Cell counting - immunofluorescence




I’m new to cell profiler and I’m trying to count retinal ganglion cells stained with NEUN and DAPI on mice retinal sections and microglial cells stained with IBA1 and DAPI on mice longitudinal optic nerve sections.

  1. I want to use the program to identify all cells in the retina that have the retinal ganglion cell bodies stained with NEUN and also co-stained with DAPI. This should be relatively easy as the shape of the retinal ganglion cell bodies are circular

Below are the two images obtained from a fluorescence microscope at x20. _c0 is the DAPI stained retina and _c3 is the NEUN stained retina

  1. and to identify all microglial cells in the optic nerve that are stained with IBA1 and co-stained with DAPI. I tried to do this with intensity because microglial cells don’t have circular shaped bodies.

Is there anyone that knows how I can do this or can provide a sample pipeline? I tried many many things without any successful…

Thank you,