Technology Feature | Published:

Tower of Babel

Nature volume 443, page 1021 (26 October 2006) | Download Citation


The Open Microscopy Environment (OME) first emerged from the recognition that an explosion in imaging data was imminent. Image files were becoming bigger and more complex, representing copious data on numerous parameters as well as experiment-specific 'metadata'. “The ability to provide links between an image, any processed versions of an image, the data describing the acquisition of that image, and any analytical results generated about that image is a critical capability,” says Jason Swedlow of the University of Dundee, UK.

When Swedlow, along with Ilya Goldberg at the US National Institute on Aging, Peter Sorger at the Massachusetts Institute of Technology, and researchers at the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin at Madison, officially launched the OME in 2001, the development of a universal file format was a top priority. “Proprietary file formats are one of the biggest problems in modern microscopy,” says the LOCI's Kevin Eliceiri. “There are about 30 or 40 major microscopy file formats, so we're speaking all of these different languages — it's the Tower of Babel.”

To combat this, the OME has developed a file format called OME-XML, which retains both image pixel data and experimental metadata in a readable XML-based file. The LOCI has since refined this format as the OME-TIFF, which still encapsulates metadata in XML but stores pixel data in a TIFF format. “We have the best of both worlds now, in that TIFF is probably the closest there is to a universal image format,” says Eliceiri.

Jason Swedlow helped launch the Open Microscopy Environment. Image: J. SWEDLOW

The OME also offers open-source software for image management and analysis, which uses these new formats. Swedlow acknowledges that OME software may prove challenging for less computer-savvy users, but says the developers are working hard to make it easier to use. Meanwhile, a growing number of commercial packages now not only recognize the OME formats, but also record data into them. Indeed, the efforts of Swedlow and his colleagues have won accolades from several manufacturers. “Maybe up to 15 or 20% of our development resources go towards reader updates,” says Michael Wussow of Bitplane in Zurich, “so we really like this idea of an Open Microscopy Environment.”

The OME also intends to tackle another weighty issue: handling and browsing increasingly bulky data sets. “We currently store about 50 terabytes of data from our imaging facility,” says Swedlow, “and the OME's goal is to provide software to handle data on this scale.” Of course, software isn't the whole answer, and significant investment in hardware and network infrastructure will be necessary for labs serious about imaging. “An enterprise-scale data-storage facility doesn't sound like hypothesis-driven research,” says Swedlow, “but it is a required tool for hypothesis-driven research using imaging.”


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