{"id":42277,"date":"2023-11-20T02:20:01","date_gmt":"2023-11-20T08:20:01","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/collection\/lung-fused-ct-pathology\/"},"modified":"2024-09-26T16:07:29","modified_gmt":"2024-09-26T21:07:29","slug":"lung-fused-ct-pathology","status":"publish","type":"tcia_collection","link":"https:\/\/stage.cancerimagingarchive.net\/collection\/lung-fused-ct-pathology\/","title":{"rendered":"LUNG-FUSED-CT-PATHOLOGY"},"featured_media":39221,"template":"","class_list":["post-42277","tcia_collection","type-tcia_collection","status-publish","has-post-thumbnail"],"cancer_types":["Lung Cancer"],"citations":[42267,42269,9225],"collection_doi":"10.7937\/k9\/tcia.2018.smt36lpn","collection_download_info":"","collection_downloads":[42271,42273,42275],"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><a href=\"https:\/\/portal.imaging.datacommons.cancer.gov\/explore\/filters\/?collection_id=lung_fused_ct_pathology\">Imaging Data Commons (IDC)<\/a> (Imaging Data)<\/li>\r\n \t<li>Source code is publicly available on Github at\u00a0<a href=\"https:\/\/github.com\/mirabelarusu\/RadPathFusionLung\">https:\/\/github.com\/mirabelarusu\/RadPathFusionLung<\/a><\/li>\r\n<\/ul>","cancer_locations":["Lung"],"collection_page_accessibility":"Public","publications_related":"","version_change_log_archived":"<h3>Version 1 (Current) Updated 2018\/07\/30<\/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,\u00a0 5.5 GB)<\/td><td colspan=\"1\"><div><p>\u00a0 <a href=\"\/wp-content\/uploads\/TCIA_Lung-Fused-CT-Pathology-2018-07-30.tcia\" download=\"TCIA_Lung-Fused-CT-Pathology-2018-07-30.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Lung-Fused-CT-Pathology\"><button><i><\/i> Search<\/button><\/a>\u00a0 \u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Lung-Fused-CT-Pathology\">\u00a0<\/a><\/p><p>(Requires\u00a0the <a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a> .)<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Annotated Whole Slide Pathology Images (TIF, 21.3 GB)<\/td><td colspan=\"1\"><div><p><a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjUyNSIsInBhc3Njb2RlIjoiYjIyM2M1M2RjZjc2ODYzODFlYTRjMWM1MjliNTcwMmQyOGE3YjgwOSIsInBhY2thZ2VfaWQiOiI1MjUiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/pathdb.cancerimagingarchive.net\/imagesearch?f[0]=collection:lung_fused_ct_pathology\"><button><i><\/i> Search<\/button><\/a>\u00a0<\/p><\/div><p>(Download and apply the\u00a0<a href=\"https:\/\/www.ibm.com\/aspera\/connect\/\">IBM-Aspera-Connect plugin\u00a0<\/a>to your browser to retrieve this faspex package)\u00a0<\/p><\/td><\/tr><tr><td colspan=\"1\">Clinical data (XLSX)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/Lung-Fused-CT-Pathology-spreadsheet.xlsx\" download=\"Lung-Fused-CT-Pathology-spreadsheet.xlsx\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><\/tr><\/tbody><\/table><p><strong> <br \/><\/strong><\/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":"1","collection_title":"Fused Radiology-Pathology Lung Dataset","date_updated":"2018-07-30","related_collection":false,"subjects":"6","analysis_results":"","collection_short_title":"Lung-Fused-CT-Pathology","data_types":["CT","Histopathology"],"version_change_log":"","collection_browse_title":"Lung-Fused-CT-Pathology","detailed_description":"<h4><u>Supporting Documentation<\/u><\/h4>\r\nThe data set is fully described in the following publications:\r\n\r\nRusu et al. <strong>Co-registration of pre-operative CT with ex vivo surgically excised ground glass nodules to define spatial extent of invasive adenocarcinoma on in vivo imaging: a proof-of-concept study<\/strong>. European Radiology (2018); PMCID:PMC5630490 DOI:<a href=\"https:\/\/doi.org\/10.1007\/s00330-017-4813-0\">10.1007\/s00330-017-4813-0<\/a>\r\n<h4><u>Histology Data Description<\/u><\/h4>\r\nThere is one folder for each patient, with the same folder name as the TCIA ID. Each folder with TCIA ID name contains 2 folders:\r\n<ul>\r\n \t<li>\u201cimages\u201d\r\n<ul>\r\n \t<li>Contains scanned histology images (in tiff format) pertinent to the TCIA ID Patient, e.g. LungFCP-01-0001_b1.tiff, LungFCP-01-0001_b2.tiff, etc<\/li>\r\n<\/ul>\r\n<\/li>\r\n \t<li>\u201cannotations\u201d\r\n<ul>\r\n \t<li>Contains the pathologist\u2019s annotations, stored as tiff file with the same image size as the scanned histology files, with 0 where there is not label, and 255 where a region was annotated. It is possible to have multiple annotations for each file, e.g. for file LungFCP-01-0001\\images\\LungFCP-01-0001_b1.tiff the following regions are available:\r\n<ul>\r\n \t<li>LungFCP-01-0001_b1_annotation_00_R000G255B000.tiff<\/li>\r\n \t<li>LungFCP-01-0001_b1_annotation_00_R255G000B000.tiff<\/li>\r\n<\/ul>\r\n<\/li>\r\n<\/ul>\r\n<\/li>\r\n<\/ul>\r\nA part of the filenames (LungFCP-01-0001_b1_annotation_00_RxxxGyyyBzzz) indicate the type of annotation:\r\n<ul>\r\n \t<li>Adenocarcinoma in Situ : R000G000B255, R001G000B255, R002G000B255<\/li>\r\n \t<li>Invasive Adenocarcinoma: R000G255B000, R001G255B000, R002G255B000, R003G255B000, R004G255B000, R005G255B000, R006G255B000<\/li>\r\n \t<li>Invasive Adenocarcinoma + Adenocarcinoma in Situ: R255G000B000<\/li>\r\n<\/ul>\r\nIf multiple files are available for the same type of annotation, e.g. Invasive Adenocarcinoma, it indicates that the pathologists has annotated multiple regions\r\n<h4><u>Content of \u201cFinalPublishedResults\u201d folder<\/u><\/h4>\r\nThe folder \u201cFinalPublishedResults\u201d contains one folder for each patient. Within each patient folder, there are 3 subfolders: \u201cCT\u201d, \u201dHistology\u201d, &amp; \u201dResults_XX\u201d where XX is a number. When expanded each patient folder appears as depicted below.\r\n<ul>\r\n \t<li>LungFCP-01-0001\r\n<ul>\r\n \t<li>CT\r\n<ul>\r\n \t<li>CT.mha\r\nCT_crop_blood_label.mha\r\nCT_label_Meta_crop.mha<\/li>\r\n<\/ul>\r\n<\/li>\r\n \t<li>histology\r\n<ul>\r\n \t<li>imgs<\/li>\r\n \t<li>masks\r\n<ul>\r\n \t<li>blood<\/li>\r\n \t<li>invasive<\/li>\r\n \t<li>lesion<\/li>\r\n \t<li>sample<\/li>\r\n \t<li>(airways)<\/li>\r\n<\/ul>\r\n<\/li>\r\n<\/ul>\r\n<\/li>\r\n \t<li>Results_XX\r\n<ul>\r\n \t<li>blood_label.mha\r\nblood_label_up.mha\r\nblood_label_up_bin.mha\r\ninvasion_label.mha\r\ninvasion_label_up.mha\r\ninvasion_label_up_bin.mha\r\nlabels_up_bin.mha\r\nlesion.mha\r\nlesion_label.mha\r\nlesion_label_up.mha\r\nlesion_label_up_bin.mha\r\nreconstruction_grayscale.mha\r\nsample_label.mha<\/li>\r\n<\/ul>\r\n<\/li>\r\n<\/ul>\r\n<\/li>\r\n \t<li>LungFCP-01-0002<\/li>\r\n \t<li>LungFCP-01-0003<\/li>\r\n \t<li>LungFCP-01-0004<\/li>\r\n \t<li>LungFCP-01-0005<\/li>\r\n \t<li>LungFCP-01-0006<\/li>\r\n<\/ul>\r\nThe folder \u201cCT\u201d contains the 3D CT volume saved as one mha file, the segmentation of the lesion obtained by majority voting for the three radiologist segmentations, and the segmentation of the blood vessels.\r\n\r\nThe folder \u201chistology\u201d has a similar content as the raw histology data, but a lower resolution, with some additional processing, e.g. applied gross rotation and flipping to correct for artifacts related to the mounting on the glass slide, and with additional annotations beside the lesion and in situ disease, e.g. blood vessels.\r\n\r\nThe folder Results_XX contain the outcome of the registration of the histopathology images and the CT.\r\n\r\n&nbsp;\r\n\r\nAll scripts used for generating these results are available at <a href=\"https:\/\/github.com\/mirabelarusu\/RadPathFusionLung\">https:\/\/github.com\/mirabelarusu\/RadPathFusionLung<\/a>\r\n\r\nPlease refer to the following publication for the methodological details:\r\n\r\nRusu M., Rajiah P., Gilkeson R., Yang M., Donatelli C., Thawani R., Jacono F.J., Linden P.,\u00a0 Madabushi A. (2017) <strong>Co-registration of pre-operative CT with ex vivo surgically excised ground glass nodules to define spatial extent of invasive adenocarcinoma on in vivo imaging: a proof-of-concept study.<\/strong> European Radiology 27:10, 4209:4217. DOI: <a href=\"https:\/\/doi.org\/10.1007\/s00330-017-4813-0\">https:\/\/doi.org\/10.1007\/s00330-017-4813-0<\/a>","supporting_data":["Image Analyses","Software\/Source Code"],"collection_featured_image":{"ID":"39221","post_author":"29","post_date":"2023-11-18 17:58:18","post_date_gmt":"2023-11-18 23:58:18","post_content":"","post_title":"Lung-Fused-CT-Pathology-featured","post_excerpt":"","post_status":"inherit","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"lung-fused-ct-pathology-featured","to_ping":"","pinged":"","post_modified":"2023-11-20 02:20:02","post_modified_gmt":"2023-11-20 08:20:02","post_content_filtered":"","post_parent":"42277","guid":"https:\/\/stage.cancerimagingarchive.net\/lung-fused-ct-pathology-featured\/","menu_order":"0","post_type":"attachment","post_mime_type":"image\/png","comment_count":"0","pod_item_id":"39221"},"collection_summary":"<p>This is the first attempt of mapping the extent of Invasive Adenocarcinoma onto in vivo lung CT. The mappings constitute ground truth of disease and may be used to further investigate the imaging signatures of Invasive Adenocarcinoma in ground glass pulmonary nodules. Patient with small ground glass nodules with &gt;2 histology slices per nodule were included. Patients with solid large nodules (&gt;40mm), with &lt;3 histology slices or with histology slices showing substantial artifacts were excluded from this study (see reference below for details). Data collection and analysis was provided by Case Western Reserve University.\u00a0<\/p><h4>References<\/h4><ul><li>All the program scripts that were used for generating the results and data in this paper have been made available at\u00a0 <a href=\"https:\/\/github.com\/mirabelarusu\/RadPathFusionLung\">https:\/\/github.com\/mirabelarusu\/RadPathFusionLung<\/a><\/li><li>This study is described in detail in the following publication:<ul><li>Rusu M., Rajiah P., Gilkeson R., Yang M., Donatelli C., Thawani R., Jacono F.J., Linden P.,\u00a0 Madabushi A. (2017) <strong>Co-registration of pre-operative CT with ex vivo surgically excised ground glass nodules to define spatial extent of invasive adenocarcinoma on in vivo imaging: a proof-of-concept study<\/strong>. European Radiology 27:10, 4209:4217. DOI:\u00a0<a href=\"https:\/\/doi.org\/10.1007\/s00330-017-4813-0\">https:\/\/doi.org\/10.1007\/s00330-017-4813-0<\/a><\/li><\/ul><\/li><\/ul>","collection_acknowledgements":"","collection_funding":"","hide_from_browse_table":"0","program":["Community"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/42277","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":2,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/42277\/revisions"}],"predecessor-version":[{"id":47367,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/42277\/revisions\/47367"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media\/39221"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=42277"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}