santiagolopezg/DeepFISH

DeepFISH

Why Deep? Because of deep-learning.

Why FISH? Because of Fluorescent in-situ Hybridization.

This repository is intended to share data and code for resolving some problems met in cytogenetics imaging such overlapping chromosomes.

Dataset

• DAPI.tif and Cy3.tif : 12 bits images of metaphasic chromosomes. The telomeres marking the end of the chromosomes are visible in the Cy3.tif image.The metaphase doesn't contain overlapping chromosomes.

• LowRes_13434_overlapping_pairs.h5 : 13434 pairs of overlapping chromosomes generated from the two previous images. This dataset is intended to train a supervised learning algorithm to resolve overlapping chromosomes. The dataset is stored as a numpy array and saved in a hdf5 file. Compared to the DAPI and Cy3 images,the resolution was decreased by two.

• overlapping_chromosomes_examples.h5: smaller dataset (~2000 images). The resolution of the images is the same than the DAPI/Cy3 images.

References

• A Geometric Approach To Fully Automatic Chromosome Segmentation
• Automated Discrimination of Dicentric and Monocentric Chromosomes by Machine Learning-based Image Processing
• An Efficient Segmentation Method for Overlapping Chromosome Images
• A Review of Cytogenetics and its Automation