Nuclei problem



I use DAPI to label nuclei of neural tissue containing glia. The glial nuclei are slightly smaller on average and a lot brighter. I am having a difficult time training CellProfiler to distinguish the two. My interest is mainly in the neurons. Any ideas short of just labeling the cells with NeuN (a neuronal nuclei marker)?

I would be pleased to give out a sample image that I am working with, but I don’t have a website to post it to. I could E-mail it though.



I would first play with MeasureObjectAreaShape and MeasureObjectIntensity modules, then you should be able to find parameters which distinguish your small and bright nuclei from the rest.



This is still giving me grief. Does the IdentifyPrimaryAuto module have to identify nuclei for the program to work well. I read in the hlep that it just makes the cell identification better. I have tried primary objects as cells instead and that works better but not perfect.