IDR: Image Data Resource

<!doctype html> <html class="no-js" lang="en" dir="ltr"> <head> <meta charset="utf-8"> <meta http-equiv="x-ua-compatible" content="ie=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>IDR: Image Data Resource</title> <link rel="shortcut icon" type="image/x-icon" href="/about/img/logos/favicon-idr.ico?1728381874421049740"> <link rel="stylesheet" type="text/css" media="all" href="https://fonts.googleapis.com/css?family=Open+Sans:400,700,400italic,700italic"> <link rel="stylesheet" type="text/css" media="all" href="https://fonts.googleapis.com/css?family=Nunito"> <link rel="stylesheet" type="text/css" media="all" href="/about/css/foundation.min.css?1728381874421049740"> <link rel="stylesheet" type="text/css" media="all" href="/about/css/responsive-tables.css?1728381874421049740"> <link rel="stylesheet" type="text/css" media="all" href="/about/css/datatables.css?1728381874421049740"> <link rel="stylesheet" type="text/css" media="all" href="/about/css/openmicroscopy.css?1728381874421049740"> <link rel="stylesheet" type="text/css" media="all" href="/about/css/idr.css?1728381874421049740"> <link rel="stylesheet" type="text/css" media="all" href="/about/css/itr.css?1728381874421049740"> <link rel="stylesheet" type="text/css" media="all" href="/about/css/fontawesome-all.css?1728381874421049740"> <script src="/about/js/vendor/jquery.js?1728381874421049740"></script> <script src="/about/js/vendor/what-input.js?1728381874421049740"></script> <script src="/about/js/vendor/foundation.js?1728381874421049740"></script> <script src="/about/js/vendor/jquery.dataTables.js?1728381874421049740"></script> <script src="/about/js/vendor/dataTables.foundation.js?1728381874421049740"></script> <script src="/about/js/app.js?1728381874421049740"></script> <script src="/about/js/tool-modal.js?1728381874421049740"></script> <script src="/about/js/responsive-tables.js?1728381874421049740"></script> <script src="/about/js/version.js?1728381874421049740"></script> </head> <body> <div class="title-bar" data-responsive-toggle="main-menu" data-hide-for="medium" style="background-color: #37474f;"> <button class="menu-icon" type="button" data-toggle></button> <div class="title-bar-title">Menu</div> </div> <div class="main-nav-bar top-bar" id="main-menu"> <div class="top-bar-left"> <ul class="dropdown menu" data-dropdown-menu> <li><a class="logo" href="https://idr.openmicroscopy.org"><img src="/about/img/logos/logo-idr.svg?1728381874421049740" alt="IDR logo"></a></li> <li> <a href="/cell/"> Cell - IDR </a> </li> <li> <a href="/tissue/"> Tissue - IDR </a> </li> </ul> </div> <div class="top-bar-right"> <ul class="dropdown menu" data-dropdown-menu> <li class="has-submenu"><a href="/about/index.html">About</a> <ul class="submenu menu vertical" data-submenu> <li><a href="/about/index.html">Overview</a></li> <li><a href="/about/studies.html">Published studies</a></li> <li><a href="/about/api.html">API Access</a></li> <li><a href="/about/download.html">Data download</a></li> <li><a href="/about/deployment.html">Deployment</a></li> <li class="has-submenu"><a href="/about/faq/">FAQ</a></li> </ul> </li> <li class="has-submenu"><a href="/about/index.html">Resources</a> <ul class="submenu menu vertical" data-submenu> <li><a href="https://idr.github.io/ome-ngff-samples/">OME-NGFF examples</a></li> <li><a href="/about/linked-resources.html">Linked resources</a></li> <li><a href="/about/itr.html">Image Tools Resource (ITR)</a></li> <li><a href="/about/analysis-environments.html">Analysis Environments</a></li> </ul> </li> <li class="has-submenu"><a href="/about/submission.html">Submissions</a> <ul class="submenu menu vertical" data-submenu> <li><a href="/about/submission.html">Overview</a></li> <li><a href="/about/screens.html">Screens</a></li> <li><a href="/about/experiments.html">Experiments</a></li> </ul> </li> </ul> </div> </div> <a name="page-top"></a>  <header class="marketing-hero"> <div class="row homepage text-center"> <div class="medium-12 columns"> <img src="/about/img/logos/logo-idr-white.svg?1728381874421049740" alt="IDR logo" class="logo-hero" /> <h1 class="hero-main-header">Image Data Resource</h1> <h2 class="hero-subheader small-10 medium-10 large-10 small-offset-1 medium-offset-1 large-offset-1"> The Image Data Resource (IDR) is a public repository of reference image datasets from published scientific studies. IDR enables access, search and analysis of these highly annotated datasets. </h2> <br> <a href="/cell/" class="large button sites-button" style="margin-right: 10px">Cell-IDR</a> <a href="/tissue/" class="large button sites-button">Tissue-IDR</a> </div> </div> </header>   <hr class="whitespace"> <div class="row column text-center"> <h2>Goal</h2> </div> <hr> <div class="row"> <div class="small-10 small-centered medium-10 medium-centered columns"> <div class="row horizontal"> <div> <p>The IDR makes datasets that have never previously been accessible publicly available, allowing the community to search, view, mine and even process and analyze large, complex, multidimensional life sciences image data. Sharing data promotes the validation of experimental methods and scientific conclusions, the comparison with new data obtained by the global scientific community, and enables data reuse by developers of new analysis and processing tools.</p> <p>You can browse the IDR without any special knowledge, but if you would like to see how the IDR can be used to obtain new biological insights from existing datasets, or a more in-depth explanation of how the IDR is set up, please see the <a href="https://dx.doi.org/10.1038/nmeth.4326">Nature Methods paper</a>.</p> <a href="https://dx.doi.org/10.1038/nmeth.4326"><img src="img/figures/idr-paper-nmeth.png" style="width:40%; float:right;" alt="Image Data Resource: a bioimage data integration and publication platform" title="Image Data Resource: a bioimage data integration and publication platform"/></a> <p>IDR datasets are annotated with author-supplied metadata (e.g., annotations, defined regions, feature vectors and ontological annotations) that are all stored and available for browsing. All metadata are also available through the <a href="https://www.openmicroscopy.org/site/support/omero5.2/developers/Modules/Api.html">OMERO API</a>. <p>If you are interested in submitting data to the IDR, see <a href="submission.html">our submission guidelines</a>.</p> </div> </div> </div> </div>   <hr class="whitespace"> <div class="row column text-center"> <h2>Examples</h2> </div> <hr> <div class="row"> <div class="small-10 small-centered medium-10 medium-centered columns"> <div class="row horizontal"> <div> <p><a href="/webclient/?show=well-45407">Datasets in human cells</a>, <a href="/webclient/?show=well-547609">Drosophila</a>, and <a href="/webclient/?show=well-590686">fungi</a> are included. The full <a href="/webclient/?show=well-771034">Mitocheck dataset</a> and a comprehensive <a href="/webclient/?show=plate-4101">chemical screen in human cells</a> are included. Imaging data from <a href="/webclient/?show=plate-4751">Tara Oceans</a>, a global survey of plankton and other marine organisms is also included.</p> <p>Wherever possible, functional annotations (e.g., 鈥渋ncreased peripheral actin") and experimental components have been converted to defined terms in the <a href="https://www.ebi.ac.uk/ols/ontologies/efo">EFO</a>, <a href="https://www.ebi.ac.uk/ols/ontologies/cmpo">CMPO</a> or other ontologies, always in collaboration with the data submitters (see example). >80% of the functional annotations have links to defined, published controlled vocabularies.</p> </div> <div class="row small-up-2 medium-up-4 large-up-4"> <div class="column"><a href="https://idr.openmicroscopy.org/webclient/?show=image-122770" target="_blank"> <img class="thumbnail" src="https://idr.openmicroscopy.org/webgateway/render_thumbnail/122770/192/" alt="idr-0008-B"> </a></div> <div class="column"><a href="https://idr.openmicroscopy.org/webclient/?show=well-37013" target="_blank"> <img class="thumbnail" alt="idr0007-A" src="https://idr.openmicroscopy.org/webgateway/render_thumbnail/95543/192/"> </a></div> <div class="column"><a href="https://idr.openmicroscopy.org/webclient/?show=image-1230008" target="_blank"> <img class="thumbnail" src="https://idr.openmicroscopy.org/webgateway/render_thumbnail/1230008/192/" alt="idr-0001-A"> </a></div> <div class="column"><a href="https://idr.openmicroscopy.org/webclient/?show=image-1484759" target="_blank"> <img class="thumbnail" src="https://idr.openmicroscopy.org/webgateway/render_thumbnail/1484759/192/" alt="idr-0013-A"> </a></div> </div> <div class="row column text-center"><a href="submission.html" class="large button sites-button">Submit your data</a></div> </div> </div> </div>   <hr class="whitespace"> <div class="row column text-center"> <h2>Technology</h2> </div> <hr> <div class="row"> <div class="small-10 small-centered medium-10 medium-centered columns"> <div class="row horizontal"> <div> <p>IDR uses OME鈥檚 <a href="https://www.openmicroscopy.org/site/products/bio-formats">Bio-Formats</a> and <a href="https://www.openmicroscopy.org/site/products/omero">OMERO</a> tools to read, manage and serve data, and provide links to EMBL-EBI鈥檚 molecular and structural resources. The resource is built upon EMBL-EBI鈥檚 OpenStack-based Embassy infrastructure. All tools used for reading and converting metadata associated with <a href="https://github.com/IDR/idr-metadata">each dataset</a> and all scripts used to build the <a href="https://github.com/IDR/infrastructure">infrastructure</a> are maintained and available. A parallel system that enables computational re-analysis of IDR data will be released soon.</p> <p>The IDR includes a <a href="/jupyter">virtual analysis environment</a> that provides full access to all data.</p> <p>Details on accessing the public IDR API are available under <a href="api.html">about/api.html</a>. </div> </div> </div> </div>   <hr class="whitespace"> <div class="row column text-center"> <h2><a class="anchor" id="funding"></a>Funding and Project Participants</h2> </div> <hr> <div class="row"> <div class="small-10 small-centered medium-10 medium-centered columns"> <div class="row horizontal"> <div> <p>The IDR Project PIs are <a href="https://www.openmicroscopy.org/site/about/development-teams/jason">Jason Swedlow (Dundee)</a>, Alvis Brazma (EMBL-EBI) and <a href="https://research-information.bristol.ac.uk/en/persons/rafael-e-carazo-salas(a7638b29-53e4-49ba-82b5-98b21d82f41f).html">Rafael Carazo Salas</a>. Construction of the IDR project was funded by the BBSRC (Ref: <a href="https://gow.bbsrc.ukri.org/grants/AwardDetails.aspx?FundingReference=BB/M018423/1">BB/M018423/1</a>) as a collaboration between the <a href="https://www.openmicroscopy.org">OME Consortium</a> at Dundee and EMBL-EBI. The IDR is part of several projects that have received funding from the European Union's Horizon 2020 research and innovation programme under grant agreements <a href="https://cordis.europa.eu/project/rcn/198825_en.html">688945</a> (<a href="https://www.eurobioimaging.eu/">Euro-BioImaging</a> Prep Phase II), <a href="https://cordis.europa.eu/project/rcn/198649_en.html">653493</a> (<a href="https://globalbioimaging.org/">Global BioImaging</a> Project) and <a href="https://www.cordis.europa.eu/project/rcn/197885_en.html">654248</a> (<a href="https://www.corbel-project.eu/home.html">CORBEL</a>). For 2018-2022, dataset submission and publication is funded by the Wellcome Trust (Ref: 212962/Z/18/Z) and integration with EMBL-EBI's BioStudies and other resources is funded by the BBSRC (Ref: <a href="https://gow.bbsrc.ukri.org/grants/AwardDetails.aspx?FundingReference=BB/R015384/1">BB/R015384/1</a>). </p> </div> </div> </div> </div>   <hr class="whitespace"> <div class="row column text-center"> <h2>Current Status</h2> </div> <hr> <div class="row"> <div class="small-10 small-centered medium-10 medium-centered columns"> <div class="row horizontal"> <div> <p>See <a href="studies.html">the full list of published studies</a> for more details.</p> </div> </div> </div> </div>   <hr class="whitespace"> <div class="row column text-center"> <h2>The IDR infrastructure</h2> </div> <hr> <div class="row"> <div class="small-10 small-centered medium-10 medium-centered columns"> <div class="row horizontal"> <div> <p>Details of the infrastructure underlying the IDR, and instructions for deploying your IDR own version are on the <a href="deployment.html">IDR Deployment page</a>.</p> </div> </div> </div> </div>  <div id="page-anchor"><a href="#page-top"><i class="fa fa-arrow-up"></i> back to top</a></div> <hr class="whitespace"> <div class="callout large secondary"> <div class="row"> <div class="row small-up-2 medium-up-5 large-up-5"> <div class="column"><a href="https://www.openmicroscopy.org/" target="_blank"><img class="thumbnail their-logo" src="/about/img/logos/ome-logo-200.png?1728381874421049740" alt="OME"></a></div> <div class="column"><a href="https://www.eurobioimaging.eu/" target="_blank"><img class="thumbnail their-logo" src="/about/img/logos/eurobioimaging_logo.png?1728381874421049740" alt="Euro-Bioimaging"></a></div> <div class="column"><a href="https://www.globalbioimaging.org/" target="_blank"><img class="thumbnail their-logo" src="/about/img/logos/globalbioimaging_logo.png?1728381874421049740" alt="Global-Bioimaging"></a></div> <div class="column"><a href="https://bbsrc.ukri.org/" target="_blank"><img class="thumbnail their-logo" src="/about/img/logos/bbsrc.png?1728381874421049740" alt="BBSRC"></a></div> <div class="column"><a href="https://www.glencoesoftware.com/" target="_blank"><img class="thumbnail their-logo" src="/about/img/logos/logo-glencoe-software-color.png?1728381874421049740" alt="Glencoe Software"></a></div> </div> <hr class="whitespace"> <div class="large-12 columns text-center"> <p>© 2016-2024 University of Dundee & Open Microscopy Environment. <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International License</a>.</p> <p>OMERO is distributed under the terms of the GNU GPL. For more information, visit <a href="https://www.openmicroscopy.org">openmicroscopy.org</a></p> </div> <hr class="whitespace"> <div> <div class="version-number float-left"> <a href="https://idr.openmicroscopy.org"><img id="version-number" src="/about/img/logos/logo-idr.svg?1728381874421049740" alt="IDR logo"></a> version: <span id="version-number-display">devel</span>. Last updated: 2024-10-08. </div> <div class="float-right"> <a href="https://www.twitter.com/idrnews" target="_blank"><i class="fab fa-fw fa-twitter"></i> @IDRnews</a> <a href="https://www.twitter.com/idrstatus" target="_blank"><i class="fab fa-fw fa-twitter"></i> @IDRstatus</a> </div> </div> </div> </div> <script> $(document).foundation(); </script> </body> </html>

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IDR: Image Data Resource