This is my pipeline:
1- Identify primary objects
2- Identify secondary objects
3- Measure size/shape of primary objects
4- Filter primary objects on Form factor and area + relabel secondary objects
The relabelling step gives unexpected output. Removed cells are not associated with removed nuclei but they seem to be randomly assigned. It seems like a bug in assigning new indexes to the secondary objects. Attached are screenshots, pipeline and sample data.
I have some problems uploading the files, so here are the links to the images
drive.google.com/folderview?id= … sp=sharing