The creation of the Open Microscopy Environment (OME) and impact of life sciences companies worldwide.
Submitting Institution
University of DundeeUnit of Assessment
Biological SciencesSummary Impact Type
TechnologicalResearch Subject Area(s)
Information and Computing Sciences: Artificial Intelligence and Image Processing
Summary of the impact
Led from Dundee by Prof Jason Swedlow FRSE, The Open Microscopy
Environment (OME) is an international consortium building tools to enable
the storage and analysis of biological image data. OME releases
Bio-Formats, an image format translation library, and OMERO, software for
the visualisation, management and analysis of image data recorded by
microscopes and high-content screening systems. OME software is
open-source and transforms the way researchers manage the vast amount of
image data routinely produced in research laboratories. Glencoe Software
is the commercial arm of OME and provides commercial licenses, support,
and customisation for OME's software tools to major industrial customers.
Underpinning research
Prof. Jason Swedlow FRSE (Professor of Quantitative Cell Biology
at the College of Life Sciences) is a world expert in the development of
pioneering new technology for viewing and analysing living cells using
digital microscopy. He has been in the vanguard of biologists adopting a
more quantitative and systematic approach to microscopy to extract
meaningful and reproducible results from image data (1,2,3). The
successful application of the green fluorescent protein (GFP) from the
jellyfish Aequorea victoria in 1994 as a genetically encoded
marker, with concomitant development of new live cell imaging systems has
also resulted in a massive increase in studies of the dynamics of
macromolecules and structures of living cells. However, the advent of this
new era in microscopy created a major problem in the management and
analysis of the substantial amounts of data collected as a result of this
innovation. Moreover, the bioinformatics tools required for
hypothesis-driven analysis of digital images were very immature in the
field.
Starting in 2000, Prof Swedlow's group at the University of Dundee
embarked on a research programme to create a pioneering image-management
system geared to the needs of quantitative microscopy that could be used
for probing cellular structure and dynamics and for performing cell based
screens. The major focus of the Open Microscopy Environment (OME) created
by Swedlow and his team was to develop software and protocols that would
allow image data from any microscope to be stored, shared and transformed
without loss of image data or information about the experimental setting,
the imaging system or the processing software. The concepts and first
implementation of OME were published in 2003 (3) and subsequent
publications from the University of Dundee have reported the development
of solutions for conventional digital microscopy and high-content
screening (4,5). Starting in 2005, Dundee's OME team started developing
OMERO, a modern open source data management system that used advanced
software engineering techniques to enable access, sharing, analysis, and
publication of complex, multi-dimensional image data. First released in
2007, OMERO has become the world-leading data management application for
light microscopy, and is now installed and in use at >3,500 sites
worldwide (6). OMERO does not replace or compete with commercial software
for controlling microscopes, acquiring images or performing image analysis
but instead serves as a neutral broker between otherwise incompatible
software. Dundee's OME team also contributes to Bio-Formats, a Java
library installed and in use at >50,000 sites worldwide that converts
>120 proprietary file formats to a common model, accessible by anyone.
In 2011, Jason Swedlow was awarded a £4.2 million Wellcome Trust
Strategic Award to continue support for the OME, as well as funding
development positions in nine satellite laboratories. In the same year,
Jason Swedlow was named BBSRC "Innovator of the Year" for the impact of
OME.
References to the research
Publications:
1. Andrews PD, Ovechkina Y, Morrice N, Wagenbach M, Duncan K, Wordeman L,
Swedlow JR. (2004) Aurora B regulates MCAK at the mitotic
centromere. Dev Cell. 6, 253-268.
(doi:10.1016/S1534-5807(04)00025-5) (Citations 271, Scopus Nov 2013)
2. Swedlow, J.R., Hu, K., Andrews, P.D., Roos, D.S., and Murray,
J.M. (2002) Measuring tubulin content in Toxoplasma gondii: a comparison
of laser-scanning confocal and wide-field fluorescence microscopy. Proc
Natl Acad Sci USA. 99, 2014-2019. (doi:10.1073/pnas.022554999)
(Citations 76, Scopus Nov 2013)
3. Swedlow, J.R., Goldberg, I., Brauner, E., and Sorger, P.K.
Informatics and quantitative analysis in biological imaging. (2003)
Science 300, 100-102 (doi:10.1126/science.1082602) (Citations 133,
Scopus Nov 2013)
4. Goldberg, I.G., Allan, C., Burel, J.M., Creager, D., Falconi, A.,
Hochheiser, H., Johnston, J., Mellen, J., Sorger, P.K. and Swedlow,
J.R. (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)
(Citations 92, Scopus Nov 2013)
5. Moore, J., Allan, C., Burel, J.M., Loranger, B., MacDonald, D., Monk,
J., and Swedlow, J.R. (2008) Open tools for storage and management
of quantitative image data. Methods Cell Biol. 85, 555-570. (doi:
10.1016/S0091-679X(08)85024-8) (Citations 16, Scopus Nov 2013)
6. 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., Patwardhan, A., Best, C., Kleywegt, G.J.,
Zanetti, G., and Swedlow, J.R. (2012) OMERO: flexible,
model-driven data management for experimental biology. Nat Methods 9,
245-253. (doi: 10.1038/nmeth.1896) (Citations 14, Scopus Nov 2013)
Key research grants relevant to this case study:
1. Wellcome Trust Technology Development Award (2002) Open image
informatics software and database for biological microscopy. Value:
£988,172. Grant Ref. 068046/Z/02/Z. Principal Grant Holder: J.R. Swedlow
2. Wellcome Trust Technology Development Award (2006) Open image
informatics software and database for biological microscopy. Value:
£612,849. Grant Ref. 080087/Z/06/Z. Principal Grant Holder: J.R. Swedlow
3. Wellcome Trust Technology Development Award (2008): The Open
Microscopy Environment: towards the development of a scientific data
management system. Value: £1,305,516. Grant Ref. 085982/Z/08/Z. Principal
Grant Holder: J.R. Swedlow
4. BBSRC Research Grant (2006): Open image informatics software
for biological microscopy. Value: £398,637. Grant Ref. BB/D00151X/1.
Principal Grant Holder: J.R. Swedlow;
5. BBSRC Research Grant (2010) Intuitive large-scale image
processing for biologists. Value: £350,064 Grant Ref. BB/I000755/1.
Principal Grant Holder: J.R. Swedlow
6. Wellcome Trust Strategic Award (2011): The open microscopy
environment — image informatics for biological sciences. Value: £4,230,140
Grant Ref. 095931/Z/11/Z. Principal Grant Holder: J.R. Swedlow.
Details of the impact
Beneficiaries (and nature of the benefits/impacts):
(a) UK Biotech (through the creation of Glencoe Software and their support
for Aridhia Informatics Ltd)
(b) Major biotechnology companies (by licensing software to PerkinElmer
(PE) and Applied Precision Inc for their commercial imaging platforms).
(c) All Pharma and Biotech companies using PE high-content screening
technology
(d) All academic translational programs using PE high-content screening
technology and/or OMERO (see (b))
(e) International publishing (by providing Rockefeller University Press
with Data Viewer solutions)
(f) The international biological and clinical research communities
handling image BigData (by providing data format, image storage and
analysis solutions)
The OME Data Model (first released in 2002), Bio-Formats (first released
in 2003) and OMERO (first released in 2007) have enabled the sharing and
analysis of image data as readily as genomic data. Some examples of how
OME is used, for example by BioBus, which provides hands-on science
education for Schools in the USA, are available on the OME web site (1). A
major impact is the uptake of OME image software and management tools by
multinational companies, which is provided to them through the Glencoe
Software spin-out, founded in late 2005 by Swedlow.
Impacts:
Glencoe Software (2) has tripled in size since its launch and by
2013 employed 13 people, with a revenue growth of 20-40% during the
assessment period. It has recently entered a partnership with Aridhia
Informatics Ltd, a Scottish-based company that specialises in
accessing, storing and analysing health-care information to create
innovative products for personalised therapies and improved patient
outcomes (3).
Glencoe Software provides commercial licenses, extensive data management
support, and customisation for OME's software tools to companies
delivering imaging solutions to their customers. OME's Bio-Formats
file translation library is the most comprehensive image file format
translator available and has been incorporated into several commercial
products. Moreover, as the data management solutions are continually
developed and supported, companies benefit by not only acquiring the right
to use them in their closed-source software but take advantage of the
open-source foundation of knowledge, specifications, and new software
produced by the OME Consortium. Examples of companies currently
distributing software platforms developed by OME and provided by Glencoe
Software through commercial licence include:
Applied Precision Inc
The first customer of Glencoe Software was Applied Precision Inc (http://www.api.com/),
which integrated the data management solutions provided by Glencoe with
its Deltavision imaging system. Glencoe Software collaborated with Applied
Precision to develop a customised version of OMERO called softWoRx DMS™,
which was installed on every DeltaVision image acquisition system sold
during the assessment period (4).
PerkinElmer
PerkinElmer, Inc. is a multinational technology corporation that operates
in 150 countries and produces instruments, diagnostics, and (bio)medical
imaging solutions. In 2008 PerkinElmer licensed OMERO from Glencoe
Software and has used it as the foundation for its successful Columbus™
platform for high-content screening and microscopy image storage,
management and analysis*. Columbus™ now dominates the market for data
management in high-content screening in Pharma and academia, and thus
makes major contributions to drug discovery and basic research (5). The
system is a commercial product, but supports the open source OME
applications. This adaptable feature enables images to be imported from
any other imaging system and is a major reason for the dominance of
Columbus™ in these markets (5,6).
*Note: PerkinElmer systems that incorporate the Columbus™ platform are
built in Cardiff.
Rockefeller University Press (RUP)
In 2008, Rockefeller University Press launched the JCB DataViewer,
the world's first on-line publication system for
multi-dimensional life sciences image data (http://jcb-dataviewer.rupress.org).
The JCB Data Viewer is a customised version of Bio-Formats and OMERO built
by Glencoe Software, in partnership with RUP. The DataViewer web browser
permits scientists to view, and share multi-dimensional image data
associated with articles published in The
Journal of Cell Biology. Currently, >280 articles and >980
figures are linked to >99,000 image datasets in the JCB DataViewer (7).
Harvard Medical School
Glencoe Software has licensed Bio-Formats and OMERO to Harvard Medical
School as the foundation for publishing data from its NIH-funded LINCS
project, which provides a resource for thousands of image-based assays of
well-known drug molecules (8) that is accessed by industry and academia.
Other measures of impact:
In 2011, the BBSRC announced Prof Swedlow as `Innovator of the Year' in
recognition OME as "a revolutionary venture into open source software"
(9). He received the prize from David Willetts MP, Minister for
Universities and Science, who spoke at the BBSRC Bioscience for Growth
business networking event in London on March 2011.
Sources to corroborate the impact
- Information about BioBus can be found on the Open Microscopy website
http://www.openmicroscopy.org/site/community/ome-stories
- Further information about Glencoe Software can be found at http://www.glencoesoftware.com
- Information about Aridhia Informatics Ltd and partnership with Glencoe
Software can be found at http://aridhia.com/about-us/our-partners
- Information regarding softWoRx DMS™ by Applied Precision Inc can be
found at
http://www.api.com/news/2008/12-13-2008.asp
- Information regarding the Columbus™ platform can be found at
http://www.perkinelmer.com/pages/020/cellularimaging/products/columbus.xhtml
- Press release by Perkin Elmer about the Columbus™ platform
http://www.perkinelmer.com/AboutUs/PressRoom/PressReleaseDetails/ArticleId/1621
- Information regarding the JCB Data Viewer provided by Rockefeller
University Press can be found at http://jcb.rupress.org/content/191/2/231.full
- Information regarding the HMS-LINCS software can be found at
http://lincs.hms.harvard.edu/resources/software/
- BBSRC Innovator of the Year announcement http://www.bbsrc.ac.uk/news/people-skills-training/2011/110325-pr-innovator-of-the-year.aspx