Automatic cell counting fluorescence quantification and colocalization

[Marion Bétizeau]

I'm analyzing z-stack pictures of 3 channels, each corresponding to a
define transcription factor (all 3 stainings are nuclear and possibly
colocalizing). Does anybody know a plug-in which does an automatic cell
count on z-stacks and which can calculate fluorescence intensities and
colocalizations on 3D ROI?
To make it even more difficult they are pictures of brain tissue where
the density and the shape of the nucleus can vary.

Thanks,

Marion