I am learning how to use QuPath for analysis of multiplex IHC images. Is it possible to create a tumor mask so that I can then move on to classifying all the cell types within that mask.
When I train a pixel classifier and do cell detection, the measurements I can export don’t seem to give me cell counts within the masks.
I’d like to create tumor/stromal masks so that I can count immune cells within those two regions.
While I am following the multiplex analysis documentation for 0.2.3, it is showing a method of identifying all the cells but not within masks. I know I can identify all the CK+ cells as tumor cells, but that doesn’t help with me being able to say there is an X% of immune cells in the tumoral and an X% of immune cells in the stromal compartments.
Maybe I am just missing something obvious?
Does anyone have any suggestions?
Thanks for your help!