OMERO: flexible, model-driven data management for experimental biology

Christopher 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

doi:10.1038/nmeth.1896

OMERO: flexible, model-driven data management for experimental biology

Christopher 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 PatwardhanChristoph Best, Gerard J. Kleywegt, Gianluigi Zanetti, Jason R. Swedlow

Research output: Contribution to journal › Article › peer-review

393 Citations (Scopus)

Abstract

Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.

Original language	English
Pages (from-to)	245-253
Number of pages	9
Journal	Nature Methods
Volume	9
Issue number	3
DOIs	https://doi.org/10.1038/nmeth.1896
Publication status	Published - 1 Mar 2012

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10.1038/nmeth.1896

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Allan, C., Burel, J.-M., Moore, J., Blackburn, C., Linkert, M., Loynton, S., MacDonald, D., Moore, W. J., Neves, C., Patterson, A., Porter, M., Tarkowska, A., Loranger, B., Avondo, J., Lagerstedt, I., Lianas, L., Leo, S., Hands, K., Hay, R. T., ... Swedlow, J. R. (2012). OMERO: flexible, model-driven data management for experimental biology. Nature Methods, 9(3), 245-253. https://doi.org/10.1038/nmeth.1896

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title = "OMERO: flexible, model-driven data management for experimental biology",

abstract = "Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.",

author = "Christopher Allan and Jean-Marie Burel and Josh Moore and Colin Blackburn and Melissa Linkert and Scott Loynton and Donald MacDonald and Moore, {William J.} and Carlos Neves and Andrew Patterson and Michael Porter and Aleksandra Tarkowska and Brian Loranger and Jerome Avondo and Ingvar Lagerstedt and Luca Lianas and Simone Leo and Katherine Hands and Hay, {Ron T.} and Ardan Patwardhan and Christoph Best and Kleywegt, {Gerard J.} and Gianluigi Zanetti and Swedlow, {Jason R.}",

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doi = "10.1038/nmeth.1896",

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Allan, C, Burel, J-M, Moore, J, Blackburn, C, Linkert, M, Loynton, S, MacDonald, D, Moore, WJ, Neves, C, Patterson, A, Porter, M, Tarkowska, A, Loranger, B, Avondo, J, Lagerstedt, I, Lianas, L, Leo, S, Hands, K, Hay, RT, Patwardhan, A, Best, C, Kleywegt, GJ, Zanetti, G & Swedlow, JR 2012, 'OMERO: flexible, model-driven data management for experimental biology', Nature Methods, vol. 9, no. 3, pp. 245-253. https://doi.org/10.1038/nmeth.1896

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T2 - flexible, model-driven data management for experimental biology

AU - Allan, Christopher

AU - Burel, Jean-Marie

AU - Moore, Josh

AU - Blackburn, Colin

AU - Linkert, Melissa

AU - Loynton, Scott

AU - MacDonald, Donald

AU - Moore, William J.

AU - Neves, Carlos

AU - Patterson, Andrew

AU - Porter, Michael

AU - Tarkowska, Aleksandra

AU - Loranger, Brian

AU - Avondo, Jerome

AU - Lagerstedt, Ingvar

AU - Lianas, Luca

AU - Leo, Simone

AU - Hands, Katherine

AU - Hay, Ron T.

AU - Patwardhan, Ardan

AU - Best, Christoph

AU - Kleywegt, Gerard J.

AU - Zanetti, Gianluigi

AU - Swedlow, Jason R.

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AB - Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.

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OMERO: flexible, model-driven data management for experimental biology

Abstract

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The Open Microscopy Environment: Image Informatics for Biological Sciences (Joint with Imperial College, Oxford University, Institut Pasteur, Carnegie-Mellon University, University of Wisconsin, Harvard Medical School & University of Edinburgh)

Aref#d: 21557. Isolation of Pooled Selected Gene Segments for Allele Discovery by Next Generation Sequencing (Tools and Resources Development Fund)

Aref#d: 21060. The Open Microscopy Environment: Towards the Development of a Scientific Data Management System

Quantitative Characterisation of Morphological and Phenotypic Changes During Microbial Cell Differentiation and Multicellular Behaviour

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OMERO: flexible, model-driven data management for experimental biology

Abstract

Access to Document

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Projects

The Open Microscopy Environment: Image Informatics for Biological Sciences (Joint with Imperial College, Oxford University, Institut Pasteur, Carnegie-Mellon University, University of Wisconsin, Harvard Medical School & University of Edinburgh)

Aref#d: 21557. Isolation of Pooled Selected Gene Segments for Allele Discovery by Next Generation Sequencing (Tools and Resources Development Fund)

Aref#d: 21060. The Open Microscopy Environment: Towards the Development of a Scientific Data Management System

Student theses

Quantitative Characterisation of Morphological and Phenotypic Changes During Microbial Cell Differentiation and Multicellular Behaviour

Cite this