I am using Cellprofiler for a task that requires to give intensity reports of each objects I defined as a list. I cannot find a module for this.
Here is how I did my previous work. I firstly identify the cytoplasm of cell by using whole cell stain and DAPI under different channels and I have successfully done that by identify primary, secondary and tertiary objects. Therefore, my tertiary object (Cytoplasm) is the whole cell outline but the nucleus area are removed. Then I need to calculate the intensity of cytoplasm of each cell. However, I only can generate the intensity value as a sum of all cytoplasm I outlined. Is there any module I can select to measure and report the intensity of every cell as a list. That will be really helpful because now I have to draw every single cell manually as region of interest on ImageJ which is killing me.
By the way, is there any function that I can manually decide the touching objects, like drawing a boundary when the software cannot split them?
That would be really helpful.