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---
layout: idr
title: Image Data Resource
redirect_from:
- about.html
---
<!-- begin marketing header -->
<header class="marketing-hero">
<div class="row homepage text-center">
<div class="medium-12 columns">
<img src="{{ "/img/logos/logo-idr-white.svg" | prepend: site.baseurl }}?{{ site.time | date: '%s%N' }}" 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>
<!-- end marketing header -->
<!-- begin Goal section -->
<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>
<!-- end Goal section -->
<!-- begin Examples section -->
<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., “increased 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>
<!-- end Examples section -->
<!-- begin Technology section -->
<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’s <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’s molecular and structural resources. The resource is built
upon EMBL-EBI’s 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>
<!-- end Technology section -->
<!-- begin Funding section -->
<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>
<!-- end Funding section -->
<!-- begin Current Status section -->
<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>
<!-- end Current Status section -->
<!-- begin Deployment section -->
<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>
<!-- end Deployment section -->