I am struggling a lot to analyze my images with CellProfiler, and I was wondering if someone could help.
I have some microscopy images containing lots of cell populations. I identify all my different populations with CP, and my goal is for each cell of each population to measure the minimal distance to the cell of another population, for each population. (Ex: I have two cell populations A and B, I want to know for each cell type A what is the closest cell type B).
I tried with the module “MeasureObjectNeighbors” but it doesn’t seem to be able to do that. I also try a plugin on imageJ but the software cashes all the time, as my images are a bit heavy.
I would be very grateful if someone had a solution!
Thanks a lot
The measurement you describe should be possible with MeasureObjectNeighbors, but is currently not working due to a bug when using different object sets. It’ll be fixed in CellProfiler 4, which we’re hoping will be available around the end of this month.
In the meantime, you can calculate the distance to neighbours by converting each set of cells to a binary image using ConvertObjectsToImage. If you use ImageMath to invert that image and then run the Morph module in ‘distance’ mode you’ll get an image in which each pixel represents the distance to the nearest cell of that set. You can then run MeasureObjectIntensity with that image and look at the MinimumIntensityEdge statistic to get the distance to the closest target cell in pixels.
Hope that helps
Thanks a lot, I’ll try !