Jason Swedlow - Abstract and Bio
Abstract
The Open Microscopy Environment: Informatics and Quantitative Analysis for Biological Microscopy
Jason R. Swedlow
Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland. jason@ifesci.dundee.ac.uk
Over the years, many advances have been made in instrumentation for light microscopy, and image analysis algorithms. However, computational cell biology remains out of reach for many investigators because file formats are proprietary, there are few facilities store, analyze and query numerical data or analysis results, integration of new algorithms into proprietary packages is difficult at best, and there are inadequate standards for sharing image data and results with colleagues. We have developed an open-source software framework to address these limitations called the Open Microscopy Environment (http://www.openmicroscopy.org). OME has three components—an open data model for biological imaging, standardised file formats and software libraries for data file conversion and software tools for image data management and analysis (http://www.openmicroscopy.org/downloads/).
The OME Data Model (http://www.ome-xml.org) has recently been updated to more fully support fluorescence filter sets, the requirement for unique identifiers, including LSIDs, and screening experiments using multi-well plates.
The OME-TIFF file format (http://www.loci.wisc.edu/ome/ome-tiff.html) and the Bio-Formats file format library (http://www.loci.wisc.edu/ome/formats.html) provide an easy-to-use set of tools for converting data from proprietary file formats. These resources enable access to data by different processing and visualization applications, and sharing of data between scientific collaborators.
The OME Server (http://openmicroscopy.org/downloads) is a Perl-based application for visualising, managing, and analysing microscope images and metadata. It includes a web browser interface, a threshold segmentation and tracking application (called "findSpots"), a MatLab interface, support for VisBio, LDAP, BioFormats. Now at version 2.6.1, the OME Server is specifically designed to support complex image analysis processes and includes a distribution system for parallel analysis.
Finally, we have recently released the Java-based OMERO server and client application suite that combines an image metadata database, a binary image data repository and an image rendering engine for rapid delivery of rendered images to the user. OMERO includes OMERO.server, a Java application running inside a JBOSS application server, a web-based OMERO.webadmin for user administration (that supports LDAP), OMERO.insight, a rich client developed in partnership with the Usable Image team (http://www.usableimage.com) for image data management, visualization, and analysis, and OMERO.importer, a client application tool that uses Bio-Formats for proprietary data file import into an instance of OMERO.server. The Current release of OMERO.server (Beta2.3; http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads) includes interfaces for C/C++ and Python to support a wider variety of client applications. This version of OMERO includes a number of new functions, including an image tagging system to allow flexible characterization and searching for image data. Demos of OMERO functionality are available at http://openmicroscopy.org/howto/. Roadmaps and future work are available at http://trac.openmicroscopy.org.uk/omero/roadmap.
Bio: Jason Swedlow
Jason Swedlow earned a BA in Chemistry from Brandeis University in 1982. He performed his PhD in Biophysics with Profs D. A. Agard and J. W. Sedat, finishing in 1994. Dr Swedlow was a postdoctoral fellow with Dr T. J. Mitchison at UCSF and then Harvard Medical School from 1994 and 1998, supported by a Damon Runyon Walter Winchell Cancer Research Fund Fellowship from 1995 to 1997. In 1998, Dr Swedlow established his own laboratory at the Wellcome Trust Biocentre, University of Dundee, Scotland as a Principal Investigator and Wellcome Trust Career Development Fellow. His lab focuses on studies of mitotic and interphase chromosome structure and dynamics and he has published numerous papers in these areas. In 2002, Dr Swedlow was awarded a Wellcome Trust Senior Research Fellowship. He participates as Faculty in the Analytical and Quantitative Microscopy Course. He is co-founder of OME (along with Peter Sorger and Ilya Goldberg).
