University of Dundee

Image of whole zebrafish embryo heralds advances in the sharing of scientific information

09 Aug 2012

Exciting new advances have been made to technology developed at the University of Dundee to enhance the sharing of scientific data for the benefit of human health.

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.

Published scientific papers form the basis for researchers to carry out future work in related and different areas. However, 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.

The JCB DataViewer, an on-line data publishing tool, allows scientists and anyone in the world to directly view and download the original scientific image data associated exciting new discoveries.

This new version of the JCB DataViewer allows authors to archive and share large tiled images, enabling the scientific community to view and browse images of 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 on the DataViewer, published today, is an image of a whole zebrafish embryo, 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 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.

Glencoe Software has developed technology platforms based on open source software built by Open Microscopy Environment, based 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.

Jason Swedlow, President of Glencoe Software and co-founder of OME, 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.

"OME and Glencoe Software are excited to be a part of this important development and milestone in scientific publishing. OME's infrastructure has many possible applications, and the whole OME team is proud of the work enabling access and sharing of important image datasets in science."

Liz Williams, Executive Editor of JCB, said, "With the publication of very large tiled image arrays images, JCB is very excited to be taking this next step in the development of new publishing tools to promote data sharing and discovery in the field of cell biology."

The JCB DataViewer is available at http://jcb-dataviewer,rupress.org.

More information about the OME can be found athttp://openmicroscopy.org.

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