Trouble identifying primary objects - high cell density

[Kinga (Kinga Bercsenyi)]

Hello,

I have some trouble identifying my primary objects; they are very dense and are difficult to separate based on intensity, or shape - could any of you point me towards the best thresholding setting within the Identify Primary Objects module?
The life database is here:

CP forum question

Thanks a million

[Minh]

Hi there,

It’s indeed a challenging case. You can try do the following:

• UnmixColors to collect the green channel
• Use some combination of Smooth and Mask, to mask the edge of the tissue out, since it’s a confusing region.
• Then clean the (remaining) green image a bit : using EnhanceOrSuppressFeatures >> Suppress, feature size 5
  
  
• Then IdentifyPrimaryObjects
  
  
  
  zoom in:
  
  

Here is the example pipeline: lif.cpproj (643.1 KB)

Good luck.

[Kinga (Kinga Bercsenyi)]

Hi Minh,

It’s working a treat, thank you!
Kinga