Calculating fluorescence intensity in cell profiler

I have a cell profiler pipeline to mark nuclei and cell boundaries and export to spreadsheet the fluorescence intensity for the different fluorescence channels.

I want to calculate the average fluorescence intensity per cell. However, the spreadsheet generates several intensity values: Integrated intensity and mean intensity. I am not sure which one should I use?

A second question I have is that Cell profiler version 3 eliminated the conserve memory module. Now my computer sometimes freezes and can not process the analysis due to lack of memory. Is there a free online server that I can use to run cell profiler.



Integrated intensity is basically sum of intensities of each pixel of the object (i.e. total intensity of object), while mean intensity is integrated intensity divided on the object area (in pixel).
Assume you have 2 objects with perfectly uniform signal distribution (i.e. each pixel has exactly the same intensity) and one object is 2 times bigger than other. In such a case, bigger object will have 2 times larger integrated intensity and exactly the same mean intensity.
Depends on the biological background of your experiment, you might be interested in either of this values.

I don’t know answer for the second question.
Good luck

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