Differentiating between stained and unstained cells


Hello, I’m new to CellProfiler. So far I have used the software in a standard method to measure nuclei and cytoplasm intensities. Cell nuclei (image “1”) are identified with primary objects, The cytoplasm (image “2”) is identified using secondary and tertiary objects. The nuclei and cytoplasm intensities are then measured in a third image (“3”). I’ve attached the sample images and pipline for this.

Out of all cells identified, I now want to break them into two categories depending on staining in a fourth image (“4”). The end result would be having separate nuclei/cytoplasm intensity measurements of cells that are stained and unstained in the 4th image. Any ideas on how I can add this extra step? Thanks!

Nuc_Cyto_Analysis.cpproj (76.7 KB)


You can add the “RelateObjects” module to relate the objects in the fourth image to objects in other images (in the example below I used cells as parent objects and stained nuclei in image 4 as child objects to have the the link between the two.)
Nuc_Cyto_AnalysisVC.cppipe (12.7 KB)