Primary Object Detection: nucleus

identifyprimary

#1

Dear All,

What is the best way to identify nucleus from the image:

Thank you in advance,
Volodymyr


Identifying epidermis and hair follicles in skin as primary objects
#2

Hi,

It’s quite a tricky mixture, with nuclei size range from small to large, bright nucleoli, and clumped cells. Until others come to help, I suggest to smooth the image first and identify nuclei with Otsu, as shown in the example pipeline example.cpproj (637.4 KB)

Hope that gives you some start.
Good luck.


#3

Would you be able to elaborate on how the smoothing helps for the detection please?

I’ve been using Ilastik a lot recently but this image has me wondering how I would deal with the clumping.


#4

The Gaussian filter smoothing with a “disk size” of about 1.5x the size of the bright nucleoli is only meant to drive the objection identification toward detecting bigger objects (which are the desired nuclei) , instead of catching the small nucleoli.
Metaphorically, if I want the segmentation to look for a mountain, instead of looking for the human with bright white hat standing on the top of the mountain, I would first blur the picture a bit, now the human is “dissolved” into the terrain and not catchy anymore.


#5

Awesome, thanks for your reply!