Per-cell stats without pre-segmentation


I was hoping this forum could help me out. I’m new to CellProfiler, so I apologise if my question has an obvious answer.

I have segmented cells using the green channel, seeded by the blue nuclear channel (IdentifyPrimaryObjects, IdentifySecondaryObjects). That works pretty well. I now want to measure the distribution in the red channel on a per-cell basis. I found I could do this using the Relate module, but as far as I can see this requires the red channel to be segmented into objects first, which is not something I want. Rather, I want to measure things inside the cell based on pixel intensities directly, without segmenting it.

Is there some way to do per-cell stats without first segmenting the image to be measured?

Thanks in advance,

Hi Ben,

You can use the cells and the red image as input into the MeasureObjectIntensity module. Even though the cells were produced from a different image, you can still measure the intensity within them against the red image and get the measurements you’re looking for.


Thought that might be a silly question. Thanks.