Distinguishing positive and negative cells for a specific marker



Hi, so I am just getting started using CellProfiler. Thank you for developing this great tool!

I´ve got tissue images and based on nuclear and membrane staining, I identified nuclei as the primary object, before identifying cells (secondary object), cytoplasm (tertiary object) and masking cells. I measured image intensity for another marker with masked cells as the input object. It is pretty obvious from the image, that some cells are clearly positive, whereas others are clearly negative for this marker.
That´s why I wondered whether it would be possible to measure signal intensity of a specific marker from masked objects just for objects being highly positive for this marker and outputting the number of positive cells, i.e. measure the number of masked objects expressing this marker above a certain threshold compared to the number of masked objects expressing the same marker below a set threshold.

Hope it is somehow clear what I mean!
Thank you very much in advance for your help!


Hello Judith,
I would check the FilterObjects module where after segmentation and measurements you can exclude the objects based on specific criteria.


Thank you very much! Did not know about this module, but it is exactly what I was looking for :slight_smile: