Thank you for checking my pipeline. I have made the changes as you have suggested - changed xeno as the image to measure and keep Xeno_nuclei as the objects to measure. When I look at the intensity output, the mean intensity I got from this is 0.044. According to the manual, this is the average pixel intensity within an object, which I believe object is referring to Xeno_nuclei (= intensity per cell) ?
The reason why I asked is because when I look back to harmony, I had 3.22 as the intensity per cell. I am not sure whether
a) are there supposed to be any intensity adjustment which I should do? or were there some inbuilt readjustment that were already been done in either CP/ilastik/Harmony?
b) or I am missing something in my CP pipeline?