Module Help

I have pictures split into 3 channels. one is nuclear staining and the other two are stains throughout the cell. I have the nucleus set as my primary object and my two other stains as secondary objects. I want to be able to subtract the intensity in the nuclear region from my two other channels so that my intensity read out is just from the area not enclosed by the nucleus. What is the best module to use?



If I understand your pipeline correctly, you want the IdentifyTertiaryObjects module. This will take the secondary object and subtract (or more correctly, mask out) the primary object, leaving the difference between the two as a new object. This tertiary object can then be used to collect measurements just like any other object. Does that sound like what you want?


I actual think i solved my problem. I masked out my primary object on both my secondary objects to collect intensity from the secondary object excluding the primary object region. I am having another problem though. When I try to collect intensity doing the reverse ( only collecting intensities from my secondary object in the region of the primary object) i get an error saying “zero-size array to min.reduce”. and im not quite sure what that means. do you have any insight


This last question is apparently a duplicate of your question here:

(And I second (third?) Mark’s suggestion to utilize IdentifyTertiaryObjects.)

Can you provide us with a pipeline, example image and the other info I requested?