OASIS: nOrmal breASt tISsue Dataset

• Dataset size: 1489 WSIs
• Contact name: Mario Parreno-Centeno
• Institution name: Kings's College London
• Institution URL: http://cancerbioinformatics.co.uk/
• Contact email: mario.parreno-centeno@kcl.ac.uk

The nOrmal breASt tISsue Dataset (OASIS) repository is a retrospectively collected dataset of 1,489 H&E-stained whole slide image (WSI) of normal breast tissue. The images were collected from following institutions, namely the King’s Health Partners Cancer Biobank (KHP, https://www.khpbiobank.co.uk/), the Netherlands Cancer Institute (NKI, https://www.nki.nl/), the Barts Cancer Institute (BCI, https://www.qmul.ac.uk/bci/), the Cathrin Brisken Lab at the École Polytechnique Fédérale de Lausanne (EPFL). We have access to WSIs from the publicly available Susan G. Komen Tissue Bank (SGK, https://komentissuebank.iu.edu/). The WSIs comprise normal breast tissue collected from:

• Normal breast tissue of healthy individuals without known germline or VUS BRCA1/2 changes (n:1k)
• Normal breast tissue of healthy individuals with known germline or VUS BRCA1/2 changes (n:151)
• Contralateral normal breast tissue of breast cancer patient with known germline or VUS BRCA1/2 changes (n:128)
• Peri-tumoral normal breast tissue of breast cancer patient with known germline or VUS BRCA1/2 changes (n:210)

Example usage

Below code demonstrates how to load WSIs programmatically using Python Openslide package

import openslide
import numpy as np
import matplotlib.pyplot as plt

#Read WSI
wsi = openslide.OpenSlide("/Path/to/wsi.ndpi")

#Get slide properties
dims=wsi.dimensions
x_resolution=wsi.properties[openslide.PROPERTY_NAME_MPP_X]
y_resolution=wsi.properties[openslide.PROPERTY_NAME_MPP_X]
base_mag=wsi.properties[openslide.PROPERTY_NAME_OBJECTIVE_POWER]


#Display thumbnail
wsi_thumbnail = wsi.get_thumbnail((1000,1000))
wsi_thumbnail=np.array(wsi_thumbnail)
plt.imshow(wsi_thumbnail)
plt.axis('off')

Credits

If you find the data useful, please cite the below paper:

@inproceedings{,
    title={},
    booktitle={},
    author={},
    year={}
}