IdentifySecondaryObjects for cell shape

Hi everyone,

I am trying to identify cell shape using the IdentifySecondaryObjects module and create objects of it. I have two image files, one for cell nuclei (Hoechst) and one for cell shape (Texas Red). However, I find it very hard to find good settings in the IdentifySecondaryObjects module. The objects do not match the cell shape correctly, no matter how I change the settings. Identifying the nuclei in IdentifyPrimaryObjects is no problem.

Could you please give suggestions on settings I can try in the IdentifySecondaryObjects module? Or is there an image pre-processing module I should try prior to objects identification?

Hoechst - n000000.tif (5.9 MB)
Texas Red - n000000.tif (5.9 MB)

These are the settings that worked the best so far, but the result is still not satisfying yet.

And this is the output I get from it.
output IdentifySecondaryObjects

Thank you!

Hi @elead,

I checked your images. There are two suggestions,

  1. You can change the method in the secondary object identification.
  2. Also you can apply a rescale intensity or minimal median filter before secondary object identification.
    I tried these settings, Of course little more optimization is required.

Hope this helps.