I’m new to Cell Profiler but i’ve heard many good things. I’m trying to see if Cell Profiler is the right tool to do a very basic but time consuming task.
Basically, I do a lot of in situ hybridization and IHC in spinal cord and dorsal root ganglia tissue. Often, the goal is to show co-expression of two or more genes and calculate percentages of overlap.
We do this by hand at the moment using Photoshop or a Matlab script we made. I know people like imageJ too, but either way, it requires manual drawing of ROIs.
it’d be great to have a tool to automatically detect cells, and determine the coexpression of different channels within the same cell.
As an example image:
I would love if Cell Profiler could find out the co-expression in panel D.
I realize neuronal cell boundaries are difficult to determine, even for humans, but I would even be happy if we conservatively drew the boundaries around nuclei (DAPI) and did coexpression that way.
Any help would be greatly appreciated.