{"id":161,"date":"2020-06-25T09:44:38","date_gmt":"2020-06-25T09:44:38","guid":{"rendered":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-service\/?page_id=161"},"modified":"2022-12-04T15:14:59","modified_gmt":"2022-12-04T15:14:59","slug":"image-and-data-analysis","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/services\/image-and-data-analysis\/","title":{"rendered":"Image and Data Analysis"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p>If you have questions, problems or projects in image analysis,<strong> please contact <a href=\"mailto:image-analysis-support@embl.de\">Image Analysis Support<\/a><\/strong>.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Analysis workstations<\/h3>\n\n\n\n<p>We offer several <a href=\"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/services\/image-and-data-analysis\/almf-embl-3dcloud-vms\/\">virtual workstations<\/a> in the <a href=\"https:\/\/www.embl.org\/about\/info\/it-services\/3d-cloud\/\">EMBL 3D cloud<\/a> (&#8216;gold&#8217; and &#8216;silver&#8217; versions ) and dedicated image analysis workstations<\/p>\n\n\n\n<p>Software packages available on our workstations include:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a rel=\"noreferrer noopener\" href=\"http:\/\/www.cellprofiler.org\/\" target=\"_blank\">CellProfiler<\/a>: Open source software for batch analysis of large microscopy data sets.<\/li><li><a rel=\"noreferrer noopener\" href=\"http:\/\/fiji.sc\/\" target=\"_blank\">Fiji<\/a> (ImageJ): Open source image analysis software with large user and developer community. Available on all workstations.<\/li><li>SVI Huygens Professional: Workstation \/ VM based deconvolution for 2D and 3D datasets, tile stitching and light sheet image fusion. For more information and access, please contact ALMF.<\/li><li><a href=\"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/services\/image-and-data-analysis\/imaris\/\" data-type=\"page\" data-id=\"184\">Imaris<\/a> (<a rel=\"noreferrer noopener\" href=\"http:\/\/www.bitplane.com\/\" target=\"_blank\">Bitplane<\/a> \/ Andor): Commercial 4D analysis and visualization tool. We offer several floating licenses.<\/li><\/ul>\n\n\n\n <a href=\"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/services\/downloads\/\" class=\"vf-button vf-button--tertiary vf-button--sm \">Downloads<\/a> \n\n\n<h2 class=\"wp-block-heading\">Training<\/h2>\n\n\n\n<p>The ALMF and <a href=\"https:\/\/www.embl.org\/topics\/bio-it-embl-centres\/#cba\">Center for Bioimage Analysis<\/a> (CBA) team up to run a number of image analysis training courses (ALMF courses, <a href=\"https:\/\/bio-it.embl.de\/centres\/cba\/cba-upcoming-events\/\">CBA upcoming events<\/a>), both regular and on demand. These include:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Basic FIJI\/Image J training, offered as part of our Basics in Microscopy courses. Additional FIJI training is provided by the <a href=\"https:\/\/www.embl.org\/topics\/bio-it-embl-centres\/#cba\">CBA<\/a>.<\/li><li>Introduction to Cellprofiler.<\/li><\/ul>\n\n\n\n<p>Training for other topics in image analysis and microscope automation can be arranged on demand, please contact <a href=\"mailto:image-analysis-support@embl.de\">image-analysis-support<\/a>.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Data and Image Analysis Support<\/h2>\n\n\n\n<p>We offer basic support in image analysis and statistical data analysis to&nbsp;our external visitors for the screens that they carry out during their visit.<\/p>\n\n\n\n<p>More general and advanced image analysis and statistical data analysis support are provided by the EMBL <a href=\"https:\/\/www.embl.de\/research\/interdisciplinary_research\/centres\/bioimage-analysis\/index.html\"><\/a><a href=\"https:\/\/www.embl.de\/research\/interdisciplinary_research\/centres\/bioimage-analysis\/index.html\">Center for Bioimage Analysis<\/a> (CBA) and the EMBL <a href=\"https:\/\/www.embl.de\/research\/interdisciplinary_research\/centres\/statistical-data-analysis\/index.html\">Centre for Statistical Data Analysis<\/a>, respectively.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">High-throughput analysis on EMBL computing cluster<\/h2>\n\n\n\n<p>For batch-analysis of large amounts of data we support distributed computing on the EMBL <a href=\"https:\/\/intranet.embl.de\/it_services\/services\/computing\/hpc_cluster\/index.html\">computing cluster<\/a>.<\/p>\n\n\n\n<p>For <strong>batch image analysis<\/strong> we currently provide a cluster workflow for <a href=\"http:\/\/www.cellprofiler.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">CellProfiler<\/a> for analysing high-throughput microscopy data generated at ALMF.<\/p>\n\n\n\n<p>For <strong>statistical analysis and visual browsing<\/strong> of the output generated by high-throughput image analysis results we provide the open source <a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/embl-cba\/shinyHTM\/blob\/master\/README.md#shinyhtm\" target=\"_blank\">shinyHTM<\/a> R-package developed by Christian Tischer, Hugo Botelho (University of Lisbon, Portugal) et al.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n<div class=\"vf-links\">\n      <h3 class=\"vf-links__heading\">Image and data analysis services<\/h3>\n    <ul class=\"vf-links__list vf-list\">\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/services\/image-and-data-analysis\/almf-embl-3dcloud-vms\/\">\n        ALMF 3Dcloud VMs      <\/a>\n      <\/li>\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.embl.org\/topics\/bio-it-embl-centres\/#cba\">\n        Center for Bioimage Analysis      <\/a>\n      <\/li>\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/services\/downloads\/\">\n        downloads      <\/a>\n      <\/li>\n    <li class=\"vf-list__item\">\n          <a class=\"vf-list__link\" href=\"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/services\/image-and-data-analysis\/imaris\/\">\n        Imaris      <\/a>\n      <\/li>\n  <\/ul>\n\n<\/div>\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"parent":114,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-161","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/pages\/161","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/comments?post=161"}],"version-history":[{"count":31,"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/pages\/161\/revisions"}],"predecessor-version":[{"id":9836,"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/pages\/161\/revisions\/9836"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/pages\/114"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/media?parent=161"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/advanced-light-microscopy-core-facility\/wp-json\/wp\/v2\/embl_taxonomy?post=161"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}