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="https://idr.openmicroscopy.org/about/img/logos/favicon-idr.ico"> <link rel="stylesheet" type="text/css" media="all" href="//fonts.googleapis.com/css?family=Open+Sans:400,700,400italic,700italic"> <link rel="stylesheet" type="text/css" media="all" href="//fonts.googleapis.com/css?family=Nunito"> <link href="/static/idr_gallery/3rdparty/foundation/foundation.min.css?_=3.11.0" rel="stylesheet"> <link href="/static/idr_gallery/css/openmicroscopy.css?_=3.11.0" rel="stylesheet"> <link href="/static/idr_gallery/css/idr.css?_=3.11.0" rel="stylesheet"> <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.8.1/css/all.css" 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class="dropdown menu" data-dropdown-menu> <li> <a class="logo" href="/"> <img src="https://idr.openmicroscopy.org/about/img/logos/logo-idr.svg" alt=""/> </a> </li> <li> <a href="/cell/" > Cell - IDR </a> </li> <li> <a href="/tissue/" > Tissue - IDR </a> </li> </ul> </div> <div id="top-bar-right" class="top-bar-right"> <ul class="dropdown menu" data-dropdown-menu> <li class="has-submenu"> <a href="https://idr.openmicroscopy.org/about/index.html">About</a> <ul class='submenu menu vertical' data-submenu> <li><a href="https://idr.openmicroscopy.org/about/index.html">Overview</a></li> <li><a href="https://idr.openmicroscopy.org/about/studies.html">Published studies</a></li> <li><a href="https://idr.openmicroscopy.org/about/api.html">API Access</a></li> <li><a href="https://idr.openmicroscopy.org/about/download.html">Data download</a></li> <li><a href="https://idr.openmicroscopy.org/about/deployment.html">Deployment</a></li> <li><a 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</div> <a name="page-top"></a> <script> // Various global constants from omero config set... var FILTER_KEYS = [{'label': 'Name (IDR number)', 'value': 'Name'}, 'Imaging Method', 'License', 'Organism', 'Publication Authors', 'Publication Title', 'Screen Technology Type', 'Screen Type', 'Study Type']; var FILTER_MAPR_KEYS = ["antibody", "cellline", "compound", "gene", "phenotype", "sirna"]; var TITLE_KEYS = ["Publication Title", "Study Title"]; var STUDY_SHORT_NAME = [{"key": "Name", "regex": "^(.*?)-.*?(.)$", "template": "$1$2"}]; // e.g. GALLEY_INDEX/api-gallery/thumbnails for loading from IDR const GALLERY_INDEX = "/"; // this is the home of this app, e.g. for GALLERY_HOME/search/ const GALLERY_HOME = "/"; const BASE_URL = "/"; const IDR_STUDIES_URL = "https://raw.githubusercontent.com/IDR/idr.openmicroscopy.org/master/_data/studies.tsv"; const CATEGORY_QUERIES = {"latest": {"label": "Light sheet fluorescence microscopy", "index": 0, "query": "Imaging Method: light sheet fluorescence microscopy OR Imaging Method: light sheet fluorescence microscopy, SPIM"}, "infection": {"label": "Infection studies", "index": 1, "query": "Study Type:infection"}, "timelapse": {"label": "Time-lapse imaging", "index": 2, "query": "Study Type:time OR Study Type:5D OR Study Type:3D-tracking"}, "lightsheet": {"label": "Light sheet fluorescence microscopy", "index": 3, "query": "Study Type:light sheet"}, "proteinlocalization": {"label": "Protein localization studies", "index": 4, "query": "Study Type:protein localization"}, "histology": {"label": "Digital pathology imaging", "index": 5, "query": "Study Type:histology"}, "yeast": {"label": "Yeast studies", "index": 6, "query": "Organism: Saccharomyces cerevisiae OR Organism:Schizosaccharomyces pombe"}, "humancellscreen": {"label": "High-content screening (human)", "index": 7, "query": "Organism:Homo sapiens AND Study Type:high content screen"}, "others": {"label": "Others", "index": 8, "query": "LAST1000:date"}}; var SUPER_CATEGORY ; const 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horizontal" style="position: relative; margin-top: 15px; margin-bottom: 15px"> <div class="stats small-12 medium-9 large-8 columns" style="position: relative"> </div> </div> <div class="row horizontal" style="position: relative;"> <div class="small-12 medium-12 large-8 columns" style> <div class="panel" id="tabs"> <ul class="tabs" data-tabs id="example-tabs"> <li class="tabs-title is-active "> <a href="#panel1" aria-selected="true" > Exploring IDR </a> </li> <li class="tabs-title "> <a href="#panel2" > Analyze Data </a> </li> </ul> <div class="tabs-content" data-tabs-content="example-tabs"> <div class="tabs-panel is-active " id="panel1"> <div class="row horizontal"> <div class="small-6 medium-6 large-6 columns" style="position: relative;"> <iframe id="youtube" width="100%" height="100%" src="https://www.youtube.com/embed/dFg2PAF3k7s" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen> </iframe> <button title="Expand video" class="expandVideo"><i class="fas fa-angle-right"></i><i class="fas fa-angle-right"></i></button> </div> <div class="columns small-6 medium-6 large-6"> <h3>From publication to IDR</h3> Find a specific IDR study from a publication. View images and Regions of Interest (ROIs) in IDR. Explore study metadata. </div> </div> <div class="row horizontal"> <div class="small-6 medium-6 large-6 columns" style="position: relative;"> <iframe id="youtube" width="100%" height="100%" src="https://www.youtube.com/embed/JboK6Kds28U" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen> </iframe> <button title="Expand video" class="expandVideo"><i class="fas fa-angle-right"></i><i class="fas fa-angle-right"></i></button> </div> <div class="columns small-6 medium-6 large-6"> <h3>From gene to phenotypes</h3> Query images by gene. Explore retrieved images and metadata, including associated phenotypes. View images in context of a plate. </div> </div> <div class="row horizontal"> <div class="small-6 medium-6 large-6 columns" style="position: relative;"> <iframe id="youtube" width="100%" height="100%" src="https://www.youtube.com/embed/stF4Q4m5GZg" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen> </iframe> <button title="Expand video" class="expandVideo"><i class="fas fa-angle-right"></i><i class="fas fa-angle-right"></i></button> </div> <div class="columns small-6 medium-6 large-6"> <h3>From compound to analytics</h3> Query images by compound. Find SARS-CoV-2 dataset. Explore images in relation to analytical data submitted by authors. </div> </div> </div> <div class="tabs-panel " id="panel2"> <p>The IDR server is built with <a target='_blank' href='https://www.openmicroscopy.org/omero/'>OMERO</a>, allowing access to all image data and metadata via an open API in Python, R, Java, MATLAB and REST/JSON. See the <a target='_blank' href='https://omero-guides.readthedocs.io/en/latest/api_usage.html'>OMERO API guide</a> for more information.</p><p>For examples of analysis tools working with OMERO to access and analyze data, see the <a target='_blank' href='https://omero-guides.readthedocs.io/en/latest/external_tools.html'>analysis tools guide</a>.</p> <div class="row horizontal"> <div class="small-6 medium-6 large-6 columns" style="position: relative;"> <iframe id="youtube" width="100%" height="100%" src="https://www.youtube.com/embed/tOgKlxyyvSc" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen> </iframe> <button title="Expand video" class="expandVideo"><i class="fas fa-angle-right"></i><i class="fas fa-angle-right"></i></button> </div> <div class="columns small-6 medium-6 large-6"> <h3>Analysis environment setup</h3> Set-up local or on-the-cloud analysis environment. Access images and metadata using API. Run analysis examples. Add your own code. </div> </div> <div class="row horizontal"> <div class="small-6 medium-6 large-6 columns" style="position: relative;"> <iframe id="youtube" width="100%" height="100%" src="https://www.youtube.com/embed/z19EE0_2JBs" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen> </iframe> <button title="Expand video" class="expandVideo"><i class="fas fa-angle-right"></i><i class="fas fa-angle-right"></i></button> </div> <div class="columns small-6 medium-6 large-6"> <h3>Segment image and compare</h3> Fetch image and labels from IDR. Segment nuclei using <a target='_blank' href='https://github.com/stardist/stardist'>StarDist</a>. Compare new labels with original. Validate software package. Save locally segmentation polygons as geojson. </div> </div> </div> </div> </div> </div> </div> </div> <script src="/static/idr_gallery/categories.js?_=3.11.0"></script> <script src="/static/idr_gallery/autocomplete.js?_=3.11.0"></script> <script> // handle expand/collapse of videos >> $("#tabs").on("click", ".expandVideo", function () { let $row = $(this).closest(".row"); // toggle from 2 columns to 1 $('.columns', $row).toggleClass("small-12 medium-12 large-12") .toggleClass("small-6 medium-6 large-6"); }); </script> <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" 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" 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" alt="Global-Bioimaging"></a></div> <div class="column"><a href="https://www.bbsrc.ac.uk/" target="_blank"><img class="thumbnail their-logo" src="/about/img/logos/bbsrc.png" 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" 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="/"><img id="version-number" src="/about/img/logos/logo-idr.svg" alt="IDR logo"></a> version: <span id="version-number-display"></span>. </div> <div class="float-right"> <a href="https://www.twitter.com/idrnews" target="_blank"><i class="fab fa-fw fa-twitter"></i> @IDRnews</a></li> <a href="https://www.twitter.com/idrstatus" target="_blank"><i class="fab fa-fw fa-twitter"></i> @IDRstatus</a></li> </div> </div> </div> </div> <script> $(document).foundation(); </script> </body> </html>

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