13 August 2012
DataViewer image goes viral
Caption: Advances in "virtual nanoscopy" enable the generation of large-scale composite images of biological tissues, as described in The Journal of Cell Biology (JCB) and made accessible through an upgrade to theJCB DataViewer web application. Users can "zoom in" from a high-resolution, composite image of a zebrafish embryo (top) to detailed images of tiny subcellular structures (bottom).
Credit: Williams, E.H., et al. 2012. J. Cell Biol. doi:10.1083/jcb.201207117
An image of a whole zebrafish embryo, available online thanks to data sharing technology developed at the University of Dundee, has been viewed millions of times since it was uploaded a week ago.
On Monday, 6th August, Glencoe Software, a company founded by the University's Professor Jason Swedlow, has announced a new update to the Journal of Cell Biology (JCB) DataViewer, the world's first system for sharing and archiving published scientific image data.
The traditional method of publishing papers has its limitations as it has been impossible to share or publish the very large, complex datasets collected in laboratories all over the world can't be shared or published, either in print, or now in the age of the internet-until now.
This new version of the JCB DataViewer allows authors to archive and share large tiled images, allowing the scientific community to view and browse images tissues or even whole plants and animals. It makes these very large datasets, often 100 Gigabytes or larger, readily available via a standard browser interface so they can be viewed and mined for information using on-line interactive tools.
The first example of the new type of image available, the whole zebrafish embryo, is made up of more than 26,000 tiled images recorded on an electron microscope. The tiles have been stitched together with software developed by scientists at the Leiden University Medical Center in the Netherlands that allows thousands of tiles to be aligned rapidly and accurately.
The image was being accessed at a rate of 300 hits per second in the aftermath of publication, with coverage of the breakthrough appearing in social and mainstream media across the globe.
Professor Swedlow, President of Glencoe Software, said, "Public availability of these datasets creates opportunities for further discovery by scientists beyond those that performed the original experiments.
"This is the first time that it has been possible to make an image of the kind mapped of a whole fish embryo by the Dutch researchers available online at this resolution. This allows scientists to view the constituents of tissues and other complex organisms, which open new directions to take their research in."
The fully stitched image comprises 281 Giga pixels. Displaying it in a web browser allows scientists the unprecedented opportunity to view the constituents of an organism at very high resolution. As tiled images are common in many different imaging applications, including light microscopy and digital pathology, the new technology also opens the doors to these new types of data.
The JCB DataViewer is built and run by Glencoe Software, from offices within the University's College of Life Sciences, using open source technology developed by the Open Microscopy Environment team at Dundee.
Founded in 2000, OME builds and releases software tools for the analysis of very large scientific image datasets. Its tools are used globally throughout the academic and scientific communities.
As a member of the OME Consortium, Glencoe Software has used OME's technology to build many different products, including the JCB DataViewer, and various other solutions for microscopy and high content screening in the academic and pharmaceutical markets.
The JCB DataViewer is available at http://jcb-dataviewer,rupress.org.
More information about the OME can be found at http://openmicroscopy.org.
To find out more about Glencoe Software visit http://glencoesoftware.com.
For media enquiries contact:
Grant Hill
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University of Dundee
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