Hello! I am new to CellProfiler and would appreciate some help.
I am trying to figure out a pipeline for counting colocalization using nuclei as the primary object/seed point. For some reason, when I try to identify secondary objects, the nuclei remain as objects when they are in a separate channel and I don’t see any major cross-channel interference.
My goal is to have a total cell count, total GFP-positive cell count (second channel), total PV-positive cell count (third channel), and total PV and GFP-positive cell counts. I am not sure what I am doing incorrectly here with my secondary object identification, and I would appreciate the help.
My (very short) pipeline and image I am trying to analyze can be found at this link.
I am using the most current version of CellProfiler, and have tried to base my pipeline on the instructions provided by David Logan on this forum.