Fluorescence image analysis using CellProfiler

Iam a beginner in CellProfiler. I want to quantify fluorescence images of yeast cells, for that i constructed one pipeline by seeing example pipelines. It includes following steps:
1) ImageMath
2) CorrectilluminationApply
3) Identify PrimaryObjects
4) IdentifySecondaryObjects
5) IdentifyTertiaryObjects
6) MeasureObjectSizeShape
but this pipeline is not working. Only inverted image was coming. If someone knows this, kindly share the idea. Here iam attaching some images which iam trying to quantify.



  1. What are you trying to quantify? What is expected outcome?
  2. Could you attach the pipeline file or screenshots of your pipeline? From your description I don’t see anything terribly wrong, should be something in details.

thanks for your kind repy.
I want to quantify the cell size and fluorescence intensity in my fluorescence images. I am unable to upload my pipeline,showing new users cant upload attachments.


You should be able to now (I just updated your trust level), if for whatever reason that still doesn’t work you can post it on GDrive, Box, Dropbox etc and link here.