{"id":5528,"date":"2023-09-04T03:01:35","date_gmt":"2023-09-04T03:01:35","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-collection\/aml-cytomorphology_mll_helmholtz\/"},"modified":"2023-09-13T11:56:00","modified_gmt":"2023-09-13T11:56:00","slug":"aml-cytomorphology_mll_helmholtz","status":"publish","type":"tcia_collection","link":"https:\/\/cm.vastapps.dev\/tcia-collection\/aml-cytomorphology_mll_helmholtz\/","title":{"rendered":"AML-CYTOMORPHOLOGY_MLL_HELMHOLTZ"},"featured_media":0,"template":"","citation-tax":[],"cancer_types":false,"citations":[4332,4333,2925],"collection_doi":"10.7937\/6PPE-4020","collection_download_info":"Click the Versions tab for more info about data releases.","collection_downloads":[4887],"full_export":"<h1 id=\"AmorphologicaldatasetofwhitebloodcellsfrompatientswithfourdifferentgeneticAMLentitiesandnonmalignantcontrols(AMLCytomorphology_MLL_Helmholtz)-Summary\">Summary<\/h1>This dataset comprises four prevalent AML subtypes with defining genetic abnormalities and typical morphological features according to the WHO 2022 classification: (i) APL with PML::RARA fusion, (ii) AML with NPM1 mutation, (iii) AML with CBFB::MYH11 fusion (without NPM1 mutation), and (iv) AML with RUNX1::RUNX1T1 fusion, as well as a control group of healthy stem cell donors.\u00a0<\/p><p>A total of 189 peripheral blood smears from the Munich Leukemia Laboratory (MLL) database from the years 2009 to 2020 were digitized.\u00a0First, all blood smears were scanned with 10x magnification and an overview image was created. Using the Metasystems Metafer platform, cell detection was performed automatically using a segmentation threshold and logarithmic color transformation. Further analysis regarding the quality of the region within the blood smear was performed automatically. Per patient, 99-500 white blood cells were then scanned in 40x magnification via oil immersion microscopy in .TIF format, corresponding to 24,9\u03bcm x 24,9\u03bcm (144x144 pixels). For this, a CMOS Color Camera from MetaSystems with a resolution of 4096x3000px and a pixel size of 3,45\u03bcm x 3,45\u03bcm was used. Four pixels were binned into one, leading to a size of 6.9\u03bcm x 6.9\u03bcm, and a resolution of 6.9\u03bcm \/ 40 (1px = 0,1725\u03bcm).\u00a0Additional information about patient age, sex and blood counts are provided in a separate .csv file.<\/p><p>To our knowledge, this dataset covers the morphological complexity of acute myeloid leukemia in peripheral blood smears in unseen quality and quantity.\u00a0<h3 id=\"AmorphologicaldatasetofwhitebloodcellsfrompatientswithfourdifferentgeneticAMLentitiesandnonmalignantcontrols(AMLCytomorphology_MLL_Helmholtz)-Acknowledgements\"><span>Acknowledgements<\/span><\/h3><ul><li><span style=\"color: rgb(32,33,36);\">All samples were collected, diagnosed and scanned at the Munich Leukemia Laboratory (MLL). Carsten Marr has received funding from the European Research Council (ERC) under the European Union\u2019s Horizon 2020 research and innovation programme (Grant agreement No. 866411). Matthias Hehr acknowledges support from Deutsche Jos\u00e9 Carreras-Leuk\u00e4mie Stiftung.<\/span><br\/><br\/><\/li><\/ul><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=\"#1457538159ba0f6d7166845d88ea4d96f32f0c097\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#14575381598a69c5e18ad4bc6830e870bde7ad1e6\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#145753815fe28d6f997f64317a780ac52342f7cd0\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#14575381574ca2fa474884476a4946bc25b29b0ed\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"1457538159ba0f6d7166845d88ea4d96f32f0c097\" active=\"true\" name=\"Data Access\" ><h3 id=\"AmorphologicaldatasetofwhitebloodcellsfrompatientswithfourdifferentgeneticAMLentitiesandnonmalignantcontrols(AMLCytomorphology_MLL_Helmholtz)-DataAccess\">Data Access<\/h3><div class=\"table-wrap\"><table class=\"wrapped relative-table confluenceTable\" style=\"width: 84.0354%;\"><colgroup><col style=\"width: 47.9418%;\"\/><col style=\"width: 30.2821%;\"\/><col style=\"width: 21.7209%;\"\/><\/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\"><strong>Data Coming Soon<\/strong><\/td><td class=\"confluenceTd\"><br\/><\/td><td class=\"confluenceTd\"><br\/><\/td><\/tr><\/tbody><\/table><\/div><p>Click the Versions tab for more info about data releases.<\/p><\/div><div class=\"tabs-pane \" id=\"14575381598a69c5e18ad4bc6830e870bde7ad1e6\" name=\"Detailed Description\" ><h3 id=\"AmorphologicaldatasetofwhitebloodcellsfrompatientswithfourdifferentgeneticAMLentitiesandnonmalignantcontrols(AMLCytomorphology_MLL_Helmholtz)-DetailedDescription\">Detailed Description<\/h3><div class=\"table-wrap\"><table class=\"wrapped confluenceTable\"><colgroup><col\/><col\/><\/colgroup><tbody><tr><th class=\"confluenceTh\"><p>Image Statistics<\/p><\/th><th class=\"confluenceTh\">Pathology Image Statistics<\/th><\/tr><tr><td class=\"confluenceTd\"><p>Modalities<\/p><\/td><td class=\"confluenceTd\"><p><br\/><\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Patients<\/p><\/td><td class=\"confluenceTd\"><p><br\/><\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Images<\/p><\/td><td class=\"confluenceTd\"><p><br\/><\/p><\/td><\/tr><tr><td class=\"confluenceTd\">Images Size (GB)<\/td><td class=\"confluenceTd\"><br\/><\/td><\/tr><\/tbody><\/table><\/div><p><strong>Data Coming Soon<\/strong><\/p><p><br\/><\/p><\/div><div class=\"tabs-pane \" id=\"145753815fe28d6f997f64317a780ac52342f7cd0\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"AmorphologicaldatasetofwhitebloodcellsfrompatientswithfourdifferentgeneticAMLentitiesandnonmalignantcontrols(AMLCytomorphology_MLL_Helmholtz)-Citations&amp;DataUsagePolicy\">Citations &amp; Data Usage Policy<\/h3><p>\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>Hehr, M., Sadafi, A., Matek, C., Lienemann, P., Pohlkamp, C., Haferlach, T., Spiekermann, K., &amp; Marr, C. (2023). A morphological dataset of white blood cells from patients with four different genetic AML entities and non-malignant controls (AML-Cytomorphology_MLL_Helmholtz) (Version 1) [Data set]. The Cancer Imaging Archive. <a href=\"https:\/\/doi.org\/10.7937\/6PPE-4020\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.7937\/6PPE-4020<\/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>Hehr, M., Sadafi, A., Matek, C., Lienemann, P., Pohlkamp, C., Haferlach, T., Spiekermann, K., &amp; Marr, C. (2023). Explainable AI identifies diagnostic cells of genetic AML subtypes. In H. Mattie (Ed.), PLOS Digital Health (Vol. 2, Issue 3, p. e0000187). Public Library of Science (PLoS). <a href=\"https:\/\/doi.org\/10.1371\/journal.pdig.0000187\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1371\/journal.pdig.0000187<\/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><span style=\"color: rgb(0,0,0);text-decoration: none;\">Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., &amp; Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045\u20131057). Springer Science and Business Media LLC.<\/span><span style=\"color: rgb(102,102,102);text-decoration: none;\"> <\/span><span style=\"color: rgb(102,102,102);text-decoration: none;\"><a href=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" title=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" class=\"external-link\" rel=\"nofollow\"><span>https:\/\/doi.org\/10.1007\/s10278-013-9622-7<\/span><\/a><\/span><\/p><\/div><\/div><h3 id=\"AmorphologicaldatasetofwhitebloodcellsfrompatientswithfourdifferentgeneticAMLentitiesandnonmalignantcontrols(AMLCytomorphology_MLL_Helmholtz)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains\u00a0<\/span><a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\" class=\"external-link\" rel=\"nofollow\">a list of publications<\/a><span> which leverage TCIA data. <\/span> If you have a manuscript you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" class=\"external-link\" rel=\"nofollow\"> contact the TCIA Helpdesk<\/a>.<\/p><\/div><div class=\"tabs-pane \" id=\"14575381574ca2fa474884476a4946bc25b29b0ed\" name=\"Versions\" ><h3 id=\"AmorphologicaldatasetofwhitebloodcellsfrompatientswithfourdifferentgeneticAMLentitiesandnonmalignantcontrols(AMLCytomorphology_MLL_Helmholtz)-Version1(Current):Updated2023\/03\/22\">Version 1 (Current): Updated 2023\/03\/22<\/h3><div class=\"table-wrap\"><table class=\"wrapped relative-table confluenceTable\" style=\"width: 40.4344%;\"><colgroup><col style=\"width: 41.8748%;\"\/><col style=\"width: 45.3423%;\"\/><col style=\"width: 12.8578%;\"\/><\/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\"><strong>Data Coming Soon<\/strong><\/td><td class=\"confluenceTd\"><br\/><\/td><td class=\"confluenceTd\"><br\/><\/td><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><\/div><p><br\/><\/p><p><br\/><\/p>","versions":false,"additional_resources":"","cancer_locations":false,"collection_page_accessibility":"Public","publications_related":"","version_change_log":"","version_change_log_archived":"","analysis_results":"","collection_status":"","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\">a list of publications<\/a> which leverage TCIA data.  If you have a manuscript you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\"> contact the TCIA Helpdesk<\/a>.","species":false,"collection_title":"A morphological dataset of white blood cells from patients with four different genetic AML entities and non-malignant controls","detailed_description":"<strong>Data Coming Soon<\/strong>\n<br\/>","related_analysis_results":false,"subjects":[],"collection_short_title":"AML-Cytomorphology_MLL_Helmholtz","data_types":false,"date_updated":"2023-09-13","collection_browse_title":"","supporting_data":false,"collection_featured_image":false,"collection_summary":"This dataset comprises four prevalent AML subtypes with defining genetic abnormalities and typical morphological features according to the WHO 2022 classification: (i) APL with PML::RARA fusion, (ii) AML with NPM1 mutation, (iii) AML with CBFB::MYH11 fusion (without NPM1 mutation), and (iv) AML with RUNX1::RUNX1T1 fusion, as well as a control group of healthy stem cell donors.\u00a0<p>A total of 189 peripheral blood smears from the Munich Leukemia Laboratory (MLL) database from the years 2009 to 2020 were digitized.\u00a0First, all blood smears were scanned with 10x magnification and an overview image was created. Using the Metasystems Metafer platform, cell detection was performed automatically using a segmentation threshold and logarithmic color transformation. Further analysis regarding the quality of the region within the blood smear was performed automatically. Per patient, 99-500 white blood cells were then scanned in 40x magnification via oil immersion microscopy in .TIF format, corresponding to 24,9\u03bcm x 24,9\u03bcm (144x144 pixels). For this, a CMOS Color Camera from MetaSystems with a resolution of 4096x3000px and a pixel size of 3,45\u03bcm x 3,45\u03bcm was used. Four pixels were binned into one, leading to a size of 6.9\u03bcm x 6.9\u03bcm, and a resolution of 6.9\u03bcm \/ 40 (1px = 0,1725\u03bcm).\u00a0Additional information about patient age, sex and blood counts are provided in a separate .csv file.<\/p><p>To our knowledge, this dataset covers the morphological complexity of acute myeloid leukemia in peripheral blood smears in unseen quality and quantity.\u00a0<\/p>","collection_acknowledgements":"<ul><li>All samples were collected, diagnosed and scanned at the Munich Leukemia Laboratory (MLL). Carsten Marr has received funding from the European Research Council (ERC) under the European Union\u2019s Horizon 2020 research and innovation programme (Grant agreement No. 866411). Matthias Hehr acknowledges support from Deutsche Jos\u00e9 Carreras-Leuk\u00e4mie Stiftung.<br\/><br\/><\/li><\/ul>","collection_funding":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections\/5528"}],"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=5528"}],"wp:term":[{"taxonomy":"tcia_citation_tax","embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/v1\/citation-tax?post=5528"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}