{"id":14,"date":"2021-04-14T14:01:45","date_gmt":"2021-04-14T14:01:45","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/template\/day-3\/"},"modified":"2022-01-26T11:04:53","modified_gmt":"2022-01-26T11:04:53","slug":"empiar","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/bioimage-databases-resources\/empiar\/","title":{"rendered":"EMPIAR"},"content":{"rendered":"\n<h3 class=\"wp-block-heading\">EMPIAR: Past, present and future &#8211; Lecture&nbsp;<\/h3>\n\n\n\n<p><strong>Trainer:<\/strong>&nbsp;<a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/trainer-biographies\/\">Gerard Kleywegt<\/a><\/p>\n\n\n\n<p><strong>Overview:<\/strong>&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/www.ebi.ac.uk\/pdbe\/emdb\/empiar\/about\" target=\"_blank\">EMPIAR<\/a>, the Electron Microscopy Public Image Archive, is a public resource for raw electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure.<\/p>\n\n\n\n<p><strong>Learning outcomes<\/strong><\/p>\n\n\n\n<p>By the end of this session you will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>List the resources and services available at EMPIAR and locate its place within the bioimage data ecosystem<\/li><li>Identify different releases of the EMPIAR archive<\/li><li>Access and visualize data in the archive<\/li><\/ul>\n\n\n\n<p><strong>Materials:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\" id=\"block-3059eaf3-d0b8-4fa5-9bf6-729e614bc3ec\"><li><a href=\"http:\/\/ftp.ebi.ac.uk\/pub\/training\/2021\/Microscopy_image_analysis_July2021\/EMPIAR\/EMPIAR_Past_Present_and_Future-Kleywegt.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">Presentation slides<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1038\/nmeth.3806\" target=\"_blank\">EMPIAR: a public archive for raw electron microscopy image data<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1038\/s41592-021-01166-8\" target=\"_blank\">REMBI: Recommended Metadata for Biological Images\u2014enabling reuse of microscopy data in biology<\/a><\/li><li><a href=\"http:\/\/ftp.ebi.ac.uk\/pub\/training\/2021\/Microscopy_image_analysis_July2021\/EMPIAR\/Data_deposition_protocols.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/www.ebi.ac.uk\/pdbe\/emdb\/empiar\/\" target=\"_blank\">Web page<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Depositing and accessing data at EMPIAR &#8211; Lecture<\/h3>\n\n\n\n<p><strong>Trainer:<\/strong>&nbsp;<a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/trainer-biographies\/\">Osman Salih<\/a><\/p>\n\n\n\n<p><strong>Overview:<\/strong>&nbsp; The Electron Microscopy Public Image Archive (<a rel=\"noreferrer noopener\" href=\"http:\/\/www.empiar.org\" target=\"_blank\">EMPIAR<\/a>) is a public resource for raw 2D image data. The lecture will guide you for using this resource.<br><\/p>\n\n\n\n<p>By the end of this session, you should be able to answer the following questions:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Where can I access raw 2D image Data?<\/li><li>How can I visualise raw 2D image Data?<\/li><li>How can I deposit &amp; download raw 2D image Data?<\/li><\/ul>\n\n\n\n<p>The lecture includes a &#8220;Step-By-Step Guide&#8221; to depositing and downloading raw 2D image data that will be followed during the practical session.<\/p>\n\n\n\n<p><strong>Materials:<\/strong> <\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"http:\/\/ftp.ebi.ac.uk\/pub\/training\/2021\/Microscopy_image_analysis_July2021\/EMPIAR\/Depositing_and_accessing_data_at_EMPIAR-Salih.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">Presentation slides<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/wwwdev.ebi.ac.uk\/pdbe\/emdb\/external_test\/master\/empiar\/deposition\/register\/\" target=\"_blank\"><strong>EMPIAR registration link<\/strong><\/a>. An <a rel=\"noreferrer noopener\" href=\"https:\/\/orcid.org\/\" target=\"_blank\">ORCID<\/a> is not compulsory to register, but is highly advised.<\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Depositing and accessing data at EMPIAR &#8211; Practical<\/h3>\n\n\n\n<p><strong>Trainer:<\/strong>&nbsp;<a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/trainer-biographies\/\">Andrii Iudin, Osman Salih &amp; Simone Weyand<\/a><\/p>\n\n\n\n<p><strong>Overview:<\/strong>&nbsp;The Electron Microscopy Public Image Archive (EMPIAR) is a public resource for raw 2D image data. The practical should increase your confidence in using this resource.<\/p>\n\n\n\n<p>During the practical session, you will follow the &#8220;Step-By-Step Guide&#8221; as described in the previous section to deposit and download raw 2D image data.<\/p>\n\n\n\n<p><strong>Materials:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"http:\/\/ftp.ebi.ac.uk\/pub\/training\/2021\/Microscopy_image_analysis_July2021\/EMPIAR\/Microscopy_data_analysis_Machine_Learning_and_the_BioImage_Archive\/\" target=\"_blank\" rel=\"noreferrer noopener\">Practical worksheets and data<\/a><\/li><li><a href=\"http:\/\/ftp.ebi.ac.uk\/pub\/training\/2021\/Microscopy_image_analysis_July2021\/EMPIAR\/Depositing_and_accessing_data_at_EMPIAR-Salih.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">Presentation slides<\/a><\/li><\/ul>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>EMPIAR: Past, present and future &#8211; Lecture&nbsp; Trainer:&nbsp;Gerard Kleywegt Overview:&nbsp;EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure. Learning outcomes By the end of this session you will be able to: List&#8230;<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":1674,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-14","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/14","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/comments?post=14"}],"version-history":[{"count":43,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/14\/revisions"}],"predecessor-version":[{"id":1904,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/14\/revisions\/1904"}],"up":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/pages\/1674"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/microscopy-image-analysis-materials\/wp-json\/wp\/v2\/media?parent=14"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}