CellProfiler- building pipelines

Hi, I am an undergraduate student in Univ of Sheffield, in UK.

I am doing a dissertation on evaluating cell tracking tools, and CellProfiler is one of my test candidates.

I have been trying to use the tool to track cells in images(jpeg). I tried creating the pipeline myself but found some difficulties.

I need to identify two different types of cells; ones in green and ones in red.

I have attached my .cp file and one of the image file.

Could I please get some help in building appropriate pipeline to track the cells in a given area(using crop).

Thank you.

p.s. I have been trying to understand the tracking methods within the tools, however I just did not really understand them. I am not doing a biological science or mathematics but im studying enterprise computing; I have a bit of programming language understanding but not at the lowest level.
It would be very very very helpful if I could get some basic description of methods and what they are advantageous at. Thanks.

DefaultOUT.mat (47.9 KB)


I’ll address your issues separately:

  • We recommend acquiring your images as TIFs or PNGs since they do not suffer from compression artifacts which degrade image quality as JPEGs do.

  • Your cells have very heterogeneous borders which will probably made identification somewhat problematic. Do you have a nuclear stain which you can use? If so, you can use IdentifyPrimaryObjects to detect the nuclei and then IdentifySecondaryObjects to find the cell body, both the red and the green.


  • Are your cells moving quickly or slowly? If there is a good amount of overlap between cells from frame to frame, you may find the Overlap method to be straightforward.

  • Whatever tacking method you chose, whether one of CellProfiler’s methods or a completely different program altogether, tracking results are only as good as the cell detection. I strongly suggest that you optimize the cell detection as mentioned above before you proceed to tracking issues.

Hope this helps!