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 & 4 others Christoph Best, Gerard J. Kleywegt, Gianluigi Zanetti, Jason R. Swedlow

    Research output: Contribution to journalArticle

    177 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 languageEnglish
    Pages (from-to)245-253
    Number of pages9
    JournalNature Methods
    Volume9
    Issue number3
    DOIs
    Publication statusPublished - 1 Mar 2012

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    Middleware
    Information management
    Electron microscopy
    Interfaces (computer)
    Optical microscopy
    Screening
    Servers
    Software
    Microscopy
    Electron Microscopy
    Genotype
    Light
    Research
    Open source software
    Datasets

    Cite this

    Allan, Christopher ; Burel, Jean-Marie ; Moore, Josh ; Blackburn, Colin ; Linkert, Melissa ; Loynton, Scott ; MacDonald, Donald ; Moore, William J. ; Neves, Carlos ; Patterson, Andrew ; Porter, Michael ; Tarkowska, Aleksandra ; Loranger, Brian ; Avondo, Jerome ; Lagerstedt, Ingvar ; Lianas, Luca ; Leo, Simone ; Hands, Katherine ; Hay, Ron T. ; Patwardhan, Ardan ; Best, Christoph ; Kleywegt, Gerard J. ; Zanetti, Gianluigi ; Swedlow, Jason R. / OMERO : flexible, model-driven data management for experimental biology. In: Nature Methods. 2012 ; Vol. 9, No. 3. pp. 245-253.
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    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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    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

    OMERO : flexible, model-driven data management for experimental biology. / Allan, Christopher; Burel, Jean-Marie; Moore, Josh; Blackburn, Colin; Linkert, Melissa; Loynton, Scott; MacDonald, Donald; Moore, William J.; Neves, Carlos; Patterson, Andrew; Porter, Michael; Tarkowska, Aleksandra; Loranger, Brian; Avondo, Jerome; Lagerstedt, Ingvar; Lianas, Luca; Leo, Simone; Hands, Katherine; Hay, Ron T.; Patwardhan, Ardan; Best, Christoph; Kleywegt, Gerard J.; Zanetti, Gianluigi; Swedlow, Jason R.

    In: Nature Methods, Vol. 9, No. 3, 01.03.2012, p. 245-253.

    Research output: Contribution to journalArticle

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    T1 - OMERO

    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.

    N1 - Copyright 2012 Elsevier B.V., All rights reserved.

    PY - 2012/3/1

    Y1 - 2012/3/1

    N2 - 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/.

    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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    U2 - 10.1038/nmeth.1896

    DO - 10.1038/nmeth.1896

    M3 - Article

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    EP - 253

    JO - Nature Methods

    JF - Nature Methods

    SN - 1548-7091

    IS - 3

    ER -

    Allan C, Burel J-M, Moore J, Blackburn C, Linkert M, Loynton S et al. OMERO: flexible, model-driven data management for experimental biology. Nature Methods. 2012 Mar 1;9(3):245-253. https://doi.org/10.1038/nmeth.1896