Colocalization DAPI NeuN



Hello everyone,

I am new to CellProfiler and I would like to make a colocalization analysis between two different channel (DAPI and NeuN). I have tried many different things so far but none of these worked. The software seems to only analyze the first slice of my stack, so my concern is that it might not be possible to do it with the slack ? Do I have to turn my stack into different images ? I already read that apparently it’s not possible to do the colocalization with 3D images, so is there any way to do this ? Otherwise I will have to go back to manual compting.

Thank you very much in advance for your help.



Please upload image sets and a pipeline; it’s hard to analyze what may be going wrong without those. Thanks!



Sorry for the late response, I was busy with other things but now I am back on Cellprofiler.
I uploaded what I’ve done so far. I’m sure that it’s probably all wrong but the only thing that i found on cell counting was for 3D monolayer, which, I think, is not really applicable for the brain slices that I am counting.

I understand that I have to do a nuclei segmentation for the DAPI channel, but I don’t really know what to do with the NeuN channel because it’s supposed to label the entire neuron and not only the membrane as for this tutorial ( I’m not very familiar with this kind of software.

Please see ithe link for the pipeline and the image (apparently I can’t join attachment because I’m a new user).

So my main problem is to identify the neuron on the NeuN channel and to make it match with the DAPI objects and to count how many “NeuN cells” are matching with DAPI.

Thanks for your help.


I just increased your trust level, so now you should be able to upload files to your posts.