I am trying to go through the multiplex analysis of immunofluorescence images.
However, I am not really happy with the cell segmentation.
I am quite confident the DAPI detection is (more or less) good, but when it comes to cell boundaries, I don’t think it gets it right at all.
I am mostly looking at CD3 positive cells (round with cell boundaries very close to the nucleus) and CD68 positive cells (big macrophages, with mostly irregular shapes). This means that the CD3 cells look bigger than I would think and the CD68 cells are either underestimated or fragmented.
The consequence is that if I have the two closely associated, they are often marked as double positive when I try to run a classifier.
Any idea of how I could change the settings to make it work?