I posted a question sometime ago with no response and I guess I was just no very clear. I have the following pipeline attached and have images that vary in illumination and stain intensity (attached).
I was successful in correct the illumination to a point where they look similar, but my nuclei counting is still very inconsistent, ecluding some clear stained nuclei and including some really poorly stained ones.
The attached pipeline is as follows
CorrectIllumCalculate (regular, all first cycle, filter “median”, size 300)
CorrectIllumCalculate (Background, size 25, each, filter “median”, size 100)
Enhance&Suppress Featrures (Enhance, Speckles, size 25) This module can be used or not.
IDPrimaryobject (Global, MoG, 0.05, automatic smoothing)
BUT I tried all the modules with the range in the size I need. Basically the methods can be ajusted, but still allow for too many false positive and false negative.
Should I use a smoothing filter for the threshold, since I already smoothed during the Illum. correction?
I also tried using some filtering for the false positive, (which is in the pipeline), but the difficulty in at least getting all the true positives in bugs me.
cell_proj.cpproj (82.5 KB)