Dear CellProfiler users and team,
I’m a new cellprofiler user. My goal is to do a colocalization between two RNA fish done on mouse brain section. Hera is a weTransfer link to see the images. I have already done a crop with ImageJ to only keep my region of interest.
So I have three channels:
- Blue for dapi staining
- Red and Green for the two FISH
My idea was first to identify primary object with the dapi staining and secondary objects with the FISH.
But I’m still stuck with the primary object segmentation. As you can see on the dapi image, cells can be clumpy and the dapi staining is not uniform inside a cell. So I first apply a smooth on the image to have a more uniform dapi:
I think that the smooth works pretty well (tell me if I’m wrong!).
After that, I tried to identify primary objects and with all the parameters that I tried, my best solution is presented here:
As you can see, I have a lot of clumpy cells that I cannot separate.
If someone can help me to optimize that, I would be super happy !