Segmenting cells in H&E staining

Hi all,

Thanks a lot in advance for your help.
I have to do something that maybe would be easy for the majority of you but not for me as a beginner unfortunately.
I have simple images of H&E staining and I would like to segment and count the cells in it. Moreover would be nice to segment cells with different features as well.
Do you have an example of pipeline that I could use?

Firstly I am trying with “UnmixColors” and then “IdentifyPrimaryObjects”. The thing is that I am not able to segment the cells at all. Maybe there is one step more to add before the Unmix one.

Last question: which format of the images would be better to upload in cellprofiler for this purpose?

Thanks a lot for your help,


Can you point to us which is the cell you want to segment? If you mean those that have the nuclei, I think your best bet is to use ilastik, demo video

Good luck.


Yes sorry I did not specified. I would like to segment and count the violet nuclei.

Thanks a lot, I will have a look at the tutorial.