I collected large 6x6 stitched images and want to identify and count nuclei using Cell Profiler. I had to black out portions of the images that are out of focus using ImageJ (selected ROIs and pressed delete). When I try to identify primary images using Cell Profiler, it identifies a lot of artifact objects along the border with the blacked out portion ( the link to access raw and processed images and the pipeline is attached). How can I solve this issue?
Your help is greatly appreciated.