Data integration with the help of the INCF Digital Atlasing Infrastructure

The goal of the INCF Digital Atlasing Program is to make the rapidly growing collection of multidimensional data widely accessible and useable to the international scientific community. A milestone of this project, the integration of three major online mouse brain resources, has now been achieved.

Digital brain atlases are useful as references, analysis tools and data integration frameworks for applications in neuroscience. Atlases and supporting tools are therefore crucial resources in facilitating and promoting data sharing. With the advance of informatics in the life sciences, neuroscientists have advocated the use of digital atlases as gateways to data of multiple modalities and from distributed locations. This infrastructure places digital atlases as hubs of a system that allows easy access to data and tools from multiple sources, and in addition, facilitates scientific discovery, data analysis and standardization. Such a framework would be both helpful to individual neuroscientists and a powerful tool for furthering neuroinformatics research.

One of the key accomplishments of the INCF Digital Atlasing Program is a standardized digital atlasing framework for sharing rodent brain data, consisting of Waxholm Space (WHS) and a supporting web-based Digital Atlasing Infrastructure (DAI). The Waxholm Space (WHS) is a spatial standard, a virtual coordinate system that unifies 3D mouse brain data from different formats and online atlases. It was developed by the INCF Standards in Digital Atlasing Task Force, based on recommendations from community representatives. The Digital Atlasing Infrastructure (DAI) supports use of the WHS via web services that allow researchers to transform images from their own data format to that of a collaborator, and to integrate different types of data from several sources at once.

Together, the WHS and DAI enable the integration of data from genetic, anatomical and functional imaging studies of the mouse brain, as well as convenient access to the data and easy conversion between data formats.

In addition, the WHS and DAI are designed so that it is reasonably straightforward to add other resources to the framework. Use of WHS data and the DAI are provided freely to the international research community.

Three major online mouse brain resources - the Allen Mouse Brain Atlas, the Edinburgh Mouse Atlas Project, and an effort from University of California San Diego (primarily the Cell Centered Database) - are now integrated with the INCF Digital Atlasing Infrastructure,  working together and accessible from multiple software clients. Any client that is WHS aware and uses components of the DAI may now access these resources. This interoperability will facilitate future research as well as increase the value of previously acquired data.

Work on a corresponding Waxholm Space framework for the rat is underway in Norway, under the direction of Prof. Jan Bjaalie at the Institute of Basic Medical Sciences, University of Oslo.


Digital Atlasing and Standardization in the Mouse Brain (2011). Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, Martone M, Ng L, Lau C, Larsen SD, Nissanov J, Puelles L, Ruffins S, Verbeek F, Zaslavsky I, Boline J. PLoS Comput Biol 7(2): e1001065.

A symmetrical Waxholm canonical mouse brain for NeuroMaps (2011) Bowden DM, Johnson GA, Zaborsky L, Green WD, Moore E, Badea A, Dubach MF, Bookstein FL. J Neurosci Methods vol. 195(2):170-5.

Waxholm space: an image-based reference for coordinating mouse brain research (2010) Johnson GA, Badea A, Brandenburg J, Cofer G, Fubara B, Liu S, Nissanov J. Neuroimage vol. 53(2):365-72. 

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