Below is per a question about the count tool in Photoshop CS3 Extended. If you have more info on ImageJ or other type of software and/or procedures, please post it!
After further checking, I’ve verified that you cannot “save” the counts image wise except through the work around I showed you (i.e. make your counts, press ALT-Print Screen, click File | New, accept default image parameters, paste into the new image, select the area you want and click Image | Crop.)
You can save total counts per image, by making your counts, click Analysis | Record Measurements and then click the Record Measurements button on the window that opens. You should have the file saved with a filename first so that the record indicates what file it goes to. For each Image or you can do it in as a group, you can export the counts to a tab delimited text file format that could be imported into Excel. You can keep multiple counts per image, but sadly it will only log the date/time of clicking the record button, document name, tool used, Scale, Units, factor and the total count.
Sad really that you cannot keep more information per point counted easily. Three other work around methods though:
1. With your image open, create a new layer. With that layer selected, choose a color and with the Pencil tool (make sure your Brush size is 1, Mode: Normal, Opacity: 100%) click every point you want to count. Once you are finished, turn off the background. Now you have a layer with only the points which you clicked (basically the same as the count tool except the points are not numbered). You can save the file and preserve both the image and the count overlay. To get the total count:
a. If the dots you created are too small, you may want to zoom in a bit on the image until you clearly see at least one of the pixels you made.
b. Turn off the background image (so only the layer with the count points is visible)
c. click Select | Color Range, the color range box will open
d. click the Info tab on your tools pallet (click Windows | Info if not showing on the right side)
e. back on your image, put your mouse (cursor should turn to the eye drop tool) over the pixel you created. In the Info window, the RGB values should show the color in which you chose (i.e. if you used black it would be R: 0 G: 0 B: 0). Click once.
f. Back on the Color Range window click OK. Now each of your pixels are selected.
g. Now click Analysis | Record Measurements and click the Record Measurements button.
i. The first line will have the total number of pixels selected.
ii. Then for each pixel, there will be a record created.
… This sounds like a lot, but actually, it’s not all that difficult and relatively quick once you’ve done it once or twice. The good thing is your counts can be saved in the image (.psd format so the layers are preserved) and thus can be reviewed or modified as needed.
2. Once you have your count with the Count tool, you can open the Info tool (Window | Info), put your cursor over each count spot and manually record the X/Y coordinate specified in the Info window in an excel spreadsheet. Tedious, but very precise info.
3. There are other image counting software out there. ImageJ (http://rsb.info.nih.gov/ij/) is a freeware app, but I think it’s based on pixel area density (counts areas that have several pixels of the same/similar color). However, there is a way to easily combine marking images in Photoshop and then analyzing those marks in ImageJ to get a total count while maintaining the count in image format. It would just be a 3 step process. You could talk to people in the Neurohumeral group.