20 March 2015 OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale
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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.
© (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Josh Moore, Josh Moore, Melissa Linkert, Melissa Linkert, Colin Blackburn, Colin Blackburn, Mark Carroll, Mark Carroll, Richard K. Ferguson, Richard K. Ferguson, Helen Flynn, Helen Flynn, Kenneth Gillen, Kenneth Gillen, Roger Leigh, Roger Leigh, Simon Li, Simon Li, Dominik Lindner, Dominik Lindner, William J. Moore, William J. Moore, Andrew J. Patterson, Andrew J. Patterson, Blazej Pindelski, Blazej Pindelski, Balaji Ramalingam, Balaji Ramalingam, Emil Rozbicki, Emil Rozbicki, Aleksandra Tarkowska, Aleksandra Tarkowska, Petr Walczysko, Petr Walczysko, Chris Allan, Chris Allan, Jean-Marie Burel, Jean-Marie Burel, Jason Swedlow, Jason Swedlow, "OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale", Proc. SPIE 9413, Medical Imaging 2015: Image Processing, 941307 (20 March 2015); doi: 10.1117/12.2086370; https://doi.org/10.1117/12.2086370
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