Identify cells as objects Cellprofiler

Hi,
I want cellprofiler to find the cells in the attached image. I have tried to do this using IdentifyPrimaryObjects. However it struggles due to the cells having irregular shape and staining. Several of the cells might have more than one nuclei, and I therefore do not think using the nuclei as primaryObject and the cells as secondaryObject would work. What do you think is the best way to find all the cell objects in this image?

Thanks in advance,
Tonje

WGA_small.tif (9.0 MB)

1 Like

Hello Tonje,
Do you have a separate nuclear stain and image as well?
In general, if you have a nuclear stain we could use that to identify the primary objects and then use this WGA stain to detect cells/secondary objects.
For multi-nuclei cells, you could smooth the cell stain channel and then use the smoothed image to detect the cells.

Yes, here are images from the same region with WGA (membrane) and Hoechst (nuclei) :slight_smile:

Hoechstsmall2.tif (11.5 MB) WGAsmall2.tif (11.5 MB)

Take a look at this quick pipeline.
ForumTestPipeline.cppipe (13.6 KB)
You can adjust/improve segmentation based on your other images.
The images in general looked a little out of focus.

To learn more about different modules and segmentation, take a look at some of our workshops.

Hope this helps!