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  • Dataset of Segmented Nuclei in Hematoxylin and Eosin Stained Histopathology Images (Pan-Cancer-Nuclei-Seg)

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Summary

Large dataset of nucleus segmentations in whole slide tissue images with quality control results are available here. There are two subsets of data: (1) automatic nucleus segmentation data of 5,060 whole slide tissue images of 10 cancer types, with quality control results. (2) manual nucleus segmentation data of 1,356 image patches from the same 10 cancer types plus additional 4 cancer types.

These 5,060 Whole Slide Images (WSIs) are from the following 10 cancer types:

BLCA Bladder urothelial carcinoma
BRCA Breast invasive carcinoma
CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma
GBM Glioblastoma Multiforme
LUAD Lung adenocarcinoma
LUSC Lung squamous cell carcinoma
PAAD Pancreatic adenocarcinoma
PRAD Prostate adenocarcinoma
SKCM Skin Cutaneous Melanoma
UCEC Uterine Corpus Endometrial Carcinoma

Note that you can also download segmentation data of following 4 cancer types, although they are not officially verified or released.

COAD Colon adenocarcinoma
READ Rectal adenocarcinoma
STAD Stomach adenocarcinoma
UVM Uveal Melanoma

Data Access

Click the Download button to be redirected to Box for downloads. Note that Box has a 15GB at one time max download restriction.

Data TypeDownload all or Query/Filter
Tissue Slide Images (SVS, 1,200 GB)

List of histopathology slides (TXT, 348.5 KB)

WSI quality control results (TXT, 151.4 KB)

Segmentation region checking results (TXT, 169.4 KB)

Click the Versions tab for more info about data releases.

Note:  Please contact help@cancerimagingarchive.net  with any questions regarding usage.

Detailed Description

Additional visual segmentation data can be found on PathDB


Manual nucleus segmentation data of 1,356 patches

These 1,356 patches are randomly extracted from all 14 cancer types mentioned above. This data contains original H&E stained histopathology image patches, and instance-level segmentation masks. Additional information is in the readme.txt file of this data. Download here


Note:  Please contact help@cancerimagingarchive.net  with any questions regarding usage.

Citations & Data Usage Policy 

These collections are freely available to browse, download, and use for commercial, scientific and educational purposes as outlined in the Creative Commons Attribution 3.0 Unported License. Questions may be directed to help@cancerimagingarchive.net. Please be sure to acknowledge both this data set and TCIA in publications by including the following citations in your work:

Dataset Citation

Le Hou, Rajarsi Gupta, John S. Van Arnam, Yuwei Zhang, Kaustubh Sivalenka, Dimitris Samaras, Tahsin M. Kurc, Joel H. Saltz (2019). Dataset of Segmented Nuclei in Hematoxylin and Eosin Stained Histopathology Images of 10 Cancer Types [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/tcia.2019.4a4dkp9u

TCIA Citation

Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. (paper)

Publication Citation

Hou, Le, Ayush Agarwal, Dimitris Samaras, Tahsin M. Kurc, Rajarsi R. Gupta, and Joel H. Saltz. "Robust Histopathology Image Analysis: To Label or to Synthesize?." In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 8533-8542. 2019. Open Access Here

Other Publications Using This Data

TCIA maintains a list of publications that leverage TCIA data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk.

CC0
To the extent possible under law, https://doi.org/10.7937/tcia.2019.4a4dkp9u has waived all copyright and related or neighboring rights to Dataset of Segmented Nuclei in Hematoxylin and Eosin Stained Histopathology Images of 10 Cancer Types (collection nucleus:segmentation). This work is published from: United States.

Version 1 (Current): 2020/08/02

Data TypeDownload all or Query/Filter
Tissue Slide Images (SVS, 1,200 GB)

List of histopathology slides (TXT, 348.5 KB)

WSI quality control results (TXT, 151.4 KB)

Segmentation region checking results (TXT, 169.4 KB)


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