Measuring image intensity


I am having trouble with optimizing my pipeline. I am trying to measure the image intensity in only one channel (red) of a merged .tif picture (blue and red) but I’d like to count the number of objects (blue) as well. Is this possible? I really just need the fluorescence intensity in the red channel of a merged image (without having to unmerge each one) but I don’t see how to change the settings of the module to do this?

Thank you very much for your time and help,


Hi avaishnavi,

Most modules in CellProfiler assume grayscale images. So CellProfiler will need to “unmerge” them, but that is only within the software and you do not need to write out the unmerged files, if that is your worry. So with a merged (color) image, in the NamesAndTypes module, be sure to set the input to “Color” and not Grayscale. Then add a ColorToGray module and Split (do not Combine) the channels into RGB. Then you can add whatever Identify and Measure modules you need. To count the blue objects, for example, use a IdentifyPrimaryObjects on the split Blue channel. And to get the intensity in the red channel add either a MeasureObjectIntensity or MeasureImageIntensity depending on whether you want to measure objects or the whole image.

Does that help?


Thank you so much! I think that should cover it, but will let you know if I have more issues. Thanks again!