Dear members of the community,
Here are the problems I encounter:
I have fluorescent images of liver stained with immunological relevant marker CD3, IL-18Ra, and TCR.
I trained the machine to get object classifiers for the three channels. Detections of CD3+ and IL-18Ra+ cells are pretty accurate with QuPath and I played a little with the different parameters of the Positive Cell Detection so I have coherent splitting of nucleus etc.
However, concerning the TCR staining, I have autofluorescence in the same channel (part of fibrosis) inducing the software to give me false positive.
I then would like to be able to use the auto-detection of CD3 and IL-18Ra and to manually assign the TCR positive (usually, the CD3 and TCR should perfectly superposed around the membrane of the cell). I am able to assign a class to a new created object but not an a cell detected by the nucleus.
Also, bonus question, I do not find (yet?) a way to sort my results in the hierarchy so I can explore them easily or reassign them (if possible? see previous concern…) to a proper class. Is it possible to sort them?
Thanks a lot in advance for those of you able to help me.