CellProfiler measure intensity multiple images




Right now I have a pipeline that looks at the average of several images (frames from an imaging session) to produce ROI’s around the cells as objects. I use the average of all images because there is ever so slight movement that I want to include.

Anyway, I want to apply this ROI to the series of ~400 frames that are individually saved as tifs in a folder. How do I use the MeasureImageIntensity tool to produce the average intensity of the objects (ROIS) across all 400 images without having to manually input all 400 images in the MeasureImageIntensity step? Right now this step spits out one AverageImageIntensity, and I want it to spit out 400 - one for each image in a table

Thank you in advance for your help!


I’m doing images over time and want the same Object to measure intensity over all time frames.



You can do this in a separate pipeline once you’ve made your ROIs; without knowing more about how your experiment is set up I can’t tell you EXACTLY how to do it, if you look at this thread, it goes into a lot of detail on how to set something like that up (essentially, the “secret sauce” is metadata matching in NamesAndTypes- the help for that module goes into detail about it too).