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| active | true |
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| title | Data Access |
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| Data Access| Data Type | Download all or Query/Filter | License |
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Tissue Slide Images (SVS,40GB) ROI Annotations (XML) |
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| url | https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/311?passcode=dabde05cb596923338b717013b335f5258a9adb3 |
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(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package)
| | | Clinical data (XLSX) |
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| url | https://wiki.cancerimagingarchive.net/download/attachments/119702524/Yale_trastuzumab_response_cohort_metadata_clean.xlsx?api=v2 |
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Click the Versions tab for more info about data releases. Additional ResourcesThe NCI Cancer Research Data Commons (CRDC) provides access to additional data and a cloud-based data science infrastructure that connects data sets with analytics tools to allow users to share, integrate, analyze, and visualize cancer research data. - Genomic Data Commons Legacy Archive (Tissue Slide Images)
- TCGA HER2 cohort: A total of 668 TCGA-BRCA HER2+/- samples with available HER2 status were downloaded from the GDC portal. Slides were visually inspected by our pathology team to exclude low quality samples with tissue folding or those that appeared to be from frozen tissue. A total of 182 samples (90 HER2- and 92 HER2+) were retained for use as independent test set. Information about which specific samples were retained from the GDC can be found the TCGA_BRCA_Filtered folder of the dataset. To download the slides, GDC recommends the following: “The TCGA case (patient) barcode can be extracted from the first 12 characters of the file names in the manifest (i.e. TCGA-BH-A0EE, TCGA-D8-A27W etc.) which can be used to match the data in the clinical files to the slide images.” Contact https://gdc.cancer.gov/support with any questions about downloading the corresponding slides.
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| title | Detailed Description |
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| Detailed DescriptionImage Statistics |
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Modalities | Pathology | Number of Patients | 273 | Number of Images | 273 | | Images Size (GB) | 40 |
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| title | Citations & Data Usage Policy |
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| Citations & Data Usage Policy| Tcia limited license policy |
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| Info |
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| Farahmand, Saman, Fernandez, Aileen I, Ahmed, Fahad Shabbir, Rimm, David L., Chuang, Jeffrey H., Reisenbichler, Emily, & Zarringhalam, Kourosh. (2022). HER2 and trastuzumab treatment response H&E slides with tumor ROI annotations (Version 3) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/E65C-AM96 |
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| title | Publication Citation |
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| Farahmand, S., Fernandez, A.I., Ahmed, F.S. et al. Deep learning trained on hematoxylin and eosin tumor region of Interest predicts HER2 status and trastuzumab treatment response in HER2+ breast cancer. Mod Pathol (2021). https://doi.org/10.1038/s41379-021-00911-w |
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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. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC. https://doi.org/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 3 (Current): Updated 2022/08/01| Data Type | Download all or Query/Filter | License |
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Tissue Slide Images (SVS,40GB) ROI Annotations (XML) |
| Tcia button generator |
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| url | https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/311?passcode=dabde05cb596923338b717013b335f5258a9adb3 |
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(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package)
| | | Clinical data (XLSX) |
| Tcia button generator |
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| url | https://wiki.cancerimagingarchive.net/download/attachments/119702524/Yale_trastuzumab_response_cohort_metadata_clean.xlsx?api=v2 |
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changes made: macros removed from all SVS images. older versions of the data no longer available for download. Version 2: updated 2022/06/28 | Data Type | Download all or Query/Filter | License |
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Tissue Slide Images (SVS,40GB) ROI Annotations (XML) | | | | Clinical data (XLSX) |
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| url | https://wiki.cancerimagingarchive.net/download/attachments/119702524/Yale_trastuzumab_response_cohort_metadata_clean.xlsx?api=v2 |
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changes made: 5 files were removed ("TCGA-A2-AOEQ-01Z-00-DX1", "TCGA-AO-AOJG-01Z-00-DX1", "TCGA-B6-A019-01Z-00-DX1”, "TCGA-EW-A1OZ-01Z-00-DX1.svs" & TCGA_BRCA_Filtered/meta.txt), 2 files were cleaned up and replaced (gdc_manifest.2022-0420.txt & HER2_TCGA.csv) and 1 file was added (case&annotation_counts_clean.xlsx). The 'HER2 Yale cohort' paragraph was updated to correct patient counts (99 negative & 93 positive for a total of 192 cases). The 'TCGA HER2 cohort' paragraph was updated to correct patient counts (92 positive & 90 negative for a total of 182 cases). The metadata CSV file was replaced with an updated XLSX file to remove duplicate patient rows. Version 1: updated 2022/03/25 | Data Type | Download all or Query/Filter | License |
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Tissue Slide Images (SVS,40GB) ROI Annotations (XML) | | | | Clinical data (CSV) | | |
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