I’ve stained my mice tissue slides with H&E and am trying to quantify the nuclei and compare between different samples. I’ve tried a few pipelines and seemed to have some luck with a simple one. Unmix Colors - EnhancedOrSurpressFeatures - Identify Primary Objects. However it did not work for all my pictures, the ones that had less hematoxylin weren’t accurate, even when I added to Color to Gray.
I’m using CellProfiler 2.1.1 on a macbook…I’ve attached an example of a picture Im using.