{"id":45803,"date":"2023-11-20T05:35:12","date_gmt":"2023-11-20T11:35:12","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/til-wsi-tcga\/"},"modified":"2024-10-31T12:14:48","modified_gmt":"2024-10-31T17:14:48","slug":"til-wsi-tcga","status":"publish","type":"tcia_analysis_result","link":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/til-wsi-tcga\/","title":{"rendered":"TIL-WSI-TCGA"},"featured_media":0,"template":"","class_list":["post-45803","tcia_analysis_result","type-tcia_analysis_result","status-publish"],"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":[45797,45799,9225],"result_doi":"10.7937\/K9\/TCIA.2018.Y75F9W1","result_download_info":"","result_downloads":[45801],"version_change_log_archived":"Version 1 (Current): 2018\/12\/17\r\n   Data TypeDownload all or Query\/FilterTIL Maps  \u00a0  H&amp;E Images and Clinical Data (external)  Clinical and Molecular Correlates (external)","versions":false,"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.\r\n<ul>\r\n \t<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>\r\n<\/ul>\r\nThe 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.\r\n<ul>\r\n \t<li>Software:\u00a0\u00a0<a href=\"https:\/\/sbu-bmi.github.io\/quip_distro\/\">QuIP Software Stack<\/a><\/li>\r\n \t<li>Software:\u00a0<a href=\"https:\/\/github.com\/SBU-BMI\/u24_lymphocyte\">TIL Classification Software<\/a><\/li>\r\n \t<li><a href=\"https:\/\/stonybrookmedicine.app.box.com\/s\/ecr7ba8czvqygw90iym0hwpnprrofoas\">TIL Maps<\/a><\/li>\r\n<\/ul>","cancer_locations":["Bladder","Breast","Pelvic Cervix","Chest","Colon","Eye","Lung","Pancreas","Prostate","Rectum","Skin","Stomach","Uterus"],"publications_related":"The Collection authors recommend these readings to give context to this dataset","result_page_accessibility":"Public","detailed_description":"","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/commons.datacite.org\/doi.org\/10.7937\/K9\/TCIA.2018.Y75F9W1\">a list of publications<\/a>\u00a0that leveraged this dataset. If you have a manuscript you\u2019d like to add please\u00a0<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact TCIA\u2019s Helpdesk<\/a>.","result_title":"Tumor-Infiltrating Lymphocytes Maps from TCGA H&E Whole Slide Pathology Images","species":false,"version_number":"1","date_updated":"2018-12-17","related_collections":[43811,44097,44187,44347,43753,43835,44129,44211,44257,44377],"result_short_title":"TIL-WSI-TCGA","subjects":"4759","related_analysis_results":false,"result_browse_title":"Tumor-Infiltrating Lymphocytes Maps from TCGA H&E Whole Slide Pathology Images (TIL-WSI-TCGA)","supporting_data":["Deep learning based computational stain for staining tumor-infiltrating lymphocytes (TILs)","Software\/Source Code","Histopathology"],"version_change_log":"","collections":"","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 href=\"\/wp-content\/uploads\/LymPipeline-FAQ.pdf\" download=\"LymPipeline-FAQ.pdf\" data-linked-resource-container-id=\"33948919\" data-linked-resource-container-version=\"33\" 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\">FAQs<\/a>\u00a0document.\r\n<h4>TCGA Tumor Types Used in this Study<\/h4>\r\n<ol>\r\n \t<li>BLCA Bladder urothelial carcinoma<\/li>\r\n \t<li>BRCA Breast invasive carcinoma<\/li>\r\n \t<li>CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma<\/li>\r\n \t<li>COAD Colon adenocarcinoma<\/li>\r\n \t<li>LUAD Lung adenocarcinoma<\/li>\r\n \t<li>LUSC Lung squamous cell carcinoma<\/li>\r\n \t<li>PAAD Pancreatic adenocarcinoma<\/li>\r\n \t<li>PRAD Prostate adenocarcinoma<\/li>\r\n \t<li>READ Rectum adenocarcinoma<\/li>\r\n \t<li>SKCM Skin Cutaneous Melanoma<\/li>\r\n \t<li>STAD Stomach adenocarcinoma<\/li>\r\n \t<li>UCEC Uterine Corpus Endometrial Carcinoma<\/li>\r\n \t<li>UVM Uveal Melanoma<\/li>\r\n<\/ol>","collection_downloads":false,"result_featured_image":false,"result_acknowledgements":"","hide_from_browse_table":"0","program":["Community"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/45803","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results"}],"about":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/types\/tcia_analysis_result"}],"version-history":[{"count":1,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/45803\/revisions"}],"predecessor-version":[{"id":47547,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/45803\/revisions\/47547"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=45803"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}