Relating cellbody with nuclei


I’m sorry for probably asking a beginner’s question (been only using CellProfiler for 2 weeks now) but I want to get CellProfiler to recognize and relate the nuclei to the cellbodies around them (I am analyzing primary human fibroblasts with DAPI/Phalloidin). I used the “Human Cells” example pipeline and went from there, it recognizes the nuclei just fine, however, I just can’t get the program to recognize the often stretched/elongated cellbodies and relate them to the nuclei.
Furthermore, I want to classify the fibroblasts in terms of morphology with CellProfiler Analyst after that.

I would be very glad if someone here was kind enough to provide me with some tips!


Hi Armando,

I would read some of the help menus in the “IdentifyTertiaryObjects” module. This is where you would identify your cell bodies and segment based on nuclei.

I find it best to do some trial and error to begin to understand how the module works. Something simple like reducing the “Threshold Correction Factor” will recognize weaker pixels and may help finding elongated cells bodies. You may also want to try a different Thresholding Method, and change some of the other choices.

Hit “Start Test Mode”, click the pause button for the module below “IdentifyTertiaryObjects”, hit run, look at the results, make a change and repeat. This will help you understand what choices to make to improve object recognition.

Also, if you upload some images someone may be able to give you more specific advice.

Rob Bukar
Fujifilm Wako Automation

This blog post may help, too: