I am having problems with the Identify Secondary Module.
As part of an experiment, we labeled three separate populations of cells with different colored membrane dyes, we then combined the populations, let them grow, fixed and added DAPI. So in any given image, I have a combination of green, red, and far red labeled membranes along with nuclei.
The Identify Prim works perfect. But since the Identify Secondary is using the Primary objects when it goes to identify the cell edges, it will “find” cell bodies that aren’t actually there. I have tried a variety of methods and haven’t come up with anything.
Attached is a sample image of my DAPI stain along with a membrane labeled image. I also included a sample of what cell profiler generates.
This seems like such a simple thing, any suggestions.