I started using/learning CellProfiler just a few days ago. My goal is to calculate the percentage of cells that stain positively (above a set threshold) for a nuclear protein.
I managed to make a pipeline until IdentifySecondaryObjects. Now, I tried to use Measurement modules to calculate the intensity of staining, and based on that the percentage of cells that display staining above certain threshold, but I did not succeed so far. In this image, 3 cells exhibit distinct staining from other cells, and I would like to reach the result of 23% of cells as positive for this nuclear protein.
Please find attached the image and the pipeline. I would appreciate help on using the measurement module to perform these calculations.
FB421_test.cp (5.68 KB)