Need help tweaking IdentifyPrimaryObject

Hi CellProfiler Team,

I have cropped one of my pictures down to two nuclei and would like the program to identify both of them as primary object; however, the entire right nuclei is not being identified, just its intense chromatin in the middle.

I realize it is probably because the right nuclei is very faint compared to the one on the left…how can I get CellProfiler to identify the whole thing?

I attached the pipeline also, in case you need it.

DefaultOUT__7PIPE.mat.cp (8.02 KB)

P.S. I’ve messed around with a couple different settings, but nothing seems to work for me. If I increase the “Typical Diameter” range it ignores the right nuclei all together.

You might want to try using a different thresholding method. In your case, you might have luck with Otsu global or adaptive with three-class thresholding, probably with the middle class assigned to the foreground.


That worked beautifully, thank you sincerely.