CellProfiler Measureimageintensity module gives very small pixel intensity



Hi all,

When using the Measureimageintensity module at the end of my pipeline in CellProfiler, the result it gives is very small numbers rather than the actual pixel value. I create a trial image which only has 9 pixels and this problem continues, is it an auto-normalization? My image is from a uint16 matrix[ 247 245 37;
41 124 108;
248 205 234], but the result shows mean intensity as 0.00252452 all other results in this kind of small scale.
If you know about this, please help, thank you!


Hi Krozard,

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. If you multiplied your mean intensity value by 65535 then the resultant value would be the average of those 9 values.

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!

As an aside to the CellProfiler team if someone from there reads it, I couldn’t really find anywhere in the manual mentioning the default rescaling where I would expect it. In the MeasureObjectIntensity section there is this paragraph.

“Keep in mind that the default behavior in CellProfiler is to rescale the image intensity from 0 to 1 by dividing all pixels in the image by the maximum possible intensity value. This “maximum possible” value is defined by the “Set intensity range from” setting in NamesAndTypes ; see the help for that setting for more details.”

But then in the NamesAndTypes section of the manual you don’t refer to this setting at all. Maybe you’ve done this on purpose but thought I’d mention it in case it was an oversight.


Thank You so much!!:grinning: