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.
Image Modified
These 5,060 Whole Slide Images (WSIs) are from the following 10 cancer types:
BLCABladder urothelial carcinoma
BRCABreast invasive carcinoma
CESCCervical squamous cell carcinoma and endocervical adenocarcinoma
GBMGlioblastoma Multiforme
LUADLung adenocarcinoma
LUSCLung squamous cell carcinoma
PAADPancreatic adenocarcinoma
PRADProstate adenocarcinoma
SKCMSkin Cutaneous Melanoma
UCECUterine 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
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title | Data Access |
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| Data AccessClick the Download button to be redirected to Box for downloads. Note that Box has a 15GB at one time max download restriction. Data Type | Download all or Query/Filter |
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Tissue Slide Images (SVS, 1,200 GB) | | List of histopathology slides (TXT, ) | | 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. |
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title | Detailed Description |
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| Detailed DescriptionAdditional 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 |
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Note: Please contact help@cancerimagingarchive.net with any questions regarding usage.
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title | Citations & Data Usage Policy |
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| 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: Info |
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| 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 |
Info |
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| 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) |
Info |
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title | Publication Citation |
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| 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 DataTCIA maintains a list of publications that leverage TCIA data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk. |
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| Version 1 (Current): 2020/02/08 |
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Data Type | Download all or Query/Filter |
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Tissue Slide Images (SVS, 1,200 GB) | | List of histopathology slides (TXT, ) | | WSI quality control results (TXT, 151.4 KB) | | Segmentation region checking results (TXT, 169.4 KB) | |
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