{"id":15856,"date":"2019-05-15T15:01:45","date_gmt":"2019-05-15T13:01:45","guid":{"rendered":"https:\/\/news.embl.de\/?p=15856"},"modified":"2024-03-22T11:05:16","modified_gmt":"2024-03-22T10:05:16","slug":"imaging-data-collection","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/imaging-data-collection\/","title":{"rendered":"Breaking the bottleneck in imaging data collection"},"content":{"rendered":"\n<p>There is a growing demand for high-throughput data acquisition in structural and cell biology research. Developments in microscopy hardware and computing performance have increased the speed and quality of transmission electron microscopy (TEM). However, until now, scientists have had to manually select the features of interest to be imaged, and identify their precise coordinates: a time-consuming task that creates a bottleneck in the data acquisition procedure.<\/p>\n\n\n\n<p>Martin Schorb, Application Engineer in EMBL\u2019s <a href=\"https:\/\/www.embl.de\/services\/core_facilities\/em\/\" target=\"_blank\" rel=\"noopener noreferrer\">Electron Microscopy Core Facility<\/a>, and colleagues from EMBL Heidelberg and the <a href=\"https:\/\/www.colorado.edu\/mcdb\/\" target=\"_blank\" rel=\"noopener noreferrer\">University of Colorado<\/a>, USA, have developed two software tools that allow automated acquisition of electron microscopy data. The tools, SerialEM and py-EM, are presented in a paper published in <em>Nature Methods<\/em>.<\/p>\n\n\n\n<p>SerialEM, which was developed by scientists at the University of Colorado, is a versatile software package for controlling microscopes and cameras, to allow automated acquisition of TEM data. The py-EM module \u2013 a collection of Python functions \u2013 interfaces with SerialEM to create feedback pipelines in specimen-specific image analysis. Py-EM and the applied workflows were developed at EMBL.<\/p>\n\n\n\n<p>Using these tools, scientists no longer need to define discrete positions on an object for data acquisition. Instead, they define whole target objects, such as cells or distinct tissue features, and the tools create automated feedback TEM workflows for these objects.<\/p>\n\n\n\n<p>The new software tools make it possible to image every entity of a specimen in a controlled way, and this opens up new possibilities for TEM applications. For example, the automated approach enables systematic screening for phenotypes within cell populations or across different conditions. It also significantly increases throughput in structural analyses of molecular complexes using <a href=\"https:\/\/news.embl.de\/science\/new-cryo-em-facility\/\" target=\"_blank\" rel=\"noopener noreferrer\">cryo-electron microscopy<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Scientists develop software tools for automated acquisition of electron microscopy data<\/p>\n","protected":false},"author":68,"featured_media":15868,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[718,136,43,598,539,410,828],"embl_taxonomy":[],"class_list":["post-15856","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-cryo-em","tag-electron-microscopy","tag-heidelberg","tag-imaging","tag-research-highlight","tag-schwab","tag-tem"],"acf":{"article_intro":"<p><span lang=\"EN-GB\">Scientists develop software tools for automated acquisition of electron microscopy data<\/span><\/p>\n","related_links":[{"link_description":"Electron Microscopy Core Facility","link_url":"http:\/\/www.embl.de\/services\/core_facilities\/em\/"},{"link_description":"Research in the Cell Biology and Biophysics Unit","link_url":"http:\/\/www.embl.de\/research\/units\/cbb\/"},{"link_description":"Research in the Structural and Computational Biology Unit","link_url":"http:\/\/www.embl.de\/research\/units\/scb\/"},{"link_description":"Molecular, Cellular & Developmental Biology, University of Colorado Boulder","link_url":"http:\/\/www.colorado.edu\/mcdb\/"},{"link_description":"EMBO|EMBL Symposium: Seeing is Believing \u2013 Imaging the Molecular Processes of Life","link_url":"http:\/\/www.embo-embl-symposia.org\/symposia\/2019\/EES19-09\/"}],"article_sources":[{"source_description":"<p><span lang=\"EN-GB\">Schorb M <i>et al.\u00a0<\/i>Software tools for automated transmission electron microscopy. <i>Nature Methods<\/i>. Published online 13 May 2019. DOI: 10.1038\/s41592-019-0396-9<\/span><\/p>\n<div class=\"page\" title=\"Page 1\">\n<div class=\"section\">\n<div class=\"layoutArea\">\n<div class=\"column\">\n<p>&nbsp;<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","source_link_url":"http:\/\/www.nature.com\/articles\/s41592-019-0396-9"}],"vf_locked":false,"featured":false,"color":"#007B53"},"embl_taxonomy_terms":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Breaking the bottleneck in imaging data collection | EMBL<\/title>\n<meta name=\"description\" content=\"Scientists at EMBL and the University of Colorado develop software tools for automated acquisition of electron microscopy data\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/imaging-data-collection\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Breaking the bottleneck in imaging data collection | EMBL\" \/>\n<meta property=\"og:description\" content=\"Scientists at EMBL and the University of Colorado develop software tools for automated acquisition of electron microscopy data\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/imaging-data-collection\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:published_time\" content=\"2019-05-15T13:01:45+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-03-22T10:05:16+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2019\/05\/Fig2_2col_cropped.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"620\" \/>\n\t<meta property=\"og:image:height\" content=\"425\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Cella Carr\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@embl\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Cella Carr\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/imaging-data-collection\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/imaging-data-collection\/\"},\"author\":{\"name\":\"Cella Carr\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/3bb76de286246270a71cf08b368e0594\"},\"headline\":\"Breaking the bottleneck in imaging data collection\",\"datePublished\":\"2019-05-15T13:01:45+00:00\",\"dateModified\":\"2024-03-22T10:05:16+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/imaging-data-collection\/\"},\"wordCount\":277,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/imaging-data-collection\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2019\/05\/Fig2_2col_cropped.jpg\",\"keywords\":[\"cryo-em\",\"electron microscopy\",\"heidelberg\",\"imaging\",\"research highlight\",\"schwab\",\"tem\"],\"articleSection\":[\"Science\",\"Science &amp; 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