Does anyone have advice on segmenting images like the ones I have attached? The problems start from the segmentation, when I try to manually set a threshold, but it inevitably captures the background or excludes the lower intensity parts of the cell.
I know I can manually draw a ROI around each cell, but I am curious if there is a way to deal with this automatically. On the Analyse particles plug-in, I tried to play around with the circularity (all my cells should have a pretty round shape which helps a lot) and by area size of course, but it still doesn’t detect only the cell.
They also have pretty uneven background, which I can try to deal with separately, but I doubt this will solve the issue with the uneven staining in the actual cell.
Any help will be appreciated