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Proceedings Paper • Open Access

OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale
Author(s): Josh Moore; Melissa Linkert; Colin Blackburn; Mark Carroll; Richard K. Ferguson; Helen Flynn; Kenneth Gillen; Roger Leigh; Simon Li; Dominik Lindner; William J. Moore; Andrew J. Patterson; Blazej Pindelski; Balaji Ramalingam; Emil Rozbicki; Aleksandra Tarkowska; Petr Walczysko; Chris Allan; Jean-Marie Burel; Jason Swedlow

Paper Abstract

The Open Microscopy Environment (OME) has built and released Bio-Formats, a Java-based proprietary file format conversion tool and OMERO, an enterprise data management platform under open source licenses. In this report, we describe new versions of Bio-Formats and OMERO that are specifically designed to support large, multi-gigabyte or terabyte scale datasets that are routinely collected across most domains of biological and biomedical research. Bio- Formats reads image data directly from native proprietary formats, bypassing the need for conversion into a standard format. It implements the concept of a file set, a container that defines the contents of multi-dimensional data comprised of many files. OMERO uses Bio-Formats to read files natively, and provides a flexible access mechanism that supports several different storage and access strategies. These new capabilities of OMERO and Bio-Formats make them especially useful for use in imaging applications like digital pathology, high content screening and light sheet microscopy that create routinely large datasets that must be managed and analyzed.

Paper Details

Date Published: 20 March 2015
PDF: 6 pages
Proc. SPIE 9413, Medical Imaging 2015: Image Processing, 941307 (20 March 2015); doi: 10.1117/12.2086370
Show Author Affiliations
Josh Moore, Univ. of Dundee (United Kingdom)
Glencoe Software, Inc. (United States)
Melissa Linkert, Glencoe Software, Inc. (United States)
Colin Blackburn, Univ. of Dundee (United Kingdom)
Mark Carroll, Univ. of Dundee (United Kingdom)
Richard K. Ferguson, Univ. of Dundee (United Kingdom)
Helen Flynn, Univ. of Dundee (United Kingdom)
Kenneth Gillen, Univ. of Dundee (United Kingdom)
Roger Leigh, Univ. of Dundee (United Kingdom)
Simon Li, Univ. of Dundee (United Kingdom)
Dominik Lindner, Univ. of Dundee (United Kingdom)
William J. Moore, Univ. of Dundee (United Kingdom)
Andrew J. Patterson, Univ. of Dundee (United Kingdom)
Blazej Pindelski, Univ. of Dundee (United Kingdom)
Balaji Ramalingam, Univ. of Dundee (United Kingdom)
Emil Rozbicki, Glencoe Software, Inc. (United States)
Aleksandra Tarkowska, Univ. of Dundee (United Kingdom)
Petr Walczysko, Univ. of Dundee (United Kingdom)
Chris Allan, Glencoe Software, Inc (United States)
Jean-Marie Burel, Univ. of Dundee (United Kingdom)
Jason Swedlow, Univ. of Dundee (United Kingdom)
Glencoe Software, Inc. (United States)

Published in SPIE Proceedings Vol. 9413:
Medical Imaging 2015: Image Processing
Sébastien Ourselin; Martin A. Styner, Editor(s)

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