I am relatively new to the CellProfiler software and I have some struggles with setting up my pipeline. I am trying to image mouse brain sections that I stained with DAPI, NeuN and for tau. I am interested in counting the number of DAPI positive cells and the tau positive area amongst other things.
I am trying to use the IdentifyPrimaryObjects module to segment the nuclei based on the DAPI staining. However, I cannot find a way to prevent oversegmenting. As you can see in the images I attached to this post, our DAPI stain results in these dots within in the nuclei. I was wondering if there is a way to work around this. I have been going through the different thresholding methods CellProfiler offers but have not figured it out yet.
I am also trying to get CellProfiler to accurately measure the signal for tau through the IdentifyPrimaryObjects module. However, as you can see the intensity for this stain is not very high and the shape of the signal varies from image to image so I am struggling to find a solution for this as well.
I have found other posts with questions about how to quantify DAPI staining, but I could not find one that specifically helped you work around these dots.
I hope that some of you with more knowledge and experience will be able to help me with this or give me some tips on how to address these problems!