{"id":46261,"date":"2023-11-20T06:03:08","date_gmt":"2023-11-20T12:03:08","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/aren0532-tumor-annotations\/"},"modified":"2025-03-20T13:33:11","modified_gmt":"2025-03-20T18:33:11","slug":"aren0532-tumor-annotations","status":"publish","type":"tcia_analysis_result","link":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/aren0532-tumor-annotations\/","title":{"rendered":"AREN0532-TUMOR-ANNOTATIONS"},"featured_media":0,"template":"","class_list":["post-46261","tcia_analysis_result","type-tcia_analysis_result","status-publish"],"cancer_types":["Wilms Tumor"],"citations":[46251,9225],"result_doi":"10.7937\/KJA4-1Z76","result_download_info":"","result_downloads":[46253,46255],"version_change_log_archived":"Version 1 (Current): Updated 2023\/08\/09\r\nData TypeDownload all or Query\/FilterLicenseAREN0532 Annotations -- Segmentations, Seed Points, and Negative Findings Assessments\u00a0(DICOM, 0.2 GB)\r\n Download\u00a0\r\n\r\n Search\u00a0\r\n(Download requires\u00a0the\u00a0NBIA Data Retriever)CC BY 4.0AREN0532 Annotation Metadata (CSV)\r\n Download\u00a0\r\nCC BY 4.0Original AREN0532 Images\u00a0used to create Segmentations and Seed Points (DICOM,\u00a0 56.4 GB)\r\n Download\u00a0\r\n(Download requires NBIA Data Retriever)NCTN\/NCORP Data Archive License (Without Collaborative Agreement)Original AREN0532 Images\u00a0used to create Negative Assessment reports (DICOM, 23.7 GB)\r\n Download\u00a0\r\n(Download requires NBIA Data Retriever)NCTN\/NCORP Data Archive License (Without Collaborative Agreement)","versions":false,"additional_resources":"<ul>\r\n \t<li>NCTN\/NCORP Data Archive provides the\u00a0<a href=\"https:\/\/nctn-data-archive.nci.nih.gov\/node\/689\">Clinical Data files<\/a>\u00a0related to these subjects, and is also where you go to request access to the entire dataset<\/li>\r\n \t<li><a href=\"https:\/\/github.com\/kirbyju\/TCIA_Notebooks\/blob\/main\/TCIA_NCTN_Annotations.ipynb\">Jupyter notebook<\/a>\u00a0demonstrating how to use the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/NBIA+Data+Retriever+Command-Line+Interface+Guide\">NBIA Data Retriever Command-Line Interface<\/a>\u00a0application and\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/Public\/NBIA+Search+with+Authentication+REST+API+Guide\">REST API (with authentication)<\/a>\u00a0to access these data<\/li>\r\n \t<li>Instructions for\u00a0<a href=\"https:\/\/github.com\/QIICR\/TCIABrowser\/raw\/master\/User%20Guide%20for%203D%20Slicer%20TCIA%20Browser.pptx\">Visualizing these data in 3D Slicer<\/a><\/li>\r\n<\/ul>","cancer_locations":["Kidney"],"publications_related":"","result_page_accessibility":"Public","detailed_description":"","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\">a list of publications<\/a> which leverage TCIA data. If you have a manuscript you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\"> contact the TCIA Helpdesk<\/a>.","result_title":"Annotations for Vincristine, Dactinomycin, and Doxorubicin With or Without Radiation Therapy or Observation Only in Treating Younger Patients Who Are Undergoing Surgery for Newly Diagnosed Stage I, II, or III Wilms' Tumor","species":["Human"],"version_number":"1","date_updated":"2023-08-09","related_collections":[45441],"result_short_title":"AREN0532-Tumor-Annotations","subjects":"543","related_analysis_results":false,"result_browse_title":"Annotations for Vincristine, Dactinomycin, and Doxorubicin With or Without Radiation Therapy or Observation Only in Treating Younger Patients Who Are Undergoing Surgery for Newly Diagnosed Stage I, II, or III Wilms' Tumor (AREN0532-Tumor-Annotations)","supporting_data":false,"version_change_log":"","collections":"Below is a list of the Collections used in these analyses:\r\n<table><colgroup> <col \/> <col \/> <col \/><\/colgroup>\r\n<tbody>\r\n<tr>\r\n<th>Source Data Type<\/th>\r\n<th>Download<\/th>\r\n<th>License<\/th>\r\n<\/tr>\r\n<tr>\r\n<td><a href=\"https:\/\/doi.org\/10.7937\/6PJ1-M859\">Original AREN0532 Images<\/a>\u00a0used to create Segmentations and Seed Points (DICOM,\u00a0 56.4 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"\/wp-content\/uploads\/AREN0532_SourceImages_SEGSandSeedpoints-manifest_2-8-2023.tcia\" download=\"AREN0532_SourceImages_SEGSandSeedpoints-manifest_2-8-2023.tcia\"><button><i><\/i> Download<\/button><\/a>\r\n\r\n(Download requires <a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)\r\n\r\n<\/div><\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"https:\/\/nctn-data-archive.nci.nih.gov\/sites\/default\/files\/DUA\/NCTN_NCORP_Data_Archive_DUA_CA_v2019-06-12.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\">NCTN\/NCORP Data Archive License (Without Collaborative Agreement)<\/a>\r\n\r\n<\/div><\/td>\r\n<\/tr>\r\n<tr>\r\n<td><a href=\"https:\/\/doi.org\/10.7937\/6PJ1-M859\">Original AREN0532 Images<\/a>\u00a0used to create Negative Assessment reports (DICOM, 23.7 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"\/wp-content\/uploads\/AREN0532_SourceImages_NegativeAssessments-manifest-2-8-2023.tcia\" download=\"AREN0532_SourceImages_NegativeAssessments-manifest-2-8-2023.tcia\"><button><i><\/i> Download<\/button><\/a>\r\n\r\n(Download requires <a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)\r\n\r\n<\/div><\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"https:\/\/nctn-data-archive.nci.nih.gov\/sites\/default\/files\/DUA\/NCTN_NCORP_Data_Archive_DUA_CA_v2019-06-12.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\">NCTN\/NCORP Data Archive License (Without Collaborative Agreement)<\/a>\r\n\r\n<\/div><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n<ul>\r\n \t<li><a href=\"https:\/\/doi.org\/10.7937\/6PJ1-M859\">Vincristine, Dactinomycin, and Doxorubicin With or Without Radiation Therapy or Observation Only in Treating Younger Patients Who Are Undergoing Surgery for Newly Diagnosed Stage I, Stage II, or Stage III Wilms' Tumor (AREN0532)<\/a><\/li>\r\n<\/ul>","result_summary":"This dataset contains image annotations derived from the NCI Clinical Trial \"<a href=\"https:\/\/doi.org\/10.7937\/6PJ1-M859\">Vincristine, Dactinomycin, and Doxorubicin With or Without Radiation Therapy or Observation Only in Treating Younger Patients Who Are Undergoing Surgery for Newly Diagnosed Stage I, Stage II, or Stage III Wilms' Tumor (AREN0532)<\/a>\u201d.\u00a0 This dataset was generated as part of an NCI project to augment TCIA datasets with annotations that will improve their value for cancer researchers and AI developers.\r\n<h3>Annotation Protocol<\/h3>\r\nFor each patient, all scans were reviewed to identify and annotate the clinically relevant time points and sequences\/series. Scans were initially annotated by an international team of radiologists holding MBBS degrees or higher, which were then reviewed by US-based board-certified radiologists to ensure accuracy. In a typical patient the following annotation rules were followed:\r\n<ol>\r\n \t<li>The primary renal tumor(s) were annotated on post-contrast axial series. Normal renal parenchyma were excluded.<\/li>\r\n \t<li>A maximum of 5 lesions were annotated per patient scan (timepoint); no more than 2 per organ. The same 5 lesions were annotated at each time point.\u00a0 RECIST 1.1 principles were generally be followed for lesion annotation, however, if &lt;5 lesions measuring &gt;1 cm were present, then smaller lesions were annotated, again up to 2 lesions per organ or 5 lesions per patient scan. Bone lesions were included if other lesions were not present.<\/li>\r\n \t<li>Lesions were labeled separately.<\/li>\r\n \t<li>Seed points were automatically generated but were reviewed by a radiologist.<\/li>\r\n \t<li>To ensure a high standard of accuracy and data quality, each annotation was reviewed by a secondary reader.<\/li>\r\n<\/ol>\r\nAt each time point:\r\n<ol>\r\n \t<li>A seed point (kernel) was created for each segmented structure. The seed points for each segmentation are provided in a separate DICOM RTSS file.<\/li>\r\n \t<li>SNOMED-CT \u201cAnatomic Region Sequence\u201d and \u201cSegmented Property Category Code Sequence\u201d and codes were inserted for all segmented structures.<\/li>\r\n \t<li>Imaging time point codes were inserted to help identify each annotation in the context of the clinical trial assessment protocol.\r\n<ol>\r\n \t<li>\u201cClinical Trial Time Point ID\u201d was used to encode time point type using one of the following strings as applicable: \u201cpre-dose\u201d or \u201cpost-chemotherapy\u201d<\/li>\r\n \t<li>Content Item in \u201cAcquisition Context Sequence\u201d was added containing \"Time Point Type\" using Concept Code Sequence (0040,A168) selected from:\r\n<ol>\r\n \t<li>(255235001, SCT, \u201cPre-dose\u201d)<\/li>\r\n \t<li>(262502001, SCT, \"Post-chemotherapy\")<\/li>\r\n<\/ol>\r\n<\/li>\r\n<\/ol>\r\n<\/li>\r\n<\/ol>\r\nWe believe that these are the most clinically useful annotations for radiologists as well as for future researchers. The selected sequences inform whether there is residual or recurrent tumor and assess response to therapy.\r\n<h3>Important supplementary information and sample code<\/h3>\r\n<ol>\r\n \t<li>A spreadsheet containing key details about the annotations is available in the\u00a0<strong>Data Access<\/strong>\u00a0section below.<\/li>\r\n \t<li>A\u00a0Jupyter notebook demonstrating how to use the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/NBIA+Data+Retriever+Command-Line+Interface+Guide\">NBIA Data Retriever Command-Line Interface<\/a>\u00a0application and the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/Public\/NBIA+Search+with+Authentication+REST+API+Guide\">REST API (with authentication)<\/a>\u00a0to access these data can be found in the\u00a0<strong>Additional Resources<\/strong>\u00a0section below.<\/li>\r\n<\/ol>","collection_downloads":[46257,46259],"result_featured_image":false,"result_acknowledgements":"","hide_from_browse_table":"0","program":["NCTN"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46261","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\/46261\/revisions"}],"predecessor-version":[{"id":47487,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46261\/revisions\/47487"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=46261"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}