FDA stained plant cells and counting their nuclei with CellProfiler

I’m first time user with CellProfiler. I’ve tried to build a pipeline to count nuclei of FDA stained plant cells. Please, see the hyperlink for the pipeline. (Unfortunately the forum does not allow first time users to upload files. The test pictures are in the attachments. I’ve gotten the pipeline to work with test picture no 4. Others do not work well (no dark background). My target is count green nuclei (cell alive) and later red nuclei/spots (dead cells).

My question is how do I export data (number of nuclei) into excel for further prossing? Are there any other points where I could improve my target recognition?


The pipeline and photos


You need to add ExportToSpreadshee module to your pipeline to export quantitative information into Excel.

You likely won’t be able to use the exact same pipeline to process images 1-3 and image 4, since they have different background colors- the UnmixColors module may help you for images 1-3.

Good luck!