Combining CellPose with CellProfiler

Hi there,

I need single-cell image analysis for one of the high throughput screen assays which require segmentation of aggregated cells. Unfortunately, I was unable to get reasonable results from CellProfiler due to uneven DAPI staining and tried CellPose which is working really neat (see attached image).

Due to the number of images involved, I want to run everything within CellProfiler. Has anyone tried running CellPose within CellProfiler (is that possible?). Or perhaps train Ilastik on CellPose and get reasonable results?

You COULD in theory, if you’re running both CellProfiler and CellPose from source, create a “RunCellPose” module that runs CellPose on CellProfiler images, but as far as I know there is not one that currently exists.

Another option would be to run your images through CellPose FIRST, then import the images + CellPose masks into CellProfiler for subsequent measurement generation; that may work entirely out-of-the-box, if not it should be reasonably easy to get working.