2164 full resolution pairs of synthetic images of two overlapping chromosomes

After having fixed the groundtruth images of the "13434" dataset, an older but full resolution dataset, has to be repaired too.

Repair of the "overlapping_chromosomes_examples.h5" dataset:

This dataset contained originally 2854 (grayscaled+groundtruth) pairs of 190x189 images, stored in a unique numpy array. Its shape was 2854x190x189x2.

The grayscaled images could suffer from two problems:

• Some grayscaled images components had black dots: those images were removed (with their corresponding groundtruth labels).

• The images dtype was int64, it is now np.uint8

The overlapping domain is also now more realistic compared with real overlapping chromosomes:

The labels of the groundtruth don't have no more spurious pixels:

Dataset format:

Once downloaded, the dataset shape is (2164, 190, 189, 2) available as:

• an hdf5 file
• a compressed (.npz) numpy array

Download the dataset with a jupyter notebook:

 

 

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)

• link to the color images
• link to the greyscaled images 
• link to the notebook

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:

Correction of uneven illumination of images of cattle nuclei at low magnification