I am currently working as a research assistant in stem cell research. My task is to extract as much useful/accurate data as possible over a large range of image sets. I have been working on and learning Cellprofiler for 4 weeks now and feel like I am progressing well much lacking a bit of knowledge.
Issues that I am experiencing:
IdentifySecondaryObjects is not accurately identifying the Cellbody’s and sometimes completely not finding them. I have had a play around with the advanced settings but can’t seem to get it to work efficiently across all images. I believe that it could be the method that I am using.
Alternatively I have tried to IdentifyPrimaryObjects then RelatedObjects however in some cases that works effectively but it relates 2 or 3 nucleus’s to the cell which is not useful data.
I have uploaded the pipeline that I am using and some example images. Hopefully somebody can guide me to a solution and I will be very grateful. Alternatively I am happy to take any improvement advice on my pipeline. I understand that my analysis is tricky because many of the images contain cells that are touching the borders and are odd shapes.
PIPELINE: MSC5x5ComplexPIPELINE.cpproj (693.5 KB)
Example IMAGES: (upload://uCkqTJI0mAXFxUE486TMX0xc0q1.cpproj) (693.5 KB)