I have made a pipline for counting number of cells in the tissue. Though it seems that CellProfiler also picks up dirt/paraffin artifacts. I Think that the issue is in the module identifying primary objects (third from top - see pipeline) i have tried diffrent kinds of thresholds (manual/global) but when I succed to get rid of the artifacts even some of the hematoxylin (Purple/blue) stained nuclei dissapear.
My aim with this is to get rid of all the artifacts and still detect all the nuclei
I have attached my pipline together with some Pictures. I would be glad if someone could tell me how to solve this
pipeline.cppipe (14.4 KB)