I am a new user of CellProfiler, attempting to count the number of cells expressing different fluorescent markers. I’ve been through the tutorials, the help modules, and the forum posts. They have been very helpful in fixing other problems, but I have not yet been able to find an answer for this particular issue.
I want to measure the intensity of my negative control image (using MeasureImageIntensity) and then subtract a percentage of that intensity from my experimental images (using ImageMath). The problem I’m encountering is that I can’t figure out how to group my images so that I can measure the control image separately from the experimental images. If I separate them using NamesAndTypes based on their metadata, I receive an error that there are not the same amount of images in each group (which I think is because it is expecting each group to consist of the different channels). If I separate them using Groups, the groups don’t show up as options further down in the pipeline. Additionally, I’ve tried to measure the control image in a separate pipeline and import the measurements, but ImageMath only takes measurements from images within the pipeline.
Any help would be appreciated! I can post the pipeline I’m working on or any example images if necessary.