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.