Tuesday, June 21, 2016

Generating images of overlapping chromosomes

Generating examples of two overlapping chromosome from single chromosomes: 

Notebook:

The idea:

Images of single chromosomes hybridized with with telomeric Cy3-probe and DAPI counterstained were extracted from the image of a metaphase:

DAPI stained chromesomes (left), (CCCTAA)3-PNA-Cy3  probes (Red)
The monochrome DAPI and Cy3 images were added. Single chromosomes were isolated:
All images are 131x128
Given two single chromosomes, examples of overlapping chromosomes were generated combining rotations and translations:


Each greyscale image of a pair of overlapping chromosomes, is associated with a mask containing labels. The pixels of value equal to 3 maps to the overlapping domain of the two chromosomes:



Then a dataset containing 2853 examples of overlapping chromosomes was generated and saved as a h5f file available here:


Once downloaded and uncompressed, the examples can be loaded as a hdf5 file as shown bellow: