Generating images of overlapping chromosomes

Generating examples of two overlapping chromosome from single chromosomes: 

Notebook:

A notebook showing the different steps to generate overlapping examples is available on kaggle. As well as the raw images.

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:

 examples of overlapping chromosomes 

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

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view raw LoadingPairsDataset.ipynb hosted with ❤ by GitHub

Modelling intersection between polygons with geogebra.

Rotate the polygons using the points B and I. Move the yellow polygon with the sliders v and w