Thursday, January 6, 2011

Good seeds, bad seeds :using watershed to label chromatids of a metacentric model chromosome

A model image of a metacentric chromosome was generated with ImageJ. The model is simplistic, it consists in X shaped binary image:
16 bits binary  image
The seeds consists in small spots in a image. To detect the chromatids, the seeds are designed as two discs labelled by two different gray level (one for each chromatid).

The initial location of the seeds, was in that first trial choosen by hand.

Initial seeds location inside the chromosome 
Gray seeds (that is a 16 bits grayscale image) are then allowed to grow using the watershed algorithm inside the chromosomes, yielding(the result is displayed with pylab):
seeds after watershed yield labelled chromatids (light blue, dark blue)

The result is nice because the initial location was purposefully chosen. What would happen with varying seeds location or orientation ?
Seeds location shifted in the lower left chromatid


After rotation, the seeds can label  p and q arms:
Upper left: the seeds are 45° rotated, the p arm (light blue) and the q arm (dark blue) are detected.
Upper, lower right: shifting vertically the seeds 
Lower left:use of three seeds p  arm (blue), centromeric region (green), q arm (yellow)