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New open standard for digital brain atlasing published in PLoS Computational Biology

Standardized framework will facilitate data sharing and integration of research results

February 3, 2011 | Download PDF

Researchers from the Allen Institute for Brain Science in collaboration with other members of the International Neuroinformatics Coordinating Facility (INCF) Working Group on Digital Atlasing have developed an open, shared standard digital atlasing framework for the mouse brain. This framework will facilitate data sharing and integration of research results across laboratories and research programs worldwide. A perspective article highlighting the work has been published in PLoS Computational Biology.

Modern brain research generates immense quantities of data across different levels of detail, from gene activity to large-scale structure, using a wide array of methods. Each method has its own type of data which is stored in different databases. Integrating findings across levels of detail and from different databases, for example to find a link between gene expression and disease, can be very challenging and time consuming. Combining data from several types of studies provides a basis for new insights and is crucial for the progress of neuroscience research. Far too often, scientific progress is hindered by barriers to integrating data from different experiments and laboratories. The work discussed in this article represents a major step forward in addressing these problems for one of the most important models in experimental neuroscience: the mouse.

The project consists of three components, a system of spatial coordinates, an imaging alignment system, and a supportive digital infrastructure to combine different types of neuroscience data. The system of spatial coordinates, called Waxholm Space (derived from the first INCF working meeting in Waxholm, Sweden), or WHS, standardizes a spatial coordinate system via logical specifications to a single origin. The imaging alignment system registers new or existing high-resolution image data, matched to its relevant WHS coordinates. The supporting Web-based Digital Atlasing Infrastructure (DAI) is a collection of distributed services intended to link data from diverse sources—from genetic, anatomical and functional imaging studies, for example—to boost progress in neuroscience research.

Michael Hawrylycz, Ph.D., senior director of data analysis and annotation at the Allen Institute for Brain Science, leads the INCF Working Group on Digital Atlasing and is lead author on the study.

Currently, 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 integrated with the INCF Digital Atlasing Infrastructure and therefore working together. They can be accessed by any scientist anywhere from multiple software clients. As more data from other research groups is integrated with this standard, it will become increasingly powerful, providing a new level of integrative understanding of brain architecture, organization and function.

Hawrylycz M, et al. (2011) Digital Atlasing and Standardization in the Mouse Brain. PLoS Comput Biol 7(2): e1001065. doi:10.1371/journal.pcbi.1001065

Brief facts

  • The Waxholm Space (WHS) is a virtual coordinate system that unifies 3D mouse brain data
  • The Digital Atlasing Infrastructure (DAI) includes web services that allow researchers to:

Transform images from their own data format to that of a collaborator

Integrate different types of data from several sources at once

  • Use of WHS data and the DAI are provided freely to the international research community
  • Work to add WHS capability for the rat is actively underway at the University of Oslo
  • Waxholm Space is named in honour of Waxholm, Sweden, the site of the first INCF Digital Atlasing Working Group, September 2008

Information resources
The Waxholm Space was developed by the INCF Standards in Digital Atlasing Task Force. A more detailed publication of this group's recommendations can be found in their report, published in September 2009. Available via the INCF Collection at Nature Precedings:

The Waxholm Space framework is being built on and expanded by the current INCF Digital Atlasing Task Forces. To find more details about these groups, standards and projects, or other recent activities see:

Scientific publications using the Waxholm Space (WHS):

  • Digital Atlasing and Standardization in the Mouse Brain. 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. 2011. 7(2): e1001065.

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

  • Waxholm space: an image-based reference for coordinating mouse brain research. Johnson GA, Badea A, Brandenburg J, Cofer G, Fubara B, Liu S, Nissanov J. Neuroimage. 2010. vol. 53(2):365-72.
More information on the community resources currently integrated with WHS can be found via these web pages: