How to separate touching cells in CellProfiler?

Hi,

I am new to CellProfiler. I have trouble separating touching cells in the following image
PicBF.tiff (126.1 KB).
I am using CellProfiler version 4.0.7. Here is the pipeline that I have been working on
CropCellsBF.cppipe (8.4 KB)
Thanks for your help.

Hi @Pallop_Huabsomboon,

For brightfield images it can be quite difficult to segment accurately without additional preprocessing. You might want to try using the Watershed module to further refine your segmentation.

In general though, we’d usually recommend approaching this with a tool like Ilastik to assist with finding the cells, then using the resulting detection in CellProfiler. There’s a tutorial on that here.

Hope that helps!

Hi David Stirling
Thank you for your fast response. I will try Ilastik and keep you inform.
Best,
Pallop