Outlining regions of interest prior to counting objects



I am trying to count a number of cells within a certain area of interest so that i can classify the different cell populations. in the intestine mucosa for example, i would be outlining the villous area and outlining the epithelium separately, then counting cells within each compartment. I tried to add a “identify objects manually” but then i couldn’t;t save the output image or ask to count within these areas in the following modules.
any help would be greatly appreciated.


Hi there, I would use the identify modules manually to delineate each one of the regions where you want to count… then I would mask the image by the regions you selected (after identifyng object manually you should get 1 object for each delineation)… additionally I would save the image of each delimited region so if the pipeline gets interrupted you can re-start from the last delineation