I am using CellProfiler to segment nuclei, bacteria and lysosome in images which have been obtained by infecting primary human macrophages with mycobacterium.
I am also interested in performing single cell analysis on these macrophages to know how many bacteria are colocalized with lysosome inside a single cell.
Now coming to the issues that I am facing:
- While segmenting lysosomes, CP fragments the lysosome into two or three parts which from naked eye we perceive as a single lysosome.
- While performing colocalization, I want to have cell as parents with two different children i.e. lysosome and bacteria and then do colocalization of these children for every parent.
But I think this doesnot exist in cellprofiler so I ended up assigning lysosome and bacteria as parent-child. If there is a way to do the two children thing please let me know.
I am attaching the pipeline that I am using.
The images can be found here dropbox.com/sh/u39h82toajrw … cH498MNxwa
The folder also contains Illumination correction images.
Please let me know if you need anything else.
P.S. You guys have done a wonderful job making this software and that too open-source. Thanks a ton
Colocalization Pipeline.cppipe (23.6 KB)