Wednesday, April 12, 2017

Modelisation of overlapping pairs of chromosomes: a dataset containing more than 200 000 pairs of images in png format.

Two datasets modelizing pair of overlapping chromosomes are available on github:
Images are available at full resolution but also at a lower resolution to reduce the memory imprint. To get a smaller memory imprint, the two componants (Cy3, DAPI) of the original image were combined into one grayscaled image.

The chromosomes were chosen to represent the different chromosomal morphologies. The training and the validation datasets were generated with different chromosomes belonging to the same metaphase (slide jp21,metaphase 3) from human normal lymphocytes couterstained with DAPI and hybridized with a telomeric Cy3-labelled PNA probe.

Low resolution images dataset: 

Training dataset

The training dataset was generated from six chromosomes:

The dataset consists in 100 085 pairs of greyscaled/groundtruth images of shape 80x82. 

Simulation of overlapping pairs of chromosomes. Sample of low resolution image dataset.

Groundtruth labels of the training dataset

Validation dataset:

The validation dataset was generated with other chromosomes from the same metaphase:

The validation dataset  contains 111 123 pairs (grey + groundtruth label) of images (8bits, png)

Full resolution dataset:

  • The training dataset contains 97 976 pairs of 201x211 images.
  • The validation dataset contains 50 543 pairs of grey / groundtruth images.

Saturday, April 1, 2017

100 overlapping, full resolution, chromosomes isolated from 14 metaphases of human lymphocytes

Metaphasics chromosomes were hybrized with a PNA telomeric probe (CCCTAA-Cy3) and an additional oligo DNA probe (Cy5) for testing purposes.

100 overlapping chromosomes can be found in that dataset (jpp21). The dataset consists of 12 bits raw greyscaled images available on the DeepFISH repository. The images of overlapping chromosomes were isolated and converted into 8bits rgb images:

Sample of 100 overlapping chromosomes (full resolution)
The overlapping images are also available as combination of DAPI and Cy3 components:

Combination DAPI+Cy3 images (inversed greyscale)

Monday, November 21, 2016

Generation of 82146 chromosomal overlappings from pairs of chromosomes

The following jupyter notebook was published on github . The aim is to generate a large dataset of overlapping chromosomes (grey scaled image + ground truth label image) to train a neural network to perform semantic segmentation on such images.
To gain a large number of images the resolution was decreased by 16. A first try proposed in the ai.on project seems to do a very good job. The results was obtained from a dataset of 13434 pair of images from a python implementation of Unet.

Monday, October 31, 2016

DeepFISH : a github repository where to find datasets, notebooks and raw images

For the opening of the topic about chromosomes segmentation on AI.ON, a github repository, DeepFISH (Sorry for the name) was created.

Today, this repo contains:
  • datasets: hope to train some kind of convolution neural network to perform semantic segmentation to resolve overlapping chromosomes. The two datasets modelize the overlapping of two chromosomes.
 
  • notebooks: for generating the dataset and for loading and displaying the datasets. The jupyter notebooks are written in python 3. Initially the notebook used to generate the datasets was written in python2.
 
  • raw images: This is additional raw images of metaphasic chromosomes staines with DAPI and labelled with a telomeric probe (PNA-Cy3).

Wednesday, October 19, 2016

chromosome segmentation problem on AI.ON

The problem of chromosomes segmentation is exposed on AI.ON.
Some data for possibly training an ANN are available at kaggle and the way to produce them too.

Wednesday, July 20, 2016

An example of modelization of overlapping chromosomes


example of generation of overlapping chromosomes.Left: greyscale image (DAPI+Telomeres). Right: red label maps to pixels belonging to the overlapping domain, blue and yellow maps to pixel belonging to single chromosomes.

This image is used for illustration on kagle.

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: