I am a new user of cell profiler and have found it quite useful already. I have some questions about improving my pipeline for images with infected cells stained by an antibody to a viral protein expressed in the ER and on the surface. I have used the pipeline to identify nuclei as primary objects than postive cells as secondary objects followed by measuring and filtering for cells above a certain intensity. I can do this reasonably well for one image, but the problem I have is when I try to do a whole set of images. The intensity of the background varies from image to image as does the intensity of the positive cells. I thought there might be a way to adapt or correct for this but I’m not sure how to go about doing it.
I’ve attached some sample images and the pipeline I am currently using.
cell counting ab.cp (12.9 KB)