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Description

Mappings of tumor-infiltrating lymphocytes (TILs), based on H&E images from 13 of The Cancer Genome Atlas (TCGA) tumor types are available here. These TIL maps are derived through computational staining, using a convolutional neural network trained to classify patches of images. In addition to the TIL Maps, the analysis codes and the software used to extract TILs are also available. The accompanying paper contains detailed information about our methods and our findings.  The source histopathology, molecular correlates and clinical data used in this study can be found on the Genomic Data Commons.  More information about the tools used to generate these results can be found  on the QuIP Software Stack and TIL Classification Software pages.  Answers to commonly asked questions about these data are contained in this FAQs document. 

TCGA Tumor Types Used in this Study

  1. BLCA Bladder urothelial carcinoma
  2. BRCA Breast invasive carcinoma
  3. CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma
  4. COAD Colon adenocarcinoma
  5. LUAD Lung adenocarcinoma
  6. LUSC Lung squamous cell carcinoma
  7. PAAD Pancreatic adenocarcinoma
  8. PRAD Prostate adenocarcinoma
  9. READ Rectum adenocarcinoma
  10. SKCM Skin Cutaneous Melanoma
  11. STAD Stomach adenocarcinoma
  12. UCEC Uterine Corpus Endometrial Carcinoma
  13. UVM Uveal Melanoma


Data Access

Data TypeDownload all or Query/Filter
TIL Maps

 

H&E Images and Clinical Data (external)

Clinical and Molecular Correlates (external)

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

Detailed Description


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:

Data Citation

Saltz, J., Gupta, R., Hou, L., Kurc, T., Singh, P., Nguyen, V., … Thorsson, V. (2018). Tumor-Infiltrating Lymphocytes Maps from TCGA H&E Whole Slide Pathology Images [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/k9/tcia.2018.y75f9w1

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)

In addition to the dataset citation above, please be sure to cite the following if you utilize these data in your research:

Publication Citation

Saltz, J., Gupta, R., Hou, L., Kurc, T., Singh, P., Nguyen, V., . . . Thorsson, V. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Reports, 23(1), 181-193.e187. https://doi.org/10.1016/j.celrep.2018.03.086

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.

Version 1 (Current): 2018/12/17

Data TypeDownload all or Query/Filter
TIL Maps

 

H&E Images and Clinical Data (external)

Clinical and Molecular Correlates (external)

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