{"id":41405,"date":"2023-11-20T00:59:48","date_gmt":"2023-11-20T06:59:48","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/collection\/ct-lymph-nodes\/"},"modified":"2024-10-16T13:54:23","modified_gmt":"2024-10-16T18:54:23","slug":"ct-lymph-nodes","status":"publish","type":"tcia_collection","link":"https:\/\/stage.cancerimagingarchive.net\/collection\/ct-lymph-nodes\/","title":{"rendered":"CT-LYMPH-NODES"},"featured_media":0,"template":"","class_list":["post-41405","tcia_collection","type-tcia_collection","status-publish"],"cancer_types":["Lymphadenopathy (non-cancer)"],"citations":[41377,41379,9225],"collection_doi":"10.7937\/K9\/TCIA.2015.AQIIDCNM","collection_download_info":"","collection_downloads":[41381,41383,41385,41387],"versions":[41397,41399,41401,41403],"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><a href=\"https:\/\/portal.imaging.datacommons.cancer.gov\/explore\/filters\/?collection_id=ct_lymph_nodes\">Imaging Data Commons (IDC)<\/a> (Imaging Data)<\/li>\r\n<\/ul>","cancer_locations":["Abdomen","Mediastinum"],"collection_page_accessibility":"Public","publications_related":"The Collection <em>authors <\/em>suggest the below will also give context to this dataset, please cite if you use them in your work:\r\n<ul>\r\n \t<li>Seff, A., Lu, L., Cherry, K.M., Roth, H.R., Liu, J., Wang, S., Hoffman, J., Turkbey, E.B., &amp; Summers, R.M. <strong>2D view aggregation for lymph node detection using a shallow hierarchy of linear classifiers<\/strong>.<em>\u00a0<\/em>Medical Image Computing and Computer-Assisted Intervention--MICCAI 2014, p544-552, 2014. (<a href=\"http:\/\/arxiv.org\/abs\/1408.3337\">http:\/\/arxiv.org\/abs\/1408.3337<\/a>)<\/li>\r\n \t<li><em>Please cite the following paper when using the segmentation masks:<\/em>\u00a0 Seff, A., Lu, L., Barbu, A., Roth, H., Shin, H.-C., &amp; Summers, R. M. (2015).<strong> Leveraging Mid-Level Semantic Boundary Cues for Automated Lymph Node Detection.<\/strong> In Lecture Notes in Computer Science\u00a0Medical Image Computing and Computer-Assisted Intervention\u2013MICCAI 2015 (pp. 53\u201361). Springer International Publishing. <a href=\"https:\/\/doi.org\/10.1007\/978-3-319-24571-3_7\">https:\/\/doi.org\/10.1007\/978-3-319-24571-3_7<\/a><\/li>\r\n<\/ul>","version_change_log_archived":"<h3>Version 5 (Current): Updated 2023\/03\/31<\/h3><table><colgroup> <col \/> <col \/> <\/colgroup><tbody><tr><th colspan=\"1\">Data Type<\/th><th colspan=\"1\">Download all or Query\/Filter<\/th><\/tr><tr><td colspan=\"1\">Image, Segmentations (DICOM, 58.4 GB)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/TCIA_CT_Lymph_Nodes_03-31-2023.tcia\" download=\"TCIA_CT_Lymph_Nodes_03-31-2023.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=CT%20Lymph%20Nodes\"><button><i><\/i> Search<\/button><\/a>\u00a0 <\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Med ABD Lymph Annotations (ZIP)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_ANNOTATIONS.zip\" download=\"MED_ABD_LYMPH_ANNOTATIONS.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Med Lymph Candidate Nodes (ZIP)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_CANDIDATES.zip\" download=\"MED_ABD_LYMPH_CANDIDATES.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Med ABD Lymph Masks (ZIP)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_MASKS.zip\" download=\"MED_ABD_LYMPH_MASKS.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><\/tbody><\/table><p>Added DICOM version of MED_ABD_LYMPH_MASKS.zip segmentations that were previously available<\/p><h3>Version 4 : Updated 2015\/12\/14<\/h3><table><colgroup> <col \/> <col \/> <\/colgroup><tbody><tr><th colspan=\"1\">Data Type<\/th><th colspan=\"1\">Download all or Query\/Filter<\/th><\/tr><tr><td colspan=\"1\">Images (DICOM, 57.8GB)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/TCIA_CT_Lymph_Nodes_06-22-2015.tcia\" download=\"TCIA_CT_Lymph_Nodes_06-22-2015.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=CT%20Lymph%20Nodes\"><button><i><\/i> Search<\/button><\/a>\u00a0 <\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Med ABD Lymph Annotations (ZIP)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_ANNOTATIONS.zip\" download=\"MED_ABD_LYMPH_ANNOTATIONS.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Med Lymph Candidate Nodes (ZIP)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_CANDIDATES.zip\" download=\"MED_ABD_LYMPH_CANDIDATES.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Med ABD Lymph Masks (ZIP)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_MASKS.zip\" download=\"MED_ABD_LYMPH_MASKS.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><\/tbody><\/table><p><em> <strong> <a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_MASKS.zip\" download=\"MED_ABD_LYMPH_MASKS.zip\">MED_ABD_LYMPH_MASKS.zip<\/a> <\/strong> <\/em>added via the wiki.<\/p><h3>Version 3: Updated 2015\/09\/14<\/h3><p><a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_CANDIDATES.zip\" download=\"MED_ABD_LYMPH_CANDIDATES.zip\">MED_ABD_LYMPH_CANDIDATES.zip<\/a> \u00a0added via the wiki.<\/p><h3>Version 2: Updated 2015\/06\/24<\/h3><p>\u00a0 <strong> <em> <a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_ANNOTATIONS.zip\" download=\"MED_ABD_LYMPH_ANNOTATIONS.zip\">MED_ABD_LYMPH_ANNOTATIONS.zip<\/a> <\/em> <\/strong> \u00a0 added via the wiki.<\/p><h3>Version 1: Updated 2015\/03\/16<\/h3><p>Image data set uploaded<\/p><p>&nbsp;<\/p>","collection_status":"Complete","publications_using":"TCIA maintains <a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\">a list of publications<\/a> which leverage our data. If you have a publication you'd like to add please <a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact TCIA's Helpdesk<\/a>.","related_analysis_results":false,"species":["Human"],"version_number":"5","collection_title":"A new 2.5 D representation for lymph node detection in CT","date_updated":"2023-03-31","related_collection":false,"subjects":"176","analysis_results":"","collection_short_title":"CT Lymph Nodes","data_types":["CT","SEG"],"version_change_log":"<p class=\"auto-cursor-target\">Added DICOM version of MED_ABD_LYMPH_MASKS.zip segmentations that were previously available<\/p>","collection_browse_title":"CT Lymph Nodes","detailed_description":"The DICOM files were created from volumetric images (Analyze and NifTI) using this from ITK: \u00a0 <strong> <em> <a href=\"http:\/\/www.itk.org\/Doxygen\/html\/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html\">http:\/\/www.itk.org\/Doxygen\/html\/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html<\/a>.<\/em> <\/strong>\r\n<h3>Annotation files<\/h3>\r\n<strong> <em> <a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_ANNOTATIONS.zip\" download=\"MED_ABD_LYMPH_ANNOTATIONS.zip\">MED_ABD_LYMPH_ANNOTATIONS.zip<\/a> <\/em> <\/strong>\u00a0(new 6\/24\/2015). The annotations include a folder for each case with text files of voxel indices, physical coordinates, size measurements and a\u00a0<a href=\"http:\/\/mitk.org\/\">MITK\u00a0<\/a>point set file (.mps), which can be visualized using the\u00a0<a href=\"http:\/\/mitk.org\/Download\">MITK workbench<\/a>\u00a0(Note: only release\u00a0<a title=\"MITK ReleaseNotes 2014.10\" href=\"http:\/\/mitk.org\/wiki\/MITK_ReleaseNotes_2014.10\">2014.10.0<\/a>\u00a0and later supports visualization of point set files using the \"point set interaction plugin\"). Abdominal size measurements\u00a0include the longest and shortest axis in axial view of a lymph node. The shortest axis is used for the RECIST criteria. The mediastinal set only includes the shortest axis.\r\n<h3>Mediastinal and abdominal lymph nodes<\/h3>\r\nComputer-generated candidate detections for mediastinal and abdominal lymph nodes (produced by methods in [K. Cherry et al., SPIE Med. Img. 2014] and [J. Liu et al., SPIE Med. Img. 2014]]). \u00a0See attached:\u00a0<a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_CANDIDATES.zip\" download=\"MED_ABD_LYMPH_CANDIDATES.zip\">MED_ABD_LYMPH_CANDIDATES.zip<\/a>\u00a0(new 9\/14\/2015).\r\n\r\n<em> <strong> <a href=\"\/wp-content\/uploads\/MED_ABD_LYMPH_MASKS.zip\" download=\"MED_ABD_LYMPH_MASKS.zip\">MED_ABD_LYMPH_MASKS.zip<\/a>\u00a0<\/strong> <\/em>(new 12\/8\/2015): These files contain a compressed NifTI image (*.nii.gz) for each patient with manually traced lymph node segmentations. Note: these segmentation masks were produced independently to the centroid annotations in MED_ABD_LYMPH_ANNOTATIONS.zip. There is an overlapping set of lymph nodes marked in both files but the indexing does not align.\u00a0 On 3\/31\/2023 (version 5) a DICOM-SEG version of these data were added to the collection.\r\n\r\nPlease cite the following paper when using the segmentation masks:\r\n\r\nA Seff, L Lu, A Barbu, H Roth, HC Shin, RM Summers. <strong>Leveraging Mid-Level Semantic Boundary Cues for Automated Lymph Node Detection<\/strong>. Medical Image Computing and Computer-Assisted Intervention\u2013MICCAI 2015, 53-61 (<a href=\"http:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-24571-3_7\">http:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-24571-3_7<\/a>)","supporting_data":["Image Analyses","Organ segmentations"],"collection_featured_image":false,"collection_summary":"<p>This collection consists of Computed Tomography (CT) images of the mediastinum and abdomen in which lymph node positions are marked by radiologists at the National Institutes of Health, Clinical Center. Radiologists at the <em> <a href=\"https:\/\/clinicalcenter.nih.gov\/meet-our-doctors\/rsummers.html\"> <strong>I<\/strong><strong>maging Biomarkers and Computer-Aided Diagnosis Laboratory<\/strong> <\/a> <\/em> labeled a total of 388 mediastinal lymph nodes in CT images of 90 patients and a total of 595 abdominal lymph nodes in 86 patients.<\/p><p>The collection is aimed at the medical image computing community for developing and assessing computer-aided detection methods. Automated detection of lymph nodes can be an important clinical diagnostic tool but is very challenging due to the low contrast of surrounding structures in CT and to their varying sizes, poses, shapes and sparsely distributed locations. This data set is made available to make direct comparison to other detection methods in order to advance the state of the art.<\/p>","collection_acknowledgements":"<ul><li>We would like to acknowledge the individuals and institutions that have provided data for this collection: National Institutes of Health, Bethesda MD. \u00a0 Special thanks to Dr. <strong>Holger R. Roth<\/strong> and Dr. <strong>Ronald Summers<\/strong>, <strong><em><a href=\"https:\/\/clinicalcenter.nih.gov\/meet-our-doctors\/rsummers.html\">Imaging Biomarkers and Computer-Aided Diagnosis Laboratory<\/a><\/em><\/strong> , Grant Magnuson Clinical Center.<\/li><li>Conversion of the segmentations into DICOM SEG representation was completed by Cosmin Ciausu using dcmqi (<a href=\"https:\/\/github.com\/QIICR\/dcmqi\">https:\/\/github.com\/QIICR\/dcmqi<\/a>), assisted by Andrey Fedorov, David Clunie, and other members of the NCI Imaging Data Commons team. NCI Imaging Data Commons consortium is supported by the contract number 19X037Q from Leidos Biomedical Research under Task Order HHSN26100071 under Contract Number HHSN261201500003l from NCI.<\/li><\/ul>","collection_funding":"","hide_from_browse_table":"0","program":["Community"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/41405","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections"}],"about":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/types\/tcia_collection"}],"version-history":[{"count":1,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/41405\/revisions"}],"predecessor-version":[{"id":49743,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/41405\/revisions\/49743"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=41405"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}