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title | Data Access |
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| Data AccessClick the Download button to save a ".tcia" manifest file to your computer, which you must open with the NBIA Data Retriever. Click the Search button to open our Data Portal, where you can browse the data collection and/or download a subset of its contents.Data Type | Download all or Query/Filter |
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Images (SVS, XX.X 30 GB) | | Supplemental Data Annotations (XML) | Image Removed | | Image Added |
ContentThe Post-NAT-BRCA dataset is composed of: • 96 whole slide images stored in an uncompressed .svs file format, standard for pathology slides. Slides were scanned at 20x objective on an Aperio slide scanner at Sunnybrook Health Sciences Centre. • An Excel (.xlsx) file containing clinical features for each patient including age, treatment, ER/PR/HER2 status etc. A key and detailed description of each column is provided in a separate tab titled "Definitions". Each row in the spreadsheet corresponds to a single (.svs) slide and anonymised patient ID's are provided in a separate column. • Manual annotations of tumor cellularity and cell labels, provided as Sedeen annotation files (.xml). Annotations are given in two directories, where the "WSI_train" folder contains WSIs annotated by a single rater and "WSI_test" was annotated by two ratersClick the Versions tab for more info about data releases. |
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title | Detailed Description |
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| Detailed Description | |
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Modalities | Pathology | Number of Patients | 64 | Number of Studies | Number of Series | Number of Images | 96 | Images Size (GB) | 30 |
Recommended SoftwareTo browse whole slide images and annotations, we highly recommend you use Pathcore's Sedeen Viewer which is available for free: https://pathcore.com/sedeen/ Please ensure that the "sedeen" folder is unzipped and placed into the same folder containing the .svs files. Sedeen Viewer loads annotations from this folder automatically when images are opened. Upon opening WSIs in Sedeen, you will notice that annotations have been color-coded according to the following key: - Pink: Healthy (0% tumor cellularity)
- Blue: Low tumor cellularity (0 - 30%)
- Yellow: Medium tumor cellularity (31 - 70%)
- Green: High tumor cellularity (70 - 100%)
- White: Contains annotations at the cell level and labeled as:
- Lymphocyte: TIL-E, TIL-S
- Normal Epithelial: normal, UDH, ADH,
- Malignant Epithelial: IDC, ILC, Muc C, DCIS 1, DCIS 2, DCIS 3, MC- E, MC - C, MC - M
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title | Citations & Data Usage Policy |
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| Citations & Data Usage PolicyAdd any special restrictions in here. 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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| DOI goes here. Create using pubhub with information from Collection Approval form |
Info |
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title | Publication Citation |
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| 1) Peikari, M., Salama, S., Nofech-Mozes, S. and Martel, A.L., 2017. Automatic cellularity assessment from post-treated breast surgical specimens. Cytometry Part A, 91(11), pp.1078-1087. |
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. DOI: 10.1007/s10278-013-9622-7 |
Other Publications Using This DataTCIA maintains a list of publications which 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): Updated 2019/0410/2601
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