Citing OME | Open Microscopy Environment (OME)

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margin-left: 10px;">Explore</a></li> <li class="show-for-small-only"><a href="/explore/">Explore</a></li> </ul> </div> </div>  <a name="top-of-page"></a> <div class="callout large primary" id="bg-image-licensing"> <div class="row column text-center"> <h1>Citing OME</h1> <p class="hero-subheader small-12 medium-12">Please cite our work in your own publications to help us secure grant funding for future development of OME products.</p> </div> </div>  <hr class="whitespace"> <div class="row"> <div class="small-12 medium-4 columns"> <h3>OME-XML & OME-TIFF</h3> </div> <div class="small-12 medium-8 columns"> <p>The 2019 article introducing the pyramidal OME-TIFF extension:</p> <p class="citation">Besson S, Leigh R, Linkert M, Allan C, Burel JM, Carroll M, Gault D, Gozim R, Li S, Lindner D, Moore J, Moore W, Walczysko P, Wong F, Swedlow JR. (2019) Bringing Open Data to Whole Slide Imaging. Digital Pathology ECDP 2019. Lecture Notes in Computer Science, vol 11435.</p> <p>DOI: <a href="https://doi.org/10.1007/978-3-030-23937-4_1" target="_blank">10.1007/978-3-030-23937-4_1</a> PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31579322/" target="_blank">31579322</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6774793/" target="_blank">PMC6774793</a> </p> <p>The 2010 article outlining the importance of metadata and introducing the OME Compliant Specification:</p> <p class="citation">Melissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782. doi: 10.1083/jcb.201004104</p> <p>DOI: <a href="https://doi.org/10.1083/jcb.201004104" target="_blank">10.1083/jcb.201004104</a> PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20513764/" target="_blank">20513764</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878938/" target="_blank">PMC2878938</a> </p> <p>The original OME Data Model paper from 2005:</p> <p class="citation">Goldberg, I., C. Allan, J.-M. Burel, D. Creager, A. Falconi, H. Hochheiser, J. Johnston, J. Mellen, P.K. Sorger, and J.R. Swedlow. (2005) The Open Microscopy Environment (OME) Data Model and XML File: Open Tools for Informatics and Quantitative Analysis in Biological Imaging. Genome Biol. 6:R47.</p> <p>DOI: <a href="https://doi.org/10.1186/gb-2005-6-5-r47" target="_blank">10.1186/gb-2005-6-5-r47</a> PMID: <a class="pmid" href="https://www.ncbi.nlm.nih.gov/pubmed/15892875/" target="_blank">15892875</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1175959/" target="_blank">PMC1175959</a> </p> </div> </div>   <hr class="whitespace"> <div class="row"> <div class="small-12 medium-4 columns"> <h3>OME-NGFF</h3> </div> <div class="small-12 medium-8 columns"> <p class="citation">Josh Moore, Chris Allan, Sébastien Besson, Jean-Marie Burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer & Jason R. Swedlow (2021). OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies. Nature methods (2021). Published: 29 November 2021</p> <p>DOI: <a href="https://doi.org/10.1038/s41592-021-01326-w" target="_blank">10.1038/s41592-021-01326-w</a> PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34845388/" target="_blank">34845388</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8648559/" target="_blank">PMC8648559</a> </p> </div> </div>   <hr class="whitespace"> <div class="row"> <div class="small-12 medium-4 columns"> <h3>Bio-Formats</h3> </div> <div class="small-12 medium-8 columns"> <p class="citation">Melissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782. doi: 10.1083/jcb.201004104</p> <p>DOI: <a href="https://doi.org/10.1083/jcb.201004104" target="_blank">10.1083/jcb.201004104</a> PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20513764" target="_blank">20513764</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878938/" target="_blank">PMC2878938</a> </p> </div> </div>   <hr class="whitespace"> <div class="row"> <div class="small-12 medium-4 columns"> <h3>OMERO server and clients</h3> </div> <div class="small-12 medium-8 columns"> <p>The original OMERO paper from 2012:</p> <p class="citation">Chris Allan, Jean-Marie Burel, Josh Moore, Colin Blackburn, Melissa Linkert, Scott Loynton, Donald MacDonald, William J Moore, Carlos Neves, Andrew Patterson, Michael Porter, Aleksandra Tarkowska, Brian Loranger, Jerome Avondo, Ingvar Lagerstedt, Luca Lianas, Simone Leo, Katherine Hands, Ron T Hay, Ardan Patwardhan, Christoph Best, Gerard J Kleywegt, Gianluigi Zanetti & Jason R Swedlow (2012) OMERO: flexible, model-driven data management for experimental biology. Nature Methods 9, 245–253. Published: 28 February 2012</p> <p>DOI: <a href="https://doi.org/10.1038/nmeth.1896" target="_blank">10.1038/nmeth.1896</a> PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22373911" target="_blank">22373911</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3437820/" target="_blank">PMC3437820</a></p> <p>OMERO for high content screening:</p> <p class="citation">Simon Li, Sébastien Besson, Colin Blackburn, Mark Carroll, Richard K. Ferguson, Helen Flynn, Kenneth Gillen, Roger Leigh, Dominik Lindner, Melissa Linkert, William J. Moore, Balaji Ramalingam, Emil Rozbicki, Gabriella Rustici, Aleksandra Tarkowska, Petr Walczysko, Eleanor Williams, Chris Allan, Jean-Marie Burel, Josh Moore, Jason R. Swedlow (2016) Metadata management for high content screening in OMERO. Methods 96, 27-32. Published: 1 March 2016</p> <p>DOI: <a href="https://doi.org/10.1016/j.ymeth.2015.10.006" target="_blank">10.1016/j.ymeth.2015.10.006</a> PMID: <a class="pmid" href="https://www.ncbi.nlm.nih.gov/pubmed/26476368/" target="_blank">26476368</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773399/" target="_blank">PMC4773399</a></p> <p>Publishing and sharing with OMERO:</p> <p class="citation">Jean-Marie Burel, Sébastien Besson, Colin Blackburn, Mark Carroll, Richard K. Ferguson, Helen Flynn, Kenneth Gillen, Roger Leigh, Simon Li, Dominik Lindner, Melissa Linkert, William J. Moore, Balaji Ramalingam, Emil Rozbicki, Aleksandra Tarkowska, Petr Walczysko, Chris Allan, Josh Moore, Jason R. Swedlow (2015) Publishing and sharing multi-dimensional image data with OMERO. Mammalian Genome 26, 441-447. Published 30 July 2015</p> <p>DOI: <a href="https://doi.org/10.1007/s00335-015-9587-6" target="_blank">10.1007/s00335-015-9587-6</a> PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26223880/" target="_blank">26223880</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602067/" target="_blank">PMC4602067</a></p> </div> </div>   <hr class="whitespace"> <div class="row"> <div class="small-12 medium-4 columns"> <h3>Image Data Resource (IDR)</h3> </div> <div class="small-12 medium-8 columns"> <p class="citation">Eleanor Williams, Josh Moore, Simon W. Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Bálint Antal, Richard K. Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E. Carazo Salas, Jason R. Swedlow (2017) The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nature Methods 14(8), 775-781. Published 19 June 2017</p> <p>DOI: <a href="https://doi.org/10.1038/nmeth.4326" target="_blank">10.1038/nmeth.4326</a> PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28775673/" target="_blank">28775673</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536224/" target="_blank">PMC5536224</a></p> </div> </div>   <hr class="whitespace"> <div class="row"> <div class="small-12 medium-4 columns"> <h3>The original OME vision</h3> </div> <div class="small-12 medium-8 columns"> <p class="citation">Swedlow JR, Goldberg I, Brauner E, Sorger PK (2003) Informatics and quantitative analysis in biological imaging. Science 300(5616), 100-2. Published 4 April 2003</p> <p>DOI: <a href="https://doi.org/10.1126/science.1082602" target="_blank">10.1126/science.1082602</a> PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12677061/" target="_blank">12677061</a> PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522889/" target="_blank">PMC3522889</a> </p> </div> </div>  <hr class="whitespace">  <div class="text-center"> <a id="back-to-top" href="#top-of-page"><i class="fa fa-arrow-up"></i> back to top</a> </div>  <hr class="whitespace"> <div id="footer" class="callout large secondary"> <div class="row"> <div class="small-12 medium-4 columns"> <div class="medium-4"><a href="/index.html"><img class="footer-logo" src="/img/logos/ome-main-nav.svg" alt="OME logo" /></a></div> <p>© 2005-2025 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>OME source code is available under the <a href="https://www.gnu.org/copyleft/gpl.html">GNU General public license</a> or more permissive open source licenses, or through commercial license from <a href="https://www.glencoesoftware.com" target="_blank">Glencoe Software Inc.</a><br/>OME, Bio-Formats, OMERO, IDR and their associated logos are trademarks of <a href="https://www.glencoesoftware.com" target="_blank">Glencoe Software Inc.</a>, which holds these marks to protect them on behalf of the OME community.</p> <p class="tiny-print" style="float:left;">[ <a href="/site-map/">Site Map</a> ]</p> <p class="tiny-print" style="float:right;">Version: 2025.02.05</p> </div> <div class="medium-2 columns"> <h6>Learn About Us</h6> <ul class="menu vertical"> <li><a href="/about/">Who We Are</a></li> <li><a href="/teams/">Our Team</a></li> <li><a href="/explore/">What We Can Do</a></li> <li><a href="/news/">What We’re Up To</a></li> <li><a href="/events/ome-community-meeting-2024/">OME 2024</a></li> <li class="hide-for-large-only"> </li> </ul> </div> <div class="medium-2 columns"> <h6>Try Our Products</h6> <ul class="menu vertical"> <li><a href="/omero/downloads/">OMERO <span class="badge">Download</span></a></li> <li><a href="/bio-formats/downloads">Bio-Formats <span class="badge">Download</span></a></li> <li><a href="/ome-files/downloads">OME Files <span class="badge">Download</span></a></li> <li class="hide-for-large-only"> </li> </ul> </div> <div class="medium-2 columns"> <h6>Knowledge Base</h6> <ul class="menu vertical"> <li><a href="/support/">Support</a></li> <li><a href="/docs/">Documentation</a></li> <li><a href="https://omero-guides.readthedocs.io/">User Guides</a></li> <li><a href="https://www.openmicroscopy.org/forums">Forum</a></li> <li><a href="https://www.openmicroscopy.org/security/advisories/">Security Advisories</a></li> <li class="hide-for-large-only"> </li> </ul> </div> <div class="medium-2 columns end"> <h6>OME Public</h6> <ul class="menu vertical"> <li><a href="https://bsky.app/profile/openmicroscopy.org" target="_blank"><i class="fa fa-brands fa-bluesky"></i> Bluesky</a></li> <li><a href="https://www.linkedin.com/company/ome---open-microscopy-environment" target="_blank"><i class="fa fa-fw fa-brands fa-linkedin-in"></i> LinkedIn</a></li> <li><a href="https://www.facebook.com/openmicroscopy" target="_blank"><i class="fa fa-fw fa-brands fa-facebook-f"></i> Facebook</a></li>  <li><a href="/on-the-web/" target="_blank"><i class="fa fa-globe"></i> On the Web</a></li> <li class="hide-for-large-only"> </li> </ul> </div> </div> </div> <script src="/js/vendor/jquery-3.7.1.min.js"></script> <script src="/js/vendor/what-input.js"></script> <script src="/js/vendor/foundation.js"></script> <script src="/js/app.js"></script> <script> $(document).foundation(); try { // helper function to filter out empty paths (trailing slash) var omitEmpty = function(el) { return el.trim() !== ''}; // extract last path bit from url var paths = document.location.pathname.split('/').filter(omitEmpty); var path = paths[paths.length-1]; // helper function to find and set active option var setActiveNavOption = function(el) { var subPaths = el.href.split('/').filter(omitEmpty); var subPath = subPaths[subPaths.length-1]; if (subPath === path) { $(el).addClass('is-active'); return true } return false; } // check if we have a .header-subnav match? var hasSubMenu = false; $(".header-subnav li a").each(function(i, el) { var isMatch = setActiveNavOption(el); if (isMatch) { hasSubMenu = true; return false; } }); // find corresponding path bit for .menu-subnav option if (hasSubMenu && paths.length > 1) { var parentPath = paths[paths.length-2]; if (parentPath !== 'omero') path = parentPath; } // set .menu-subnav option $(".menu-subnav li a").each(function(i, el) { if (setActiveNavOption(el)) return false; }); } catch(ignored) {} </script> </body> </html>

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Citing OME | Open Microscopy Environment (OME)