{"id":5595,"date":"2023-09-04T03:11:13","date_gmt":"2023-09-04T03:11:13","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-collection\/prostate-fused-mri-pathology\/"},"modified":"2023-09-13T11:59:01","modified_gmt":"2023-09-13T11:59:01","slug":"prostate-fused-mri-pathology","status":"publish","type":"tcia_collection","link":"https:\/\/cm.vastapps.dev\/tcia-collection\/prostate-fused-mri-pathology\/","title":{"rendered":"PROSTATE-FUSED-MRI-PATHOLOGY"},"featured_media":0,"template":"","citation-tax":[],"cancer_types":["Prostate Cancer"],"citations":[4471,4472,4473,4474,4475,2925],"collection_doi":"10.7937\/k9\/TCIA.2016.tlpmr1am","collection_download_info":"<br\/>\nClick the Versions tab for more info about data releases.","collection_downloads":[5039,5041,5042,5043],"full_export":"<h2 id=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-Summary\">Summary<\/h2>This collection comprises a total of 28 3 Tesla T1-weighted, T2-weighted, Diffusion weighted and Dynamic Contrast Enhanced prostate MRI along with accompanying digitized histopathology (H&amp;E stained) images of corresponding radical prostatectomy specimens. The MRI scans also have a mapping of extent of prostate cancer on them [<a style=\"text-decoration: none;\" href=\"https:\/\/doi.org\/10.1002\/jmri.24975\" class=\"external-link\" rel=\"nofollow\">10.1002\/jmri.24975<\/a>]. Each surgically excised prostate specimen was originally sectioned and quartered resulting in 4 slides for each section. Each of these individual slides was digitized at 20x magnification using an Aperio slide scanner resulting in a set of 4 .svs images. Each of the 4 .svs images were then digitally stitched together to constitute a pseudo-whole mount section (.tiff) using the program in [PMCID: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4023035\/\" class=\"external-link\" rel=\"nofollow\">PMC4023035<\/a>]. Annotations of cancer presence on the pseudo-whole mount sections were made by an expert pathologist. Slice correspondences were established between the individual T2w MRI and stitched pseudo-whole mount sections by the program in [<a href=\"https:\/\/doi.org\/10.1016\/j.compmedimag.2010.12.003\" class=\"external-link\" rel=\"nofollow\">10.1016\/j.compmedimag.2010.12.003<\/a>] and checked for accuracy by an expert pathologist and radiologist. Deformable co-registration [<span class=\"identifier pmc\"><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/pmc3078156\/\" style=\"text-decoration: none;\" class=\"external-link\" rel=\"nofollow\">PMC3078156<\/a><\/span>] was employed to spatially co-registered the corresponding radiologic and histopathologic tissue sections to map disease extent onto the corresponding MRI scans.<h3 id=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-Acknowledgement\">Acknowledgement<\/h3><ul><li>Data collection and analysis was provided by Anant Madabhushi, PhD, Case Western Reserve University and Michael D. Feldman, MD, PhD, Hospital at the University of Pennsylvania.\u00a0<\/li><li>This work was supported by NIH R01CA136535.<\/li><\/ul><p><br\/><\/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=\"#236915147cb815ce996743b9ba812a9f720a65f4\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#23691514bb164164ca0142f99d275154d37a310c\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#23691514198bdfbf81e044a68e2aa7d290b4bf95\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#23691514623e7edc4aae4e16abd21b612dff549c\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"236915147cb815ce996743b9ba812a9f720a65f4\" active=\"true\" name=\"Data Access\" ><h3 id=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-DataAccess\">Data Access\u00a0<\/h3><div class=\"table-wrap\"><table class=\"wrapped relative-table confluenceTable\" style=\"width: 58.0963%;\"><colgroup><col style=\"width: 37.584%;\"\/><col style=\"width: 35.6794%;\"\/><col style=\"width: 26.6643%;\"\/><\/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, 4.4 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\/23691514\/doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia?version=1&amp;modificationDate=1534787026838&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:\/\/nbia.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Prostate%20Fused-MRI-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=Prostate Fused-MRI-Pathology\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><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><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Annotated Whole Slide Pathology Images &amp; Annotations (Tiff, XML 76.8 GB)<\/p><\/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\/72?passcode=3da9391db835cc0937cd309ea568755c2153b056\" 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:prostate_fused_mri_pathology\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/72?passcode=3da9391db835cc0937cd309ea568755c2153b056\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a>\u00a0<a href=\"https:\/\/pathology.cancerimagingarchive.net\/pathdata\/cw_flex2\/index.php\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><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><\/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><tr><td class=\"confluenceTd\">Fused Rad-Path Matlab Files<\/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\/23691514\/fused_prostate_matlab.zip?version=1&amp;modificationDate=1476802701461&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><tr><td class=\"confluenceTd\">Correspondence tables (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\/23691514\/histo_MR_Correspondence.xlsx?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><br\/><\/p><p>Click the Versions tab for more info about data releases.<\/p><p>\n<h3 id=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-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=prostate_fused_mri_pathology\" class=\"external-link\" rel=\"nofollow\">Imaging Data Commons (IDC)<\/a> (Imaging Data)<\/li><\/ul><\/div><div class=\"tabs-pane \" id=\"23691514bb164164ca0142f99d275154d37a310c\" name=\"Detailed Description\" ><h3 id=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-DetailedDescription\">Detailed Description<\/h3><div class=\"table-wrap\"><table class=\"wrapped fixed-table confluenceTable\"><colgroup> <col style=\"width: 160.0px;\"\/> <col style=\"width: 133.0px;\"\/> <col style=\"width: 135.0px;\"\/> <\/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 style=\"text-align: center;\">Radiology Image Statistics<\/p><\/div><\/th><th style=\"text-align: center;\" 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>MRI<\/p><\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">Pathology, Matlab<\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Participants<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>28<\/p><\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">16<\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Studies<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>29<\/p><\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">N\/A<\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Series<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\">325<\/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>32,508<\/p><\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">114<\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Image Size (GB)<\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">4.4<\/td><td style=\"text-align: center;\" colspan=\"1\" class=\"confluenceTd\">76.8<\/td><\/tr><\/tbody><\/table><\/div><h4 id=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-SupportingDocumentation\">Supporting Documentation<\/h4><p>The data set is fully described in the following publications:<\/p><ol><li><p class=\"auto-cursor-target\">Singanamalli, A. , Rusu, M. , Sparks, R. E., Shih, N. N., Ziober, A. , Wang, L. , Tomaszewski, J. , Rosen, M. , Feldman, M. and Madabhushi, A. (2016), <strong>Identifying in vivo DCE MRI markers associated with microvessel architecture and gleason grades of prostate cancer.<\/strong> J. Magn. Reson. Imaging, 43: 149-158. doi: <a href=\"https:\/\/doi.org\/10.1002\/jmri.24975\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1002\/jmri.24975<\/a> <span style=\"letter-spacing: 0.0px;\">(PMID:26110513).<\/span><\/p><\/li><li>Toth, R, Feldman, M, Yu, D, Tomaszewski, J, Madabhushi, A, <strong>\u201cHistostitcher\u2122: An Informatics Software Platform for Reconstructing Whole-Mount Prostate Histology using the Extensible Imaging Platform (XIP\u2122) Framework,\u201d<\/strong> Journal of Pathology Informatics, vol. 5, pg. 8, 2014 (PMID: 24843820, PMCID: PMC4023035). <a href=\"https:\/\/doi.org\/10.4103\/2153-3539.129441\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.4103\/2153-3539.129441<\/a><\/li><li>Xiao, G, Bloch, N, Chappelow, J, Genega, E, Rofsky, N, Lenkinsky, R, Tomaszewski, J, Feldman, M, Rosen, M, Madabhushi, A, <strong>\u201cDetermining Histology-MRI Slice Correspondences for Defining MRI-based Disease Signatures of Prostate Cancer,\u201d<\/strong> Special Issue of Computerized Medical Imaging and Graphics on Whole Slide Microscopic Image Processing, vol. 35[7-8], pp. 568-78, 2011 (PMID: 21255974). <a href=\"https:\/\/doi.org\/10.1016\/j.compmedimag.2010.12.003\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1016\/j.compmedimag.2010.12.003<\/a><\/li><li>Chappelow, J, Bloch, N., Rofsky, N, Genega, E, Lenkinski, R, DeWolf, W, Madabhushi, A,\u00a0\u00a0 <strong>\u201cElastic Registration of Multimodal Prostate MRI and Histology via Multi-Attribute Combined Mutual Information,\u201d<\/strong> Medical Physics, vol. 38[4], pp. 2005-2018, 2011 (PMID: 21626933). <a href=\"https:\/\/doi.org\/10.1118\/1.3560879\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1118\/1.3560879<\/a><\/li><\/ol><p><br\/><\/p><\/div><div class=\"tabs-pane \" id=\"23691514198bdfbf81e044a68e2aa7d290b4bf95\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-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><span style=\"color: rgb(0,0,0);\">Madabhushi, A.<\/span>, &amp; <span style=\"color: rgb(0,0,0);\">Feldman, M<\/span>. (2016). <strong> <span style=\"color: rgb(0,0,0);\">Fused Radiology-Pathology Prostate Dataset (Prostate Fused-MRI-Pathology)<\/span> <\/strong>. The Cancer Imaging Archive. doi;\u00a0<a href=\"http:\/\/doi.org\/10.7937\/k9\/TCIA.2016.tlpmr1am\" class=\"external-link\" rel=\"nofollow\">10.7937\/k9\/TCIA.2016.tlpmr1am<\/a><\/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><span style=\"color: rgb(28,29,30);\">Singanamalli, A. , Rusu, M. , Sparks, R. E., Shih, N. N., Ziober, A. , Wang, L. , Tomaszewski, J. , Rosen, M. , Feldman, M. and Madabhushi, A. (2016), <strong>Identifying in vivo DCE MRI markers associated with microvessel architecture and gleason grades of prostate cancer.<\/strong> J. Magn. Reson. Imaging, 43: 149-158. doi:<\/span> <a style=\"text-decoration: none;\" href=\"https:\/\/doi.org\/10.1002\/jmri.24975\" class=\"external-link\" rel=\"nofollow\">10.1002\/jmri.24975<\/a>\u00a0(PMID:26110513).<\/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>Toth, R, Feldman, M, Yu, D, Tomaszewski, J, Madabhushi, A, \u201c<strong>Histostitcher\u2122: An Informatics Software Platform for Reconstructing Whole-Mount Prostate Histology using the Extensible Imaging Platform (XIP\u2122) Framework<\/strong>,\u201d <em>Journal of Pathology Informatics, <\/em>vol. 5, pg. 8, 2014 (PMID: 24843820, PMCID: PMC4023035). <a href=\"https:\/\/doi.org\/10.4103\/2153-3539.129441\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.4103\/2153-3539.129441<\/a><\/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>Xiao, G, Bloch, N, Chappelow, J, Genega, E, Rofsky, N, Lenkinsky, R, Tomaszewski, J, Feldman, M, Rosen, M, Madabhushi, A, \u201c<strong>Determining Histology-MRI Slice Correspondences for Defining MRI-based Disease Signatures of Prostate Cancer<\/strong>,\u201d Special Issue of Computerized Medical Imaging and Graphics on Whole Slide Microscopic Image Processing, vol. 35[7-8], pp. 568-78, 2011 (PMID: 21255974).\u00a0<a href=\"https:\/\/doi.org\/10.1016\/j.compmedimag.2010.12.003\" title=\"Persistent link using digital object identifier\" style=\"text-decoration: underline;\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1016\/j.compmedimag.2010.12.003<\/a><\/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>Chappelow, J, Bloch, N., Rofsky, N, Genega, E, Lenkinski, R, DeWolf, W, Madabhushi, A,\u00a0\u00a0 \u201c<strong>Elastic Registration of Multimodal Prostate MRI and Histology via Multi-Attribute Combined Mutual Information<\/strong>,\u201d Medical Physics, vol. 38[4], pp. 2005-2018, 2011 (PMID: 21626933). <a href=\"https:\/\/doi.org\/10.1118\/1.3560879\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1118\/1.3560879<\/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=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-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><ol><li>Brunese, L., Mercaldo, F., Reginelli, A., &amp; Santone, A. (2020). Formal methods for prostate cancer gleason score and treatment prediction using radiomic biomarkers. Magnetic resonance imaging, 66, 165-175. doi:<a href=\"https:\/\/doi.org\/10.1016\/j.mri.2019.08.030\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1016\/j.mri.2019.08.030<\/a><\/li><li>Chatzoudis, P. (2018). MRI prostate cancer radiomics: Assessment of effectiveness and perspectives. (Master of Biomedical Engineering). Delft University of Technology, Delft, Netherlands. Retrieved from <a href=\"http:\/\/resolver.tudelft.nl\/uuid:b8459bdb-1761-4f17-8807-e3b1cf7da629\" class=\"external-link\" rel=\"nofollow\">http:\/\/resolver.tudelft.nl\/uuid:b8459bdb-1761-4f17-8807-e3b1cf7da629<\/a>\u00a0<\/li><li>Duran, A., Dussert, G., Rouviere, O., Jaouen, T., Jodoin, P. M., &amp; Lartizien, C. (2022). ProstAttention-Net: A deep attention model for prostate cancer segmentation by aggressiveness in MRI scans. Medical image analysis, 77, 102347. doi:<a href=\"https:\/\/doi.org\/10.1016\/j.media.2021.102347\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1016\/j.media.2021.102347<\/a>\u00a0<\/li><\/ol><p><br\/><\/p><\/div><div class=\"tabs-pane \" id=\"23691514623e7edc4aae4e16abd21b612dff549c\" name=\"Versions\" ><h3 id=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-Version2(Current)2023-04-10:\">Version 2 (Current) 2023-04-10:<\/h3><div class=\"table-wrap\"><table class=\"relative-table wrapped confluenceTable\" style=\"width: 58.0963%;\"><colgroup><col style=\"width: 43.229%;\"\/><col style=\"width: 36.6487%;\"\/><col style=\"width: 20.0934%;\"\/><\/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, 4.4 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\/23691514\/doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia?version=1&amp;modificationDate=1534787026838&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:\/\/nbia.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Prostate%20Fused-MRI-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=Prostate Fused-MRI-Pathology\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><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><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Annotated Whole Slide Pathology Images &amp; Annotations (Tiff, XML 76.8 GB)<\/p><\/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\/72?passcode=3da9391db835cc0937cd309ea568755c2153b056\" 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:prostate_fused_mri_pathology\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/72?passcode=3da9391db835cc0937cd309ea568755c2153b056\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a>\u00a0<a href=\"https:\/\/pathology.cancerimagingarchive.net\/pathdata\/cw_flex2\/index.php\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><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><\/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><tr><td class=\"confluenceTd\">Fused Rad-Path Matlab Files<\/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\/23691514\/fused_prostate_matlab.zip?version=1&amp;modificationDate=1476802701461&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><tr><td class=\"confluenceTd\">Correspondence tables (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\/23691514\/histo_MR_Correspondence.xlsx?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>Added a correspondence xlsx between MR and Pathology slides, imaging data are unchanged.\u00a0<\/p><h3 id=\"FusedRadiologyPathologyProstateDataset(ProstateFusedMRIPathology)-Version1(Current):Updated2016-11-30\">Version 1 (Current): Updated 2016-11-30<\/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, 4.4 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:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/23691514\/doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia?version=1&amp;modificationDate=1534787026838&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:\/\/nbia.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Prostate%20Fused-MRI-Pathology\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span>\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Prostate Fused-MRI-Pathology\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Annotated Whole Slide Pathology Images &amp; Annotations (Tiff, XML 76.8 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\/72?passcode=3da9391db835cc0937cd309ea568755c2153b056\" 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:prostate_fused_mri_pathology\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/72?passcode=3da9391db835cc0937cd309ea568755c2153b056\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a>\u00a0\u00a0\u00a0 \u00a0\u00a0<\/p><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\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Fused Rad-Path MATLAB Files<\/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\/23691514\/fused_prostate_matlab.zip?version=1&amp;modificationDate=1476802701461&amp;api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\u00a0<a href=\"https:\/\/pathology.cancerimagingarchive.net\/pathdata\/\" class=\"external-link\" rel=\"nofollow\">\u00a0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><\/div><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=prostate_fused_mri_pathology\">Imaging Data Commons (IDC)<\/a> (Imaging Data)<\/li><\/ul>","cancer_locations":["Prostate"],"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>.\n<ol><li>Brunese, L., Mercaldo, F., Reginelli, A., &amp; Santone, A. (2020). Formal methods for prostate cancer gleason score and treatment prediction using radiomic biomarkers. Magnetic resonance imaging, 66, 165-175. doi:<a href=\"https:\/\/doi.org\/10.1016\/j.mri.2019.08.030\">https:\/\/doi.org\/10.1016\/j.mri.2019.08.030<\/a><\/li><li>Chatzoudis, P. (2018). MRI prostate cancer radiomics: Assessment of effectiveness and perspectives. (Master of Biomedical Engineering). Delft University of Technology, Delft, Netherlands. Retrieved from <a href=\"http:\/\/resolver.tudelft.nl\/uuid:b8459bdb-1761-4f17-8807-e3b1cf7da629\">http:\/\/resolver.tudelft.nl\/uuid:b8459bdb-1761-4f17-8807-e3b1cf7da629<\/a>\u00a0<\/li><li>Duran, A., Dussert, G., Rouviere, O., Jaouen, T., Jodoin, P. M., &amp; Lartizien, C. (2022). ProstAttention-Net: A deep attention model for prostate cancer segmentation by aggressiveness in MRI scans. Medical image analysis, 77, 102347. doi:<a href=\"https:\/\/doi.org\/10.1016\/j.media.2021.102347\">https:\/\/doi.org\/10.1016\/j.media.2021.102347<\/a>\u00a0<\/li><\/ol>\n<br\/>","species":["Human"],"collection_title":"Fused Radiology-Pathology Prostate Dataset","detailed_description":"<h4>Supporting Documentation<\/h4>\nThe data set is fully described in the following publications:\n<ol><li><p>Singanamalli, A. , Rusu, M. , Sparks, R. E., Shih, N. N., Ziober, A. , Wang, L. , Tomaszewski, J. , Rosen, M. , Feldman, M. and Madabhushi, A. (2016), <strong>Identifying in vivo DCE MRI markers associated with microvessel architecture and gleason grades of prostate cancer.<\/strong> J. Magn. Reson. Imaging, 43: 149-158. doi: <a href=\"https:\/\/doi.org\/10.1002\/jmri.24975\">https:\/\/doi.org\/10.1002\/jmri.24975<\/a> (PMID:26110513).<\/p><\/li><li>Toth, R, Feldman, M, Yu, D, Tomaszewski, J, Madabhushi, A, <strong>\u201cHistostitcher\u2122: An Informatics Software Platform for Reconstructing Whole-Mount Prostate Histology using the Extensible Imaging Platform (XIP\u2122) Framework,\u201d<\/strong> Journal of Pathology Informatics, vol. 5, pg. 8, 2014 (PMID: 24843820, PMCID: PMC4023035). <a href=\"https:\/\/doi.org\/10.4103\/2153-3539.129441\">https:\/\/doi.org\/10.4103\/2153-3539.129441<\/a><\/li><li>Xiao, G, Bloch, N, Chappelow, J, Genega, E, Rofsky, N, Lenkinsky, R, Tomaszewski, J, Feldman, M, Rosen, M, Madabhushi, A, <strong>\u201cDetermining Histology-MRI Slice Correspondences for Defining MRI-based Disease Signatures of Prostate Cancer,\u201d<\/strong> Special Issue of Computerized Medical Imaging and Graphics on Whole Slide Microscopic Image Processing, vol. 35[7-8], pp. 568-78, 2011 (PMID: 21255974). <a href=\"https:\/\/doi.org\/10.1016\/j.compmedimag.2010.12.003\">https:\/\/doi.org\/10.1016\/j.compmedimag.2010.12.003<\/a><\/li><li>Chappelow, J, Bloch, N., Rofsky, N, Genega, E, Lenkinski, R, DeWolf, W, Madabhushi, A,\u00a0\u00a0 <strong>\u201cElastic Registration of Multimodal Prostate MRI and Histology via Multi-Attribute Combined Mutual Information,\u201d<\/strong> Medical Physics, vol. 38[4], pp. 2005-2018, 2011 (PMID: 21626933). <a href=\"https:\/\/doi.org\/10.1118\/1.3560879\">https:\/\/doi.org\/10.1118\/1.3560879<\/a><\/li><\/ol>\n<br\/>","related_analysis_results":false,"subjects":"28","collection_short_title":"Prostate Fused-MRI-Pathology","data_types":["MR","Pathology"],"date_updated":"2023-09-13","collection_browse_title":"","supporting_data":["Image Analyses"],"collection_featured_image":false,"collection_summary":"This collection comprises a total of 28 3 Tesla T1-weighted, T2-weighted, Diffusion weighted and Dynamic Contrast Enhanced prostate MRI along with accompanying digitized histopathology (H&amp;E stained) images of corresponding radical prostatectomy specimens. The MRI scans also have a mapping of extent of prostate cancer on them [<a href=\"https:\/\/doi.org\/10.1002\/jmri.24975\">10.1002\/jmri.24975<\/a>]. Each surgically excised prostate specimen was originally sectioned and quartered resulting in 4 slides for each section. Each of these individual slides was digitized at 20x magnification using an Aperio slide scanner resulting in a set of 4 .svs images. Each of the 4 .svs images were then digitally stitched together to constitute a pseudo-whole mount section (.tiff) using the program in [PMCID: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4023035\/\">PMC4023035<\/a>]. Annotations of cancer presence on the pseudo-whole mount sections were made by an expert pathologist. Slice correspondences were established between the individual T2w MRI and stitched pseudo-whole mount sections by the program in [<a href=\"https:\/\/doi.org\/10.1016\/j.compmedimag.2010.12.003\">10.1016\/j.compmedimag.2010.12.003<\/a>] and checked for accuracy by an expert pathologist and radiologist. Deformable co-registration [<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/pmc3078156\/\">PMC3078156<\/a>] was employed to spatially co-registered the corresponding radiologic and histopathologic tissue sections to map disease extent onto the corresponding MRI scans.","collection_acknowledgements":"<ul><li>Data collection and analysis was provided by Anant Madabhushi, PhD, Case Western Reserve University and Michael D. Feldman, MD, PhD, Hospital at the University of Pennsylvania.\u00a0<\/li><li>This work was supported by NIH R01CA136535.<\/li><\/ul>\n<br\/>","collection_funding":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections\/5595"}],"collection":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections"}],"about":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/types\/tcia_collection"}],"wp:attachment":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media?parent=5595"}],"wp:term":[{"taxonomy":"tcia_citation_tax","embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/v1\/citation-tax?post=5595"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}