CellProfiler program has been an incredible tool that our lab has started to recently use and it has made our analysis hit a level of granularity we haven’t used before in image analysis. We have gotten a lot of data out of our images that have been extremely useful, but since we always wonder what else this program can do, we were hoping another level of analysis would be possible.
In short, we are doing Fluorescent In Situ Hybridization (FISH) which visualizes RNA strands (puncta) within nuclei of neurons. This results in spots/speckles that we’ve been counting (which has worked fantastically so far). We’ve identified the nuclei, puncta, and colocalized them.
We wondered if it would be possible to measure the percent of each cell that was covered by each kind of puncta we’re looking for. In other words, can we get an output of each neuron and the percent it is covered by each puncta.
The closest thing I’ve been able to find is “MeasureImageAreaOccupied” which gives the total coverage of objects (puncta) we want from a masked image. This is good, but we really would like this on a per-cell basis, rather than per-image, if possible. Does anyone know how to do this? Ideally we would have something where it gave each cell number and then (x% covered by Puncta 1 and y% covered by Puncta 2)
Thanks for any help anyone can give me! All help is appreciated.