I am a new user of cellprofiler and love it. I have been using this to quantity cell number by nuclear counting, among other uses. Recently, I have acquired some images using a high content imaging system and the images contain a well region with nuclear stained cells and a region outside the well (please see the attached image). This thus creates two backgrounds, one inside the well and one outside the well. My pipeline worked well with images that don’t contain this extrawell space but doesn’t work on images with a second background. I don’t know how to tell the pipeline to regard that as background. Help please!
Thank you very much!