I am trying to set up an Ilastik classifyer with three labels in order to identidy cells with a full circle cellular membrane, cells without a full membrane and negative areas (outside the section, blood vessels, folds, etc). My strategy so far has been the following:
Label one: negative areas
Label two: cell membrane
Label three: cytoplasms (no nucleus in the inside)
Any ideas on how to compile that or is there is an existing pipeline for that? Also, is there any step to set up automatically flourescence intensity and background reducing?