Analyze ImageIntensity

Hi everyone,

I am facing a new problem: To analyze the intensity using CellProfiler or ImageJ is quite simple, but reveals totally different results in my case.

CellProfiler: I use “MeasureImageIntensity”-module for DAPI with the following results:

Once I use ImageJ (Analyze->Measure) it shows me this:

Since ImageJ is more or less the “gold standard” for this I would like to understand the different results. Could anybody help with it?


Hi @Mahuesi,

It’s the default behaviour of CellProfiler to rescale the pixel intensity values of your image to between 0 and 1 by the maximum possible intensity in your images. Looks to me like your images are 16-bit as 103.860/65535 = 0.00158

The behaviour of the rescaling is defined in the NamesAndTypes module with the setting “Set intensity range from…”. If you click the ? button to the right you will get a help window which will explain how the options you can set.

Hope that helps!


Hi Laura,

you are right!

By using ImageMath (multiply by 65535 for 16bit) I got the same results compared to ImageJ.

Thanks a lot for your help!


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