08:50:40 -0400 Message-Id: <9310201250.AA08900@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 20 Oct 1993 08:29:02 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: VideoSpigot This is the first I have been aware that QuickTime movies could be >brought into NIH-Image. I don't have any plans to do this, but it raises a >simple question: Does Image automatically make 8-bit data out of what I >assume is higher-than-8-bit (i.e., color) images? Yes. You convert the QuickTime movie to PICS using the QuickTime<->PICS utility on zippy.nimh.nih.gov and then open the PICS file as an Image stack. >If so, is the LUT the same for every image in the movie? All slices in the stack use the same LUT since there is only one LUT for the entire stack. --wayne From Scott.Wurcer@analog.com Wed Oct 20 05:06:06 1993 Received: from nic.near.net by nx1.soils.umn.edu (5.65c) id AA29486; Wed, 20 Oct 1993 08:35:23 -0500 Return-Path: Received: from [137.71.23.11] by nic.near.net id aa04969; 20 Oct 93 9:06 EDT Received: from nwd2sun1.analog.com ([137.71.22.41]) by adi.analog.com Received: from titania.adsdesign.analog.com by nwd2sun1.analog.com (4.1/SMI-4.1) Message-Id: <9310201304.AA25649@nwd2sun1.analog.com> Received: from hermia.adsdesign.analog.com by titania.adsdesign.analog.com Date: Wed, 20 Oct 93 09:06:06 EDT From: Scott Wurcer To: nih-image@soils.umn.edu Subject: Re: Data Output I've also had great success using the error-diffusion halftones along with bicubic spline scaling from Photoshop to get rid of jaggies in blown-up images. Even 128x128 images can look pretty good at 4x. From @ibm.gwdg.de:rfritsc@gwdgv1.dnet.gwdg.de Wed Oct 20 15:34:58 1993 Received: from ibm.gwdg.de by nx1.soils.umn.edu (5.65c) id AA29587; Wed, 20 Oct 1993 08:46:13 -0500 Return-Path: <@ibm.gwdg.de:rfritsc@gwdgv1.dnet.gwdg.de> Message-Id: <199310201346.AA29587@nx1.soils.umn.edu> Received: from IBM.GWDG.DE by ibm.gwdg.de (IBM VM SMTP R1.2.2MX) with BSMTP id 6162; Wed, 20 Oct 93 14:34:59 MEZ Received: from dnet.gwdg.de by IBM.GWDG.DE (Mailer R2.08) with BSMTP id 3458; Wed, 20 Oct 93 14:34:58 MEZ Date: Wed, 20 Oct 1993 14:34:58 +0100 From: "GWDGV1::RFRITSC" To: nih-image@soils.umn.edu Subject: Kodak DCS200/Zeiss Microscope Dear Image users, We are trying to set up a system for routine documentation using the Kodak DCS 200 camera. I remember there has been some discussion on this list about using the Kodak DCS 200 camera for microscopy (via Photoshop plug in). Could anybody who is using such a setup specify how they connected the camera to a Zeiss Axiophot microscope? How to compensate for the small CCD chip? The chip has only 1/4 of the area of film and the adapters we got from Zeiss to connect the camera to the microscope is for film so we can capture only a small part of the slide we see in the eyepiece. Any suggestions? Thanks! Ruediger Fritsch Max-Planck-Institut f. biophysikalische Chemie Am Fassberg 37077 Goettingen Germany email rfritsc@gwdgv1.dnet.gwdg.de From waheeschen@dow.com Wed Oct 20 06:19:20 1993 Received: from na1.dow.com (na2.dow.com) by nx1.soils.umn.edu (5.65c) id AA29894; Wed, 20 Oct 1993 09:18:10 -0500 Return-Path: Received: by na1.dow.com id AA03041 (InterLock SMTP Gateway 1.1 for nih-image@soils.umn.edu); Wed, 20 Oct 1993 09:05:35 -0500 Message-Id: <199310201405.AA03041@na1.dow.com> Date: Wed, 20 Oct 1993 10:19:20 -0400 From: waheeschen@dow.com (Bill Heeschen (517)636-4005 PMRC/ASL) To: nih-image@soils.umn.edu Subject: Re: Too many constants in enumerated type / MPW vs Think X-Vms-To: SMTP%"nih-image@soils.umn.edu" Did I just hear Carl raise his hand to volunteer.... 8-) ========================== Bill Heeschen / Analytical Sciences - Materials Characterization 1897-D Building / The Dow Chemical Company Midland, MI 48667 U.S.A. phone: (517)636-4005 fax: (517)636-5453 Email: waheeschen@dow.com ========================== From mvivino@helix.nih.gov Wed Oct 20 06:22:41 1993 Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c) id AA29960; Wed, 20 Oct 1993 09:21:14 -0500 Return-Path: Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0)) id AA18813; Wed, 20 Oct 93 10:22:41 -0400 Date: Wed, 20 Oct 93 10:22:41 -0400 Message-Id: <9310201422.AA18813@helix.nih.gov> X-Sender: mvivino@128.231.2.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mvivino@helix.nih.gov (Mark Vivino) Subject: Re: IPLab Spectrum >Has anyone tried using IPLab Spectrum, by Signal Analytics Corp? If so, how >does it compare with NIH Image? One difference is that the former can work >with greater than 256 grey levels, but otherwise it appears quite similar, >based on the demo version. It does do a fourier transform and a few other things, although DIP Station does these as well or better and they are in your area. If I were adding 50 images together I might use IPLab. IPlab has a few hardware interfaces that Image does not have, such as for photometrics and others. It has some interesting color transforms too. Mark Vivino NIH/DCRT mvivino@helix.nih.gov From mschindl@Physik.TU-Muenchen.DE Wed Oct 20 16:38:21 1993 Received: from srv.cip.physik.tu-muenchen.de by nx1.soils.umn.edu (5.65c) id AA00248; Wed, 20 Oct 1993 09:36:56 -0500 Return-Path: Received: from ss3.cip.physik.tu-muenchen.de by srv.cip.physik.tu-muenchen.de with SMTP id AA14185 for (5.65c/IDA-1.4.4/bs-02); Wed, 20 Oct 1993 15:38:22 +0100 Received: by ss3.cip.physik.tu-muenchen.de (4.1/SMI-4.1) id AA06294; Wed, 20 Oct 93 15:38:21 +0100 Date: Wed, 20 Oct 93 15:38:21 +0100 From: Mathias.Schindl@Physik.TU-Muenchen.DE Message-Id: <9310201438.AA06294@ss3.cip.physik.tu-muenchen.de> To: nih-image@soils.umn.edu Subject: "Metaphor" Hi, has anybody out there ever heard of an image processing system / software called "Metaphor" or something like that? I would appreciate any little hint or information about it. Thank you. Mathias Schindl, Ph.D. student Physics Department, Biophysics Group E22 Technische Universitaet Muenchen, 85747 Garching, Germany From Carl.Gustafson@cbis.ece.drexel.edu Wed Oct 20 06:50:08 1993 Received: from cbis.ece.drexel.edu by nx1.soils.umn.edu (5.65c) id AA00326; Wed, 20 Oct 1993 09:48:43 -0500 Return-Path: Received: from n1-5-228-ece-ipc.ece.drexel.edu by cbis.ECE.Drexel.EDU (5.67/1.34) id AA17209; Wed, 20 Oct 93 10:50:08 EDT Date: Wed, 20 Oct 93 10:50:08 EDT Message-Id: <9310201450.AA17209@cbis.ECE.Drexel.EDU> To: nih-image@soils.umn.edu From: Carl.Gustafson@cbis.ece.drexel.edu (Carl Gustafson) X-Sender: cgustafs@CoE.Drexel.EDU Subject: Re: Too many constants in enumerated type / MPW vs Think >Did I just hear Carl raise his hand to volunteer.... 8-) > >========================== >Bill Heeschen / Analytical Sciences - Materials Characterization >1897-D Building / The Dow Chemical Company >Midland, MI 48667 U.S.A. >phone: (517)636-4005 fax: (517)636-5453 >Email: waheeschen@dow.com >========================== Carl was firmly sitting on his hands when he sent that message. Quite a trick to type that way What I may do is work on an MPW Tool to convert TP to MPW. This would be the more general approach, and doesn't require freezing versions. Probably won't be too difficult; problem is finding time. Carl Gustafson =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I only speak for myself =============================================================================== From djm@cidmv1.wustl.edu Wed Oct 20 04:55:55 1993 Received: from wugate.wustl.edu by nx1.soils.umn.edu (5.65c) id AA00417; Wed, 20 Oct 1993 10:00:12 -0500 Return-Path: Received: by wugate.wustl.edu (5.67a+/WUSTL-0.3) with DECnet id AA04558; Wed, 20 Oct 1993 09:55:55 -0500 Date: Wed, 20 Oct 1993 09:55:55 -0500 Message-Id: <199310201455.AA04558@wugate.wustl.edu> From: djm@cidmv1.wustl.edu (D.J. Meyer) To: nih@wugate.wustl.edu Subject: # of colors on monitor hi, i just put a 24bit video card in our IIfx for our imaging needs. now, nih gives me an error message that the monitor *must* be configured for 256 colors or gray scales. the documentation says it will handle 24 bit images. but not display them? is there a way around this? 8 bit display is not acceptable for what we need to do with our images. thanks dj meyer djm@cidmv1.wustl.edu From bbug1@cc.swarthmore.edu Wed Oct 20 07:26:33 1993 Received: from oak.cc.swarthmore.edu by nx1.soils.umn.edu (5.65c) id AA00766; Wed, 20 Oct 1993 10:25:09 -0500 Return-Path: Received: from [130.58.70.116] (mac01.martin2.swarthmore.edu [130.58.70.116]) by oak.cc.swarthmore.edu (8.6.2/8.6.2) with SMTP id LAA16264 for ; Wed, 20 Oct 1993 11:26:33 -0400 Date: Wed, 20 Oct 1993 11:26:33 -0400 Message-Id: <199310201526.LAA16264@oak.cc.swarthmore.edu> X-Mailer: Eudora/Swarthmore 1.3b116 To: nih-image@soils.umn.edu From: Bill Bug Subject: Re: Kodak DCS200/Zeiss Microscope >The chip(Kodak DCS 200 camera) has only 1/4 of the area of film and the >adapters we >got from Zeiss to connect the camera to the microscope is for >film so we can capture >only a small part of the slide we see in the eyepiece. >Any suggestions? >Thanks! > >Ruediger Fritsch >Max-Planck-Institut f. biophysikalische Chemie >Am Fassberg >37077 Goettingen >Germany >email rfritsc@gwdgv1.dnet.gwdg.de Herr Fritsch, We have had been able to get all the optical coupling components we need to interface our cooled CCD camera (Photometrics, LTD) with a Zeiss Axioskop from Diagnostic Instruments (6540 Burroughs St., Sterling Heights, MI, 48314, USA - phone:(313) 731-6000; fax: (313) 731-6469). Speak with Patrick Merlo at DI. He's not only knowledgable of the phyisics involved in such optical devices, he also has many years experience applying that knowledge to the specifications of various microscopes. He should be able to give you all the pros and cons of using a low power elements (< 1x) to bring more of the field on to the CCD chip. Many people actually have a higher power camera coupling (2.5x) in order to exclude the less well corrected, outer portion of the objective field from the imaging device. Good luck! Cheers, Bill Bug ************************* * Bill Bug * * Dept. of Biology * * Swarthmore College * ************************* From kartenh@Sdsc.Edu Wed Oct 20 15:47:45 1993 Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA00963; Wed, 20 Oct 1993 10:46:23 -0500 Return-Path: Date: Wed, 20 Oct 93 15:47:45 GMT From: kartenh@Sdsc.Edu (Harvey Karten) Message-Id: <931020154745.204074d9@m5.sdsc.edu> Subject: IPL and AxoVideo To: nih-image@soils.umn.edu X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu" Both IPL and Axovideo (Axon Instruments) include software for Calcium ratio imaging. Has anyone developed a complete set of macros for NIH Image for this purpose? Harvey Karten Harvey J. Karten, M.D. Dept. Neurosciences UCSD 0608 La Jolla, CA 92093 Phone (619)-534-4938 FAX (619)-534-6602 E-Mail KARTENH@SDSC.EDU From keller@micros.mrd.bldrdoc.gov Wed Oct 20 03:56:51 1993 Received: from central.bldrdoc.gov by nx1.soils.umn.edu (5.65c) id AA01096; Wed, 20 Oct 1993 10:55:40 -0500 Return-Path: Received: from pascal.mrd.bldrdoc.gov by central.bldrdoc.gov (4.1/SMI-DDN) id AA04013; Wed, 20 Oct 93 09:57:07 MDT Received: from micros.mrd.bldrdoc.gov by pascal.mrd.bldrdoc.gov (4.1/SMI-3.2) id AA00502; Wed, 20 Oct 93 09:57:46 MDT Message-Id: <9310201557.AA00502@pascal.mrd.bldrdoc.gov> Date: Wed, 20 Oct 93 09:56:51 MDT From: Bob Keller Subject: Re: IPLab Spectrum To: nih-image@soils.umn.edu X-Mailer: LeeMail 1.2.4 >>Has anyone tried using IPLab Spectrum, by Signal Analytics Corp? > >It does do a fourier transform and a few other things, although DIP Station >does these as well or better and they are in your area. If I were adding 50 >images together I might use IPLab. IPlab has a few hardware interfaces that >Image does not have, such as for photometrics and others. It has some >interesting color transforms too. Thanks for the info. Where can I find out more about DIP Station? Bob Keller NIST Boulder keller@micros.mrd.bldrdoc.gov From djm@cidmv1.wustl.edu Wed Oct 20 07:11:32 1993 Received: from wugate.wustl.edu by nx1.soils.umn.edu (5.65c) id AA01773; Wed, 20 Oct 1993 12:10:17 -0500 Return-Path: Received: by wugate.wustl.edu (5.67a+/WUSTL-0.3) with DECnet id AA10976; Wed, 20 Oct 1993 12:11:33 -0500 Date: Wed, 20 Oct 1993 12:11:32 -0500 Message-Id: <199310201711.AA10976@wugate.wustl.edu> From: djm@cidmv1.wustl.edu (D.J. Meyer) To: nih@wugate.wustl.edu Subject: tif or pict are they both 24bit? From russ@mat.mte.ncsu.edu Wed Oct 20 09:16:43 1993 Received: from mat.mte.ncsu.edu by nx1.soils.umn.edu (5.65c) id AA01805; Wed, 20 Oct 1993 12:15:32 -0500 Return-Path: Received: by mat.mte.ncsu.edu (5.57/Ultrix3.0-C) id AA09975; Wed, 20 Oct 93 13:16:43 -0400 Date: Wed, 20 Oct 93 13:16:43 -0400 Message-Id: <9310201716.AA09975@mat.mte.ncsu.edu> To: nih-image@soils.umn.edu From: russ@mat.mte.ncsu.edu Subject: Re: "Metaphor" you may be referring to Metamorph, an image analysis package (software and boards) that runs on a PC. It is available from Universal Imaging Universal Imaging Corp, 502 Brandywine Parkway, West Chester, PA 19380, (215) 344-9410; fax: 215-344-9515; ask for Ted Inoue __________________________________________________ John Russ (John_Russ@ncsu.edu) or (russ@mat.mte.ncsu.edu) Materials Science and Engineering Department, North Carolina State Univ., Raleigh, NC 27695-7907 phone: 919-515-3328 fax: 919-515-7724 From kyzy@rice.edu Wed Oct 20 07:24:09 1993 Received: from moe.rice.edu by nx1.soils.umn.edu (5.65c) id AA01891; Wed, 20 Oct 1993 12:22:49 -0500 Return-Path: Received: from [128.42.105.7] (erinna.rice.edu) by moe.rice.edu (AA10112); Wed, 20 Oct 93 12:24:09 CDT Date: Wed, 20 Oct 93 12:24:09 CDT Message-Id: <9310201724.AA10112@moe.rice.edu> To: nih-image@soils.umn.edu From: kyzy@rice.edu Subject: Re: # of colors on monitor D.J Meyer writes >i just put a 24bit video card in our IIfx for our imaging needs. now, >nih gives me an error message that the monitor *must* be configured for >256 colors or gray scales. the documentation says it will handle 24 >bit images. but not display them? is there a way around this? >8 bit display is not acceptable for what we need to do with our >images. I have experienced a similar problem when I use my Powerbook 180 (4-bit screen but 8-bit external video) for interactive presentations using Image. If I configure my external video (LCD display panel) as a second monitor, Image will not start from my screen since it is not 8-bit deep. So I have to configure my external video to mirror my Powerbook screen, thus wasting lots of premium screen space for my presentations (Powerbook has only 640x400 display). Don't ask me why the 180 will not allow me to specify the external video (LCD panel) as the startup monitor... Wayne, is there a way around this ? Can Image be made to refuse to display 8-bit images on a screen that is not 8-bits deep, but (a) start from a monitor that is 1-bit or 4-bit deep, (b) allow you to display 8-bit images on a second 8-bit monitor and (b) allow you to display graphics or text on the main 1-bit or 4-bit monitor ? ------------------------------------------------------------------------ | Kyriacos Zygourakis, Ph.D. | Phone: (713) 527-8750 Ext. 3509 Dept. of Chemical Engineering | FAX: (713) 285-5478 Rice University | e-mail: kyzy@rice.edu Houston, Texas 77251-1892 | | ------------------------------------------------------------------------ From mvivino@helix.nih.gov Wed Oct 20 09:24:30 1993 Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c) id AA01897; Wed, 20 Oct 1993 12:23:03 -0500 Return-Path: Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0)) id AA21868; Wed, 20 Oct 93 13:24:30 -0400 Date: Wed, 20 Oct 93 13:24:30 -0400 Message-Id: <9310201724.AA21868@helix.nih.gov> X-Sender: mvivino@128.231.2.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mvivino@helix.nih.gov (Mark Vivino) Subject: Re: IPLab Spectrum >Thanks for the info. Where can I find out more about DIP Station? >From the About NIH Image manual: DIP Station (Medical image analysis, 16-bits, surface rendering) Hayden Image Processing Group Boulder, Colorado 303-449-3433 (whc@po.cwru.edu) From morilak@cmgm.stanford.edu Wed Oct 20 03:43:10 1993 Received: from cmgm.Stanford.EDU by nx1.soils.umn.edu (5.65c) id AA02057; Wed, 20 Oct 1993 12:35:53 -0500 Return-Path: Received: from (P159-macplus.Stanford.EDU) by cmgm.stanford.edu (4.1/1.34) id AA15051; Wed, 20 Oct 93 10:37:15 PDT Date: Wed, 20 Oct 1993 10:43:10 PDT From: QR Subject: MSRS catalog of primary antibodoes To: nih-image@soils.umn.edu In-Reply-To: Your message of Thu, 14 Oct 1993 14:08:38 -0500 Message-Id: I have received several questions regarding the MSRS catalog of Primary Antibodies that I mentioned in a previous transmission, so I am sending this to both the microscopy and NIH image distribution lists. The MSRS catalog is indeed a catalog of primary antisera, both those available commercially and those available from individual labs who choose to have their antisera listed. I have found it to be an extremely useful first reference, though it is, as might be expected, not 100% comprehensive. I often will call the sources listed to find out what else they have available that is not in the catalog (e.g. polyclonals vs monoclonals, different host species, different epitopes etc.). I ordered it at last years Neuroscience meeting, and an update (I am told) will be available approximately annually. The cost was somewhere around $75 (US). (MSRS stands for "Manufacturer's Specifications and Reference Synopsis"). I don't have a phone number, but here is the address off the order form: MSRS catalog of Primary Antibodies AERIE Corporation Box 1356 Birmingham, MI 48012-1356 ------- From wayne@helix.nih.gov Wed Oct 20 12:42:58 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA02119; Wed, 20 Oct 1993 12:44:23 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA09666; Wed, 20 Oct 93 13:04:36 -0400 Message-Id: <9310201704.AA09666@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 20 Oct 1993 12:42:58 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: # of colors on monitor >i just put a 24bit video card in our IIfx for our imaging needs. now, >nih gives me an error message that the monitor *must* be configured for >256 colors or gray scales. the documentation says it will handle 24 >bit images. but not display them? is there a way around this? >8 bit display is not acceptable for what we need to do with our >images. NIH Image requires that the monitor be in 8-bit (256 color) mode. I would suggest using Photoshop for editing and displaying 24-bit color images. There is a utility in the /pub/util directory on zippy.nimh.nih.gov called DepthGage that allows you to quickly and easily switch between 8-bit mode and 24-bit mode. --wayne From russ@mat.mte.ncsu.edu Wed Oct 20 10:46:31 1993 Received: from mat.mte.ncsu.edu by nx1.soils.umn.edu (5.65c) id AA02736; Wed, 20 Oct 1993 13:45:15 -0500 Return-Path: Received: by mat.mte.ncsu.edu (5.57/Ultrix3.0-C) id AA10315; Wed, 20 Oct 93 14:46:31 -0400 Date: Wed, 20 Oct 93 14:46:31 -0400 Message-Id: <9310201846.AA10315@mat.mte.ncsu.edu> To: nih-image@soils.umn.edu From: russ@mat.mte.ncsu.edu Subject: Re: # of colors on monitor Kyriacos Zygourakis writes > >I have experienced a similar problem when I use my Powerbook 180 (4-bit >screen but 8-bit external video) for interactive presentations using Image. >If I configure my external video (LCD display panel) as a second monitor, >Image will not start from my screen since it is not 8-bit deep. So I have >to configure my external video to mirror my Powerbook screen, thus wasting >lots of premium screen space for my presentations (Powerbook has only >640x400 display). Don't ask me why the 180 will not allow me to specify the >external video (LCD panel) as the startup monitor... > No problem to do this. I do it all the time, using either an external color monitor or a Sharp LCD panel as the second screen on my 180. Set the second monitor up NOT to mirror the screen but as a second monitor. Open monitors and drag the menu bar from the internal to external monitor. Then depress the option key (the happy Mac icon will appear). Drag that icon to the second monitor as well. Now the external monitor (or panel) will be the primary screen, where the "welcome to mac" message and the menu bars appear. the nice thing about this is that if you use the powerbook without the external monitor connected, it reverts to the internal screen, but the next time you boot up with the second monitor connected, it will use it without any further fiddling around. __________________________________________________ John Russ (John_Russ@ncsu.edu) or (russ@mat.mte.ncsu.edu) Materials Science and Engineering Department, North Carolina State Univ., Raleigh, NC 27695-7907 phone: 919-515-3328 fax: 919-515-7724 From wayne@helix.nih.gov Wed Oct 20 14:11:49 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA03011; Wed, 20 Oct 1993 14:13:14 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA09891; Wed, 20 Oct 93 14:33:28 -0400 Message-Id: <9310201833.AA09891@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 20 Oct 1993 14:11:49 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: tif or pict >are they both 24bit? Both can be 1, 8 or 24-bits deep. NIH Image reads 1, 8 and 24-bit PICT files, but only writes 8-bit PICTs. Note that reading 24-bit PICTs requires the QuickTime INIT and doesn't always work. NIH Image can read uncompressed 8 and 16-bit TIFF files and writes uncompressed 8-bit TIFF files. --wayne From roper@lamar.ColoState.EDU Wed Oct 20 09:39:55 1993 Received: from lamar.ColoState.EDU by nx1.soils.umn.edu (5.65c) id AA04171; Wed, 20 Oct 1993 16:39:08 -0500 Return-Path: Received: from [129.82.126.25] by lamar.ColoState.EDU (AIX 3.2/UCB 5.64/4.03) id AA17373; Wed, 20 Oct 1993 15:39:55 -0600 Date: Wed, 20 Oct 1993 15:39:55 -0600 Message-Id: <9310202139.AA17373@lamar.ColoState.EDU> To: nih-image@soils.umn.edu From: roper@lamar.ColoState.EDU Subject: Re: Kodak DCS200/Zeiss Microscope >Dear Image users, >We are trying to set up a system for routine documentation using the Kodak DCS >200 camera. I have the Kodak DCS200 camera attached to a Zeiss Axiophot microscope. I had to purchase several hundred dollars of special adapter pieces designed to connect a Nikon camera to the zeiss TV port, including an extension tube, a Zeiss eyepiece (10X), and a few adapter pieces. I am told that Zeiss is now making an adapter directly for the Kodak camera, but I have no information on it. You may wish to contact Dennis Runyan, Technical Sales Rep, Carl Zeiss Inc, Microscope Division, San Leandro Office, 14751 Catalina St., San Leandro, CA 94577, phone 800-832-3800. He is familiar with all the recent adapter stuff, I believe. To compensate for the small chip, I merely use a lower mag objective than for a conventional camera back. You can, of course, view the image through the ground glass screen of the Kodak (Nikon) camera back to make sure you have everything you want in the frame. I connect the Kodak camera to my Mac Quadra 800 and use PhotoShop to capture the results. I can obtain publication-quality (well, nearly so) prints by sending the resulting image via ftp to my campus's Tektronix dye sublimation printer (Phase IISD). The cost for an 8x10 is $3.95. This sure beats conventional darkroom methodology in time and money (except for the expensive Zeiss adapters!). -------------------------------------------- Stephen Roper, Professor of Anatomy and Neurobiology, Colorado State University, Ft. Collins CO 80523 INTERNET: Roper@Lamar.ColoState.Edu FAX:(303) 491-7907 PHONE: (303) 491-7808 From herro001@maroon.tc.umn.edu Wed Oct 20 12:14:07 1993 Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c) id AA04503; Wed, 20 Oct 1993 17:22:11 -0500 Return-Path: Message-Id: <199310202222.AA04503@nx1.soils.umn.edu> Received: from rash.med.umn.edu by maroon.tc.umn.edu id SMTP-0012cc5b81f012435; Wed, 20 Oct 93 17:13:57 -0500 From: "Mike Herron" Reply-To: "Mike Herron" <@staff.tc.umn.edu> To: nih-image@soils.umn.edu Subject: Re: MSRS catalog of primary antibodoes Date: Wed, 20 Oct 93 17:14:07 -0500 Do you have any idea how the MSRS compares with the Linscott's Directory as far as completeness, accuracy or timely nature of the information? I have used the Linscott's directory for years, and have been quite happy with it. In message writes: > I have received several questions regarding the MSRS catalog of Primary > Antibodies that I mentioned in a previous transmission, so I am sending this > to both the microscopy and NIH image distribution lists. The MSRS catalog is > indeed a catalog of primary antisera, both those available commercially and > those available from individual labs who choose to have their antisera > listed. > I have found it to be an extremely useful first reference, though it is, as > might be expected, not 100% comprehensive. I often will call the sources > listed to find out what else they have available that is not in the catalog > (e.g. polyclonals vs monoclonals, different host species, different epitopes > etc.). I ordered it at last years Neuroscience meeting, and an update (I am > told) will be available approximately annually. The cost was somewhere around > $75 (US). (MSRS stands for "Manufacturer's Specifications and Reference > Synopsis"). I don't have a phone number, but here is the address off the > order > form: > > > MSRS catalog of Primary Antibodies > AERIE Corporation > Box 1356 > Birmingham, MI 48012-1356 > ------- > ______________________________________________ / Mike Herron, U of MN, Dept. of Dermatology / / herro001@maroon.tc.umn.edu / / 612-625-8935 Box 124 UMHC, Mpls MN 55455 / ______________________________________________ From morilak@cmgm.stanford.edu Wed Oct 20 09:47:14 1993 Received: from cmgm.Stanford.EDU by nx1.soils.umn.edu (5.65c) id AA05123; Wed, 20 Oct 1993 18:39:51 -0500 Return-Path: Received: from (P159-macplus.Stanford.EDU) by cmgm.stanford.edu (4.1/1.34) id AA22342; Wed, 20 Oct 93 16:41:17 PDT Date: Wed, 20 Oct 1993 16:47:14 PDT From: _` Subject: Re: MSRS catalog vs Linscott's To: nih-image@soils.umn.edu In-Reply-To: Your message of Wed, 20 Oct 1993 17:28:41 -0500 Message-Id: In response to Mike Herron's query, I can't compare the MSRS to the Linscott's directory as I have not used Linscott's. Maybe someone else could comment? -David Morilak P.S. I apologize again for the bizarre "From" headers my messages are generating. I thought I had the problem fixed, but our mailer seems to have had something of a psychotic break! ------- From mt1ntg@fencer.cis.dsto.gov.au Thu Oct 21 19:50:04 1993 Received: from fencer.cis.dsto.gov.au by nx1.soils.umn.edu (5.65c) id AA05195; Wed, 20 Oct 1993 18:48:48 -0500 Return-Path: Message-Id: <199310202348.AA05195@nx1.soils.umn.edu> Received: from [160.64.14.216] by fencer.cis.dsto.gov.au with SMTP; Thu, 21 Oct 1993 10:01:41 +1000 (EST) Date: Thu, 21 Oct 1993 09:50:04 +1000 To: nih-image@soils.umn.edu From: NoelGoldsmith (Noel Goldsmith) Subject: Re: Kodak DCS200/Zeiss Microscope >Dear Image users, >We are trying to set up a system for routine documentation using the Kodak DCS >200 camera. I remember there has been some discussion on this list about using >the Kodak DCS 200 camera for microscopy (via Photoshop plug in). Could anybody >who is using such a setup specify how they connected the camera to a Zeiss >Axiophot microscope? How to compensate for the small CCD chip? The chip has >only 1/4 of the area of film and the adapters we got from Zeiss to connect the >camera to the microscope is for film so we can capture only a small part of the >slide we see in the eyepiece. Any suggestions? >Thanks! > >Ruediger Fritsch >Max-Planck-Institut f. biophysikalische Chemie >Am Fassberg >37077 Goettingen >Germany >email rfritsc@gwdgv1.dnet.gwdg.de Ruediger, I have had some fun here interfacing a variety of cameras to a variety of lenses, microscopes and so-on. The essential principles you must keep in mind are as follows. You need a real image on the chip/chips in focus, which covers the field you want. How do you do this when the chip/chips are buried some 30 mm deep in the camera. I think the DCS200 has similar back focal distance to a 35mm SLR, so if you use a typical C mount adaptor then you will get a small field of view. Solution. Project an image from your microscope onto a piece of card which has a rectangle on it the same size as your chip. (you might need to turn out the lights). Adjust the distance between the card and the eyepiece or camera port until the field of view on the chip rectangle is what you need. Focus this as well as you can, the image is small. Now take a lens, for a trial use a 50mm enlarger lens or a 50mm lens from an SLR camera. Place this lens 100 mm away from the card and place the ccd chip 100 mm behind the lens. Remove the card. This will relay the image at 1 magnification (or at 1:1) into the ccd chip. If you want to get a different scale vary the distances on each side of the lens. Enlarger lenses are good for this sort of work, as they are designed to work at ratios around 1:1, whereas ordinary camera lenses are computed for infinity. The optimum solution will use a process lens, designed for 1:1 and similar. Of course in this application, the field need to be covered is small in angular terms and consequently any lens will work quite well. The problem with this method is that it is not a compact solution, and requires a bit of machining of tubes etc for a good permanent set-up. An advantage is that you can make telescoping tubes and achieve large fields or small fields, with one lens. Commercial solutions are often expensive, and may be designed to work with C mount cameras which employ a lens to ccd distance which is around 10mm and make coupling easier. Commercial solutions may be compact. Leica, Zeiss and so-on all have some lenses for adapting cameras to stereo microscopes and these come in a variety of magnifications, using numbers such as 0.6. Such a 0.6 lens is a strong positive objective (about a 10x magnifier) which relays the image smaller, and does so in a fairly compact way) Lenses for cameras such as the Sony DXC-930 P which is a 3 chip colour ccd employ an optical design strategy known a retro-focus, whereby a zoom lens with a focal length of 8-80 mm say is positioned in front of a window in the camera, with the focal plane being located some 30mm behind. There is a relay lens which transfers the image, at the required scale. Hope this helps. Noel Noel T Goldsmith DSTO Aeronautical Research Laboratory 506 Lorimer Street Port Melbourne Vic 3207 Australia From huff@MCCLB0.MED.NYU.EDU Thu Oct 21 01:10:05 1993 Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c) id AA08202; Thu, 21 Oct 1993 05:07:43 -0500 Return-Path: Received: from DialupEudora (ANNEX1.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU (PMDF V4.2-14 #2884) id <01H4D4ATA09C0027I1@MCCLB0.MED.NYU.EDU>; Thu, 21 Oct 1993 06:08:56 EDT Date: Thu, 21 Oct 1993 06:10:05 -0500 From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff) Subject: Re: IPL and AxoVideo To: nih-image@soils.umn.edu Message-Id: <01H4D4AU37KI0027I1@MCCLB0.MED.NYU.EDU> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT >Both IPL and Axovideo (Axon Instruments) include software for Calcium >ratio imaging. >Has anyone developed a complete set of macros for NIH Image >for this purpose? > Harvey Karten I developed a User.p which supports 32 bit real images, and steven@cell.BIH.Harvard.Edu (Steven Blechner) wrote macros that use the macro commands I provided, and I believe has been doing Calcium ratio imaging using that package. I plan to move that code from User.p into UMPixel32r.p in Image UMX so that the macro commands each have their own names instead of UserCode(code#,...) but haven't gotten to it yet. That package also supports the Scion 1200 board collecting 32fps images onto a DayStar RAM card and later integrates them into 16 bit images. -- Edward J. Huff huff@mcclb0.med.nyu.edu (212)998-8465 Keck Laboratory for Biomolecular Imaging NYU Chemistry Department, 31 Washington Place, New York NY 10003 From sarmienu@rnisd0.DNET.roche.com Thu Oct 21 03:36:16 1993 Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c) id AA08560; Thu, 21 Oct 1993 06:34:53 -0500 Return-Path: Received: by gatekeeper.roche.com (5.65/fma-120691); id AA28870; Thu, 21 Oct 93 07:36:18 -0400 Received: by mailgate.roche.com (5.65/fma-120691); id AA18164; Thu, 21 Oct 93 07:32:23 -0400 From: sarmienu@rnisd0.DNET.roche.com Message-Id: <9310211132.AA18164@mailgate.roche.com> Received: from rnisd0.enet; by inet.enet; Thu, 21 Oct 93 07:36:16 EDT Date: Thu, 21 Oct 93 07:36:16 EDT To: nih-image@soils.umn.edu Apparently-To: nih-image@soils.umn.edu Subject: Linscott's catalogue Could we get the address (phone number) to obtain the Linscott's catalogue too... ?? Thank you Juan I. Sarmiento Department of Toxicology and Pathology Hoffmann-La Roche, INC. 340 Kingsland street Nutley, NJ 07110 Sarmienu@RNISD0.DNET.ROCHE.COM From jladwig@soils.umn.edu Thu Oct 21 03:19:26 1993 Received: from saturn.soils.umn.edu by nx1.soils.umn.edu (5.65c) id AA09238; Thu, 21 Oct 1993 08:19:31 -0500 Return-Path: Received: by saturn.soils.umn.edu (4.1) id AA04542; Thu, 21 Oct 93 08:19:26 CDT Date: Thu, 21 Oct 93 08:19:26 CDT From: "John Ladwig" Message-Id: <9310211319.AA04542@saturn.soils.umn.edu> To: nih-image@soils.umn.edu Subject: Re: John Crum - electron microscope images ------- Start of forwarded message ------- Reply to question by John Crum at SDSU: 4pi Analysis in North Carolina makes a board for the Macintosh computer that will scan an image on an electron microscope and collect a digital image. Image size can be anything up to 4096x4096 with 14 bits per pixel. Included is a plug-in for Adobe Photoshop to do the scanning and collect the image. This plug-in also works with NIH Image and runs faster than in Photoshop. The board also contains all the hardware to be used as a multi-channel analyzer for EDS analysis. The NIST/NIH Desktop Spectrum Analysis (DTSA) program runs with this board to make a complete multichannel analyzer with many simulation and analysis features. The board from 4pi costs about $5000 and the DTSA program costs $815 from NIST. 4pi Analysis, Inc. 3500 Westgate Drive Suite 403 Durham, NC 27707 Phone: 919-489-1757 DTSA information: Phone: 301-975-3906 (Bob Myklebust) email: myklebust@gapnet.nist.gov Bob Myklebust ------- End of forwarded message ------- From kartenh@Sdsc.Edu Thu Oct 21 13:39:54 1993 Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA09458; Thu, 21 Oct 1993 08:38:42 -0500 Return-Path: Date: Thu, 21 Oct 93 13:39:54 GMT From: kartenh@Sdsc.Edu (Harvey Karten) Message-Id: <931021133954.20404251@m5.sdsc.edu> Subject: Re: IPL and AxoVideo To: nih-image@soils.umn.edu X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu" X-St-Vmsmail-Cc: KARTENH Edward Huff writes: "package also supports the Scion 1200 board collecting 32fps images onto a DayStar RAM card and later " What is the Scion 1200 board? I was only aware of their LG-3. Also: " lan to move that code from User.p into UMPixel32r.p in Image UMX so that the macro commands each have their own names instead of UserCode(code#,...) " Look forward to seeing it on Zippy. Many thanks, Harvey Karten Harvey J. Karten, M.D. Dept. Neurosciences UCSD 0608 La Jolla, CA 92093 Phone (619)-534-4938 FAX (619)-534-6602 E-Mail KARTENH@SDSC.EDU From @YaleVM.YCC.Yale.Edu:Mike_Schwartz@QUICKMAIL.CIS.YALE.EDU Mon Oct 21 06:27:31 1993 Received: from YALEVM.YCC.YALE.EDU by nx1.soils.umn.edu (5.65c) id AA09913; Thu, 21 Oct 1993 09:27:08 -0500 Return-Path: <@YaleVM.YCC.Yale.Edu:Mike_Schwartz@QUICKMAIL.CIS.YALE.EDU> Message-Id: <199310211427.AA09913@nx1.soils.umn.edu> Received: from quickmail.yale.edu by YaleVM.YCC.Yale.Edu (IBM VM SMTP V2R2) with TCP; Thu, 21 Oct 93 10:26:36 EDT Date: 21 Oct 1993 10:27:31 -0400 From: "Mike Schwartz" Subject: 4pi Analysis in North Carol To: "Image List" Return-Receipt-To: "Mike Schwartz" Subject: Time:10:15 AM OFFICE MEMO 4pi Analysis in North Carolina makes_ Date:10/21/93 >4pi Analysis in North Carolina makes a board for the Macintosh >computer that will scan an image on an electron microscope and collect >a digital image. Image size can be anything up to 4096x4096 with 14 >bits per pixel. What camera do you use to take advantage of the 4096x4096 resolution and how do you mount the camera? What printer do you use to obtain hardcopy and are the resulting prints of publication quality? Mike Schwartz Sect. of Neurobiology Yale Univ. Sch. of Med. Mike Schwartz@qm.yale.edu From djm@cidmv1.wustl.edu Thu Oct 21 06:15:03 1993 Received: from wugate.wustl.edu by nx1.soils.umn.edu (5.65c) id AA10589; Thu, 21 Oct 1993 11:13:40 -0500 Return-Path: Received: by wugate.wustl.edu (5.67a+/WUSTL-0.3) with DECnet id AA22037; Thu, 21 Oct 1993 11:15:04 -0500 Date: Thu, 21 Oct 1993 11:15:03 -0500 Message-Id: <199310211615.AA22037@wugate.wustl.edu> From: djm@cidmv1.wustl.edu (D.J. Meyer) To: nih@wugate.wustl.edu Subject: illumination hi, we do a lot of processing of retinas, and are frequently using our ccd camera so the other lab members can watch the surgeries, disections, etc. we also capture a lot of images. these are shot through binoculars. i am having a problem with illumination, particularly reflections. the eyes are as you know, roughly sperical, and we use fiber lights to illuminate inside. however, we are getting a lot of reflections no matter what kind of dish we use to hold the eye. i've tried glass petri dishes. beakers. styrofoam. even a plastic bottle cap, but i can't seem to get the illumination right with the eyes. grabbing images from the slide microscope works perfectly, but its easy to get equal illumination from a microscope. any suggestions on lighting and containers? thanks dj meyer From herro001@maroon.tc.umn.edu Thu Oct 21 08:38:24 1993 Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c) id AA11806; Thu, 21 Oct 1993 13:36:56 -0500 Return-Path: Message-Id: <199310211836.AA11806@nx1.soils.umn.edu> Received: from rash.med.umn.edu by maroon.tc.umn.edu id SMTP-0012cc6d6ff024112; Thu, 21 Oct 93 13:37:54 -0500 From: "Mike Herron" Reply-To: "Mike Herron" <@staff.tc.umn.edu> To: nih-image@soils.umn.edu Subject: Re: illumination Date: Thu, 21 Oct 93 13:38:24 -0500 How about a polarizer filter? In message <199310211615.AA22037@wugate.wustl.edu> writes: > > hi, > we do a lot of processing of retinas, and are frequently using our ccd > camera so the other lab members can watch the surgeries, disections, etc. > we also capture a lot of images. these are shot through binoculars. > > i am having a problem with illumination, particularly reflections. the eyes > are as you know, roughly sperical, and we use fiber lights to illuminate > inside. however, we are getting a lot of reflections no matter what kind > of dish we use to hold the eye. > i've tried glass petri dishes. beakers. styrofoam. even a plastic bottle cap, > but i can't seem to get the illumination right with the eyes. > grabbing images from the slide microscope works perfectly, but its easy to > get equal illumination from a microscope. > any suggestions on lighting and containers? > thanks > dj meyer > ______________________________________________ / Mike Herron, U of MN, Dept. of Dermatology / / herro001@maroon.tc.umn.edu / / 612-625-8935 Box 124 UMHC, Mpls MN 55455 / ______________________________________________ From wayne@helix.nih.gov Thu Oct 21 15:35:57 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA12606; Thu, 21 Oct 1993 15:37:26 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA16471; Thu, 21 Oct 93 15:57:41 -0400 Message-Id: <9310211957.AA16471@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 21 Oct 1993 15:35:57 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: grain counting macros >Hi. > >I'm a new member of 'the list' and don't know if this has been covered yet. >Has anyone tried the grain-counting macros that Karl Beykirch put up for >anonymous ftp transfer? >I've been trying them, and having some difficulty. In particular, when >using the 'Count Grains in Area (F7) macro, it is graying out my entire >selection and counting it as -one- grain. Perhaps I am not calibrating >the area/grain properly. I am not macro-literate (yet), so any info >that you can offer is appreciated. Send me a sample image and I will see if I can figure out what is going on. You can either upload it to the contrib directory on Zippy or email it in binhex format. --wayne From glenmac@u.washington.edu Thu Oct 21 09:40:00 1993 Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c) id AA13637; Thu, 21 Oct 1993 18:46:27 -0500 Return-Path: Received: by carson.u.washington.edu (5.65/UW-NDC Revision: 2.29 ) id AA04781; Thu, 21 Oct 93 16:47:54 -0700 X-Sender: glenmac@carson.u.washington.edu Date: Thu, 21 Oct 1993 16:40:00 -0700 (PDT) From: Glen Macdonald Subject: Re: Linscott's catalogue info. To: nih-image@soils.umn.edu Cc: Multiple recipients of list In-Reply-To: <9310211132.AA18164@mailgate.roche.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=us-ascii Linscott's Directory 4877 Grange Rd. Santa Rosa, CA 95404 USA (707) 544-95555 Subscriptions are $60/yr. and provides a main book with 3 or 4 quarterly updates. It lists monoclonal and polyclonal antibodies by antigen type,tissues, cytokines, lectins, venoms, etc. and cell cultures, immunoassay kits, and contract/custome services. Glen MacDonald Hearing Development Labs University of WAshington From pruskyg@hg.uleth.ca Thu Oct 21 10:17:51 1993 Received: from holly.cc.uleth.ca by nx1.soils.umn.edu (5.65c) id AA13831; Thu, 21 Oct 1993 19:14:08 -0500 Return-Path: Received: by holly.cc.uleth.ca; id AA28511; Thu, 21 Oct 1993 18:14:24 -0600 Message-Id: <9310220014.AA28511@holly.cc.uleth.ca> Date: Thu, 21 Oct 1993 18:17:51 -0800 To: nih-image@soils.umn.edu From: pruskyg@hg.uleth.ca (Glen Prusky) X-Sender: pruskyg@pop.uleth.ca Subject: Sweet wishes Wayne et al., I am an evangelical user and supporter of Image, but there are always things that could be added to any program to enhance its features to match one's particular application. I was wondering if anyone out there has written a macro or if Wayne could incorporate into the program the following utility: I use image to capture dye-filled neurons on a fluorescence microscope. The processes of these neurons have the unfortunate poperty of coursing in and out of the plane of focus at high magnifications, and at low magnifications, the inherent low resolution of video results in unsatisfactory images. In order to get around this, I end up taking a series of images at high magnification at different focal planes and cutting and pasting to create a 2D image of the cellular processes. Haig Keshishian (HKESHIS@YALEVM.YCC.YALE.EDU) has encountered a similar problem and has written code for his DOS-based system to help rectify this problem. First he captures an image. Then he selects an area on this image that is out of focus. This and only this area can then be placed into live capture mode, allowing you to focus on that particular part of the specimin and then capture that area and paste it into the original image. This can be done a number of times to give you a completely focussed 2D image. This has the advantage of maintaining perfect alignment among pieces of a photomontage, it saves a lot of time since you don't have to cut and paste together peices of different original images, and the resulting image has few areas of abrupt changes in background because you are capturing new areas of the image at the same time under the same lighting conditions. Confocal microscopy, that allows you to collapse different planes of an image into 2D, can solve this problem, but for those of us without such a machine who would like to have this kind of utility, would do cartwheels if it were part of Image. I have talked with Haig and he would be happy to share how he accomplished this feature in his software. I know of many people who use Image in a similar capacity that I do, so I suspect that a feature such as this in Image would meet with widespread approval. Keep up the great work! Glen T. Prusky Ph.D. Department of Psychology The University of Lethbridge 4401 University Drive Lethbridge, AB, Canada T1K 3M4 pruskyg@hg.uleth.ca Office-403-329-2402 Lab-403-329-2410 Fax-403-329-2410 From rms@acsu.buffalo.edu Thu Oct 21 17:08:05 1993 Received: from lictor.acsu.buffalo.edu by nx1.soils.umn.edu (5.65c) id AA14138; Thu, 21 Oct 1993 20:06:40 -0500 Return-Path: Received: from rms@localhost by lictor.acsu.buffalo.edu (8.5/8.5) id VAA23789; Thu, 21 Oct 1993 21:08:05 -0400 Date: Thu, 21 Oct 1993 21:08:05 -0400 From: "Robert M. Straubinger" Message-Id: <199310220108.VAA23789@lictor.acsu.buffalo.edu> To: nih-image@soils.umn.edu, nih-image@soils.umn.edu Subject: Re: IPL and AxoVideo H. Karten wrote: *Has anyone developed a complete set of macros for NIH Image *for [the] purpose [of ratio imaging]. Since the exchanges on this list a couple weeks back, we've made a couple macros to load a stack of alternating-wavelength images, and create a new stack of ratioed images. The trouble is that the 'divide' routine currently automatically scales the resulting image to the widest possible dynamic range (ie. stretches the max/min ratios to 256/0, respectively), as best I understand. This creates problems as we need to keep the scaling uniform through our image series. Otherwise the calibration curve will mean nothing. Wayne wrote that he was contemplating a fix for this problem. Bob Straubinger Pharmaceutics SUNY/Buffalo From kartenh@Sdsc.Edu Fri Oct 22 03:26:06 1993 Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA14826; Thu, 21 Oct 1993 22:24:47 -0500 Return-Path: Date: Fri, 22 Oct 93 03:26:06 GMT From: kartenh@Sdsc.Edu (Harvey Karten) Message-Id: <931022032606.20407f33@m5.sdsc.edu> Subject: RE: Sweet wishes To: nih-image@soils.umn.edu X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu" X-St-Vmsmail-Cc: KARTENH How accurate a reconstruction does this method produce? How does it deal with collateral branches in the same ROI but in different focal planes? Harvey Karaten Harvey J. Karten, M.D. Dept. Neurosciences UCSD 0608 La Jolla, CA 92093 Phone (619)-534-4938 FAX (619)-534-6602 E-Mail KARTENH@SDSC.EDU From mt1ntg@fencer.cis.dsto.gov.au Sat Oct 23 02:40:17 1993 Received: from fencer.cis.dsto.gov.au by nx1.soils.umn.edu (5.65c) id AA15764; Fri, 22 Oct 1993 01:39:04 -0500 Return-Path: Message-Id: <199310220639.AA15764@nx1.soils.umn.edu> Received: from [160.64.14.216] by fencer.cis.dsto.gov.au with SMTP; Fri, 22 Oct 1993 16:52:00 +1000 (EST) Date: Fri, 22 Oct 1993 16:40:17 +1000 To: nih-image@soils.umn.edu From: NoelGoldsmith (Noel Goldsmith) Subject: Re: Sweet wishes >Wayne et al., >I am an evangelical user and supporter of Image, but there are always >things that could be added to any program to enhance its features to match >one's particular application. I was wondering if anyone out there has >written a macro or if Wayne could incorporate into the program the >following utility: I use image to capture dye-filled neurons on a >fluorescence microscope. The processes of these neurons have the >unfortunate poperty of coursing in and out of the plane of focus at high >magnifications, and at low magnifications, the inherent low resolution of >video results in unsatisfactory images. In order to get around this, I end >up taking a series of images at high magnification at different focal >planes and cutting and pasting to create a 2D image of the cellular >processes. Haig Keshishian (HKESHIS@YALEVM.YCC.YALE.EDU) has encountered a >similar problem and has written code for his DOS-based system to help >rectify this problem. First he captures an image. Then he selects an area >on this image that is out of focus. This and only this area can then be >placed into live capture mode, allowing you to focus on that particular >part of the specimin and then capture that area and paste it into the >original image. This can be done a number of times to give you a completely >focussed 2D image. This has the advantage of maintaining perfect alignment >among pieces of a photomontage, it saves a lot of time since you don't have >to cut and paste together peices of different original images, and the >resulting image has few areas of abrupt changes in background because you >are capturing new areas of the image at the same time under the same >lighting conditions. Confocal microscopy, that allows you to collapse >different planes of an image into 2D, can solve this problem, but for those >of us without such a machine who would like to have this kind of utility, >would do cartwheels if it were part of Image. >I have talked with Haig and he would be happy to share how he accomplished >this feature in his software. I know of many people who use Image in a >similar capacity that I do, so I suspect that a feature such as this in >Image would meet with widespread approval. Keep up the great work! > >Glen T. Prusky Ph.D. >Department of Psychology >The University of Lethbridge >4401 University Drive >Lethbridge, AB, Canada >T1K 3M4 >pruskyg@hg.uleth.ca >Office-403-329-2402 >Lab-403-329-2410 >Fax-403-329-2410 Well, I have done this for opaque reflective specimens. This code is not yet quite mature. I (the place where I work) are considering the financial implications of commercialisng it. Another much more difficult problem is how do you cope with constant changes in Image. I am thinking that if we package our method in a plug in it may do. Or we could put it in NIHUMX, which would put all of the extra code in one module. May I recommend the following references for those who want to do a bit of library digging. As you might guess I am writing a paper on the topic. Peiper, R.J., and Korpel, A. (1983) Image Processing for extended depth of field. Applied Optics 22, 1449-1453. Sugimoto, S.A. and Ichioka, Y. (1985) Digital composition of images with increased depth of focus considering depth information. Applied Optics 24, 2076-2080. Hausler, G. and Korner, E. (1987) Imaging with expanded depth of focus. Zeiss Information, Vol 29, pp. 1-32. Carl Zeiss, Oberkochen, Germany. Itoh, K., Hayashi, A. and Ichioka, Y. (1989) Digitized optical microscopy with extended depth of field. Applied Optics. 28, 3487-3493. Vollath, D., The Influence of the scene parameters and of noise on the behaviour of automatic focusing algorithms. Journal of Microscopy, Vol. 151, Pt 2, August 1988, pp. 133-146. Erteza, A., Sharpness index and its application to focus control. Applied Optics Vol 15, No. 4, April 1976. pp 877-881. Erteza, A., Depth of convergence of a sharpness index autofocus system Applied Optics Vol 16, No. 8, August 1977. pp 2273-2278. Born, M. and Wolf, E., Principles of Optics, Pergamon Press, 1980, pp 435-442. Goss, R., Holm, J., Thin Section Photomicrography, Kodak TechBits 1, 1992, pp 4-7. Conrady, A. E. Applied optics and optical design Part 2 Dover Publications 1960 pp 627-628. Hope this helps. Noel Noel T Goldsmith DSTO Aeronautical Research Laboratory 506 Lorimer Street Port Melbourne Vic 3207 Australia From sarmienu@rnisd0.DNET.roche.com Fri Oct 22 04:07:44 1993 Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c) id AA17386; Fri, 22 Oct 1993 07:06:21 -0500 Return-Path: Received: by gatekeeper.roche.com (5.65/fma-120691); id AA04797; Fri, 22 Oct 93 08:07:47 -0400 Received: by mailgate.roche.com (5.65/fma-120691); id AA28363; Fri, 22 Oct 93 08:04:13 -0400 From: sarmienu@rnisd0.DNET.roche.com Message-Id: <9310221204.AA28363@mailgate.roche.com> Received: from rnisd0.enet; by inet.enet; Fri, 22 Oct 93 08:07:44 EDT Date: Fri, 22 Oct 93 08:07:44 EDT To: nih-image@soils.umn.edu Apparently-To: nih-image@soils.umn.edu Subject: IP-Lab Spectrum and LG-3 I thought this may be of some interest: IP-Lab now supports the frame grabber that we have been using for NIH Image. This is interesting in that the software is not that expensive and may be used in addition to or instead of NIH Image. Furthermore, I will be looking into validation for FDA approval for this program as well as PrismView (more expensive). For more information, contact: Signal Analytics Corp., 440 Maple Avenue East, Suite 201, Vienna VA 22180, phone 703-281-3277, fax 703-281-2509. Ask for Dr. Michael Mort. Their email address via internet is D6196@Applelink.Apple.Com From mvivino@helix.nih.gov Fri Oct 22 05:58:56 1993 Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c) id AA18040; Fri, 22 Oct 1993 08:57:31 -0500 Return-Path: Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0)) id AA21731; Fri, 22 Oct 93 09:58:56 -0400 Date: Fri, 22 Oct 93 09:58:56 -0400 Message-Id: <9310221358.AA21731@helix.nih.gov> X-Sender: mvivino@128.231.2.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mvivino@helix.nih.gov (Mark Vivino) Subject: Re: illumination >hi, >we do a lot of processing of retinas, and are frequently {deleted} >i am having a problem with illumination, particularly reflections. {deleted} Aside from polarisers, what about all the instrumentation that has been designed exactly for the purpose of looking at the retina? As far as comes to mind there is an indirect ophthalmoscope, fundus camera and probably others. These are routinely used here at NIH for studies such as macular edema, etc. Mark Vivino NIH/DCRT mvivino@helix.nih.gov From COIN@NIEHS.NIH.GOV Fri Oct 22 06:52:42 1993 Received: from NIEHS.NIH.GOV (vaxe.niehs.nih.gov) by nx1.soils.umn.edu (5.65c) id AA18461; Fri, 22 Oct 1993 09:50:30 -0500 Return-Path: Received: from NIEHS.NIH.GOV by NIEHS.NIH.GOV (PMDF V4.2-13 #3461) id <01H4ESFZ9ZOW90OASF@NIEHS.NIH.GOV>; Fri, 22 Oct 1993 10:52:42 EDT Date: Fri, 22 Oct 1993 10:52:42 -0400 (EDT) From: Patrick Coin Subject: cell scoring macro? To: NIH-IMAGE@SOILS.UMN.EDU Message-Id: <01H4ESFZA9C290OASF@NIEHS.NIH.GOV> X-Vms-To: IN%"NIH-IMAGE@SOILS.UMN.EDU" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Howdy. I'd like to use Image as a semi-automated scoring system for immuno-stained cells. I have cells on a slide that are either unlabelled (blue counter- staining) or labelled (brown). These differences show up clearly in the 8-bit indexed color when I capture a color image. I would then like to take the crosshair tool and MANUALLY score each cell by clicking on it and have the program keep count of labelled, unlabelled, and total cells. (I'd like to differentiate the two by holding down the option key or something.) I know there might be a fancy way to use automated particle counting to do this, but this is too slow and it is too hard to screen out the frequent pieces of junk on the slide. These are easy to screen out by eye. My main interest in using the digitizer is to reduce eye strain. This is a serious problem when counting 100 or 200 cells/slide and then counting 20 slides for a single experiment. So have any of you macro mavens out there seen a macro to do this? Alternatively, does anybody have an idea where to start to write a macro to do this? Many thanks Patrick Coin COIN@NIEHS.NIH.GOV Laboratory of Pulmonary Pathobiology National Institute of Environmental Health Sciences (a lesser known part of your friendly National Institutes of Health) From pruskyg@hg.uleth.ca Fri Oct 22 02:04:24 1993 Received: from holly.cc.uleth.ca by nx1.soils.umn.edu (5.65c) id AA18900; Fri, 22 Oct 1993 11:03:02 -0500 Return-Path: Received: by holly.cc.uleth.ca; id AA00282; Fri, 22 Oct 1993 10:00:58 -0600 Message-Id: <9310221600.AA00282@holly.cc.uleth.ca> Date: Fri, 22 Oct 1993 10:04:24 -0800 To: nih-image@soils.umn.edu From: pruskyg@hg.uleth.ca (Glen Prusky) X-Sender: pruskyg@pop.uleth.ca Subject: RE: Sweet wishes >How accurate a reconstruction does this method produce? How does it deal with >collateral branches in the same ROI but in different focal planes? > Harvey Karaten > Harvey J. Karten, M.D. > Dept. Neurosciences > UCSD 0608 > La Jolla, CA 92093 > Phone (619)-534-4938 > FAX (619)-534-6602 > E-Mail KARTENH@SDSC.EDU Harvey, My brain might be frozen this morning, but I am not sure what you mean by ROI. This method of capturing an image is much better than cutting and pasting individual peices of many images together to form a montage. Basically you rely on your judgement of when an area is in focus. If a process rapidly moves through the depth of a piece if tissue, then you simply make smaller boxes and follow that process to its end. Of course it is not perfect because it is not truly slicing the tissue, but many times you would like the detail of a higher magnification and the depth of field of lower magnification. This is one compromize. The kind of tissue that I use and I think that most people use is a slice of tissue 100-300 uM thick and most of the time, this procedure works well. I know Haig uses this technique to follow neurons and muscles in whole fly and grasshopper embyos with great success. See the covers of The Journal of Neurobiology, Vol 24 #6, June 1993 and the cover of Trends in Neurosciences, Vol 16, #7[181], July 1993. All of the work in the papers in these journals was done using this technique. It works extremely well! Glen Prusky Glen T. Prusky Ph.D. Department of Psychology The University of Lethbridge 4401 University Drive Lethbridge, AB, Canada T1K 3M4 pruskyg@hg.uleth.ca Office-403-329-2402 Lab-403-329-2410 Fax-403-329-2410 From pruskyg@hg.uleth.ca Fri Oct 22 02:23:38 1993 Received: from holly.cc.uleth.ca by nx1.soils.umn.edu (5.65c) id AA19076; Fri, 22 Oct 1993 11:19:52 -0500 Return-Path: Received: by holly.cc.uleth.ca; id AA00347; Fri, 22 Oct 1993 10:20:12 -0600 Message-Id: <9310221620.AA00347@holly.cc.uleth.ca> Date: Fri, 22 Oct 1993 10:23:38 -0800 To: nih-image@soils.umn.edu From: pruskyg@hg.uleth.ca (Glen Prusky) X-Sender: pruskyg@pop.uleth.ca Subject: Re: Sweet wishes Noel Writes: >Well, I have done this for opaque reflective specimens. This code is not >yet quite mature. I (the place where I work) are considering the financial >implications of commercialisng it. Another much more difficult problem is >how do you cope with constant changes in Image. I am thinking that if we >package our method in a plug in it may do. Or we could put it in NIHUMX, >which would put all of the extra code in one module. >May I recommend the following references for those who want to do a bit of >library digging. As you might guess I am writing a paper on the topic. > Peiper, R.J., and Korpel, A. (1983) Image Processing for extended depth >of field. Applied Optics 22, 1449-1453. > Sugimoto, S.A. and Ichioka, Y. (1985) Digital composition of images with >increased depth of focus considering depth information. Applied Optics 24, >2076-2080. > Hausler, G. and Korner, E. (1987) Imaging with expanded depth of focus. >Zeiss Information, Vol 29, pp. 1-32. Carl Zeiss, Oberkochen, Germany. > Itoh, K., Hayashi, A. and Ichioka, Y. (1989) Digitized optical microscopy >with extended depth of field. Applied Optics. 28, 3487-3493. > Vollath, D., The Influence of the scene parameters and of noise on the >behaviour of automatic focusing algorithms. Journal of Microscopy, Vol. >151, Pt 2, August 1988, pp. 133-146. > Erteza, A., Sharpness index and its application to focus control. Applied >Optics Vol 15, No. 4, April 1976. pp 877-881. > Erteza, A., Depth of convergence of a sharpness index autofocus system >Applied Optics Vol 16, No. 8, August 1977. pp 2273-2278. > Born, M. and Wolf, E., Principles of Optics, Pergamon Press, 1980, pp 435-442. > > Goss, R., Holm, J., Thin Section Photomicrography, Kodak TechBits 1, 1992, >pp 4-7. > Conrady, A. E. Applied optics and optical design Part 2 Dover >Publications 1960 pp 627-628. >Hope this helps. >Noel >Noel T Goldsmith >DSTO >Aeronautical Research Laboratory >506 Lorimer Street >Port Melbourne >Vic 3207 >Australia Noel, See my reply to Harvey Karten. In terms of the actual code to accomplish this within Image, my preference would be to have another option in the Special menu that simply allowed you to capture images in this manner, just like you can average, integrate or subtract background. This could be called something like 'Build Image'. First you would capture an original and then use the area selection items (probably the box or the elipse would be fine; Haig's system uses the box) to select the area of the image that you would like to focus. That area would have live camera input that you could see over the original image , allowing you to focus that area with the surrounding areas of the original image, and then paste it in. Just like in the normal capture mode you could terminate the live video either by a carriage return or the mouse button, or by using the same average or integrate settings that were used to capture the original image. This maintains consistency in the quality of the image across the resulting montage. If this mode of capture were part of the normal capturing menu, plug ins would not be necessary. Obviously, to accomplish this, it would have to be placed in Wayne's queue of priorities for updates. I think that this would be a very nice addition to the program. What do you think Wayne? Glen Prusky Glen T. Prusky Ph.D. Department of Psychology The University of Lethbridge 4401 University Drive Lethbridge, AB, Canada T1K 3M4 pruskyg@hg.uleth.ca Office-403-329-2402 Lab-403-329-2410 Fax-403-329-2410 From morilak@cmgm.stanford.edu Fri Oct 22 02:53:11 1993 Received: from cmgm.Stanford.EDU by nx1.soils.umn.edu (5.65c) id AA19283; Fri, 22 Oct 1993 11:47:25 -0500 Return-Path: Received: from (P159-macclassic.Stanford.EDU) by cmgm.stanford.edu (4.1/1.34) id AA25671; Fri, 22 Oct 93 09:48:49 PDT From: morilak@cmgm.stanford.edu (David Morilak) Date: Fri, 22 Oct 1993 09:53:11 PDT Subject: Re: live paste? To: nih-image@soils.umn.edu In-Reply-To: Your message of Fri, 22 Oct 1993 10:05:18 -0500 Message-Id: In response to the question about doing a "photomontage" in Image to bring different focal planes into focus (sorry, I mistakenly deleted the original so I can't reference the sender), wouldn't the Live Paste function do the trick? Even if items in different focal planes existed within a ROI, that subregion could be selected again from the camera window and then refocused in a live paste. I guess the main limitations would be that rectangular selections only are allowed, and that if there were huge differences in focal plane, there might also be an apparent size change, meaning that edges might not line up exactly right. I gave this a quick and limited try before responding, and it seemed to work. But, being fairly new at this, I'm more than happy to be corrected... David Morilak Dept of Psychiatry Stanford Univ morilak@cmgm.stanford.edu ------- From bright@ENH.NIST.GOV Fri Oct 22 10:20:33 1993 Received: from enh.nist.gov by nx1.soils.umn.edu (5.65c) id AA19925; Fri, 22 Oct 1993 13:20:20 -0500 Return-Path: Received: from [129.6.98.4] (dsb-mac.nist.gov) by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01H4EZQPD4Q8002EFP@ENH.NIST.GOV>; Fri, 22 Oct 1993 14:20:33 EDT Date: Fri, 22 Oct 1993 14:20:33 -0400 (EDT) Date-Warning: Date header was inserted by ENH.NIST.GOV From: bright@ENH.NIST.GOV Subject: Re: 4pi Analysis in North Carol To: nih-image@soils.umn.edu Message-Id: <01H4EZQPO46Q002EFP@ENH.NIST.GOV> Content-Transfer-Encoding: 7BIT > Subject: Time:10:15 AM > OFFICE MEMO 4pi Analysis in North Carolina makes_ Date:10/21/93 >>4pi Analysis in North Carolina makes a board for the Macintosh >>computer that will scan an image on an electron microscope and collect >>a digital image. Image size can be anything up to 4096x4096 with 14 >>bits per pixel. > >What camera do you use to take advantage of the 4096x4096 resolution and how >do you mount the camera? What printer do you use to obtain hardcopy and are the >resulting prints of publication quality? > >Mike Schwartz >Sect. of Neurobiology >Yale Univ. Sch. of Med. >Mike Schwartz@qm.yale.edu The 4Pi board controls the scanning of the beam and gets the signal (scattered electron count, or whatever) directly from the microscope. There is no camera involved, which is why this type of thing is so nice: large images and large dynamic range for the data. :8o) Dave ------------------------------------------------------------- David S. Bright bright@enh.nist.gov Microanalysis Research Group Chem. A113 National Institute of Standards & Technology (NIST, formerly NBS) Gaithersburg, MD 20899-0001 USA 301-975-3911 - voice, 301-216-1134 - fax From wayne@helix.nih.gov Fri Oct 22 14:25:05 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA20511; Fri, 22 Oct 1993 14:26:40 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA18210; Fri, 22 Oct 93 14:46:55 -0400 Message-Id: <9310221846.AA18210@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 22 Oct 1993 14:25:05 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: IPL and AxoVideo >Since the exchanges on this list a couple weeks back, we've >made a couple macros to load a stack of alternating-wavelength >images, and create a new stack of ratioed images. The trouble >is that the 'divide' routine currently automatically scales >the resulting image to the widest possible dynamic range (ie. >stretches the max/min ratios to 256/0, respectively), as >best I understand. This creates problems as we need to keep >the scaling uniform through our image series. Otherwise the >calibration curve will mean nothing. > >Wayne wrote that he was contemplating a fix for this problem. There is a new command in the latest beta on Zippy called Image Math that does image arithmetic between two images and allows you to specify the scale and offset needed to scale back to 8-bits. There is a corresponding macro routine that has the form "ImageMath('divide', pic1, pic2, scale, offset, 'Result')", where pic1 and pic2 are pic numbers or pid numbers. --wayne From wayne@helix.nih.gov Fri Oct 22 16:20:52 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA21357; Fri, 22 Oct 1993 16:22:38 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA18638; Fri, 22 Oct 93 16:42:41 -0400 Message-Id: <9310222042.AA18638@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 22 Oct 1993 16:20:52 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Sweet wishes >See my reply to Harvey Karten. In terms of the actual code to accomplish >this within Image, my preference would be to have another option in the >Special menu that simply allowed you to capture images in this manner, just >like you can average, integrate or subtract background. This could be >called something like 'Build Image'. First you would capture an original >and then use the area selection items (probably the box or the elipse would >be fine; Haig's system uses the box) to select the area of the image that >you would like to focus. That area would have live camera input that you >could see over the original image , allowing you to focus that area with >the surrounding areas of the original image, and then paste it in. Just >like in the normal capture mode you could terminate the live video either >by a carriage return or the mouse button, or by using the same average or >integrate settings that were used to capture the original image. This >maintains consistency in the quality of the image across the resulting >montage. If this mode of capture were part of the normal capturing menu, >plug ins would not be necessary. Obviously, to accomplish this, it would >have to be placed in Wayne's queue of priorities for updates. I think that >this would be a very nice addition to the program. What do you think Wayne? I would like to see someone put this feature into Image so we can see how difficult it is to implement and how well it works. If it works well and looks like it would be useful to a lot people then I can put it into the production version. --wayne From kartenh@sdsc.edu Fri Oct 22 23:41:55 1993 Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA22022; Fri, 22 Oct 1993 18:40:39 -0500 Return-Path: Message-Id: <199310222340.AA22022@nx1.soils.umn.edu> Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET; Fri, 22 Oct 93 23:41:54 GMT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: kartenh@Sdsc.Edu Subject: Re: 4pi Analysis in North Carol Date: Fri, 22 Oct 93 23:41:55 GMT > >The 4Pi board controls the scanning of the beam and gets the signal >(scattered electron count, or whatever) directly from the microscope. >There is no camera involved, which is why this type of thing is so nice: >large images and large dynamic range for the data. >:8o) Dave Are you referring tro the output of an SEM or a TEM? That was the nature of my question. I had assumed that you were referring to a TEM, where the image is commonly imaged onto a film plane. Harvey Karten Harvey J. Karten, M.D. Dept. of Neurosciences Univ.California San Diego La Jolla, CA 92093-0608 EMail: Kartenh@sdsc.edu Phone: (619)-534-4938 FAX: (619)-534-6602 From CMSABEL@minna.acc.iit.edu Thu Oct 21 12:09:31 1993 Received: from harpo.acc.iit.edu by nx1.soils.umn.edu (5.65c) id AA04191; Sat, 23 Oct 1993 22:31:51 -0500 Return-Path: Received: from minna.acc.iit.edu by minna.acc.iit.edu (PMDF V4.2-12 #3556) id <01H4DRACW3AO8ZHTTX@minna.acc.iit.edu>; Thu, 21 Oct 1993 17:09:31 CDT Date: Thu, 21 Oct 1993 17:09:31 -0500 (CDT) From: CMSABEL@minna.acc.iit.edu Subject: Re: grain counting macros To: nih-image@soils.umn.edu Message-Id: <01H4DRACX5VM8ZHTTX@minna.acc.iit.edu> X-Vms-To: IN%"nih-image@soils.umn.edu" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Wayne, thanks for the offer. I , with the help of a colleague , have been working on modifying the macro to suit our needs. I think we are very close. So, I won't bother you with it at the moment. If we get it worked out, I'll upload it (the modified macro)...and if we don't, I'll e-mail you with specific questions. Thanks again, Marc From sc@wiko-berlin.DE Sun Oct 24 13:18:55 1993 Received: from sc.ZIB-Berlin.DE by nx1.soils.umn.edu (5.65c) id AA07564; Sun, 24 Oct 1993 06:16:04 -0500 Return-Path: Received: from wiko-berlin.DE ([192.55.244.98]) by sc.ZIB-Berlin.DE (4.1/SMI-4.0-sc/03.06.93) id AA01139; Sun, 24 Oct 93 12:17:26 +0100 Received: from [192.55.244.93] (quadra) by wiko-berlin.DE (4.1/SMI-4.0-MHS-6.0) id AA21218; Sun, 24 Oct 93 12:18:55 +0100 Date: Sun, 24 Oct 93 12:18:55 +0100 Message-Id: <9310241118.AA21218@wiko-berlin.de> From: "Scott Camazine" To: NIH-IMAGE@soils.umn.edu Subject: Images Dear NIH-Image users: I am new to this list but would like to make a request. I am trying to get some interesting high resolution black and white 8-bit images of medical pathology that I can enhance by applying various palettes with PalEdit, Spyglass and similar programs. I would like to use these images for lectures and possibly in publications. The contributions I have submitted to the anonymous ftp (zippy.nimh.nih.gov) are examples of the kind of images I am interested in. I have acquired these images by scanning black and white 35mm slides of xrays, CAT scans, and MRIs that I have access to at the hospitals where I work. If any of you have images (preferably in the form of scans at a resolution of at least 1000 dpi, which would give a file size of several megabytes for a 35mm slide) which I could use without infringing upon anyone's copyrights, I would like to hear from you. I have also been trying to get some nice images of molecules. I have been using Alchemy and Chem3D which give pretty space-filling molecules. I was wondering if anyone knew who contributed the image titled "molecule" to the anonymous ftp address. I would like to find out what software was used to generate that image. Thanks, Scott Camazine (sc@wiko-berlin.de) From mt1ntg@fencer.cis.dsto.gov.au Tue Oct 26 01:08:00 1993 Received: from fencer.cis.dsto.gov.au by nx1.soils.umn.edu (5.65c) id AA13627; Mon, 25 Oct 1993 00:06:45 -0500 Return-Path: Message-Id: <199310250506.AA13627@nx1.soils.umn.edu> Received: from [160.64.14.216] by fencer.cis.dsto.gov.au with SMTP; Mon, 25 Oct 1993 15:08:06 +1000 (EST) Date: Mon, 25 Oct 1993 15:08:00 +1000 To: nih-image@soils.umn.edu From: NoelGoldsmith (Noel Goldsmith) Subject: Re: Sweet wishes Glen writes >Noel, >See my reply to Harvey Karten. In terms of the actual code to accomplish >this within Image, my preference would be to have another option in the >Special menu that simply allowed you to capture images in this manner, just >like you can average, integrate or subtract background. This could be >called something like 'Build Image'. First you would capture an original >and then use the area selection items (probably the box or the elipse would >be fine; Haig's system uses the box) to select the area of the image that >you would like to focus. That area would have live camera input that you >could see over the original image , allowing you to focus that area with >the surrounding areas of the original image, and then paste it in. Just >like in the normal capture mode you could terminate the live video either >by a carriage return or the mouse button, or by using the same average or >integrate settings that were used to capture the original image. This >maintains consistency in the quality of the image across the resulting >montage. If this mode of capture were part of the normal capturing menu, >plug ins would not be necessary. Obviously, to accomplish this, it would >have to be placed in Wayne's queue of priorities for updates. I think that >this would be a very nice addition to the program. What do you think Wayne? > >Glen Prusky Glen, I see now that what you want to do is different to what I do. I want to get all of the surface of an opaque rough object in focus on one image. You want to follow a structure through a translucent object so as to produce a 2D of it. The process I use relies on no operator decisions, it knows when a piece of an image is in the best focus for the z series. I have not tried this out on specimens like yours, our microscopes work with incident light, yours with transmitted. Also, by restricting the activity to a simple cut and paste on the selected area of the image, the speed of the computations becomes a non-issue. In your response to Harvey Karten you affirm that the results of the operation you propose are superior to a cut and paste from a z series. When my procedure is used it works much better than a manual cut and paste, mainly because my patience and manual dexterity is not as good as that of the TOM (totally obedient moron ) or computer. The down side on what I do is that if there is noise in the images, it is favoured in the montage. Maybe you could email me some Z series and I will have a go at them if you like. If you use a mailer like Eudora I think you can enclose images, or you could turn them into giffs. Noel. Noel T Goldsmith DSTO Aeronautical Research Laboratory 506 Lorimer Street Port Melbourne Vic 3207 Australia From pierre.trebbia@univ-reims.fr Mon Oct 25 10:49:06 1993 Received: from cleo.univ-reims.fr by nx1.soils.umn.edu (5.65c) id AA14543; Mon, 25 Oct 1993 03:50:22 -0500 Return-Path: Message-Id: <199310250850.AA14543@nx1.soils.umn.edu> Received: from centre01.univ-reims.fr by cleo.univ-reims.fr with SMTP (1.37.109.4/16.2) id AA08343; Mon, 25 Oct 93 09:52:20 +0100 Received: from [193.50.208.72] by centre01.univ-reims.fr with SMTP (1.37.109.4/16.2) id AA16987; Mon, 25 Oct 93 09:49:06 +0100 Date: Mon, 25 Oct 93 09:49:06 +0100 To: nih-image@soils.umn.edu From: pierre.trebbia@univ-reims.fr (Pierre TREBBIA) X-Sender: trebbia@centre01 Subject: Re: grain counting macros Big problem! I got (and I'm getting) about 30 times the same message. Please check what's wrong. >Wayne, > >thanks for the offer. I , with the help of a colleague , have been working >on modifying the macro to suit our needs. I think we are very close. So, I >won't bother you with it at the moment. If we get it worked out, I'll >upload it (the modified macro)...and if we don't, I'll e-mail you with >specific questions. > >Thanks again, > >Marc -------------- Pierre Trebbia, LASSI/GRSM, Universite de Reims, F51062 Reims cedex, France Email : pierre.trebbia@univ-reims.fr Phone : (33) 26 05 33 62 FAX : (33) 26 05 32 50 From @cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be Mon Oct 25 11:38:22 1993 Received: from cc1.kuleuven.ac.be by nx1.soils.umn.edu (5.65c) id AA14808; Mon, 25 Oct 1993 04:38:50 -0500 Return-Path: <@cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be> Received: from rc1.vub.ac.be by cc1.kuleuven.ac.be (IBM VM SMTP V2R2) with TCP; Mon, 25 Oct 93 10:39:13 +0100 Received: from dec5.ulb.ac.be (dbmdec5) by rc1.vub.ac.be (4.1/RC1-930922) id AA09125; Mon, 25 Oct 93 10:40:27 +0100 Received: by dec5.ulb.ac.be (5.65/ULB.920908) id AA14535; Mon, 25 Oct 1993 10:38:23 +0100 From: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN) Message-Id: <9310250938.AA14535@dec5.ulb.ac.be> Subject: Illegal Instruction on Quadra To: nih-image@soils.umn.edu Date: Mon, 25 Oct 1993 10:38:22 +0100 (WET DST) Cc: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN) In-Reply-To: <199310250850.AA14543@nx1.soils.umn.edu> from "Pierre TREBBIA" at Oct 25, 93 03:50:39 am X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 581 Hi everybody, I have a problem when I want to work on Image sources with a Quadra 800. When I use the Measure command, I get an 'Illegal Instruction' error message, with the finger pointing to the runtime.lib file. This error does not exist on the compiled version (even when compiled on the quadra). The source error is also absent when I run the sources on a fx. Has anyone experienced this kind of problem ? Should I choose special settings in the compile or source options for working on sources with the Quadra ? Thanks, Jacques van Helden jvanheld@dbmdec5.ulb.ac.be From John_Mansfield@mse.engin.umich.edu Mon Oct 25 09:58:54 1993 Received: from mse.engin.umich.edu by nx1.soils.umn.edu (5.65c) id AA16664; Mon, 25 Oct 1993 09:58:54 -0500 Return-Path: Message-Id: <199310251458.AA16664@nx1.soils.umn.edu> Date: 25 Oct 1993 10:47:46 U From: "John Mansfield" Subject: Re: 660av Screen Capture & To: nih-image@soils.umn.edu Reply_ RE>>660av Screen Capture & 840av too Reply from: John Mansfield North Campus Electron Microbeam Analysis Laboratory University of Michigan 2455 Hayward Ann Arbor MI 48109-2143 Phone: (313)936-3352 jfmjfm@engin.umich.edu or John_Mansfield@mse.engin.umich.edu I have tried out the 840av with a VCR and a good quality TV camera. The problem I have is that, as everyone has pointed out, the avs are optimized for Quicktime. There is no single frame acquisition software that comes with the machine. The only way I could grab a whole 640 by 480 frame was to display the video in "full screen" mode in the "Video Monitor" application and then do a command-c. You hear the "camera shutter" sound and the next video frame is copied to the clipboard. You can then past this image into NIH-Image. The image quality isnt as good as the Scion LG-3 board, but it's not too bad compared with the old early Scion boards we also have. Too bad there isnt some software to average a few consecutive video frames as that would help clean up the image noise and would make the 660av a good buy for low end frame grabbing. It's perfect for student labs! Built in frame grabbing, video and ethernet! What more do you want? (Yes, I know... the sun and moon and.....) Does anyone know if anyone is working on a plug-in for these machines? John Mansfield. From glenmac@u.washington.edu Mon Oct 25 04:22:09 1993 Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c) id AA18883; Mon, 25 Oct 1993 13:32:36 -0500 Return-Path: Received: by carson.u.washington.edu (5.65/UW-NDC Revision: 2.29 ) id AA16497; Mon, 25 Oct 93 11:26:47 -0700 X-Sender: glenmac@carson.u.washington.edu Date: Mon, 25 Oct 1993 11:22:09 -0700 (PDT) From: Glen Macdonald Subject: Re: cell scoring macro? To: nih-image@soils.umn.edu Cc: Multiple recipients of list In-Reply-To: <01H4ESFZA9C290OASF@NIEHS.NIH.GOV> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=us-ascii Take a look at the Cavalieri macro in the UserMacros dir on Zippy. You may be able to use it as is, simply counting all of one category, then counting the other label category. Or, take it apart and use the core counting code to be able to incorporate an option-click so you can mix your counts. Read the Cavalieri doc also in that directory. Glen MacDonald Hearing Development Labs University of Washington From Joel_Boymel@tpdmgate.amgen.com Fri Oct 25 06:46:16 1993 Received: from relay1.UU.NET by nx1.soils.umn.edu (5.65c) id AA20332; Mon, 25 Oct 1993 15:51:35 -0500 Return-Path: Received: from amgen.com (via ns.amgen.com) by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AA29199; Mon, 25 Oct 93 16:52:48 -0400 Received: from tpdmgate.amgen.com by amgen.com (4.1/SMI-4.1) id AA06690; Mon, 25 Oct 93 13:52:43 PDT Message-Id: <9310252052.AA06690@amgen.com> Date: 25 Oct 1993 14:46:16 -0800 From: "Joel Boymel" Subject: None To: "NIH Image" Mail*Link(r) SMTP None help set From mmoberg%11.59.dnet.smhi.se@lurch.smhi.se Tue Oct 26 08:37:40 1993 Received: from palantir.p.tvt.se by nx1.soils.umn.edu (5.65c) id AA28337; Tue, 26 Oct 1993 01:36:25 -0500 Return-Path: Received: from gatekeeper.smhi.se by palantir.p.tvt.se with smtp (Smail3.1.28.1 #2) id m0ori5q-000ABsC; Tue, 26 Oct 93 07:41 WET Received: by gatekeeper.smhi.se (5.65/DEC-Ultrix/4.3) id AA00781; Tue, 26 Oct 1993 07:38:18 +0100 Received: by lurch.smhi.se (5.65/DEC-Ultrix/4.3) id AA09354; Tue, 26 Oct 1993 07:37:40 +0100 Date: Tue, 26 Oct 1993 07:37:40 +0100 Message-Id: <9310260637.AA09354@lurch.smhi.se> From: mmoberg%11.59.dnet.smhi.se@lurch.smhi.se (mmoberg@lurch.smhi.se) To: "nih-image@soils.umn.edu"%LURCH.dnet.smhi.se@lurch.smhi.se Cc: mmoberg@lurch.smhi.se Subject: Another LUT-question I am in need of a function that let me use colour-LUTs from other Image processing system in NIH Image. A convenient way of defining a LUT is by means of a formatted file (256 lines long) that in every line has information about: digital count Red amount Green amount Blue amount Is there any possibility to include a function in NIH Image that, similar to Macro-making, will make a LUT from a text window - e.g. "Load LUT from window"? M Moberg, mmoberg@smhi.se From bonnot@jouy.inra.fr Tue Oct 26 17:02:52 1993 Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c) id AA01372; Tue, 26 Oct 1993 08:54:24 -0500 Return-Path: Received: from inra.inra.fr by chenas.inria.fr (5.65c8d/92.02.29) via Fnet-EUnet id AA26453; Tue, 26 Oct 1993 14:55:40 +0100 (MET) Received: from jouy.jouy.inra.fr by inra.inra.fr, Tue, 26 Oct 93 14:55:15 +0100 Received: from [134.214.101.173] (bio2.insa-lyon.fr) by jouy.jouy.inra.fr, Tue, 26 Oct 93 14:52:55 +0100 Message-Id: <9310261352.AA01017@jouy.jouy.inra.fr> X-Sender: bonnot@jouy.inra.fr (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 26 Oct 1993 16:02:52 +0100 To: nih-image@soils.umn.edu From: bonnot@jouy.inra.fr Subject: about projections I am attempting to make 3D reconstruction of aphid gut circonvolutions from histological slices. In order to better see the outer gut loops I tried to project my stack using the z axis for rotation and find this projection does not work as expected. All what I get is a rotating frontal projection (from front to back); the way th ex or y axis projection works lets me think (it's what I need) that z projection would project the stack from a lateral point of view while turning around the object. I probably don't have understood everything. does someone has other solution than reslicing repetitively my stack to constitute a longitudinal sliced stack using a macro (it would be perhaps better to return back to the microtome). Thanks for any suggestions ######################################################## # Guy Bonnot phone: +33 - 72 43 83 56 # # INRA - INSA fax: +33 - 72 43 85 11 # # Biologie 406 internet: bonnot@lyon.inra.fr # # 20, av. A. Einstein =bonnot@jouy.inra.fr # # 69621 Villeurbanne cedex # # France # ######################################################## From RBLYSTON@VM1.TUCC.TRINITY.EDU Tue Oct 26 05:43:37 1993 Received: from vm1.tucc.trinity.edu by nx1.soils.umn.edu (5.65c) id AA02295; Tue, 26 Oct 1993 10:43:30 -0500 Return-Path: Message-Id: <199310261543.AA02295@nx1.soils.umn.edu> Received: from VM1.tucc.trinity.edu by VM1.TUCC.TRINITY.EDU (IBM VM SMTP V2R2) with BSMTP id 9085; Tue, 26 Oct 93 10:44:35 CDT Received: from TRINITY.EDU (RBLYSTON) by VM1.tucc.trinity.edu (Mailer R2.10 ptf000) with BSMTP id 9084; Tue, 26 Oct 93 10:44:34 CDT Date: Tue, 26 Oct 93 10:43:37 CDT From: rblyston Subject: Re: about projections To: nih-image@soils.umn.edu In-Reply-To: Message of Tue, 26 Oct 1993 09:04:41 -0500 from To Guy Bonnet: Which version of Image are you using? and have you looked at SpyGlass? It might do what you want. Blystone in Texas ********************** ROBERT V. BLYSTONE PHONE:(210)736-7243 DEPARTMENT OF BIOLOGY FAX:(210)736-7229 Trinity University E-Mail:RBlyston@Trinity.edu 715 Stadium Drive San Antonio, TX, 78212 From bonnot@jouy.inra.fr Tue Oct 26 20:31:10 1993 Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c) id AA03196; Tue, 26 Oct 1993 12:22:41 -0500 Return-Path: Received: from inra.inra.fr by chenas.inria.fr (5.65c8d/92.02.29) via Fnet-EUnet id AA10899; Tue, 26 Oct 1993 18:23:57 +0100 (MET) Received: from jouy.jouy.inra.fr by inra.inra.fr, Tue, 26 Oct 93 18:23:32 +0100 Received: from [134.214.101.173] (bio2.insa-lyon.fr) by jouy.jouy.inra.fr, Tue, 26 Oct 93 18:21:13 +0100 Message-Id: <9310261721.AA04583@jouy.jouy.inra.fr> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 26 Oct 1993 19:31:10 +0100 To: nih-image@soils.umn.edu From: bonnot@jouy.inra.fr Subject: Re: about projections >To Guy Bonnet: Which version of Image are you using? and have you looked at >SpyGlass? It might do what you want. Blystone in Texas > >********************** >ROBERT V. BLYSTONE PHONE:(210)736-7243 >DEPARTMENT OF BIOLOGY FAX:(210)736-7229 >Trinity University E-Mail:RBlyston@Trinity.edu >715 Stadium Drive >San Antonio, TX, 78212 Thank you. I use NIH Image 1.52. How to access to SpyGlass? . I never see this program in catalogs in France. ######################################################## # Guy Bonnot phone: +33 - 72 43 83 56 # # INRA - INSA fax: +33 - 72 43 85 11 # # Biologie 406 internet: bonnot@lyon.inra.fr # # 20, av. A. Einstein =bonnot@jouy.inra.fr # # 69621 Villeurbanne cedex # # France # ######################################################## From CHARLEST@macc.wisc.edu Tue Oct 26 08:26:00 1993 Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c) id AA03746; Tue, 26 Oct 1993 13:26:21 -0500 Return-Path: Received: from VMSmail by vms2.macc.wisc.edu; Tue, 26 Oct 93 13:26 CDT Message-Id: <23102613265529@vms2.macc.wisc.edu> Date: Tue, 26 Oct 93 13:26 CDT From: Charles Thomas Subject: Re: about projections To: nih-image@soils.umn.edu X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST Spyglass, Inc. P.O. Box 6338 Champaign, IL 61826 (217) 355-6000 USA We have used Spyglass Dicer in limited applications and have found it very useful. It allows you to show 2D planes through your specimen at any orientation, view surfaces, cut chunks out of volumes to see inner details, etc. It makes a very nice compliment to Voxel View/Mac and NIH-Image. Feel free to call or Email me directly with any specific questions. Charles Thomas Integrated Microscopy Resource University of Wisconsin, Madison 608-263-8481 P.S. I have made a demonstration video tape outlining many of Spyglass Dicer's features. I could arrange to have it sent to you if it would be helpful. From RBLYSTON@VM1.TUCC.TRINITY.EDU Tue Oct 26 08:31:16 1993 Received: from vm1.tucc.trinity.edu by nx1.soils.umn.edu (5.65c) id AA03881; Tue, 26 Oct 1993 13:38:37 -0500 Return-Path: Message-Id: <199310261838.AA03881@nx1.soils.umn.edu> Received: from VM1.tucc.trinity.edu by VM1.TUCC.TRINITY.EDU (IBM VM SMTP V2R2) with BSMTP id 1732; Tue, 26 Oct 93 13:39:43 CDT Received: from TRINITY.EDU (RBLYSTON) by VM1.tucc.trinity.edu (Mailer R2.10 ptf000) with BSMTP id 1731; Tue, 26 Oct 93 13:39:41 CDT Date: Tue, 26 Oct 93 13:31:16 CDT From: RBlystone Subject: Re: about projections To: nih-image@soils.umn.edu In-Reply-To: Message of Tue, 26 Oct 1993 12:34:28 -0500 from To Guy: Obviously you are using the most current full version of Image. Spyglass is a commercial product. Its Email address is D5717@applelink.apple.co m. FAX is 217-355-8925 and regular phone 217-355-1665. Address is P.O. Box 6388 Champaign, IL. 61826 USA A person to speak to is Brand Fortner. SpyGlass has an interesting application called Dicer and it can be used to create animated rotations. There is another early version of SpyGlass that is public domain called NCSA Dataslice. You can find that at ftp.ncsa.uiuc.edu. I find SpyGlass very useful for rotations of histological reconstructions of se rial sections. Blystone in Texas ********************** ROBERT V. BLYSTONE PHONE:(210)736-7243 DEPARTMENT OF BIOLOGY FAX:(210)736-7229 Trinity University E-Mail:RBlyston@Trinity.edu 715 Stadium Drive San Antonio, TX, 78212 From NSafford@scigen.co.uk Tue Oct 26 19:11:59 1993 Received: from eros.Britain.EU.net by nx1.soils.umn.edu (5.65c) id AA04320; Tue, 26 Oct 1993 14:21:37 -0500 Return-Path: Received: from scigen.co.uk by eros.britain.eu.net with UUCP id ; Tue, 26 Oct 1993 19:20:58 +0000 Received: from [192.9.200.40] (sg_quadra_800) by scigen.co.uk (4.1/SMI-4.1) id AA08412; Tue, 26 Oct 93 19:11:23 GMT Message-Id: <9310261911.AA08412@ scigen.co.uk> Date: Tue, 26 Oct 1993 19:11:59 +0000 To: nih-image@soils.umn.edu From: NSafford@scigen.co.uk (Nick Safford) X-Sender: nas1@jasper Subject: Re: 660av Screen Capture. >>>I am thinking about purchasing a 660av to use NIH Image and was wondering >>>about the quality of screen capture. >>> >>>Is the 660av a poorman's viable alternative to a frame grabber card? >> >>Like the Video Spigot, it's a good if you wan't to hook up a camcorder to >>your Mac and make a color QuickTime movie. (The AV Macs use the same chip >>set as the Video Spigot.) You can convert the QuickTime movie into PICS >>format to get it into NIH Image. >> >>--wayne > >Does anyone know the actual performance specs of the 660av/840av on a >monochrome image from a decent video camera? Linear resolution, contrast >range, etc. > Harvey Karten > > Harvey J. Karten, M.D. > Dept. of Neurosciences > Univ.California San Diego > La Jolla, CA 92093-0608 > EMail: Kartenh@sdsc.edu > Phone: (619)-534-4938 > FAX: (619)-534-6602 For what it's worth, I've tried the 840AV against a Scion (and also QuickImage, QuickCapture, VideoSpigot). As I recall the order of quality goes: QuickCapture, Scion LG-3 Quadra 840AV QuickImage VideoSpigot. This is using the S-video input on the Quadra. The composite is not nearly as good (not surprisingly). The biggest problem with the 840AV's internal grabber (which I imagine is similar/identical to the 660) is that it's 16 bit (5 bits per gun and one that gets thrown away) and you do get obvious 'oatmeal' effects from this, as the greyscale information is really only 5 bits. For scientific purposes this is obviously a drawback. The resolution is pretty good - subjective sharpness is better than on the Scion but this is only because the contrast I achieved was higher (too high) with the 840AV. The true resolution is just about the same. Writing code to grab frames through the Quicktime routines is pretty easy, although I haven't done it myself in Pascal. I'm thinking of doing some kind of rudimentary photoshop plugin BUT as far as I'm aware you HAVE to be working with your monitor set to 16 bit to use it. This will make Image feel uncomfortable. (It might be possible to do something nasty with getting the code to switch modes on the way in and out of the plugin in the hope that Image won't notice the horrid thing you've done). The 16 bit display requirement is because the grabber stuffs its 16 bit data straight into VRAM. It's really quite fast. You can get full speed, full frame video onto your monitor (ie into your VRAM) and it's pretty amazing to look at (no lag!). Using sequential buffering on an 840av we nearly got full speed video into main RAM (rather than VRAM) - but not quite. You wouln't get so close with a 660av. This was PAL format - I'm not sure how this would work in NTSC format, as NTSC is a higher framing rate (but fewer lines, so the data rate you have to sustain is only 18Mb/sec instead of about 22Mb/sec). You clearly can't put data at these rates onto disc; Apple say you can get 1/4 frame onto disc at a sustained 30 fps. Hope this is of some use to somebody. Nick Safford (NSafford@scigen.co.uk) Scientific Generics Phone 0223 424425 King's Court Fax 0223 424281 Kirkwood Road Cambridge CB4 2PF UK From philp@physiol.su.oz.au Wed Oct 27 21:40:27 1993 Received: from cortex.physiol.su.OZ.AU by nx1.soils.umn.edu (5.65c) id AA07063; Tue, 26 Oct 1993 20:39:18 -0500 Return-Path: Received: by cortex.physiol.su.oz.au (5.57/Ultrix3.0-C) id AA05190; Wed, 27 Oct 93 11:40:27 +1000 Date: Wed, 27 Oct 93 11:40:27 +1000 From: philp@physiol.su.oz.au (Philip Poronnik) Message-Id: <9310270140.AA05190@cortex.physiol.su.oz.au> To: nih-image@soils.umn.edu Subject: edge detection Hi out there, does anyone have/know of an edge detection or edge following macro or algorithm to run under Image. The problem I have is that I am trying to follow volume changes in a clump of cells. At the moment I just trace around the perimeter and measure the number of pixels inside - infortunately I have literally thousands of images and some sort of automation would be more than appropriate. these are bright field images so it is very difficult to use a mask. I would rather be able to define an edge and let a macro just follow it around. Any help would be more than appreciated thanks philp From @cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be Wed Oct 27 12:45:03 1993 Received: from cc1.kuleuven.ac.be by nx1.soils.umn.edu (5.65c) id AA10828; Wed, 27 Oct 1993 06:35:06 -0500 Return-Path: <@cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be> Received: from rc1.vub.ac.be by cc1.kuleuven.ac.be (IBM VM SMTP V2R2) with TCP; Wed, 27 Oct 93 12:34:23 +0100 Received: from dec5.ulb.ac.be (dbmdec5) by rc1.vub.ac.be (4.1/RC1-930922) id AA24902; Wed, 27 Oct 93 12:35:42 +0100 Received: by dec5.ulb.ac.be (5.65/ULB.920908) id AA06516; Wed, 27 Oct 1993 11:45:04 +0100 From: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN) Message-Id: <9310271045.AA06516@dec5.ulb.ac.be> Subject: Re: edge detection To: nih-image@soils.umn.edu Date: Wed, 27 Oct 1993 11:45:03 +0100 (WET DST) Cc: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN) In-Reply-To: <9310270140.AA05190@cortex.physiol.su.oz.au> from "Philip Poronnik" at Oct 26, 93 08:39:39 pm X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 515 Hi, there is a routine I developed specially for tracing cell edges on bright field images. It is not a macro but a Pascal routine, which is integrated in NIH-Image. The compiled version, as well as the source code, are on zippy, in the contrib directory. The name of the file is Quantile_Crest.sit.hqx The archive includes an example stack. In this example, the edge finding is based on cell fluorescence, but it also works with bright field images. Good luck, Jacques van Helden jvanheld@dbmdec5.ulb.ac.be From wayne@helix.nih.gov Wed Oct 27 16:39:31 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA16303; Wed, 27 Oct 1993 16:41:09 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA16654; Wed, 27 Oct 93 17:01:47 -0400 Message-Id: <9310272101.AA16654@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Oct 1993 16:39:31 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: 660av Screen Capture. >For what it's worth, I've tried the 840AV against a Scion (and also >QuickImage, QuickCapture, VideoSpigot). Have you tried the Movie Movie card from Sigma Designs. It got a good write up in the latest MacUser and is only $300. >Writing code to grab frames through the Quicktime routines is pretty easy, >although I haven't done it myself in Pascal. I'm thinking of doing some >kind of rudimentary photoshop plugin BUT as far as I'm aware you HAVE to be >working with your monitor set to 16 bit to use it. I you sure of this? I thought the QuickTime capture program that comes with the AV Macs (Video Fusion?) requires that the monitor be in 8-bit mode. I would love to see a plug-in that uses QuickTime to capture images, particularly one that came with source code so I could see how it was done. I assume it would also work with any capture card with a QuickTime driver, such as the Video Spigot and the Movie Movie. --wayne From mhowland@alsvid.une.edu.au Thu Oct 28 21:49:45 1993 Received: from alsvid.une.edu.au by nx1.soils.umn.edu (5.65c) id AA18040; Wed, 27 Oct 1993 20:48:31 -0500 Return-Path: Received: from [129.180.146.5] (mac146_5.nr.une.edu.au) by alsvid.une.edu.au with SMTP id AA27807 (5.65c8+/IDA-1.4.4 for ); Thu, 28 Oct 1993 11:49:45 +1000 Date: Thu, 28 Oct 1993 11:49:45 +1000 Message-Id: <199310280149.AA27807@alsvid.une.edu.au> X-Sender: mhowland@pophost.nr.une.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mhowland@alsvid.une.edu.au (Mick Howland) Subject: source code What version of Think Pascal is the source code for Image written in. I have v4.0 and it doesn't seem to be able to open the Image project. _____________________________________________________________ Michael Howland, Faculty of Resource Science & Management UNE - Northern Rivers, P.O. Box 157, Lismore, NSW, Australia. Phone: +61-66-203037 Fax: +61-66-212669 E-mail: mhowland@alsvid.une.edu.au _____________________________________________________________ From huff@MCCLB0.MED.NYU.EDU Thu Oct 28 02:27:00 1993 Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c) id AA21830; Thu, 28 Oct 1993 06:24:35 -0500 Return-Path: Received: from [128.122.250.23] (EDHUFF.DIAL.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU (PMDF V4.2-14 #2884) id <01H4MZ0HI2BK0031CA@MCCLB0.MED.NYU.EDU>; Thu, 28 Oct 1993 07:25:48 EDT Date: Thu, 28 Oct 1993 07:27:00 -0500 From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff) Subject: Re: source code To: nih-image@soils.umn.edu Message-Id: <01H4MZ0IL6HU0031CA@MCCLB0.MED.NYU.EDU> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT >What version of Think Pascal is the source code for Image written in. I >have v4.0 and it doesn't seem to be able to open the Image project. V4.0.1 is used. I don't know if lack of the update prevents opening the project. I just uploaded the updater to zippy.nimh.nih.gov into /pub/nih-image/contrib, file name ThP_4.0.1_TCL_1.1.2_Update.sea.hqx. -- Edward J. Huff huff@mcclb0.med.nyu.edu (212)998-8465 Keck Laboratory for Biomolecular Imaging NYU Chemistry Department, 31 Washington Place, New York NY 10003 From husemoj@ccsmtp.ccf.org Thu Oct 28 03:54:37 1993 Received: from ccfadm.eeg.ccf.org by nx1.soils.umn.edu (5.65c) id AA22470; Thu, 28 Oct 1993 07:55:24 -0500 Return-Path: Received: from ccsmtp.ccf.org by ccfadm.eeg.ccf.org with SMTP (1.37.109.4/16.2) id AA04370; Thu, 28 Oct 93 08:54:53 -0400 Received: from cc:Mail by ccsmtp.ccf.org (1.30/SMTPLink) id A10072; Thu, 28 Oct 93 08:54:37 EST Date: Thu, 28 Oct 93 08:54:37 EST From: John Husemoller Message-Id: <9310280854.A10072@ccsmtp.ccf.org> To: wayne%helix.nih.gov@relay.tc.umn.edu, nih-image@soils.umn.edu Subject: Re: image documents corrupted?-Please Help I had a system crash just after I saved several documents I had scanned and worked with in Image 1.53b7. After the restart, These images and every image after them (listed alphabetically) in the same folder was corrupted somehow. Several of these files weren't even open, and the ones before the corrupted ones(again listed alphabetically) are completley fine I can see with any number of utilities that these documents are ~70k and show the correct file and creator codes, in the finder they show up as 2k TIFF Image documents and give an I/O error of( -83 or -73 or something like that-I can't exactly remember) when I open them in image. I'm running on a quad 700, sys7.1 HSU 2.1, standard inits, and working off of a bernoulli drive. ANY help would be greatly appreciated. Thanks, John From NSafford@scigen.co.uk Thu Oct 28 16:39:17 1993 Received: from eros.Britain.EU.net by nx1.soils.umn.edu (5.65c) id AA25441; Thu, 28 Oct 1993 12:24:24 -0500 Return-Path: Received: from scigen.co.uk by eros.britain.eu.net with UUCP id ; Thu, 28 Oct 1993 16:51:01 +0000 Received: from [192.9.200.40] (sg_quadra_800) by scigen.co.uk (4.1/SMI-4.1) id AA12493; Thu, 28 Oct 93 16:38:38 GMT Message-Id: <9310281638.AA12493@ scigen.co.uk> Date: Thu, 28 Oct 1993 16:39:17 +0000 To: nih-image@soils.umn.edu From: NSafford@scigen.co.uk (Nick Safford) X-Sender: nas1@jasper Subject: Re: 660av Screen Capture. >Have you tried the Movie Movie card from Sigma Designs. It got a good write >up in the latest MacUser and is only $300. No, but I'm interested! >I you sure of this? I thought the QuickTime capture program that comes with >the AV Macs (Video Fusion?) requires that the monitor be in 8-bit mode. I >would love to see a plug-in that uses QuickTime to capture images, >particularly one that came with source code so I could see how it was done. >I assume it would also work with any capture card with a QuickTime driver, >such as the Video Spigot and the Movie Movie. > >--wayne I think you may be right - I think my initial assessment was hasty. I'll be investigating capture modes other than 16 bit shortly. Further investigation of the chipset specs leads me to believe that it ought to be possible to capture decent 8 bit greyscale. I don't need to do that right now, but doubtless very soon I will. Nick Safford (NSafford@scigen.co.uk) Scientific Generics Phone 0223 424425 King's Court Fax 0223 424281 Kirkwood Road Cambridge CB4 2PF UK From pruskyg@hg.uleth.ca Thu Oct 28 04:24:02 1993 Received: from holly.cc.uleth.ca by nx1.soils.umn.edu (5.65c) id AA25991; Thu, 28 Oct 1993 13:21:14 -0500 Return-Path: Received: by holly.cc.uleth.ca; id AA12479; Thu, 28 Oct 1993 12:20:22 -0600 Message-Id: <9310281820.AA12479@holly.cc.uleth.ca> Date: Thu, 28 Oct 1993 12:24:02 -0800 To: nih-image@soils.umn.edu From: pruskyg@hg.uleth.ca (Glen Prusky) X-Sender: pruskyg@pop.uleth.ca Subject: Re: sweet dreams (re:David Morilak) >Glen: > >Sorry, I misplaced (i.e. deleted) your original message, so I couldn't refer >to you directly in the following message, which I have submitted to the NIH >Image mailing list. Is Live Paste something you might be able to use for the >purpose you describe?? > >David Morilak > > > >From: morilak%cmgm.stanford.edu@relay.tc.umn.edu (David Morilak) >To: Multiple recipients of list >Subject: Re: live paste? >X-Listprocessor-Version: 6.0 -- ListProcessor by Anastasios Kotsikonas >X-Comment: NIH Image Distribution List > >In response to the question about doing a "photomontage" in Image to bring >different focal planes into focus (sorry, I mistakenly deleted the original so >I can't reference the sender), wouldn't the Live Paste function do the trick? >Even if items in different focal planes existed within a ROI, that subregion >could be selected again from the camera window and then refocused in a live >paste. I guess the main limitations would be that rectangular selections only >are allowed, and that if there were huge differences in focal plane, there >might also be an apparent size change, meaning that edges might not line up >exactly right. I gave this a quick and limited try before responding, and it >seemed to work. But, being fairly new at this, I'm more than happy to be >corrected... > >David Morilak >Dept of Psychiatry >Stanford Univ >morilak@cmgm.stanford.edu >------- >------- David, Thanks for your interest in this feature. I think that the live paste function could easily be beefed-up to do what I am proposing. It does allow you to select part of a field and then independently control the focus of the live image in that selected area. That is step one in the process. However, there are two limitations with it as it currently exists in order to easily produce 2D photomontages. First, it does not give you the option of pasting the selected area into the exact X-Y coordinates that it came from in the camera window. You still must align the images by hand or remember the coordinates from the camera window as you move the selected area in image that you are building. Second, it only allows you to grab one frame. Most times you want to average or integrate the capture of your image to reduce noise or increase gain. You can do this, of course, with the original image, but you can not use the same parameters in live paste mode; it only allows you to grab one frame. I think that it would be relatively easy to encorporate these simple features into the live paste window that 1, Allows you to automatically paste the selection from the camera window into the same coordinates in the new window and 2, Allows you to control the input parameters of the live paste in the same way that you can in the capture window. Wayne, is this possible? There may already be utilities that I do not know about that could accomplish this that could be controlled with a macro. Does such a Macro exist? Thanks a million, Glen! Glen T. Prusky Ph.D., Department of Psychology, The University of Lethbridge 4401 University Drive, Lethbridge, AB, Canada T1K 3M4 pruskyg@hg.uleth.ca Office-403-329-2402 Lab-403-329-2410 Fax-403-329-2410 From MEZY301@utxvms.cc.utexas.edu Thu Oct 28 09:36:38 1993 Received: from orange.cc.utexas.edu by nx1.soils.umn.edu (5.65c) id AA26680; Thu, 28 Oct 1993 14:37:42 -0500 Return-Path: Received: from utxvms.cc.utexas.edu by utxvms.cc.utexas.edu (PMDF V4.2-12 #4544) id <01H4NDWJPBQ88WXE9L@utxvms.cc.utexas.edu>; Thu, 28 Oct 1993 14:36:39 CDT Date: Thu, 28 Oct 1993 14:36:38 -0500 (CDT) From: MEZY301@utxvms.cc.utexas.edu Subject: Re: sweet dreams (re:David Morilak) To: nih-image@soils.umn.edu Message-Id: <01H4NDWJRGW28WXE9L@utxvms.cc.utexas.edu> X-Envelope-To: nih-image@soils.umn.edu X-Vms-To: IN%"nih-image@soils.umn.edu" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT I have compiled a long list of useful macros, as well as a couple different working versions of Image. I just discovered I can keep my "Image Macros" file in the System Folder which means I don't have to have multiple copies for each version of Image I run. My question how big can this "Image Macros" file get, how many macros can Image load in this manner??? Peter J. Joyce Office Phone (512) 471-5724 email= Received: from [129.180.146.5] (mac146_5.nr.une.edu.au) by alsvid.une.edu.au with SMTP id AA19172 (5.65c8+/IDA-1.4.4 for ); Fri, 29 Oct 1993 11:43:11 +1000 Date: Fri, 29 Oct 1993 11:43:11 +1000 Message-Id: <199310290143.AA19172@alsvid.une.edu.au> X-Sender: mhowland@pophost.nr.une.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: mhowland@alsvid.une.edu.au (Mick Howland) Subject: Re: source code >>What version of Think Pascal is the source code for Image written in. I >>have v4.0 and it doesn't seem to be able to open the Image project. > >V4.0.1 is used. I don't know if lack of the update prevents opening the >project. I just uploaded the updater to zippy.nimh.nih.gov into >/pub/nih-image/contrib, file name ThP_4.0.1_TCL_1.1.2_Update.sea.hqx. > Thanks, thing are now working fine. _____________________________________________________________ Michael Howland, Faculty of Resource Science & Management UNE - Northern Rivers, P.O. Box 157, Lismore, NSW, Australia. Phone: +61-66-203037 Fax: +61-66-212669 E-mail: mhowland@alsvid.une.edu.au _____________________________________________________________ From huff@MCCLB0.MED.NYU.EDU Thu Oct 28 17:35:30 1993 Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c) id AA29811; Thu, 28 Oct 1993 21:33:05 -0500 Return-Path: Received: from [128.122.250.23] (EDHUFF.DIAL.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU (PMDF V4.2-14 #2884) id <01H4NUQN7ZN4003861@MCCLB0.MED.NYU.EDU>; Thu, 28 Oct 1993 22:34:17 EDT Date: Thu, 28 Oct 1993 22:35:30 -0500 From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff) Subject: Live paste to camera coordinates To: nih-image@soils.umn.edu Message-Id: <01H4NUQVA592003861@MCCLB0.MED.NYU.EDU> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT Select a region on the camera window, copy, then switch to the destination image and type command 4 (restore selection). Then paste. -- Edward J. Huff huff@mcclb0.med.nyu.edu (212)998-8465 Keck Laboratory for Biomolecular Imaging NYU Chemistry Department, 31 Washington Place, New York NY 10003 From huff@MCCLB0.MED.NYU.EDU Thu Oct 28 17:35:37 1993 Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c) id AA29820; Thu, 28 Oct 1993 21:33:13 -0500 Return-Path: Received: from [128.122.250.23] (EDHUFF.DIAL.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU (PMDF V4.2-14 #2884) id <01H4NUQN7ZN4003861@MCCLB0.MED.NYU.EDU>; Thu, 28 Oct 1993 22:34:24 EDT Date: Thu, 28 Oct 1993 22:35:37 -0500 From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff) Subject: Macro file size limitations To: nih-image@soils.umn.edu Message-Id: <01H4NUR01CFU003861@MCCLB0.MED.NYU.EDU> X-Envelope-To: nih-image@soils.umn.edu Content-Transfer-Encoding: 7BIT There is a limit on the number of macros, and a limit on the file size. Text edit restricts files to 32k bytes, and the text windows are implemented with text edit. My version of 1.44 (markup) lifts the file size restriction and doubles the number of macros, but the scrolling menu got a little unreasonable. A few seconds to get down to the bottom... [That version also fixed the else if "feature". In the present version, you must write "else begin ...", never "else if" or "else repeat". 1.44markup fixes that at the expense of a slightly slower macro processor. Now that the segment size limitation of the amount of code in Macros1.p has been lifted, this fix ought to be incorporated... Or at least the program should give a macro error if "else" is followed by "if" or "repeat".] I think a good fix for all of these restrictions would be to create a hierarchal menu under special with one hierarchal menu item for each macro file. Thus, the 32k file size limit need not be removed, and the number of macros per file limit need not be removed. But you can still have essentially unliminted number of macros and essentially unlimited file space. Each macro set would have its own global variables. They could communicate by stuffing values into a scratch image. -- Edward J. Huff huff@mcclb0.med.nyu.edu (212)998-8465 Keck Laboratory for Biomolecular Imaging NYU Chemistry Department, 31 Washington Place, New York NY 10003 From robday@uniwa.uwa.edu.au Fri Oct 29 19:05:35 1993 Received: from uniwa.uwa.edu.au by nx1.soils.umn.edu (5.65c) id AA00259; Thu, 28 Oct 1993 22:04:24 -0500 Return-Path: Received: from localhost (robday@localhost) by uniwa.uwa.edu.au (8.6.3/8.6.2) id LAA27825 for nih-image@soils.umn.edu; Fri, 29 Oct 1993 11:05:37 +0800 From: Robert Day Message-Id: <199310290305.LAA27825@uniwa.uwa.edu.au> Subject: Errors (?) in length of skeletonised image To: nih-image@soils.umn.edu Date: Fri, 29 Oct 1993 11:05:35 +0800 (WST) X-Mailer: ELM [version 2.4 PL11] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 811 We have been using Image to do histomorphometry on trabecular bone in vertebral bodies. In the course of this work, we are wanting to measure the length of a skeletonised network of trabeculae. We have tried using the analyse particles selection with Area and Length/Perimeter checked, but the results don't seem right. To check the results, we then drew a series of straight 1 pixel wide lines and tried to measure them. Vertical lines have almost the right area, and slightly overestimated perimeters. Horizontal lines are a little worse, and lines at any other angle are way off (30 %). Does anyone know what we are doing wrong, or how to get correct length measurements of a skeletonised network out of Image ? Steve Edmondston Rob Day (robday@uniwa.uwa.edu.au) Royal Perth Hospital Perth Australia From bab6@cornell.edu Fri Oct 29 02:13:13 1993 Received: from POSTOFFICE.MAIL.CORNELL.EDU by nx1.soils.umn.edu (5.65c) id AA03388; Fri, 29 Oct 1993 06:11:54 -0500 Return-Path: Received: from [128.253.111.209] by postoffice.mail.cornell.edu with SMTP id AA17979 (5.67a/IDA-1.5 for ); Fri, 29 Oct 1993 07:13:08 -0400 Message-Id: <199310291113.AA17979@postoffice.mail.cornell.edu> Date: Fri, 29 Oct 1993 07:13:13 -0500 To: Multiple recipients of list From: bab6@cornell.edu (Barry Ball) X-Sender: bab6@postoffice.mail.cornell.edu Subject: CCD cameras We are interested in obtaining a slide scanner for image acquisition from both color and B&W 35-mm format slides and negatives. We might also use the scanner for digitizing images from larger format films, but only on an occassional basis. Does anyone have experience with particular hardware in this area and if so what type of equipment are you using. Any information would be helpful. Thanks, bab6@cornell.edu (Barry Ball) From enater@soils.umn.edu Fri Oct 29 03:03:52 1993 Received: from forsoil.soils.umn.edu by nx1.soils.umn.edu (5.65c) id AA04136; Fri, 29 Oct 1993 08:00:49 -0500 Return-Path: Received: by forsoil.soils.umn.edu (4.1) id AA02345; Fri, 29 Oct 93 08:03:53 CDT From: "Ed Nater" Message-Id: <9310291303.AA02345@forsoil.soils.umn.edu> Subject: ImageFractal Problems To: nih-image@soils.umn.edu (Image newsletter) Date: Fri, 29 Oct 1993 08:03:52 -0500 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1398 We are having a couple of problems while running NIH-ImageFractal and hope someone in netland can help. Our application is trying to assess the fractal nature of the pore network in soils. The images are large (3.4 Mb) fluorescent images of a soil pore network. Our setup is a Quadra 950 with 32 Mb RAM running system 7.1. In order to accommodate the images, the application memory size has been expanded to 20,000 Kb with a minimum size of 10,000 Kb, and the Undo and Clipboard Buffer Size has been expanded to 5,000 Kb. The two problems we have been experiencing are: (1) When we try to run the Grid-Screen fractal analysis (under the Fractal menu item) the program dies and gives a type 1 error. There seems to be no way around this particular bomb. (2) We would also like to run the Caliper and the GridXY methods of analysis (also under the Fractal menu item) on the whole image. Although they seem to work properly, they *only* work on one selected particle at a time (each image has several hundred pa rticles). Does anyone know if there is a way to get these items to measure all particles in an image at a single stroke? Thanks for the help. Ed -- Ed Nater Soil Science Department Associate Professor University of Minnesota Soil Genesis/Clay Mineralogy St. Paul, MN 55108 U.S.A. Internet: ed.nater@soils.umn.edu From CHARLEST@macc.wisc.edu Fri Oct 29 04:55:00 1993 Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c) id AA05124; Fri, 29 Oct 1993 09:55:25 -0500 Return-Path: Received: from VMSmail by vms2.macc.wisc.edu; Fri, 29 Oct 93 09:55 CDT Message-Id: <23102909555482@vms2.macc.wisc.edu> Date: Fri, 29 Oct 93 09:55 CDT From: Charles Thomas Subject: Harvey Karten To: nih-image@soils.umn.edu X-Vms-To: image,CHARLEST Two things... If anyone (including Harvey himself) can get me Harvey Karten's email address, I would be most grateful. Secondly, the instructions I got a month or two back on how to access old NIH Image email group posts from gopher don't seem to be working for me. Under Univeristy of Minnesota, Computer Information, General, I don't see a folder for NIH Image messages. Thanks, as always. Charles Thomas Charlest@macc.wisc.edu 608-263-8481 P.S. I'm looking for Harvey in regard to a Ludl Mac 1000 stage drive we have. Nothing to fret about. :) From jladwig@soils.umn.edu Fri Oct 29 06:36:51 1993 Received: from saturn.soils.umn.edu by nx1.soils.umn.edu (5.65c) id AA05965; Fri, 29 Oct 1993 11:37:10 -0500 Return-Path: Received: by saturn.soils.umn.edu (4.1) id AA08292; Fri, 29 Oct 93 11:36:51 CDT Date: Fri, 29 Oct 93 11:36:51 CDT From: "John Ladwig" Message-Id: <9310291636.AA08292@saturn.soils.umn.edu> To: nih-image@soils.umn.edu Subject: Re: Harvey Karten In-Reply-To: Charles Thomas's message <23102909555482@vms2.macc.wisc.edu> of 29 October 1993 References: <23102909555482@vms2.macc.wisc.edu> >>>>> On Fri, 29 Oct 1993 09:57:19 -0500, Charles Thomas said: Charles> If anyone (including Harvey himself) can get me Harvey Charles> Karten's email address, I would be most grateful. kartenh@Sdsc.Edu (From the Gopher archives) Charles> Secondly, the instructions I got a month or two back on Charles> how to access old NIH Image email group posts from gopher Charles> don't seem to be working for me. Charles> Under Univeristy of Minnesota, Computer Information, Charles> General, I don't see a folder for NIH Image messages. It's there if you connect to the UMN *Soil Science* gopher (gopher.soils.umn.edu). The path from the UMN "mother" gopher is: Other Gopher and Information Servers/ North America/ USA/ minnesota/ University of Minnesota Soil Science Gopher Information Service/ Computer Information/ General Information/ Search Nih-Image Mailing List Archives or Selected Electronic Mailing List Archives/ Nih-image/ From kartenh@sdsc.edu Fri Oct 29 17:10:46 1993 Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c) id AA06291; Fri, 29 Oct 1993 12:09:42 -0500 Return-Path: Message-Id: <199310291709.AA06291@nx1.soils.umn.edu> Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET; Fri, 29 Oct 93 17:10:45 GMT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: nih-image@soils.umn.edu From: kartenh@Sdsc.Edu Subject: Re: Harvey Karten Date: Fri, 29 Oct 93 17:10:46 GMT \ >If anyone (including Harvey himself) can get me Harvey Karten's email address, >I >would be most grateful. Dear Charles, From himself, (but not the black Irishman), How can I help you on the Ludl 1000? regards, Harvey Karten Harvey J. Karten, M.D. Dept. of Neurosciences Univ.California San Diego La Jolla, CA 92093-0608 EMail: Kartenh@sdsc.edu Phone: (619)-534-4938 FAX: (619)-534-6602 From wayne@helix.nih.gov Fri Oct 29 12:14:08 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA06327; Fri, 29 Oct 1993 12:15:55 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA03655; Fri, 29 Oct 93 12:36:33 -0400 Message-Id: <9310291636.AA03655@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 29 Oct 1993 12:14:08 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Harvey Karten >If anyone (including Harvey himself) can get me Harvey Karten's email address, >I >would be most grateful. You can get a list (with email addresses) of all subscribers to the NIH Image mailing list be sending a message containing the line "recipients nih-image" to listserv@soils.umn.edu. --wayne From wayne@helix.nih.gov Fri Oct 29 13:11:50 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA06925; Fri, 29 Oct 1993 13:13:31 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA03811; Fri, 29 Oct 93 13:34:15 -0400 Message-Id: <9310291734.AA03811@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 29 Oct 1993 13:11:50 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Macro file size limitations >There is a limit on the number of macros, and a limit on the file size. The maximum number of macros per file is 100 and the maximum macro file size is 30,000 bytes. >My version of 1.44 (markup) lifts the file size restriction and doubles the >number of macros, but the scrolling menu got a little unreasonable. A few >seconds to get down to the bottom... > >[That version also fixed the else if "feature". In the present version, >you must write "else begin ...", never "else if" or "else repeat". >1.44markup fixes that at the expense of a slightly slower macro processor. >Now that the segment size limitation of the amount of code in Macros1.p has >been lifted, this fix ought to be incorporated... Or at least the program >should give a macro error if "else" is followed by "if" or "repeat".] The latest NIH Image beta (1.53b33) reports an error if an "else" is followed by either "if" or "repeat". --wayne From hammer@wana.pbrc.Hawaii.Edu Fri Oct 29 13:47:46 1993 Received: from wana.pbrc.Hawaii.Edu by nx1.soils.umn.edu (5.65c) id AA07304; Fri, 29 Oct 1993 13:47:46 -0500 Return-Path: Received: from [128.171.24.10] (McHammer.pbrc.Hawaii.Edu) by wana.pbrc.Hawaii.Edu (4.1/SMI-4.1) id AA20414; Fri, 29 Oct 93 08:48:52 HST Date: Fri, 29 Oct 93 08:48:51 HST Message-Id: <9310291848.AA20414@wana.pbrc.Hawaii.Edu> To: Multiple recipients of list From: Ron Hammer Subject: Voxel View/Mac If anyone is interested, Vital Images (515-472-7726) has a demo version of Voxel View/Mac which does everything except save files. Sample data sets are included. The Mac version sells for $1295 (a scaled down, less expensive form of the SGI version). Thanks to Charles Thomas for answering my questions about Voxel View/Mac. Ron Hammer From wayne@helix.nih.gov Fri Oct 29 16:43:27 1993 Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c) id AA09071; Fri, 29 Oct 1993 16:45:08 -0500 Return-Path: Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0) id AA04383; Fri, 29 Oct 93 17:05:53 -0400 Message-Id: <9310292105.AA04383@zippy.nimh.nih.gov> X-Sender: wayne@128.231.98.32 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 29 Oct 1993 16:43:27 +0000 To: nih-image@soils.umn.edu From: wayne@helix.nih.gov(Wayne Rasband) Subject: Re: Errors (?) in length of skeletonised image >We have been using Image to do histomorphometry on trabecular bone in >vertebral bodies. > >In the course of this work, we are wanting to measure the length of a >skeletonised network of trabeculae. We have tried using the analyse >particles selection with Area and Length/Perimeter checked, but the >results don't seem right. To check the results, we then drew a series >of straight 1 pixel wide lines and tried to measure them. Vertical >lines have almost the right area, and slightly overestimated perimeters. >Horizontal lines are a little worse, and lines at any other angle are >way off (30 %). > >Does anyone know what we are doing wrong, or how to get correct length >measurements of a skeletonised network out of Image ? You get these errors because, for example, a horizontal line and a diagonal line are both drawn using the same number of pixels. In this example ##### # # # # # both lines have the same area in pixels (5), but the diagonal line is longer. Bert Smit (SMIT@CABO.AGRO.nl), an NIH Image user in the Netherlands figured out a conversion factor to correct for these errors, assuming the line segments are at random angles. He was trying to measure the lengths of plant roots. You might also consider using a program that is better at morhometrics, such as PrismView, which is now available for Signal Analytics, the IPLab people. PrismView measures about 50 particle features, including length. --wayne From honig@leland.Stanford.EDU Sun Oct 31 09:08:52 1993 Received: from cardinal.Stanford.EDU by nx1.soils.umn.edu (5.65c) id AA28717; Sun, 31 Oct 1993 19:07:40 -0600 Return-Path: Received: from localhost (honig@localhost) by cardinal.Stanford.EDU (8.5/8.5) id RAA10338; Sun, 31 Oct 1993 17:08:53 -0800 From: "Lawrence S. Honig" Message-Id: <199311010108.RAA10338@cardinal.Stanford.EDU> Subject: Re: Errors apparent in handling "Results meaurements" To: nih-image@soils.umn.edu Date: Sun, 31 Oct 1993 17:08:52 -0800 (PST) In-Reply-To: <9310292105.AA04383@zippy.nimh.nih.gov> from "Wayne Rasband" at Oct 29, 93 04:50:42 pm X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1072 To Wayne Rasband - I seem to have uncovered an error in handling of Results Measurements in version 1.52. Firstly, in preface... NIH Image seems to have a great difficulty handling large (>64K ?) results of measurements files... For example, if one makes more than about 371 measurements (with my options which include: number, average, int density, bak, min/max, user1 and user2) , then one cannot use "ShowResults" to see more than the first 371 .. However the program does correctly save the entire (1000 plus) set of measurements. Secondly, MORE IMPORTANTLY, but probably related to the above (?), if one tries to "Delete a measurement" such as measurement 1 to 10 (i.e. early measurements) , one is unable to do so as far as I can tell... That is, normally it is no problem to delete any specified measurement, but in big result files, it no longer seems possible (the program just deletes the last measurement done, instead of the measurement number specified!) My compliments regarding the program in general... Thanks .... Larry Honig From honig@leland.Stanford.EDU Sun Oct 31 09:10:37 1993 Received: from cardinal.Stanford.EDU by nx1.soils.umn.edu (5.65c) id AA28735; Sun, 31 Oct 1993 19:09:24 -0600 Return-Path: Received: from localhost (honig@localhost) by cardinal.Stanford.EDU (8.5/8.5) id RAA10447; Sun, 31 Oct 1993 17:10:38 -0800 From: "Lawrence S. Honig" Message-Id: <199311010110.RAA10447@cardinal.Stanford.EDU> Subject: Re: Errors apparent in handling "Results meaurements" (fwd) To: nih-image@soils.umn.edu Date: Sun, 31 Oct 1993 17:10:37 -0800 (PST) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1517 Forwarded message: >From honig Sun Oct 31 17:08:52 1993 Subject: Re: Errors apparent in handling "Results meaurements" To: nih-image@soils.umn.edu Date: Sun, 31 Oct 1993 17:08:52 -0800 (PST) In-Reply-To: <9310292105.AA04383@zippy.nimh.nih.gov> from "Wayne Rasband" at Oct 29, 93 04:50:42 pm X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1073 To Wayne Rasband - I seem to have uncovered an error in handling of Results Measurements in version 1.52. Firstly, in preface... NIH Image seems to have a great difficulty handling large (>64K ?) results of measurements files... For example, if one makes more than about 371 measurements (with my options which include: number, average, int density, bak, min/max, user1 and user2) , then one cannot use "ShowResults" to see more than the first 371 .. However the program does correctly save the entire (1000 plus) set of measurements. Secondly, MORE IMPORTANTLY, but probably related to the above (?), if one tries to "Delete a measurement" such as measurement 1 to 10 (i.e. early measurements) , one is unable to do so as far as I can tell... That is, normally it is no problem to delete any specified measurement, but in big result files, it no longer seems possible (the program just deletes the last measurement done, instead of the measurement number specified!) My compliments regarding the program in general... Thanks .... Larry Honig