The Open Microscopy Environment

Open image informatics for the biological sciences

Colin Blackburn, Chris Allan, Sébastien Besson, Jean Marie Burel, Mark Carroll, Richard K. Ferguson, Helen Flynn, David Gault, Kenneth Gillen, Roger Leigh, Simone Leo, Simon Li, Dominik Lindner, Melissa Linkert, Josh Moore, William J. Moore, Balaji Ramalingam, Emil Rozbicki, Gabriella Rustici, Aleksandra Tarkowska & 3 others Petr Walczysko, Eleanor Williams, Jason R. Swedlow

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

Original languageEnglish
Title of host publicationSoftware and Cyberinfrastructure for Astronomy IV
PublisherSPIE-International Society for Optical Engineering
Volume9913
ISBN (Electronic)9781510602052
DOIs
Publication statusPublished - 26 Jul 2016
EventSPIE Astronomical Telescopes + Instrumentation: Software and Cyberinfrastructure for Astronomy IV - Edinburgh International Conference Centre, Edinburgh, United Kingdom
Duration: 26 Jun 201630 Jun 2016
https://spie.org/conferences-and-exhibitions/past-conferences-and-exhibitions/astronomical-instrumentation-and-telescopes-2016 (Link to Conference details)

Conference

ConferenceSPIE Astronomical Telescopes + Instrumentation
CountryUnited Kingdom
CityEdinburgh
Period26/06/1630/06/16
Internet address

Fingerprint

Microscopy
format
Microscopic examination
microscopy
Imaging techniques
Imaging
files
application programming interface
platforms
Application programming interfaces (API)
Data structures
Data Model
Servers
Visualization
Java
Sharing
Astronomy
metadata
data management
Pathology

Keywords

  • Data management
  • File formats
  • Image analysis
  • Image management
  • Image repositories
  • Multi-dimensional data
  • Open-source software

Cite this

Blackburn, C., Allan, C., Besson, S., Burel, J. M., Carroll, M., Ferguson, R. K., ... Swedlow, J. R. (2016). The Open Microscopy Environment: Open image informatics for the biological sciences. In Software and Cyberinfrastructure for Astronomy IV (Vol. 9913). [991324] SPIE-International Society for Optical Engineering. https://doi.org/10.1117/12.2232291
Blackburn, Colin ; Allan, Chris ; Besson, Sébastien ; Burel, Jean Marie ; Carroll, Mark ; Ferguson, Richard K. ; Flynn, Helen ; Gault, David ; Gillen, Kenneth ; Leigh, Roger ; Leo, Simone ; Li, Simon ; Lindner, Dominik ; Linkert, Melissa ; Moore, Josh ; Moore, William J. ; Ramalingam, Balaji ; Rozbicki, Emil ; Rustici, Gabriella ; Tarkowska, Aleksandra ; Walczysko, Petr ; Williams, Eleanor ; Swedlow, Jason R. / The Open Microscopy Environment : Open image informatics for the biological sciences. Software and Cyberinfrastructure for Astronomy IV. Vol. 9913 SPIE-International Society for Optical Engineering, 2016.
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Blackburn, C, Allan, C, Besson, S, Burel, JM, Carroll, M, Ferguson, RK, Flynn, H, Gault, D, Gillen, K, Leigh, R, Leo, S, Li, S, Lindner, D, Linkert, M, Moore, J, Moore, WJ, Ramalingam, B, Rozbicki, E, Rustici, G, Tarkowska, A, Walczysko, P, Williams, E & Swedlow, JR 2016, The Open Microscopy Environment: Open image informatics for the biological sciences. in Software and Cyberinfrastructure for Astronomy IV. vol. 9913, 991324, SPIE-International Society for Optical Engineering, SPIE Astronomical Telescopes + Instrumentation, Edinburgh, United Kingdom, 26/06/16. https://doi.org/10.1117/12.2232291

The Open Microscopy Environment : Open image informatics for the biological sciences. / Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

Software and Cyberinfrastructure for Astronomy IV. Vol. 9913 SPIE-International Society for Optical Engineering, 2016. 991324.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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AU - Linkert, Melissa

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AU - Ramalingam, Balaji

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AU - Rustici, Gabriella

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AU - Swedlow, Jason R.

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Blackburn C, Allan C, Besson S, Burel JM, Carroll M, Ferguson RK et al. The Open Microscopy Environment: Open image informatics for the biological sciences. In Software and Cyberinfrastructure for Astronomy IV. Vol. 9913. SPIE-International Society for Optical Engineering. 2016. 991324 https://doi.org/10.1117/12.2232291