I have cells where the nuclei are marked with DAPI, and the cytoplasmic regions are marked with an anti-enolase stain. My goal is to identify all of the individual cytoplasmic regions as separate primary objects.
Some cells are clustered, while others are isolated. The isolated cells are segmented properly, with the cytoplasm highlighted and the nucleus present as an empty circle.
However, when there are multiple adjacent cells, the segmentation fails—my pipeline combines half of one cell’s cytoplasm, and half of another cell’s cytoplasm, into a single cell. The nuclei are wrongly identified as empty space at the edge of a cell, and are used for segmentation. I’m new to CellProfiler. How do I fix this? Thanks in advance. I have attached my basic pipeline and some example images.
Test_Pipeline_2_S3W4.cpproj (649.2 KB)