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?