I am working with images that show groups that differ in the intensity of junctional proteins. The set of images I have with high junctional intensity I can get secondary objects from by inverting the image with ImageMath, but this doesn’t work with the other set of images as there are no clear dividing lines between cells. To try and quantify this, I created a pipeline (attached below) that just expands the nuclei by a few pixels to create secondary objects for both sets of images and compares the intensity in the junctional image channel within those borders. This pipeline shows minor differences between the groups, but not nearly to the degree I would expect when looking at the images by eye. I thought perhaps this could be due to the region that is measured still being mostly low intensity (as only the very border of the cells is stained) which would bring the mean intensity down in both groups and limit the difference between the groups in my results, but I am unsure how to combat this. I tried using an upper quartile intensity measurement instead of a mean intensity measurement, but it didn’t seem to help much. I included screenshots of one image in each group so you can get a better idea of what I’m talking about.
Thanks for any help, I really appreciate it!
TestPipeline.cpproj (495.2 KB)