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/.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    et al. Metadata matters: access to image data in the real world. J. Cell Biol. 189, 777–782 (2010).

  2. 2.

    & Open source bioimage informatics for cell biology. Trends Cell Biol. 19, 656–660 (2009).

  3. 3.

    et al. The open microscopy environment (OME) data model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome Biol. 6, R47 (2005).

  4. 4.

    , & Bioimage informatics for experimental biology. Annu. Rev. Biophys. 38, 327–346 (2009).

  5. 5.

    et al. Unifying biological image formats with HDF5. Commun. ACM 52, 42–47 (2009).

  6. 6.

    et al. Scientific Data Management in the Coming Decade (Microsoft Research, Inc., 2005).

  7. 7.

    et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).

  8. 8.

    et al. Visualizing plant development and gene expression in three dimensions using optical projection tomography. Plant Cell 18, 2145–2156 (2006).

  9. 9.

    et al. The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251–1255 (2007).

  10. 10.

    , , , & Bisque: a platform for bioimage analysis and management. Bioinformatics 26, 544–552 (2010).

  11. 11.

    , , & Informatics and quantitative analysis in biological imaging. Science 300, 100–102 (2003).

  12. 12.

    et al. Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis. Nat. Genet. 42, 495–497 (2010).

  13. 13.

    Missing data imputation and haplotype phase inference for genome-wide association studies. Hum. Genet. 124, 439–450 (2008).

  14. 14.

    , , & Genotype imputation. Annu. Rev. Genomics Hum. Genet. 10, 387–406 (2009).

  15. 15.

    Announcing the JCB DataViewer, a browser-based application for viewing original image files. J. Cell Biol. 183, 969–970 (2008).

  16. 16.

    et al. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res. 39, D456–D464 (2011).

  17. 17.

    , & Image processing with ImageJ. Biophotonics International 11, 36–42 (2004).

  18. 18.

    et al. Engineering and algorithm design for an image processing API: a technical report on ITK—the insight toolkit. in Proceedings of Medicine Meets Virtual Reality (ed., J. Westwood) 586–592 (IOS Press, Amsterdam, 2002).

  19. 19.

    , , & An open-source software for navigating in multidimensional DICOM images. J. Digit. Imaging 17, 205–216 (2004).

  20. 20.

    et al. Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat. Methods 8, 246–249 (2011).

Download references

Acknowledgements

We thank E. Hill for helpful comments on the manuscript. Work on OME, Bio-Formats and OMERO in J.R.S.'s laboratory is supported by the Wellcome Trust (085982 and 095931) and the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/G022585 and BB/I000755). Work on OMERO Electron Microscopy Data Bank at the European Bioinformatics Institute is supported by the BBSRC (BB/G022577). Work on OMERO at the John Innes Center, Norwich is supported by Joint Information Systems Committee (REXDAT03).

Author information

Author notes

    • Christoph Best

    Present address: Google UK Ltd., London, UK.

Affiliations

  1. Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland, UK.

    • Chris Allan
    • , Jean-Marie Burel
    • , Colin Blackburn
    • , Scott Loynton
    • , Donald MacDonald
    • , William J Moore
    • , Andrew Patterson
    • , Michael Porter
    • , Aleksandra Tarkowska
    • , Brian Loranger
    • , Katherine Hands
    • , Ron T Hay
    •  & Jason R Swedlow
  2. Glencoe Software, Inc., Seattle, Washington, USA.

    • Chris Allan
    • , Jean-Marie Burel
    • , Josh Moore
    • , Melissa Linkert
    • , Carlos Neves
    •  & Jason R Swedlow
  3. John Innes Centre Norwich Research Park, Norwich, UK.

    • Jerome Avondo
  4. European Molecular B iology Laboratory– European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

    • Ingvar Lagerstedt
    • , Ardan Patwardhan
    • , Christoph Best
    •  & Gerard J Kleywegt
  5. CRS4, Pula, Italy.

    • Luca Lianas
    • , Simone Leo
    •  & Gianluigi Zanetti

Authors

  1. Search for Chris Allan in:

  2. Search for Jean-Marie Burel in:

  3. Search for Josh Moore in:

  4. Search for Colin Blackburn in:

  5. Search for Melissa Linkert in:

  6. Search for Scott Loynton in:

  7. Search for Donald MacDonald in:

  8. Search for William J Moore in:

  9. Search for Carlos Neves in:

  10. Search for Andrew Patterson in:

  11. Search for Michael Porter in:

  12. Search for Aleksandra Tarkowska in:

  13. Search for Brian Loranger in:

  14. Search for Jerome Avondo in:

  15. Search for Ingvar Lagerstedt in:

  16. Search for Luca Lianas in:

  17. Search for Simone Leo in:

  18. Search for Katherine Hands in:

  19. Search for Ron T Hay in:

  20. Search for Ardan Patwardhan in:

  21. Search for Christoph Best in:

  22. Search for Gerard J Kleywegt in:

  23. Search for Gianluigi Zanetti in:

  24. Search for Jason R Swedlow in:

Competing interests

C.A., J.-M.B., J.M., C.N., M.L. and J.R.S. are affiliated with Glencoe Software, Inc., an open-source US-based commercial company that contributes to OMERO.

Corresponding author

Correspondence to Jason R Swedlow.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Note

About this article

Publication history

Published

DOI

https://doi.org/10.1038/nmeth.1896

Further reading