{"id":5594,"date":"2023-09-04T03:11:09","date_gmt":"2023-09-04T03:11:09","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-collection\/lung-fused-ct-pathology\/"},"modified":"2023-09-13T11:58:59","modified_gmt":"2023-09-13T11:58:59","slug":"lung-fused-ct-pathology","status":"publish","type":"tcia_collection","link":"https:\/\/cm.vastapps.dev\/tcia-collection\/lung-fused-ct-pathology\/","title":{"rendered":"LUNG-FUSED-CT-PATHOLOGY"},"featured_media":8574,"template":"","citation-tax":[],"cancer_types":["Lung Cancer"],"citations":[4469,4470,2925],"collection_doi":"10.7937\/k9\/tcia.2018.smt36lpn","collection_download_info":"Click the Versions tab for more info about data releases.","collection_downloads":[5035,5037,5038],"full_export":"<h2 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-Summary\">Summary<\/h2><p><span class=\"confluence-embedded-file-wrapper image-right-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image image-right\" draggable=\"false\" width=\"500\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/Public\/Fused%20Radiology-Pathology%20Lung%20Dataset%20(Lung-Fused-CT-Pathology)\/10.png?api=v2\"><\/span><\/p><div class=\"tableauPlaceholder\"><br\/><\/div><p>This is the first attempt of mapping the extent of Invasive Adenocarcinoma onto <em>in vivo<\/em> 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.\u00a0Patient 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).\u00a0Data collection and analysis was provided by Case Western Reserve University.\u00a0<\/p><h3 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-References\"><span style=\"color: rgb(255,102,0);\"> <span style=\"color: rgb(0,51,102);\">References<\/span> <\/span><\/h3><ul><li>All the program scripts that were used for generating the results and data in this paper have been made available at\u00a0<span class=\"ExternalRef\"> <a rel=\"nofollow\" href=\"https:\/\/github.com\/mirabelarusu\/RadPathFusionLung\" class=\"external-link\">https:\/\/github.com\/mirabelarusu\/RadPathFusionLung<\/a> <\/span><\/li><li><span class=\"ExternalRef\">This study is described in detail in the following publication:<\/span><ul><li><span class=\"ExternalRef\">Rusu M., Rajiah P., Gilkeson R., Yang M., Donatelli C., Thawani R., Jacono F.J., Linden P.,\u00a0 Madabushi A. (2017) 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. European Radiology 27:10, 4209:4217. DOI:\u00a0<a rel=\"nofollow\" class=\"external-link\" href=\"https:\/\/doi.org\/10.1007\/s00330-017-4813-0\">https:\/\/doi.org\/10.1007\/s00330-017-4813-0<\/a> <\/span><\/li><\/ul><\/li><\/ul><p><span class=\"ExternalRef\"> <br\/><\/span><\/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=\"#398787029cd7bdf0d1b84eca93e764fc72b342c4\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#398787026034b10e65034f248b25dafd262caee7\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#39878702eefeb453a19646f790bcb1ad016ae5dc\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#3987870212beccd1426b4365b5e526974a5662a0\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"398787029cd7bdf0d1b84eca93e764fc72b342c4\" active=\"true\" name=\"Data Access\" ><h3 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-DataAccess\">Data Access<\/h3><div class=\"table-wrap\"><table class=\"wrapped relative-table confluenceTable\" style=\"width: 70.6706%;\"><colgroup><col style=\"width: 26.9062%;\"\/><col style=\"width: 42.1666%;\"\/><col style=\"width: 30.8896%;\"\/><\/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\">Images (DICOM, 5.5 GB)<\/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:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/39878702\/TCIA_Lung-Fused-CT-Pathology-2018-07-30.tcia?version=1&amp;modificationDate=1541510138720&amp;api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Lung-Fused-CT-Pathology\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><span class=\"confluence-link\">\u00a0<\/span>\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Lung-Fused-CT-Pathology\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><\/div><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><span class=\"confluence-link\"><span class=\"confluence-link\">\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><br\/><\/span><\/span><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Annotated Whole Slide Pathology Images (TIF, 21.3 GB)<\/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:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/80?passcode=2e2eb188bbddd4b7d145fde0f6696493cf8a229e\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/pathdb.cancerimagingarchive.net\/imagesearch?f[0]=collection:lung_fused_ct_pathology\" 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><p>(Download and apply the\u00a0<a href=\"https:\/\/www.ibm.com\/aspera\/connect\/\" class=\"external-link\" rel=\"nofollow\">IBM-Aspera-Connect plugin\u00a0<\/a>to your browser to retrieve this faspex package)\u00a0<\/p><\/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><tr><td class=\"confluenceTd\">Clinical data (XLSX)<\/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:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/39878702\/Lung%20Fused-CT-Pathology%20spreadsheet.xlsx?version=1&amp;modificationDate=1532544176723&amp;api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/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>Click the Versions tab for more info about data releases.<\/p><p>\n<h3 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-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><\/p><ul><li class=\"auto-cursor-target\"><a href=\"https:\/\/portal.imaging.datacommons.cancer.gov\/explore\/filters\/?collection_id=lung_fused_ct_pathology\" class=\"external-link\" rel=\"nofollow\">Imaging Data Commons (IDC)<\/a> (Imaging Data)<\/li><\/ul><p style=\"text-align: left;\">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.<\/p><ul style=\"text-align: left;\"><li>Source code is publicly available on Github at<span class=\"ExternalRef\">\u00a0<a class=\"external-link\" rel=\"nofollow\" href=\"https:\/\/github.com\/mirabelarusu\/RadPathFusionLung\">https:\/\/github.com\/mirabelarusu\/RadPathFusionLung<\/a><\/span><\/li><\/ul><\/div><div class=\"tabs-pane \" id=\"398787026034b10e65034f248b25dafd262caee7\" name=\"Detailed Description\" ><h3 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-DetailedDescription\">Detailed Description<\/h3><div class=\"table-wrap\"><table class=\"wrapped fixed-table confluenceTable\"><colgroup> <col style=\"width: 168.0px;\"\/> <col style=\"width: 210.0px;\"\/> <col style=\"width: 211.0px;\"\/> <\/colgroup><tbody><tr><th class=\"confluenceTh\"><div class=\"tablesorter-header-inner\"><p>Collection Statistics<\/p><\/div><\/th><th class=\"confluenceTh\"><div class=\"tablesorter-header-inner\"><p>\u00a0Radiology Image Statistics<\/p><\/div><\/th><th colspan=\"1\" class=\"confluenceTh\">Pathology Image Statistics<\/th><\/tr><tr><td class=\"confluenceTd\"><p>Modalities<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>CT, Histology compartments mapped on CT (DICOM)<\/p><\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">Pathology<\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Participants<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>6<\/p><\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">6<\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Studies<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\">6<\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">6<\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Series<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\">52<\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">N\/A<\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Images<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>11,210<\/p><\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">25<\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Image Size (GB)<\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">5.5<\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">21.3<\/td><\/tr><\/tbody><\/table><\/div><h4 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-SupportingDocumentation\"><u>Supporting Documentation<\/u><\/h4><p>Within the directory CT_Segmentations_and_annotations\/CT_Segmentations\/&lt;ptID&gt;\/ there are five directories:<\/p><ol><li>BloodVessels (derived from CT)<\/li><li>Nodule (derived from CT)<\/li><li>MappedFromHistologyBloodVessels<\/li><li>MappedFromHistologyInvasion<\/li><li>MappedFromHistologyLesion<\/li><\/ol><p>The data set is fully described in the following publications:<\/p><p><span>Rusu et al. 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. European Radiology (2018); PMCID:PMC5630490 DOI:<a href=\"https:\/\/doi.org\/10.1007\/s00330-017-4813-0\" class=\"external-link\" rel=\"nofollow\">10.1007\/s00330-017-4813-0<\/a> <\/span><\/p><h4 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-HistologyDataDescription\"><u>Histology Data Description<\/u><\/h4><p>There is one folder for each patient, with the same folder name as the TCIA ID. Each folder with TCIA ID name contains 2 folders:<\/p><ul><li>\u201cimages\u201d<ul><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><\/ul><\/li><li>\u201cannotations\u201d<ul><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:<ul><li>LungFCP-01-0001_b1_annotation_00_R000G255B000.tiff<\/li><li>LungFCP-01-0001_b1_annotation_00_R255G000B000.tiff<\/li><\/ul><\/li><\/ul><\/li><\/ul><p>A part of the filenames (LungFCP-01-0001_b1_annotation_00_RxxxGyyyBzzz) indicate the type of annotation:<\/p><ul><li>Adenocarcinoma in Situ : R000G000B255, R001G000B255, R002G000B255<\/li><li>Invasive Adenocarcinoma: R000G255B000, R001G255B000, R002G255B000, R003G255B000, R004G255B000, R005G255B000, R006G255B000<\/li><li>Invasive Adenocarcinoma + Adenocarcinoma in Situ: R255G000B000<\/li><\/ul><p>If multiple files are available for the same type of annotation, e.g. Invasive Adenocarcinoma, it indicates that the pathologists has annotated multiple regions<\/p><h4 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-Descriptionofthecontentof\u201cFinalPublishedResults\u201dfolder\"><u>Description of the content of \u201cFinalPublishedResults\u201d folder<\/u><\/h4><p>The 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. When expanded each patient folder\u00a0 appears as depicted below.<\/p><ul><li>LungFCP-01-0001<ul><li>CT<\/li><li>Histology<\/li><li>Results_XX<\/li><\/ul><\/li><li>LungFCP-01-0002<\/li><li>LungFCP-01-0003<\/li><li>LungFCP-01-0004<\/li><li>LungFCP-01-0005<\/li><li>LungFCP-01-0006<\/li><\/ul><p>The 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.<\/p><p>The 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.<\/p><p>The folder Results contain the outcome of the registration of the histopathology images and the CT. All scripts used for generating these results are available at\u00a0<a href=\"https:\/\/github.com\/mirabelarusu\/RadPathFusionLung\" class=\"external-link\" rel=\"nofollow\">https:\/\/github.com\/mirabelarusu\/RadPathFusionLung<\/a><\/p><p>Please refer to the following publication for the methodological details:<\/p><p>Rusu M., Rajiah P., Gilkeson R., Yang M., Donatelli C., Thawani R., Jacono F.J., Linden P.,\u00a0 Madabushi A. (2017) 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. European Radiology 27:10, 4209:4217. DOI: <a href=\"https:\/\/doi.org\/10.1007\/s00330-017-4813-0\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1007\/s00330-017-4813-0<\/a><\/p><\/div><div class=\"tabs-pane \" id=\"39878702eefeb453a19646f790bcb1ad016ae5dc\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-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>Madabhushi, A., &amp; Rusu, M. (2018).<span>\u00a0<\/span><strong>Fused Radiology-Pathology Lung (Lung-Fused-CT-Pathology)\u00a0(Version 1) [Data set]<\/strong>. The Cancer Imaging Archive.<span> <a style=\"text-decoration: none;\" href=\"https:\/\/doi.org\/10.7937\/k9\/tcia.2018.smt36lpn\" class=\"external-link\" rel=\"nofollow\">\u00a0https:\/\/doi.org\/10.7937\/k9\/tcia.2018.smt36lpn<\/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>Rusu, M., Rajiah, P., Gilkeson, R., Yang, M., Donatelli, C., Thawani, R., Jacono, F. J., Linden, P., &amp; Madabhushi, A. (2018) <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 (Vol. 27, Issue 10, pp. 4209\u20134217). \u00a0PMCID:PMC5630490 DOI:\u00a0<a href=\"https:\/\/doi.org\/10.1007\/s00330-017-4813-0\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1007\/s00330-017-4813-0<\/a><\/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>Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F.\u00a0<strong>The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository<\/strong>, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. DOI: <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><\/p><\/div><\/div><h3 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains <a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\" class=\"external-link\" rel=\"nofollow\">a list of publications<\/a> which leverage our data. <\/span>If you have a publication you'd like to add, please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" class=\"external-link\" rel=\"nofollow\"> contact TCIA's Helpdesk<\/a>.<\/p><\/div><div class=\"tabs-pane \" id=\"3987870212beccd1426b4365b5e526974a5662a0\" name=\"Versions\" ><h3 id=\"FusedRadiologyPathologyLungDataset(LungFusedCTPathology)-Version1(Current)Updated07-30-2018\">Version 1 (Current) Updated 07-30-2018<\/h3><div class=\"table-wrap\"><table class=\"wrapped confluenceTable\"><colgroup> <col\/> <col\/> <\/colgroup><tbody><tr><th colspan=\"1\" class=\"confluenceTh\">Data Type<\/th><th colspan=\"1\" class=\"confluenceTh\">Download all or Query\/Filter<\/th><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Images (DICOM,\u00a0 5.5 GB)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><span class=\"confluence-link\">\u00a0<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/39878702\/TCIA_Lung-Fused-CT-Pathology-2018-07-30.tcia?version=1&amp;modificationDate=1541510138720&amp;api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Lung-Fused-CT-Pathology\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><span class=\"confluence-link\"> <\/span>\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Lung-Fused-CT-Pathology\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><p><span class=\"confluence-link\">(Requires\u00a0<span>the <\/span> <a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a> <span>.<\/span>)<br\/><\/span><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Annotated Whole Slide Pathology Images (TIF, 21.3 GB)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/80?passcode=2e2eb188bbddd4b7d145fde0f6696493cf8a229e\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/pathdb.cancerimagingarchive.net\/imagesearch?f[0]=collection:lung_fused_ct_pathology\" 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><p>(Download and apply the\u00a0<a href=\"https:\/\/www.ibm.com\/aspera\/connect\/\" class=\"external-link\" rel=\"nofollow\">IBM-Aspera-Connect plugin\u00a0<\/a>to your browser to retrieve this faspex package)\u00a0<\/p><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Clinical data (XLSX)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/39878702\/Lung%20Fused-CT-Pathology%20spreadsheet.xlsx?version=1&amp;modificationDate=1532544176723&amp;api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p class=\"auto-cursor-target\"><strong> <br\/><\/strong><\/p><\/div><\/div><\/div><\/div><p><br\/><\/p><p><br\/><\/p><p><br\/><\/p><p><br\/><\/p><p><br\/><\/p>","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.\n \n<ul><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><\/ul>\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.\n<ul><li>Source code is publicly available on Github at\u00a0<a href=\"https:\/\/github.com\/mirabelarusu\/RadPathFusionLung\">https:\/\/github.com\/mirabelarusu\/RadPathFusionLung<\/a><\/li><\/ul>","cancer_locations":["Lung"],"collection_page_accessibility":"Public","publications_related":"","version_change_log":"","version_change_log_archived":"","analysis_results":"","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>.","species":["Human"],"collection_title":"Fused Radiology-Pathology Lung Dataset","detailed_description":"<h4><u>Supporting Documentation<\/u><\/h4>\nWithin the directory CT_Segmentations_and_annotations\/CT_Segmentations\/&lt;ptID&gt;\/ there are five directories:\n<ol><li>BloodVessels (derived from CT)<\/li><li>Nodule (derived from CT)<\/li><li>MappedFromHistologyBloodVessels<\/li><li>MappedFromHistologyInvasion<\/li><li>MappedFromHistologyLesion<\/li><\/ol>\nThe data set is fully described in the following publications:\nRusu et al. 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. European Radiology (2018); PMCID:PMC5630490 DOI:<a href=\"https:\/\/doi.org\/10.1007\/s00330-017-4813-0\">10.1007\/s00330-017-4813-0<\/a>\n<h4><u>Histology Data Description<\/u><\/h4>\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:\n<ul><li>\u201cimages\u201d<ul><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><\/ul><\/li><li>\u201cannotations\u201d<ul><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:<ul><li>LungFCP-01-0001_b1_annotation_00_R000G255B000.tiff<\/li><li>LungFCP-01-0001_b1_annotation_00_R255G000B000.tiff<\/li><\/ul><\/li><\/ul><\/li><\/ul>\nA part of the filenames (LungFCP-01-0001_b1_annotation_00_RxxxGyyyBzzz) indicate the type of annotation:\n<ul><li>Adenocarcinoma in Situ : R000G000B255, R001G000B255, R002G000B255<\/li><li>Invasive Adenocarcinoma: R000G255B000, R001G255B000, R002G255B000, R003G255B000, R004G255B000, R005G255B000, R006G255B000<\/li><li>Invasive Adenocarcinoma + Adenocarcinoma in Situ: R255G000B000<\/li><\/ul>\nIf multiple files are available for the same type of annotation, e.g. Invasive Adenocarcinoma, it indicates that the pathologists has annotated multiple regions\n<h4><u>Description of the content of \u201cFinalPublishedResults\u201d folder<\/u><\/h4>\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. When expanded each patient folder\u00a0 appears as depicted below.\n<ul><li>LungFCP-01-0001<ul><li>CT<\/li><li>Histology<\/li><li>Results_XX<\/li><\/ul><\/li><li>LungFCP-01-0002<\/li><li>LungFCP-01-0003<\/li><li>LungFCP-01-0004<\/li><li>LungFCP-01-0005<\/li><li>LungFCP-01-0006<\/li><\/ul>\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.\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.\nThe folder Results contain the outcome of the registration of the histopathology images and the CT. All scripts used for generating these results are available at\u00a0<a href=\"https:\/\/github.com\/mirabelarusu\/RadPathFusionLung\">https:\/\/github.com\/mirabelarusu\/RadPathFusionLung<\/a>\nPlease refer to the following publication for the methodological details:\nRusu M., Rajiah P., Gilkeson R., Yang M., Donatelli C., Thawani R., Jacono F.J., Linden P.,\u00a0 Madabushi A. (2017) 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. 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>","related_analysis_results":false,"subjects":"6","collection_short_title":"Lung-Fused-CT-Pathology","data_types":["CT","Pathology"],"date_updated":"2023-09-13","collection_browse_title":"","supporting_data":["Image Analyses"],"collection_featured_image":{"ID":"8574","post_author":"6","post_date":"2023-09-13 04:15:56","post_date_gmt":"2023-09-13 04:15:56","post_content":"","post_title":"image2021-2-9_23-4-10","post_excerpt":"","post_status":"inherit","comment_status":"open","ping_status":"closed","post_password":"","post_name":"image2021-2-9_23-4-10","to_ping":"","pinged":"","post_modified":"2023-09-13 11:58:59","post_modified_gmt":"2023-09-13 11:58:59","post_content_filtered":"","post_parent":"5594","guid":"https:\/\/cm.vastapps.dev\/wp-content\/uploads\/image2021-2-9_23-4-10.png","menu_order":"0","post_type":"attachment","post_mime_type":"image\/png","comment_count":"0","pod_item_id":"8574"},"collection_summary":"<br\/>\nThis is the first attempt of mapping the extent of Invasive Adenocarcinoma onto <em>in vivo<\/em> 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.\u00a0Patient 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).\u00a0Data collection and analysis was provided by Case Western Reserve University.\u00a0\n<h3> References <\/h3>\n<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) 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. 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>\n<br\/>","collection_acknowledgements":"","collection_funding":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections\/5594"}],"collection":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections"}],"about":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/types\/tcia_collection"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media\/8574"}],"wp:attachment":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media?parent=5594"}],"wp:term":[{"taxonomy":"tcia_citation_tax","embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/v1\/citation-tax?post=5594"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}