The attached pipeline was created to identify puncta stained with the fluorescent dye LysoTracker (which labels acidic organelles). I have also attached 2 image sets (DAPI files are of Nuclei, Cy3 files are of LysoTracker).
I think the identification of Nuclei works fine, but I am wondering if anyone has any advice on improving the identification of LysoTracker puncta.
Additionally, this pipeline was created on CellProfiler 2.2.0 but it does not seem compatible with CellProfiler 3. I think this is an issue with the different thresholding strategies when Identifying Primary Objects but I am not sure how to modify the pipeline to make it compatible with CellProfiler 3. I would really appreciate any help in this!
iN7 Lysotracker Analysis.cpproj (1.0 MB)