Thank you for all your work on CellProfiler, it really is a wonderful tool to use.
I seem to have reached an impasse in regards to identifying the specific section I want.
I am only interested in the basal layer of the skin tissue, which is the bottommost line of nuclei (not including any free-floating keratinocytes). Using this basal layer, I was attempting to use the program to count the number of DAPI stained nuclei and the related number of Ki67 stained nuclei as well.
What I was attempting to do was to crop out all of the unnecessary layers and preserve the basal layer. The problem arose when I tried to use the crop function to do this. The image is not perfectly straight up and down so using the ellipse and rectangle crop functions did not work.
The next step I tried was to use the module IdentifyObjectsManually. Unfortunately, I got an error when I tried to save the resulting crop: “object cpi is not defined”. Being unable to save the resulting cropped image made IdentifyObjectsManually not useful to me.
Attached are example images I have tried working around with. Any comments/suggestions would be much appreciated!
Involucrin_Ki67_June28.cp (8.54 KB)