Please cite our work in your own publications to help us secure grant funding for future development of OME products.
The 2019 article introducing the pyramidal OME-TIFF extension:
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.
DOI: 10.1007/978-3-030-23937-4_1 PMID: 31579322 PMCID: PMC6774793
The 2010 article outlining the importance of metadata and introducing the OME Compliant Specification:
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
DOI: 10.1083/jcb.201004104 PMID: 20513764 PMCID: PMC2878938
The original OME Data Model paper from 2005:
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.
DOI: 10.1186/gb-2005-6-5-r47 PMID: 15892875 PMCID: PMC1175959
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
DOI: 10.1038/s41592-021-01326-w PMID: 34845388 PMCID: PMC8648559
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
DOI: 10.1083/jcb.201004104 PMID: 20513764 PMCID: PMC2878938
The original OMERO paper from 2012:
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
DOI: 10.1038/nmeth.1896 PMID: 22373911 PMCID: PMC3437820
OMERO for high content screening:
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
DOI: 10.1016/j.ymeth.2015.10.006 PMID: 26476368 PMCID: PMC4773399
Publishing and sharing with OMERO:
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
DOI: 10.1007/s00335-015-9587-6 PMID: 26223880 PMCID: PMC4602067
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
DOI: 10.1038/nmeth.4326 PMID: 28775673 PMCID: PMC5536224
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
DOI: 10.1126/science.1082602 PMID: 12677061 PMCID: PMC3522889
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OME source code is available under the GNU General public license or more permissive open source licenses, or through commercial license from Glencoe Software Inc.
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Version: 2024.10.24