Metaphasic chromosomes preparations contain most of the time overlapping chromosomes as follow :

A cluster of two overlapping chromosomes 
Here a cluster of two chromosomes was isolated and the two chromosomes were segmented using a contour based method implemented in an ipython notebook.
First a polygonal approximation of the contour is performed and negative corners are extracted
as previously:

Polygonal approximation of the cluster contour (red line). Negative corners (yellow dots), positive corners (red dots). 
The quadrilateral is converted to an image (overlapp domain:right image) and substracted from the original thresholded image yielding here four chromosomal elements (left image):
The four chromosomal elements are labelled:

Left:labelled chromosomal elements (the size is figured above the image). Right: labelled overlapping domain. 
and isolated:
The idea is to used combinations of elements to build candidate chromosomes. Here the image is supposed to contain two chromosomes, so combinations of two elements in a set of four elements yield the following candidates:
For each candidate, several descriptors are computed: the number of connected components (cc), the eccentricity (ecc), the ratio chromosome area over its convex hull area (r) and the number of negative corner on the contour.
The two first highest ratio correspond to the two overlapping chromosomes which can be isolated: