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  • Tumor-Infiltrating Lymphocytes Maps from TCGA H&E Whole Slide Pathology Images (TIL-WSI-TCGA)

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changes.mady.by.user Quasar Jarosz

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changes.mady.by.user Tracy Nolan

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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

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Localtab Group



Localtab
activetrue
titleData Access

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.


Collections Used in this Third Party Analysis
Below is a list of the Collections used in these analyses:




Localtab
titleDetailed Description

Detailed Description





Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy 

Public collection license

Info
titleData Citation

Saltz, J., Gupta, R., Hou, L., Kurc, T., Singh, P., Nguyen, V., … , Samaras, D., Shroyer, K. R., Zhao, T., Batiste, R., Van Arnam, J., The Cancer Genome Atlas Research Network, Shmulevich, I., Rao, A. U. K., Lazar, A. J., Sharma, A., & 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/k9K9/tciaTCIA.2018.y75f9w1Y75F9W1


Info
titleTCIA Publication 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:

Info
titlePublication Citation

Saltz, J., Gupta, R., Hou, L., Kurc, T., Singh, P., Nguyen, V., . . . Thorsson, V. Spatial Saltz, J., Gupta, R., Hou, L., Kurc, T., Singh, P., Nguyen, V., Samaras, D., Shroyer, K. R., Zhao, T., Batiste, R., Van Arnam, J., The Cancer Genome Atlas Research Network, Shmulevich, I., Rao, A. U. K., Lazar, A. J., Sharma, A., Thorsson, V. (2018). Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Reports, 23(1), 181-193.e187e7. https://doi.org/10.1016/j.celrep.2018.03.086


Info
titleTCIA 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. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. Journal of Digital Imaging, 26(6), 1045–1057. https://doi.org/10.1007/s10278-013-9622-7


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



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.




Localtab
titleVersions

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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