I need help identifying cells


I am working on a pipeline identifying cytoplasmic speckles.

In the end I want to derive a “speckles per cell” ratio and therefore I need to relate the child objects “speckles” as accurately as possible to the parent objects “cytoplasm”. I have some difficulties identifying the cells itself. No matter which settings I use, the labeled image is not what I want to see.

I attached some screenshots to my post to clarify what I mean.

I would appreciate any help! Thank you!

Hello again,

I attached a simplified pipeline to clarify the difficulties I have.

The name of the pipeline is “2012-10-29.cp”.

“overlays.png” is a new screenshot.

The TIF-files are the corresponding pictures.

Thank you very much!

2012-10-29.cp (7.32 KB)


I’m attaching a pipeline which should help; it is largely based on the Speckles pipeline located on our Examples page. I also had to change the identification method in IdentifySecondaryObjects; it’s not perfect since your cell borders are a bit indistinct in areas, but using Propagation with a lower regularization distance seems to look better than before.

2012_11_06.cp (9.72 KB)


thank you for your help! I really appreciate your time.

Is there any stain out there you can thoroughly recommend for cell border identification?

Something similar to a phalloidin or cellmask stain should do the trick.