Open image informatics software for biological microscopy

Lead Research Organisation: University of Dundee


Biological microscopy has always required an imaging capability: traditionally, an image of a sample was drawn on paper, or with the advent of light-sensitive film, recorded on media that conveniently allowed reproduction. However, the application of digital detectors to microscopy has converted the biological microscope into a quantitative assay device. The clinical and research applications for digital imaging microscopy are enormous, but these applications generate large amounts of data/a single time-lapse image can easily be 500 Mbytes. Four years ago, we began developing a data management tool for digital biological microscopy. Our project, the Open Microscopy Environment (OME; is now the leading provider of open source image management software for biological microscopy. This proposal seeks funds to support the integration of image data storage technology created by OME with genome sequencing data generated over the last ten years. The genome sequences of humans and many of the organisms used in modern biomedical research are now known and available on the Web (e.g., However, there is an increasingly rich set of accessory images showing effects of genetic mutations, gene expression, etc. that should be served by these sites, but no standard data format is available to allow delivery or sharing of this information with or between researchers. We will therefore incorporate the experimental data models built by other projects into the existing OME Data Model that describes the results of an imaging experiment, and develop tools to help scientists record experimental data about an imaging experiment (e.g., kinds of cells, gene mutations) in a single, coherent, shareable format. Finally, as the OME project grows, we have real need for resources for generating user-targeted documentation, FAQ's, etc., as well as managing user and developer questions. Currently, our developers are providing these services, but we have no resources for managing or logging contacts, and ensuring coherent support is provided. This support will go a long way to ensuring the usefulness and dissemination of the OME tools.

Technical Summary

Biological imaging is now used as an assay technique, most recently in time-lapse multichannel fluorescence imaging of cellular dynamics and in high-content genomic or small molecule screens. Maintaining critical contextual descriptions (e.g., cell lines, mutants, microscope configuration), the relationships between images, annotations and quantitative analyses while preventing data loss during file format migration or data exchange with collaborators is a major challenge for any cell biologist. Our project, the Open Microscopy Environment (OME; solves this problem with a Data Model that simultaneously defines the relationships between complex data types and provides a mechanism for changes to the Data Model to support changing experimental requirements. However, the OME Data Model is focused on capturing image metadata. Now that mature experimental ontologies are available from MGED, GO, and OBO, we will incorporate the appropriate parts of these models into the OME Data Model to generate a fully functional data model for biological microscopy. In addition, we will evaluate, and if necessary update existing freely available tools for data capture (e.g., Protege) so that not only microscope image data, but also all experimental metadata, are easily entered by the user into the data management tools provide by OME. Finally, we will initiate a user and developer support system for OME, to ensure that feedback and requests are properly managed and supported.


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Linkert M (2010) Metadata matters: access to image data in the real world. in The Journal of cell biology

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Swedlow JR (2009) Bioimage informatics for experimental biology. in Annual review of biophysics

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Swedlow JR (2009) Open source bioimage informatics for cell biology. in Trends in cell biology

Description OME's efforts are focussed completely on data models, specifications and software tools for biological microscopy. We have deliberately limited the scope of our work, and especially our data modelling to imaging-essentially, our tools are focussed on everything that occurs AFTER a user sits down at a microscope, and have left the modelling and definition of experimental protocols, reagents, biological systems to others. In this project (BB/D00151/X), we proposed the extension of OME's tools, with the aim of integrating many of the existing tools and specifications from other projects into OME applications, specifically with the aim of integrating experimental definitions like MAGE-ML and specific ontologies into OME applications. This work has been successful, with the development and release of OMERO.editor, a cross-platform Java application that uses defined templates and protocols to capture experimental data, provides an indexed search facility, and serves as a bridge between a user's own customised descriptions and defined data specifications and ontologies. A full description of the use and scope of the EXISTING application is available ( and a demonstration of this application is available as a screencast video ( OMERO.editor was first released in June 2008 as a standalone application that integrated a user's own definitions and protocols, defined data models (e.g., MAGE-ML, OME-XML, Gel-ML), and any ontology available on OLS ( With the release of OMERO-Beta3.1 (Oct 2008), the standalone OMERO.editor has been enhanced to include a smart text parser to convert text protocols into fields in OMERO.editor (and thus parseable and searchable data structures) and CSV importer that enables any spreadsheet file (including tab-delimited MAGE-TAB) to be imported into OMERO.editor (see Moreover, OMERO.editor files can be uploaded to an OMERO server and indexed using the facility, and viewed within the data management, visualization, and analysis client application, OMERO.insight.
Exploitation Route OMERO.editor is a standalone experimental metadata application that can be used to store data for many different experiments. Several novel uses in many different areas have been mentioned on our OME Forums.
Sectors Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology

Description This was the first example of using structured annotations, defined by ontologies available in the Ontology Lookup Service in the OMERO system. This was then translated by Glencoe Software into the CELL Image Library ( which used the underlying annotation technology to annotation several thousand publicly submitted images with terms from a defined set of ontologies.
First Year Of Impact 2008
Sector Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology
Impact Types Societal

Title OMERO.editor 
Description We developed developed and released OMERO.editor, a cross-platform Java application that uses defined templates and protocols to capture experimental data, provides an indexed search facility, and serves as a bridge between a user?s own customised descriptions and defined data specifications and ontologies. 
Type Of Technology Software 
Year Produced 2008 
Impact No actual Impacts realised to date 
Title The OMERO Platform 
Description OME Remote Objects (OMERO) is a modern client-server software platform for visualizing, managing, and annotating scientific image data. OMERO lets you import and archive your images, annotate and tag them, record your experimental protocols, and export images in a number of formats. It also allows you to collaborate with colleagues anywhere in the world by creating user groups with different permission levels. OMERO consists of a Java server, several Java client applications, as well as Python and C++ bindings and a Django-based web application. 
Type Of Technology Software 
Year Produced 2009 
Open Source License? Yes  
Impact OMERO powers a large number of public image data repositories, and is installed in >4,000 sites worldwide. Please note-- the year of output realisation is incorrect, as it is has been a development project running since 2005. 
Company Name Glencoe Software Ltd & Glencoe Software Inc 
Description Glencoe Software is the commercial arm of the OME Consortium., providing commercial direct and OEM licensing of OME's software, Bio-Formats and OMERO. 
Year Established 2005 
Impact Glencoe Software licenses OMERO to PerkinElmer Inc as the foundation for Columbus, the market-leading image data management fproduct for high content screening and multi-dimensional microscopy. ( Glencoe Software customised OMERO to build the JCB DataViewer, the world's first on-line scientific image data publication system. (