I’m trying to carry out a DNA content analysis using optical densitometry of stained nuclei. To find out DNA content I need to find the IOD for each nuclei.
Currently I have a pipeline that gives me a kind of surrogate of integrated optical density, by dividing the mean background intensity by the mean nuclear intensity, and taking a log10 of this number.
This isn’t the exact IOD however, which is the sum of (nuclear pixel intensity/mean background intensity) for each pixel in the nucleus.
I’m really struggling to find a way to do this and was wondering if anyone had any ideas? (I think I might need to find a way to get individual pixel intensity observations for each nuclear pixel?)
I’ve attached my pipeline and an example image.
LymphocyteOptimisedpipelineforbluefeulgen.cp (12.4 KB)