...) checkbox
command to select either Swiss-2DPAGE, UniProt, iProClass or iProLink
servers. If you measure a spot (select a spot in an active image and
then type C-M) (and are connected to the Internet), it will
lookup the Swiss-Prot protein (accession name, and protein id) on the
Swiss-2DPAGE server. Then, if you enable "Click to access DB", it will
pop up the particular active DB server you have selected. An
additional option is to enable the (Edit | Auto measure, protein lookup and Web page
popup) checkbox command. Then when you click on a spot in an
active image (associated with a Web database), it will: 1. measure the
spot and add it to the spot list; 2. lookup the Swiss-Prot (name, id);
and 3. pop up the Web server on the currently selected active DB
server.
1. NOTE: we changed the old (C-I) short-cut command to (C-K). The (C-I) is NOW used to bring up a short edit form to define or change the spot annotation 'id' fields for the measured spot(s) selected in the image(s). The same id value you enter is assigned to both spots if you are editing two spots (selected from the left and right images). The full command is (Quantify | Measure by circle | Edit selected spot(s) 'id' fields from spot list(s) (C-I)). We fixed some bugs where the circle size shown was different between the circles in a list of measured spots and in the non-list spot measurement. The data was the same.
2. NOTE: we find it useful to adjust the circle size around a spot, by temporarily turning off the (View | Set view overlays | View measurements |
View
list-of-spots else trial-spot measurement mode (C-J)) while
leaving the (CView | Set view overlays | View measurements | View measurement circle) on. Then click
on a spot and type (C-M) to get a trial spot measurement. As
you adjust the "meas circle" size diameter scroller, it will redraw
the circle around the spot as well as display the new integrated
density in the image title (if (C-G) was enabled. 3. NOTE: the (View | Set view overlays | View measurements |
View list of spot measurements)
has been moved to the Quantify menu and renamed (Quantify | View list-of-spots else trial-spot
measurement mode (C-J)) and given a (C-J) short-cut key to
make toggling between modes easier. Fixed problem of trying to save
an unsaved spot list on exit if you had never defined the .flk startup
file (it now prompts you for a .flk file name). Fixed the problem
where the scroller states for the images was not setup in the correct
order and was being overloaded with the default state.
- View measurement circle for (C-B and (C-M) trial spots
- View list of spot measurement for viewing spot lists
- Use 'Circle' for spot locations OR
- Use '+ for spot locations OR neither.
- Use 'spot number' for spot annotations AND/OR
- Use 'spot identifier for spot annotations OR neither.
We added a new scroller "measure circle size" to the parameter scrollers. This is equivalent to going into the (Quantify | Measure by circle | Circular mask size (pixels) | ...) and selecting a size. However it is more convenient and gives you better visual feedback.[Thanks to suggestions by Enrico De Toni].
Calibration of grayscale in other units (e.g., optical density)
We have activated the grayscale calibration using an neutral density
(or other known standard) step-wedge scanned with the material (e.g.,
2D-gel) when it was scanned. You must know the calibration values
(e.g., OD or CPM, etc.) corresponding to the step wedge. You set the
computing window Region Of Interest (ROI) over the step wedge and then
use the (Quantify | Calibrate | Optical density by step wedge)
command. To demonstrate this process, we have built in four sample
ROI's and the corresponding OD values corresponding to the step wedge
scanned with the four demo gels (Leukemia-AML, Leukemia-ALL,
Leukemia-CLL, Leukemia-HCL). To use this demo, first set the
(Quantify | Calibrate | Use demo leukemia gels ND wedge calibration
preloads) first. Then, use the (Quantify | Calibrate | Optical
density by step wedge) command. We will be adding discussion and
documentation on calibration in the reference manual and we plan to
add vignettes.
View spot measurements and the
Windmp [183:203, 168:188] Center (193,178) 20X20 size,
sampled: 1 pixels, data-radix: Decimal
Image: Images\plasmaH.gif
X 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203
Y --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
168 71 61 57 55 54 54 56 57 56 50 46 42 42 43 45 42 43 48 53 67 80
169 71 53 50 48 45 48 50 55 60 56 46 42 40 43 42 40 37 41 47 54 65
170 88 49 44 42 40 42 45 53 56 61 50 41 40 39 39 37 34 37 38 45 54
171 97 49 41 39 39 40 43 53 60 61 54 43 39 38 37 36 34 36 37 43 50
172 106 47 39 37 36 37 39 53 72 78 72 50 43 38 37 35 33 34 35 39 44
173 84 41 38 37 34 33 35 50 82 94 84 58 48 41 40 37 34 35 35 39 44
174 66 39 38 37 35 33 35 50 84 96 84 59 48 41 40 39 35 37 37 39 44
175 47 41 43 40 36 34 34 49 78 84 71 56 50 43 44 43 38 37 37 47 46
176 50 46 46 46 39 34 35 56 91 95 77 61 58 54 57 54 47 43 41 43 47
177 53 49 51 50 42 37 38 69 117 122 98 74 66 62 65 62 51 47 44 45 50
178 58 59 65 65 53 43 46 106 171 174 139 94 78 71 67 65 57 54 50 48 54
179 63 77 97 97 82 59 55 104 163 164 120 76 64 58 62 62 61 58 55 52 56
180 67 90 122 124 106 72 60 86 132 132 95 64 59 55 64 62 61 59 57 53 57
181 76 140 189 193 174 128 94 59 70 68 60 55 55 54 59 63 60 60 58 55 58
182 82 167 214 215 195 137 97 50 47 49 52 53 53 53 53 56 55 57 59 57 61
183 73 142 194 194 160 97 67 42 44 46 51 52 52 50 53 52 54 57 60 62 63
184 51 62 81 80 60 46 39 38 44 46 51 52 52 51 54 54 66 69 78 80 77
185 48 50 52 52 46 40 39 40 45 48 51 52 51 53 56 57 56 65 70 72 72
186 49 49 50 50 46 41 40 40 42 46 49 51 51 53 55 56 53 62 60 61 61
187 51 55 63 62 56 46 43 40 40 41 45 51 53 57 58 55 50 48 52 49 50
188 70 90 97 90 71 57 52 47 41 40 46 56 61 66 64 60 51 46 48 47 50
Use sum density else
mean density). Added (Quantify | Measure by circle | Delete
selected spot from the spot list) so you can edit the
list. Changed the default trial object color from yellow to orange
which is a little easier to see. Changed the default circular mask
size from 5x5 to 11x11. Changed the default measurement circular mask
color from yellow to red.
Use
measurement counter) has been added to let you track your
measurements in the report log more easily.