Monday, December 13, 2010

Chromatids segmentation with ImageJ

Let's perform high pass filtering on the DAPI image previously processed:

After thresholding and connected component labeling, we get:

If prior image labelling, watershed is performed, the chromosomes are broken into particles that corresponds mainly to the chromatids of the largest chromosomes:

We can see that most of the chromatids are well detected in large chromosomes but less accurately in small chomosomes such HSA 19 or HSA21:

Some pieces of chromatids are well detected, let's paint ("Human labeling") them by hand:
  • in green or blue for the chromatids 
  • in red for the centromeric labeling
  • in yellow, for the badly segmented chromatids.

Yellow regions needs to be reaffected to blue / green or red region. By hands, it gives:

Can we imagine an algorithm capable to perform that task?
A low level image opening finally yields:

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