I am looking for advice on how best to identify CD3+ T cells in hematoxylin-costained IHC tissue sections. The pipeline I have set up right now seems to do a decent job but would anyone have suggestions on how to improve the object identification?
Also, the pipeline I have set up now has the user manually draw an ROI before quantifying T cells in that area. In practice we draw ROIs in the Aperio Webscope program to quantify tumor area. I’d like to be able to submit to CellProfiler screenshots or snapshots of tumors with an ROI already drawn around it (see example) so that the user would not need to manually redefine this area each time. Is that possible using CellProfiler? Any advice or suggestions would be much appreciated!
AL_DABCD3_wROI.cpproj (651.7 KB)