{"id":5771,"date":"2023-09-04T03:36:55","date_gmt":"2023-09-04T03:36:55","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/til-wsi-tcga\/"},"modified":"2023-09-13T12:09:42","modified_gmt":"2023-09-13T12:09:42","slug":"til-wsi-tcga","status":"publish","type":"tcia_analysis_result","link":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/til-wsi-tcga\/","title":{"rendered":"TIL-WSI-TCGA"},"featured_media":0,"template":"","cancer_types":["Bladder Urothelial Carcinoma","Breast Invasive Carcinoma","Cervical Squamous Cell Carcinoma","Endocervical Adenocarcinoma","Colon adenocarcinoma","Lung Adenocarcinoma","Lung Squamous Cell Carcinoma","Pancreatic adenocarcinoma","Prostate Adenocarcinoma","Rectum Adenocarcinoma","Skin Cutaneous Melanoma","Stomach Adenocarcinoma","Uterine Corpus Endometrial Carcinoma","Uveal Melanoma"],"citations":[4772,4773,2925],"full_export":"<h2 id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-Summary\">Summary<\/h2><p><span> <span style=\"color: rgb(0,0,0);\">Mappings of tumor-infiltrating lymphocytes (TILs), based on H&amp;E images from 13 of <a href=\"https:\/\/www.cancer.gov\/about-nci\/organization\/ccg\/research\/structural-genomics\/tcga\" class=\"external-link\" rel=\"nofollow\">The Cancer Genome Atlas (TCGA)<\/a> 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.\u00a0<\/span> <\/span>The accompanying paper contains detailed information about our methods and our findings.\u00a0 The source histopathology, molecular correlates and clinical data used in this study can be found on the <a href=\"https:\/\/portal.gdc.cancer.gov\/\" class=\"external-link\" rel=\"nofollow\">Genomic Data Commons<\/a>.\u00a0 More information about the tools used to generate these results can be found\u00a0 on the <a href=\"https:\/\/sbu-bmi.github.io\/quip_distro\/\" class=\"external-link\" rel=\"nofollow\">QuIP Software Stack<\/a> and <a href=\"https:\/\/github.com\/SBU-BMI\/u24_lymphocyte\" class=\"external-link\" rel=\"nofollow\">TIL Classification Software<\/a> pages.\u00a0 Answers to commonly asked questions about these data are contained in this\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/33948919\/LymPipeline%20FAQ.pdf?version=1&amp;modificationDate=1531946493666&amp;api=v2\" data-linked-resource-id=\"39879041\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"LymPipeline FAQ.pdf\" data-nice-type=\"PDF Document\" data-linked-resource-content-type=\"application\/pdf\" data-linked-resource-container-id=\"33948919\" data-linked-resource-container-version=\"32\">FAQs<\/a>\u00a0document.\u00a0<\/p><h4 style=\"text-align: justify;\" id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-TCGATumorTypesUsedinthisStudy\"><span style=\"color: rgb(0,0,0);\">TCGA Tumor Types Used in this Study<\/span><\/h4><ol><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">BLCA<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Bladder urothelial carcinoma<\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">BRCA<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Breast invasive carcinoma<\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">CESC<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Cervical squamous cell carcinoma and endocervical adenocarcinoma<\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">COAD<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Colon adenocarcinoma<\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">LUAD<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Lung adenocarcinoma<br\/><\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">LUSC<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Lung squamous cell carcinoma<br\/><\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">PAAD<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Pancreatic adenocarcinoma<br\/><\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">PRAD<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Prostate adenocarcinoma<br\/><\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">READ<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Rectum adenocarcinoma<br\/><\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">SKCM<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Skin Cutaneous Melanoma<br\/><\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">STAD<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Stomach adenocarcinoma<br\/><\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">UCEC<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Uterine Corpus Endometrial Carcinoma<br\/><\/span><\/li><li style=\"text-align: justify;\"><span style=\"color: rgb(0,0,0);\">UVM<\/span> <span style=\"color: rgb(0,0,0);\"> <\/span> <span style=\"color: rgb(0,0,0);\">Uveal Melanoma<\/span><\/li><\/ol><p style=\"text-align: justify;\"><br\/><\/p><div class=\"tab-style-builtin\"><div class=\"localtabs-macro\"><div class=\"aui-tabs horizontal-tabs\" role=\"application\" data-aui-responsive=\"true\"><ul class=\"tabs-menu\"><li class=\"menu-item bv-localtab  active-tab \"><a href=\"#33948919036220c66a5a436f90e4a0b54367bfae\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#33948919e703f075658f4b0a9f03aeca877d7f4b\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#33948919d170e52bc57d4c67b747b57bf88c460f\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#33948919aa756e3841914e7da45eadb37096a710\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"33948919036220c66a5a436f90e4a0b54367bfae\" active=\"true\" name=\"Data Access\" ><h3 id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-DataAccess\"><span style=\"color: rgb(23,43,77);\">Data Access<\/span><\/h3><div class=\"table-wrap\"><table class=\"fixed-table wrapped confluenceTable\"><colgroup><col style=\"width: 336.0px;\"\/><col style=\"width: 303.0px;\"\/><col style=\"width: 303.0px;\"\/><\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><th class=\"confluenceTh\">License<\/th><\/tr><tr><td class=\"confluenceTd\">TIL Maps<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/cancerimagingarchive.net\/datascope\/TCGA_TilMap\/ \" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p style=\"text-align: left;\">Click the Versions tab for more info about data releases.<\/p><h3 style=\"text-align: left;\" id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-AdditionalResourcesforthisDatasetTheNCICancerResearchDataCommons(CRDC)providesaccesstoadditionaldataandacloud-baseddatascienceinfrastructurethatconnectsdatasetswithanalyticst\">\n<h3 id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-AdditionalResourcesforthisDataset\">Additional Resources for this Dataset<\/h3>\n<p>The 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.<\/p><\/h3><ul><li>Genomic Data Commons: (<a href=\"https:\/\/gdc.cancer.gov\/node\/1006\/\" class=\"external-link\" rel=\"nofollow\">Genomic data<\/a>, <span style=\"color: rgb(33,37,41);\">H&amp;E Images , Clinical, and <a href=\"https:\/\/gdc.cancer.gov\/about-data\/publications\/tilmap\" class=\"external-link\" rel=\"nofollow\">molecular correlate Data<\/a><\/span>)<\/li><\/ul><h3 style=\"text-align: left;\" id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-Additionalresources:\">Additional resources:<\/h3><p><span style=\"color: rgb(33,37,41);\">The following external resources have been made available by the data submitters.\u00a0 These are not hosted or supported by TCIA, but may be useful to researchers utilizing this collection.<\/span><\/p><ul><li>Software:<span>\u00a0<\/span><span style=\"color: rgb(33,37,41);\"><span>\u00a0<\/span><\/span><a href=\"https:\/\/sbu-bmi.github.io\/quip_distro\/\" style=\"text-decoration: none;text-align: left;\" rel=\"nofollow\" class=\"external-link\">QuIP Software Stack<\/a><\/li><li><span style=\"color: rgb(33,37,41);\"><span>Software:\u00a0<\/span><\/span><a rel=\"nofollow\" style=\"text-decoration: none;text-align: left;\" class=\"external-link\" href=\"https:\/\/github.com\/SBU-BMI\/u24_lymphocyte\">TIL Classification Software<\/a><span style=\"color: rgb(33,37,41);\"><span>\u00a0<\/span><\/span><\/li><li><span style=\"color: rgb(33,37,41);\"><span><a href=\"https:\/\/stonybrookmedicine.app.box.com\/s\/ecr7ba8czvqygw90iym0hwpnprrofoas\" class=\"external-link\" rel=\"nofollow\">TIL Maps<\/a> <\/span><\/span><\/li><\/ul><p style=\"text-align: left;\"><strong><span style=\"color: rgb(29,28,29);text-decoration: none;\">Collections Used in this Third Party Analysis<\/span><\/strong><\/p><p style=\"text-align: left;\"><br style=\"text-decoration: none;text-align: left;\"\/><span style=\"color: rgb(29,28,29);text-decoration: none;\">Below is a list of TCIA Collections used in these analyses:<\/span><\/p><ul style=\"text-align: left;\"><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a style=\"text-decoration: none;text-align: left;\" href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.8LNG8XDR\" class=\"external-link\" rel=\"nofollow\">TCGA-BLCA<\/a><span style=\"color: rgb(103,103,103);\">,<span>\u00a0<\/span><\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a style=\"text-decoration: none;text-align: left;\" href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.AB2NAZRP\" class=\"external-link\" rel=\"nofollow\">TCGA-BRCA<\/a><span style=\"color: rgb(103,103,103);\">,<span>\u00a0<\/span><\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.SQ4M8YP4\" style=\"text-decoration: none;text-align: left;\" class=\"external-link\" rel=\"nofollow\">TCGA-CESC<\/a><span style=\"color: rgb(103,103,103);\">,<span>\u00a0<\/span><\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.HJJHBOXZ\" style=\"text-decoration: none;text-align: left;\" class=\"external-link\" rel=\"nofollow\">TCGA-COAD<\/a><span style=\"color: rgb(103,103,103);\">,<\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.JGNIHEP5\" style=\"text-decoration: none;text-align: left;\" class=\"external-link\" rel=\"nofollow\">TCGA-LUAD<\/a><span style=\"color: rgb(103,103,103);\">,<span>\u00a0<\/span><\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.TYGKKFMQ\" style=\"text-decoration: none;text-align: left;\" class=\"external-link\" rel=\"nofollow\">TCGA-LUSC<\/a><span style=\"color: rgb(103,103,103);\">, <\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><span style=\"color: rgb(103,103,103);\">TCGA-PAAD,<span>\u00a0<\/span><\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a style=\"text-decoration: none;text-align: left;\" href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.YXOGLM4Y\" class=\"external-link\" rel=\"nofollow\">TCGA-PRAD<\/a><span style=\"color: rgb(103,103,103);\">,<\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a style=\"text-decoration: none;text-align: left;\" href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.F7PPNPNU\" class=\"external-link\" rel=\"nofollow\">TCGA-READ<\/a><span style=\"color: rgb(103,103,103);\">, <\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><span style=\"color: rgb(103,103,103);\">TCGA-SKCM,<span>\u00a0<\/span><\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.GDHL9KIM\" style=\"text-decoration: none;text-align: left;\" class=\"external-link\" rel=\"nofollow\">TCGA-STAD<\/a><span style=\"color: rgb(103,103,103);\">,<span>\u00a0<\/span><\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.GKJ0ZWAC\" style=\"text-decoration: none;text-align: left;\" class=\"external-link\" rel=\"nofollow\">TCGA-UCEC<\/a><span style=\"color: rgb(103,103,103);\">, <\/span><\/span><\/span><\/li><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><span style=\"color: rgb(51,122,183);\"><span style=\"color: rgb(103,103,103);\">TCGA-UVM<\/span><\/span><\/span><\/li><\/ul><\/div><div class=\"tabs-pane \" id=\"33948919e703f075658f4b0a9f03aeca877d7f4b\" name=\"Detailed Description\" ><h3 id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-DetailedDescription\">Detailed Description<\/h3><p><br\/><\/p><p><span style=\"color: rgb(33,37,41);\">Please contact <a href=\"mailto:help@cancerimagingarchive.net\" class=\"external-link\" rel=\"nofollow\">help@cancerimagingarchive.net<\/a> with any questions regarding usage.<\/span><\/p><\/div><div class=\"tabs-pane \" id=\"33948919d170e52bc57d4c67b747b57bf88c460f\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-Citations&amp;DataUsagePolicy\">Citations &amp; Data Usage Policy\u00a0<\/h3><p class=\"auto-cursor-target\">\n<p>\nUsers must abide by the <a href=\"https:\/\/wiki.cancerimagingarchive.net\/x\/c4hF\" class=\"external-link\" rel=\"nofollow\">TCIA Data Usage Policy and Restrictions<\/a>. Attribution should include references to the following citations:\n<\/p><\/p><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Data Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span style=\"color: rgb(102,102,102);\">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., &amp; Thorsson, V. (2018). <strong>Tumor-Infiltrating Lymphocytes Maps from TCGA H&amp;E Whole Slide Pathology Images [Data set]<\/strong>. The Cancer Imaging Archive. <a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.Y75F9W1\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.Y75F9W1<\/a><\/span><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Publication Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p class=\"EndNoteBibliography\"><span style=\"color: rgb(102,102,102);\">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). <strong>Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images<\/strong>. Cell Reports, 23(1), 181-193.e7. <a href=\"https:\/\/doi.org\/10.1016\/j.celrep.2018.03.086\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1016\/j.celrep.2018.03.086<\/a><\/span><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">TCIA Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span style=\"color: rgb(102,102,102);\">Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., &amp; Prior, F. (2013). <strong>The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository<\/strong>. Journal of Digital Imaging, 26(6), 1045\u20131057. <a href=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1007\/s10278-013-9622-7<\/a><\/span><\/p><\/div><\/div><h3 id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains<\/span> <a class=\"external-link\" rel=\"nofollow\" href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\"> a list of publications<\/a> <span> which leverage TCIA data. <\/span> If you have a publication you'd like to add please<a class=\"external-link\" rel=\"nofollow\" href=\"http:\/\/www.cancerimagingarchive.net\/support\/\"> contact TCIA's Helpdesk<\/a>.<\/p><\/div><div class=\"tabs-pane \" id=\"33948919aa756e3841914e7da45eadb37096a710\" name=\"Versions\" ><h3 id=\"TumorInfiltratingLymphocytesMapsfromTCGAH&amp;EWholeSlidePathologyImages(TILWSITCGA)-Version1(Current):2018\/12\/17\">Version 1 (Current): 2018\/12\/17<\/h3><div class=\"table-wrap\"><table class=\"fixed-table wrapped confluenceTable\"><colgroup> <col style=\"width: 336.0px;\"\/> <col style=\"width: 303.0px;\"\/> <\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><\/tr><tr><td class=\"confluenceTd\">TIL Maps<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/stonybrookmedicine.app.box.com\/s\/ecr7ba8czvqygw90iym0hwpnprrofoas\" class=\"external-link\" rel=\"nofollow\"> <span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/Tumor-Infiltrating%20Lymphocytes%20Maps%20from%20TCGA%20H&amp;E%20Whole%20Slide%20Pathology%20Images%20(TIL-WSI-TCGA)\/tcia_wiki_download_button.png?api=v2\"><\/span> <\/a>\u00a0<a href=\"https:\/\/cancerimagingarchive.net\/datascope\/TCGA_TilMap\/\" class=\"external-link\" rel=\"nofollow\"> <span class=\"confluence-embedded-file-wrapper\"><img class=\"confluence-embedded-image confluence-external-resource\" draggable=\"false\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/2621477\/tcia_wiki_search_button.png?version=1&amp;modificationDate=1450207093851&amp;api=v2\" data-image-src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/2621477\/tcia_wiki_search_button.png?version=1&amp;modificationDate=1450207093851&amp;api=v2\"><\/span> <\/a><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">H&amp;E Images and Clinical Data (external)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/portal.gdc.cancer.gov\/\" class=\"external-link\" rel=\"nofollow\"> <span class=\"confluence-embedded-file-wrapper\"><img class=\"confluence-embedded-image confluence-external-resource\" draggable=\"false\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/2621477\/tcia_wiki_search_button.png?version=1&amp;modificationDate=1450207093851&amp;api=v2\" data-image-src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/2621477\/tcia_wiki_search_button.png?version=1&amp;modificationDate=1450207093851&amp;api=v2\"><\/span> <\/a><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Clinical and Molecular Correlates (external)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/gdc.cancer.gov\/about-data\/publications\/tilmap\" class=\"external-link\" rel=\"nofollow\"> <span class=\"confluence-embedded-file-wrapper\"><img class=\"confluence-embedded-image confluence-external-resource\" draggable=\"false\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/2621477\/tcia_wiki_search_button.png?version=1&amp;modificationDate=1450207093851&amp;api=v2\" data-image-src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/2621477\/tcia_wiki_search_button.png?version=1&amp;modificationDate=1450207093851&amp;api=v2\"><\/span> <\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><\/div>","make_new_version_button":"","related_collections":["TCGA-BLCA","TCGA-BRCA","TCGA-CESC","TCGA-COAD","TCGA-LUAD","TCGA-LUSC","TCGA-PRAD","TCGA-READ","TCGA-STAD","TCGA-UCEC"],"result_doi":"10.7937\/K9\/TCIA.2018.Y75F9W1","versions":false,"cancer_locations":["Bladder","Breast","Pelvic Cervix","Chest","Colon","Eye","Lung","Pancreas","Prostate","Rectum","Skin","Stomach","Uterus"],"publications_related":"","result_download_info":"Click the Versions tab for more info about data releases.\n<h3>\n<\/h3>","result_downloads":[5393],"result_page_accessibility":"Public","version_change_log_archived":"","additional_resources":"The 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.\n<ul><li>Genomic Data Commons: (<a href=\"https:\/\/gdc.cancer.gov\/node\/1006\/\">Genomic data<\/a>, H&amp;E Images , Clinical, and <a href=\"https:\/\/gdc.cancer.gov\/about-data\/publications\/tilmap\">molecular correlate Data<\/a>)<\/li><\/ul>","date_updated":"2018-12-17","publications_using":"TCIA maintains <a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\"> a list of publications<\/a>  which leverage TCIA data.  If you have a publication you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\"> contact TCIA's Helpdesk<\/a>.","result_title":"Tumor-Infiltrating Lymphocytes Maps from TCGA H&E Whole Slide Pathology Images","subjects":"4759","detailed_description":"<br\/>\nPlease contact <a href=\"mailto:help@cancerimagingarchive.net\">help@cancerimagingarchive.net<\/a> with any questions regarding usage.","result_short_title":"TIL-WSI-TCGA","supporting_data":["Deep learning based computational stain for staining tumor-infiltrating lymphocytes (TILs)"],"version_change_log":"","collections":"","result_browse_title":"","version_number":[],"collection_downloads":false,"result_summary":"Mappings of tumor-infiltrating lymphocytes (TILs), based on H&amp;E images from 13 of <a href=\"https:\/\/www.cancer.gov\/about-nci\/organization\/ccg\/research\/structural-genomics\/tcga\">The Cancer Genome Atlas (TCGA)<\/a> 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.\u00a0 The accompanying paper contains detailed information about our methods and our findings.\u00a0 The source histopathology, molecular correlates and clinical data used in this study can be found on the <a href=\"https:\/\/portal.gdc.cancer.gov\/\">Genomic Data Commons<\/a>.\u00a0 More information about the tools used to generate these results can be found\u00a0 on the <a href=\"https:\/\/sbu-bmi.github.io\/quip_distro\/\">QuIP Software Stack<\/a> and <a href=\"https:\/\/github.com\/SBU-BMI\/u24_lymphocyte\">TIL Classification Software<\/a> pages.\u00a0 Answers to commonly asked questions about these data are contained in this\u00a0<a data-linked-resource-container-id=\"33948919\" data-linked-resource-container-version=\"32\" data-linked-resource-content-type=\"application\/pdf\" data-linked-resource-default-alias=\"LymPipeline FAQ.pdf\" data-linked-resource-id=\"39879041\" data-linked-resource-type=\"attachment\" data-linked-resource-version=\"1\" data-nice-type=\"PDF Document\" download=\"\" href=\"\/wp-content\/uploads\/LymPipeline-FAQ.pdf\" target=\"_blank\">FAQs<\/a>\u00a0document.\u00a0\n<h4>TCGA Tumor Types Used in this Study<\/h4>\n<ol><li>BLCA   Bladder urothelial carcinoma<\/li><li>BRCA   Breast invasive carcinoma<\/li><li>CESC   Cervical squamous cell carcinoma and endocervical adenocarcinoma<\/li><li>COAD   Colon adenocarcinoma<\/li><li>LUAD   Lung adenocarcinoma<br\/><\/li><li>LUSC   Lung squamous cell carcinoma<br\/><\/li><li>PAAD   Pancreatic adenocarcinoma<br\/><\/li><li>PRAD   Prostate adenocarcinoma<br\/><\/li><li>READ   Rectum adenocarcinoma<br\/><\/li><li>SKCM   Skin Cutaneous Melanoma<br\/><\/li><li>STAD   Stomach adenocarcinoma<br\/><\/li><li>UCEC   Uterine Corpus Endometrial Carcinoma<br\/><\/li><li>UVM   Uveal Melanoma<\/li><\/ol>\n<br\/>","result_featured_image":false,"result_acknowledgements":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/analysis-results\/5771"}],"collection":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/analysis-results"}],"about":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/types\/tcia_analysis_result"}],"wp:attachment":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media?parent=5771"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}