The unit and definition of the intensity in CellProfiler



I have analyzed some photos with the CellProfiler. Now I’m writing the manuscript. I want to know the unit and definition of the intensity in MeasureObjectIntensity of CellProfiler.

Thanks a lot.


Glad you’ve had good luck with CellProfiler on your project!

Units of intensity from microscopy images are usually described as “Intensity units”. It’s also important to state whether you are reporting the mean or integrated intensity, so you might say “Mean intensity units” or “Integrated intensity units”. Because microscopes vary so much from each other and are not calibrated to an absolute scale, it’s not feasible to state units more specifically, like “number of photons”, as you can imagine! For this reason, many people would add the word “Arbitrary”, like “Arbitrary pixel intensity units”.

Thanks for your question, we will add this to the help for the module.

p.s. Don’t forget to cite the CellProfiler paper when you publish your work. Here is the paper:

You could also submit your CellProfiler pipeline to the journal as “supplementary data” so that there is never any doubt of exactly what measurement you have made!