{"id":18546,"date":"2020-02-28T09:04:35","date_gmt":"2020-02-28T08:04:35","guid":{"rendered":"https:\/\/news.embl.de\/?p=18546"},"modified":"2024-03-22T11:11:44","modified_gmt":"2024-03-22T10:11:44","slug":"finding-your-way-around-platynereis-dumerilii","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/finding-your-way-around-platynereis-dumerilii\/","title":{"rendered":"Finding your way around Platynereis dumerilii"},"content":{"rendered":"\n<p>The segmented marine worm <em>Platynereis dumerilii<\/em> is an ideal organism for the study of the nervous system. At EMBL Heidelberg, researchers have developed a resource that enables completely new insights into the biology of this organism. <em>PlatyBrowser<\/em> is an interactive atlas of the entire animal that allows scientists to travel virtually to any cell found in a young <em>Platynereis<\/em> worm, inspect the cell\u2019s ultrastructure in its anatomical context, and display the genes that are expressed in that cell. The resource and all the data have been made available both <a href=\"https:\/\/github.com\/platybrowser\/mmb-fiji#mmb-fiji\">online<\/a> and in a <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.02.26.961037v1\">preprint<\/a>. The researchers invite feedback from users, who can also add their own datasets to the atlas.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Electron microscopy meets gene expression data<\/h2>\n\n\n\n<p>The novel <em>Platynereis <\/em>atlas \u2013 a collaborative project involving researchers from EMBL\u2019s Arendt and Kreshuk groups, Schwab team and Electron Microscopy Core Facility, and Centre for Bioimage Analysis \u2013 is based on volume electron microscopy (EM) data acquired from a whole six-day-old worm. \u201cWe acquired high-resolution volume EM data of an entire animal, which provides ultrastructural detail,\u201d explains Detlev Arendt, EMBL group leader and one of the coordinators of the project. \u201cWe\u2019re also bringing together spatial expression profiling and volume EM for the first time at this scale.\u201d<\/p>\n\n\n\n<p>The study was made possible by recent advances in EM technology and data analysis. In collaboration with Christel Genoud and Rainer Friedrich at the Friedrich Miescher Institute for Biomedical Research (FMI) in Basel, Switzerland, who have developed a new software tool called <a href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fncir.2018.00054\/full\"><em>SBEMimage<\/em><\/a>, the researchers managed to acquire the several terabytes of data required to image a complete specimen at nanometre resolution. Novel algorithms were used to automatically segment all 12&nbsp;000 cells and their nuclei across all tissues in <em>Platynereis<\/em>. \u201cDevelopments in the field of connectomics, which studies neuronal structures by EM, pioneered these methods, but we had to develop new approaches for segmentation of very diverse tissues across the whole organism, which is really challenging,\u201d explains EMBL group leader Anna Kreshuk. \u201cSo far, nobody had done this for non-neuronal tissues or multiple tissue types at once.\u201d<\/p>\n\n\n\n<p>The nuclear segmentation pattern could then be used to align the EM data with a <a href=\"https:\/\/www.pnas.org\/content\/114\/23\/5878\">previously published<\/a> and expanded gene expression dataset for hundreds of genes. This enables users to zoom in on single cells to simultaneously investigate their structure, composition, and the genes expressed within them. \u201cWe now have a full overlay of gene expression data onto an anatomical atlas at nanometric resolution,\u201d says EMBL team leader Yannick Schwab. \u201cThis is the first time such a detailed match has been obtained for an entire organism.\u201d<\/p>\n\n\n\n<p>To make the combined gene expression and EM data easily explorable, the team has developed a new Fiji plugin that allows browsing of large multimodal datasets. \u201cWe collaborated with EMBL\u2019s IT department to use the latest developments in cloud data storage to enable remote public access to terabyte-sized image datasets,\u201d explains Christian Tischer, who runs EMBL\u2019s Centre for Bioimage Analysis. The <a href=\"https:\/\/github.com\/platybrowser\/mmb-fiji#mmb-fiji\">PlatyBrowser plugin<\/a> is available for anyone to install as open source software.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">A model for interdisciplinary research<\/h2>\n\n\n\n<p>The current research project is a team effort across EMBL units and research groups, as well as with external collaborators. It unites expertise in <em>Platynereis<\/em> biology, EM technology, automated image processing, and machine learning from the Arendt and Kreshuk groups, the Schwab team, EMBL\u2019s Centre for Bioimage Analysis, and the collaborators at FMI Basel. Bringing together this expertise has not only allowed the researchers to overcome the technical challenges, but has already revealed novel insights into <em>Platynereis <\/em>biology. \u201cWe can now cluster segmented cells that show similar gene expression, and we find that these clusters follow morphological boundaries in the animal\u2019s body. There is a high coherence between gene expression at the tissue level and the anatomical units in the body. This type of insight has not been possible before,\u201d says Arendt.<\/p>\n\n\n\n<p>The biggest strength of the new resource, though, is its multi-modality. \u201cThis means that several types of data can be combined,\u201d Arendt explains. \u201cAt the moment, we have gene expression and the ultrastructure, but our resource allows other modalities, such as metabolomics or proteomics datasets, or X-ray tomography data to be easily added.\u201d This way, <em>PlatyBrowser<\/em> enables researchers to perform multidisciplinary analyses and add their own research data. The EMBL researchers invite the whole <em>Platynereis <\/em>community to use the resource and provide feedback. \u201cOur resource is expandable; it\u2019s not a fixed resource,\u201d Schwab concludes. \u201cIt will keep growing with more knowledge being added to it in the future.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"<p>EMBL researchers combine multiple datasets to develop expandable atlas of an entire animal<\/p>\n","protected":false},"author":81,"featured_media":18554,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[417,227,565,602,926,539,410],"embl_taxonomy":[],"class_list":["post-18546","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-arendt","tag-core-facility","tag-developmental-biology","tag-kreshuk","tag-platynereis-dumerilii","tag-research-highlight","tag-schwab"],"acf":{"article_intro":"<p>EMBL researchers combine multiple datasets to develop expandable atlas of an entire animal<\/p>\n","related_links":[{"link_description":"PlatyBrowser Fiji Plugin","link_url":"https:\/\/github.com\/platybrowser\/mmb-fiji#mmb-fiji"},{"link_description":"Mapping gene expression, cell by cell","link_url":"https:\/\/news.embl.de\/science\/1706-mapping-gene-expression-cell-by-cell\/"},{"link_description":"Research in the Arendt group","link_url":"https:\/\/www.embl.de\/research\/units\/dev_biology\/arendt\/index.html"},{"link_description":"Research in the Kreshuk group","link_url":"https:\/\/www.embl.de\/research\/units\/cbb\/kreshuk\/index.html"},{"link_description":"Research in the Schwab team","link_url":"https:\/\/www.embl.de\/research\/units\/cbb\/schwab\/index.html"},{"link_description":"EMBL Centre for Bioimage Analysis","link_url":"https:\/\/www.embl.de\/research\/interdisciplinary_research\/centres\/bioimage-analysis\/index.html"}],"article_sources":[{"source_description":"<p>Vergara HM, Pape C, Meechan K, Zinchenko V, Genoud C, Wanner AA, Titze B, Templin R, Bertucci PY, Simakov O, Machado P, Savage EL, Schwab Y, Friedrich RW, Kreshuk A, Tischer C &amp; Arendt D (2020). Whole-body integration of gene expression and single-cell morphology. Preprint, bioRxiv 2020.02.26.961037. doi: 10.1101\/2020.02.26.961037<\/p>\n","source_link_url":"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.02.26.961037v1"},{"source_description":"<p>Vergara HM, Bertucci PY, Hantz P, Tosches MA, Achim K, Vopalensky P &amp; Arendt D (2017). Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord of <em>Platynereis dumerilii<\/em>. Proc Natl Acad Sci USA 114(23):5878-5885. doi: 10.1073\/pnas.1610602114<\/p>\n","source_link_url":"https:\/\/www.pnas.org\/content\/114\/23\/5878"},{"source_description":"<p>Titze B, Genoud C &amp; Friedrich RW (2018). SBEMimage: versatile acquisition control software for serial block-face electron microscopy. Frontiers in Neural Circuits 12:54. doi: 10.3389\/fncir.2018.00054<\/p>\n","source_link_url":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fncir.2018.00054\/full"}],"description_pdf_archive_link":"","pdf_archive_link":"","vf_locked":false,"featured":true,"color":"#15153b"},"embl_taxonomy_terms":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Finding your way around Platynereis dumerilii | EMBL<\/title>\n<meta name=\"description\" content=\"PlatyBrowser is an interactive atlas that allows scientists to travel virtually to any cell found in a young Platynereis dumerilii worm\" \/>\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\/finding-your-way-around-platynereis-dumerilii\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Finding your way around Platynereis dumerilii | EMBL\" \/>\n<meta property=\"og:description\" content=\"PlatyBrowser is an interactive atlas that allows scientists to travel virtually to any cell found in a young Platynereis dumerilii worm\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/finding-your-way-around-platynereis-dumerilii\/\" \/>\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=\"2020-02-28T08:04:35+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-03-22T10:11:44+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2020\/02\/2002_research-highlight_platybrowser_ib.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=\"Marius Bruer\" \/>\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=\"Marius Bruer\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"4 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/finding-your-way-around-platynereis-dumerilii\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/finding-your-way-around-platynereis-dumerilii\/\"},\"author\":{\"name\":\"Marius Bruer\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/702350187d61d3ff4dd6541c7d212e86\"},\"headline\":\"Finding your way around Platynereis dumerilii\",\"datePublished\":\"2020-02-28T08:04:35+00:00\",\"dateModified\":\"2024-03-22T10:11:44+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/finding-your-way-around-platynereis-dumerilii\/\"},\"wordCount\":757,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/finding-your-way-around-platynereis-dumerilii\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2020\/02\/2002_research-highlight_platybrowser_ib.jpg\",\"keywords\":[\"arendt\",\"core facility\",\"developmental biology\",\"kreshuk\",\"platynereis dumerilii\",\"research highlight\",\"schwab\"],\"articleSection\":[\"Science\",\"Science &amp; 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The broad shadings show the expression of genes found in the muscles (red) and neuropile (cyan). Cell chromatin is highlighted in various colours. 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