The Open Microscopy Environment (OME): Open Image Informatics for the Biological Sciences

Abstract

Event Abstract Back to Event The Open Microscopy Environment (OME): Open Image Informatics for the Biological Sciences Jason R. Swedlow1* 1 University of Dundee, Centre for Gene Regulation and Expression, United Kingdom OME is a multi-site collaborative effort across academic laboratories and commercial entities that produces open tools to support data visualization, management, and analysis for biological imaging. All OME specifications and software are free, and all source code is available under GNU public "copyleft" licenses. With a strong foundation for biological light microscopy in place, OME has begun extending its coverage to High Content Screening (HCS), electron microscopy, scanning probe microscopy, digital pathology, and other emerging modes of biological imaging. OME develops and releases: • The OME Data Model and OME-TIFF file format (http://www.openmicroscopy.org/site/support/file-formats) provide a specification for saving and exchanging metadata in biological imaging. • The Bio-Formats file format library (http://openmicroscopy.org/site/products/bio-formats) provides an plug-in for ImageJ, Matlab, and many other software tools for converting data from proprietary file formats into an open, accessible format. Bio-Formats is installed and in use at >60,000 sites worldwide. (Linkert et al, 2010). • OMERO (http://openmicroscopy.org/site/products/omero) is a Java-based client-server application suite that combines an image metadata database, a binary image data repository and high performance visualization and analysis. OMERO works as an image data management system for a laboratory, department or institution. For computational analysis of biological image data, OMERO’s standardised interface and Bio-Formats provide a single mechanism for accessing image data and metadata regardless of original file format. OMERO includes interfaces for Java, C++ and Python to support standard image processing tools like ImageJ, Matlab, and CellProfiler, a scripting facility for Python-based data processing, and custom clients that enable remote image viewing, processing and analysis. Processed images, calculated regions-of-interest, and quantitative measurements can be stored using OMERO’s internal databases or in an HDF5-based tabular data store. Users can control access to their data, and make specific datasets as public or private as necessary. OMERO is installed and in use at >3,500 sites worldwide and powers several institutional image data repositories (e.g., http://srdr.stowers.org/). (Allan et al. 2012). OMERO and Bio-Formats are used in a number of commercial products, and run the JCB DataViewer (http://jcb-dataviewer.rupress.org), the first publication system for original image data in the life sciences. More information is available at http://openmicroscopy.org. Acknowledgements Work on OME, Bio-Formats and OMERO in JRS's lab is supported by the Wellcome Trust (Ref: 095931) and the BBSRC (Ref: BB/G022585 & BB/I000755). References Linkert, M., C.T. Rueden, C. Allan, J.M. Burel, W. Moore, A. Patterson, B. Loranger, J. Moore, C. Neves, D. Macdonald, A. Tarkowska, C. Sticco, E. Hill, M. Rossner, K.W. Eliceiri, and J.R. Swedlow. 2010. Metadata matters: access to image data in the real world. J. Cell. Biol. 189:777-782. Allan, C., J.M. Burel, J. Moore, C. Blackburn, M. Linkert, S. Loynton, D. Macdonald, W.J. Moore, C. Neves, A. Patterson, M. Porter, A. Tarkowska, B. Loranger, J. Avondo, I. Lagerstedt, L. Lianas, S. Leo, K. Hands, R.T. Hay, A. Patwardhan, C. Best, G.J. Kleywegt, G. Zanetti, and J.R. Swedlow. 2012. OMERO: flexible, model-driven data management for experimental biology. Nature methods. 9:245-253. Keywords: image informatics, Microscopy, data management, Open Source Software, digital pathology Conference: Imaging the brain at different scales: How to integrate multi-scale structural information?, Antwerp, Belgium, 2 Sep - 6 Sep, 2013. Presentation Type: Special topic or demo Topic: Handling of light and magnetic resonance microscopy data sets Citation: Swedlow JR (2013). The Open Microscopy Environment (OME): Open Image Informatics for the Biological Sciences. Front. Neuroinform. Conference Abstract: Imaging the brain at different scales: How to integrate multi-scale structural information?. doi: 10.3389/conf.fninf.2013.10.00017 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 01 Jul 2013; Published Online: 30 Aug 2013. * Correspondence: Prof. Jason R Swedlow, University of Dundee, Centre for Gene Regulation and Expression, Dundee, DD1 5EH, United Kingdom, j.r.swedlow@dundee.ac.uk Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Jason R Swedlow Google Jason R Swedlow Google Scholar Jason R Swedlow PubMed Jason R Swedlow Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.