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.