{"id":42305,"date":"2023-11-20T02:21:26","date_gmt":"2023-11-20T08:21:26","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/collection\/prostate-fused-mri-pathology\/"},"modified":"2024-09-26T16:14:36","modified_gmt":"2024-09-26T21:14:36","slug":"prostate-fused-mri-pathology","status":"publish","type":"tcia_collection","link":"https:\/\/stage.cancerimagingarchive.net\/collection\/prostate-fused-mri-pathology\/","title":{"rendered":"PROSTATE-FUSED-MRI-PATHOLOGY"},"featured_media":0,"template":"","class_list":["post-42305","tcia_collection","type-tcia_collection","status-publish"],"cancer_types":["Prostate Cancer"],"citations":[42279,42281,42283,42285,42287,9225],"collection_doi":"10.7937\/k9\/TCIA.2016.tlpmr1am","collection_download_info":"","collection_downloads":[42289,42291,42293,42295],"versions":[42303],"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=prostate_fused_mri_pathology\">Imaging Data Commons (IDC)<\/a> (Imaging Data)<\/li>\r\n<\/ul>","cancer_locations":["Prostate"],"collection_page_accessibility":"Public","publications_related":"","version_change_log_archived":"<h3>Version 2 (Current): Updated 2023\/04\/10<\/h3><table><colgroup><col \/><col \/><col \/><\/colgroup><tbody><tr><th>Data Type<\/th><th>Download all or Query\/Filter<\/th><th>License<\/th><\/tr><tr><td>Images (DICOM, 4.4 GB)<\/td><td><div><p><a href=\"\/wp-content\/uploads\/doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia\" download=\"doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/nbia.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Prostate%20Fused-MRI-Pathology\"><button><i><\/i> Search<\/button><\/a>\u00a0 \u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Prostate Fused-MRI-Pathology\">\u00a0<\/a><\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><td><div><p><a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td><p>Annotated Whole Slide Pathology Images &amp; Annotations (Tiff, XML 76.8 GB)<\/p><\/td><td><div><p><a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjUzNSIsInBhc3Njb2RlIjoiMGUwNWFjMmU0MWNkYWRmZTA1ZGYxNzZjNjRiMzM5MDc3OGNjMTI5MyIsInBhY2thZ2VfaWQiOiI1MzUiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/pathdb.cancerimagingarchive.net\/imagesearch?f[0]=collection:prostate_fused_mri_pathology\"><button><i><\/i> Search<\/button><\/a>\u00a0 <a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/72?passcode=3da9391db835cc0937cd309ea568755c2153b056\">\u00a0<\/a>\u00a0<a href=\"https:\/\/pathology.cancerimagingarchive.net\/pathdata\/cw_flex2\/index.php\">\u00a0<\/a><\/p><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><\/div><\/td><td><div><p><a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td>Fused Rad-Path Matlab Files<\/td><td><div><p><a href=\"\/wp-content\/uploads\/fused_prostate_matlab.zip\" download=\"fused_prostate_matlab.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><td><div><p><a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td>Correspondence tables (XLSX)<\/td><td><div><p><a href=\"\/wp-content\/uploads\/histo_MR_Correspondence.xlsx\" download=\"histo_MR_Correspondence.xlsx\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><td><div><p><a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><p>Added a correspondence xlsx between MR and Pathology slides, imaging data are unchanged.\u00a0<\/p><h3>Version 1: Updated 2016\/11\/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, 4.4 GB)<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia\" download=\"doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/nbia.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Prostate%20Fused-MRI-Pathology\"><button><i><\/i> Search<\/button><\/a>\u00a0 \u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/nbia-search\/?CollectionCriteria=Prostate Fused-MRI-Pathology\">\u00a0<\/a><\/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\">Annotated Whole Slide Pathology Images &amp; Annotations (Tiff, XML 76.8 GB)<\/td><td colspan=\"1\"><div><p><a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjUzNSIsInBhc3Njb2RlIjoiMGUwNWFjMmU0MWNkYWRmZTA1ZGYxNzZjNjRiMzM5MDc3OGNjMTI5MyIsInBhY2thZ2VfaWQiOiI1MzUiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/pathdb.cancerimagingarchive.net\/imagesearch?f[0]=collection:prostate_fused_mri_pathology\"><button><i><\/i> Search<\/button><\/a>\u00a0 <a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/72?passcode=3da9391db835cc0937cd309ea568755c2153b056\">\u00a0<\/a>\u00a0\u00a0\u00a0 \u00a0\u00a0<\/p><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\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/p><\/div><\/td><\/tr><tr><td colspan=\"1\">Fused Rad-Path MATLAB Files<\/td><td colspan=\"1\"><div><p><a href=\"\/wp-content\/uploads\/fused_prostate_matlab.zip\" download=\"fused_prostate_matlab.zip\"><button><i><\/i> Download<\/button><\/a>\u00a0 \u00a0<a href=\"https:\/\/pathology.cancerimagingarchive.net\/pathdata\/\">\u00a0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table>","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>.\r\n<h4>The below were found to have cited this dataset:<\/h4>\r\n<ol>\r\n \t<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>\r\n \t<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><\/li>\r\n \t<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><\/li>\r\n<\/ol>\r\n<h4><strong>The authors recommend<\/strong> that the below publications fully describe the data:<\/h4>","related_analysis_results":false,"species":["Human"],"version_number":"2","collection_title":"Fused Radiology-Pathology Prostate Dataset","date_updated":"2023-04-10","related_collection":false,"subjects":"28","analysis_results":"","collection_short_title":"Prostate Fused-MRI-Pathology","data_types":["MR","Histopathology"],"version_change_log":"Added a correspondence xlsx between MR and Pathology slides, imaging data are unchanged.","collection_browse_title":"Prostate Fused-MRI-Pathology","detailed_description":"","supporting_data":["Image Analyses"],"collection_featured_image":false,"collection_summary":"<p>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.<\/p>","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>","collection_funding":"","hide_from_browse_table":"0","program":["Community"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/42305","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\/42305\/revisions"}],"predecessor-version":[{"id":47351,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/42305\/revisions\/47351"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=42305"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}