Identification of nuclei shape without direct nuclei stain

Hi,

I want to identify the nuclei as objects from the ER staining which originally also displays the outer nuclear membrane itself together with its peripheral ER membrane (please see the attached fileC2-Image123.tif (1.0 MB) ).
Unfortunately, the image does not have a nuclei stain.

As the nuclei shape is distinctively recognized from the ER stain itself, I thought I could find the way of identification of nuclei in cellprofiler, too. But I failed.

Initially,

  1. I invert the image using ImageMath
  2. use Gaussian filter of sigma 6
  3. use enhancedEdge module
  4. then, perform IdentififyingPrimaryObject under condition of Global, Robustbackgroud…etc.

The above approach allows me to identify couple of nuclei, but not efficient.

Does anyone have a better idea and would you help me out?

Many thanks in advance and I would appreciate any possible help,

Best
Wonyul

Hi @Wonyul,

I tried another way as follows,

  1. Gaussian filter
  2. Invert the image
  3. EnhanceSuppressfeature - Enhance the dark holes (with the size cutoff)
  4. Identify Primary object with similar setting as you had mentioned.

Here is the screenshot & pipeline. You might have to try with many samples. You can play around with teh gaussian filter too if needed.


nuclei.cpproj (135.6 KB)

Hope this helps.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

Hi Lakshmi,

that looks very nice! That’s exactly what I wanted. :grinning:
I will try it by myself with those approaches in the batch scale.

Thanks again for your help!

Best wishes,
Wonyul

Hi @Wonyul,

You are welcome!!

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging