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JIC and JISC effort to promote open bioimaging

5 April 2011

The field of biological imaging has seen incredible advances due to new imaging techniques and molecular markers. This is producing large amounts of data, and storing, manipulating and processing this data presents a challenge to science.

A solution to this problem is the Open Microscopy Environment (OME). OME is a multi-site collaborative effort among academic laboratories and a number of commercial entities that produces open tools to support data management for biological light microscopy. OME is developed as a joint project between research-active laboratories at Dundee, NIA Baltimore, Harvard Medical School and LOCI. In addition, OME has active collaborations with many imaging and informatics groups.

JIC Bio-imaging data

JIC Bio-imaging data, provided by Karen Lee and Jerome Avondo

The John Innes Centre, in partnership with JISC, the body responsible for funding information and communications technology (ICT) services for further education and research councils are working to contribute to the OME effort. A platform is being developed at the JIC to allow for better management of the imaging data, for instance by recording the processing algorithms and parameters that are used to produce results. This ensures that there is a strong link between images, software and results, which is of vital importance in the scientific field.

As part of the project, the JIC team is working with partners on the Norwich Research Park, within the Biotechnology and Biological Sciences Research Council (BBSRC) and also the wider bio-imaging community to disseminate their experiences and contribute to the wider adoption of the OME platform. As part of this, the John Innes Centre and the OME team are organising a series of lectures and workshops to allow users and developers to learn more about the OME platform.

Among the speakers is Professor Jason Swedlow of the University of Dundee, co-founder of the Open Microscopy Environment. Jason was recently named as the BBSRC's Innovator of the Year for his work on this. Jerome Avondo of the John Innes Centre will talk about how he is integrating his tools with OME to extend the visualisation and analysis capabilities.

Other speakers will talk about how OME is used at Imperial College London, the University of Geneva as well as the European Bioinformatics Institute, where a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures has been set up.  This will be followed by a two-day workshop run by OME and the JIC experts, who will give personal tuition demonstrating the functionality of the platform.

The event is sponsored by B2net, Perkin Elmer and Mathworks.

  • B2net has a long history of working with research sector customers. Many of its clients have faced similar challenges including high performance requirements for data processing, peaks in system load at key times within projects, increasing financial, management and sharing constraints. All this makes putting together the correct solution a huge challenge. B2net believe that the best way to approach these issues is to begin with gaining an in-depth understanding of their clients' data requirements, then applying skills and years of experience to ensure that they deliver the correct solution using proven technology and at an acceptable cost.
  • PerkinElmer uses OMERO for its Columbus® Image Data Management and Analysis System. Columbus allows scientists to manage, view, annotate and measure images from anywhere via the Internet. The system utilizes the OMERO server, developed by the
    OME, which enables it to support a wide range of file formats, allowing flexible, rapid and high performance analysis of images
    regardless of their origin.
  • MathWorks produces mathematical computing software for engineers, scientists, mathematicians, and researchers. MATLAB, the language of technical computing, is a programming environment for algorithm development, data analysis, visualization, and numeric computation which plays a central role the scientific workflow



BBSRC is the UK funding agency for research in the life sciences. Sponsored by Government, BBSRC annually invests around £470M in a wide range of research that makes a significant contribution to the quality of life in the UK and beyond and supports a number of important industrial stakeholders, including the agriculture, food, chemical, healthcare and pharmaceutical sectors.

BBSRC provides institute strategic research grants to the following:

  • The Babraham Institute
  • Institute for Animal Health
  • Institute of Biological, Environmental and Rural Sciences (Aberystwyth University)
  • Institute of Food Research
  • John Innes Centre
  • The Genome Analysis Centre
  • The Roslin Institute (University of Edinburgh)
  • Rothamsted Research

The Institutes conduct long-term, mission-oriented research using specialist facilities. They have strong interactions with industry, Government departments and other end-users of their research.

External contact

11 October 2005

The following stories appear in the October 2005 edition of Business, the quarterly magazine of research highlights from the Biotechnology and Biological Sciences Research Council (BBSRC).

Controlling 'superpests'
Scientists have developed a new technique that helps make pesticides more effective by removing insects’ ability to exhibit resistance. Their research will extend the effective life of current pesticides, reduce the amount that needs to be sprayed and remove the need for farmers to move to stronger and more harmful chemicals. The new technique relies on applying a chemical to block the insect’s processes that can degrade a pesticide. With the pests newly rendered helpless farmers can apply pesticide to kill them.
(Page 13)

Dr Graham Moores, Rothamsted Research, Tel: 01582 763133 ext 2483,

Fruit fly studies open new avenue in cancer research
Researchers have discovered a family of amino acid transporters that are powerful growth promoters in fruit flies. When the transporters were overexpressed in a fly, its cells became hypersensitive to insulin-like molecules in the body that have a long-term role in promoting cell growth in development and cancer, and the cells grew excessively. If the equivalent genes in humans have the same effect then this discovery could lead to new drugs or even dietary advice that could block their activity and slow down the growth of tumours.
(Page 20)

Dr Deborah Goberdhan, University of Oxford, Tel: 01865 282662, e-mail:

Gene delivery vehicle for skeletal regeneration
UK scientists are working on new methods to regenerate cartilage and bone by delivering genes to stem cells within the body to instruct them to turn into bone cells. The new research will use tiny nanoscopic systems that cross the surface of a stem cell and then deliver the genes into that prompt the cell to turn into a bone cell. This method of gene delivery could provide significant healthcare benefits as trauma, degenerative disease and bone loss with old age all lead to patients needing orthopaedic procedures that require new bone.
(Page 26)

Professor Richard Oreffo, University of Southampton, Tel: 023 8079 8502, e-mail:

'Ending up' with antibody production
Scientists are pioneering a new technique to produce large numbers of antibodies quickly and reliably and this is being used to help the study of dangerous bacteria. The new technique harnesses the unique properties of the C-terminus of a protein to produce a large number of antibodies that will only bind to a specific protein. The antibodies can then be used to identify, count and track the proteins. Proteins are central to many areas of bioscience research as they are often the targets for vaccines, the raw materials for bioprocessing or are employed as environmental biomarkers. Production of panels of antibodies that previously took years may now be possible in just weeks.
(Page 14)

Dr Rob Edwards, Imperial College Hammersmith Hospital, Tel: 020 8383 2055,

Building proteins on demand
A multidisciplinary team of researchers is developing new tools to direct the evolution of proteins, a move that will help the search for new anti-HIV drugs. The scientists have developed an efficient methodology for generating every possible mutation of a single protein and then assembling this into a library to identify which variations are resistant to drugs and which are not. This information can then be used to develop and validate new drugs.
(Page 9)

Dr Cameron Neylon, University of Southampton, e-mail:

Bringing physical forces to bear
World-leading laser facilities at the Rutherford Appleton Laboratory in Oxfordshire will be harnessed for biological studies thanks to joint funding from two Research Councils. A new laser system will study the bonds between atoms by looking at the unique frequency of their vibration. The new system will be able to take measurements of these ‘vibrational fingerprints’ at a scale so small that they will by able to study how cells repair damaged DNA, how proteins fold and develop new ways of detecting cancerous and pre-cancerous cells.
(Page 6)

Professor Tony Parker, CCLRC Rutherford Appleton Laboratory, Tel: 01235 445109, e-mail:

‘Model gut’ moves to commercialisation
Researchers at the Institute of Food Research in Norwich are moving closer to turning ten years of research on the workings of the human gut into a computer controlled model that will enable scientists to predict the digestive processes of human gut using real food and medicines. The result will be a revolutionary research tool that will enable researchers to examine the physical, chemical and biochemical functions of the gut as a whole.
(Page 3)

Zoe Dunford, Institute of Food Research, Tel: 01603 255111, e-mail:



The Biotechnology and Biological Sciences Research Council (BBSRC) is the UK funding agency for research in the life sciences. Sponsored by Government, BBSRC annually invests around £380 million in a wide range of research that makes a significant contribution to the quality of life for UK citizens and supports a number of important industrial stakeholders including the agriculture, food, chemical, healthcare and pharmaceutical sectors.