{"id":4742,"date":"2022-12-27T10:11:20","date_gmt":"2022-12-27T10:11:20","guid":{"rendered":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/?page_id=4742"},"modified":"2025-10-01T09:47:34","modified_gmt":"2025-10-01T09:47:34","slug":"image-analysis-software","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/image-analysis-software\/","title":{"rendered":"Image Analysis Software"},"content":{"rendered":"\n<p>For analysing the data generated using our electron microscopes, the EMCF makes use of EMBL&#8217;s compute resources located at the IT datacenter. Image data is stored and backed-up centrally. Dedicated virtual workstations in the <a href=\"https:\/\/www.embl.org\/about\/info\/it-services\/3d-cloud\/\">3DCloud<\/a> offer a broad collection of software used for reconstruction or segmentation of EM data. These include <a href=\"https:\/\/www.thermofisher.com\/de\/de\/home\/electron-microscopy\/products\/software-em-3d-vis\/amira-software.html\">Amira<\/a>, <a href=\"https:\/\/bio3d.colorado.edu\/imod\/\">IMOD<\/a>, <a href=\"https:\/\/www.ilastik.org\/\">Ilastik<\/a>, <a href=\"https:\/\/www.blender.org\/\" data-type=\"link\" data-id=\"https:\/\/www.blender.org\/\">Blender<\/a> and <a href=\"http:\/\/mib.helsinki.fi\/\">MIB<\/a>. Certain analysis pipelines are also implemented using the <a href=\"https:\/\/www.embl.org\/about\/info\/it-services\/what-people-need\/\">compute cluster<\/a> infrastructure speeding up the processing tremendously. In addition, we work closely with EMBL&#8217;s <a href=\"https:\/\/bio-it.embl.de\/centres\/cba\/\">Centre for Bioimage Analysis<\/a> for tailor-made image processing workflows.We make our data publicly available on public archives such as <a href=\"https:\/\/www.ebi.ac.uk\/empiar\/\">EMPIAR<\/a> and share it using <a href=\"https:\/\/mobie.github.io\/\">MoBIE<\/a>, an interactive viewer <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.05.27.493763v1\">developed at EMBL<\/a> for exactly these purposes. You can find a collection of published projects within MoBIE.<\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>For analysing the data generated using our electron microscopes, the EMCF makes use of EMBL&#8217;s compute resources located at the IT datacenter. Image data is stored and backed-up centrally. Dedicated virtual workstations in the 3DCloud offer a broad collection of software used for&hellip;<\/p>\n","protected":false},"author":8,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-4742","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/wp-json\/wp\/v2\/pages\/4742","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/wp-json\/wp\/v2\/users\/8"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/wp-json\/wp\/v2\/comments?post=4742"}],"version-history":[{"count":2,"href":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/wp-json\/wp\/v2\/pages\/4742\/revisions"}],"predecessor-version":[{"id":21775,"href":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/wp-json\/wp\/v2\/pages\/4742\/revisions\/21775"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/wp-json\/wp\/v2\/media?parent=4742"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/electron-microscopy-core-facility\/wp-json\/wp\/v2\/embl_taxonomy?post=4742"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}