Bringing Data into the INCF Digital Atlas-based Sharing Framework
Jyl Boline (Informed Minds, USA), Richard Baldock (MRC Human Genetics Unit and IGMM, UK), Rembrandt Bakker (Radboud University, Netherlands), Janis Breeze (INCF, Sweden), Albert Burger (MRC Human Genetics Unit and Heriot-Watt University), James Gee (University of Pennsylvania, Philadelphia, USA), Christian Haselgrove (University of Massachusetts Medical Center, USA), Mike Hawrylycz (Allen Institute for Brain Science, USA), Andreas Hess (Institute of Experimental and Clinical Pharmacology and Toxicology, Germany), Luis Ibanez (Kitware Inc., Clifton Park, USA), G. Allan Johnson (Duke Center for In Vivo Microscopy, USA), Stephen Larson (University of California, USA), Lydia Ng (Allen Institute for Brain Science, USA), Yuko Okamura-Oho (RIKEN Advanced Science Institute, Wako, Japan), Seth Ruffins (Biological Imaging Center, California Institute of Technology, USA), Fons Verbeek (Leiden Institute of Advanced Computer Science, Leiden University, Netherlands), Ilya Zaslavsky (San Diego Supercomputer Center, University of California, USA)
The INCF Digital Atlasing Program (http://incf.org/core/programs/atlasing), is an International Neuroinformatics Coordinating Facility (INCF, http://incf.org) collaborative effort to create an atlas-based framework to make the rapidly growing collection of multidimensional data of the rodent brain more widely accessible and usable to the research community (Boline et al, 2007, Nature Precedings, doi:10.1038/npre.2007.1046.1). It includes two task forces, the Waxholm Space (WHS) Task Force, and the Digital Atlasing infrastructure (DAI) Task Force. These two groups are building an atlas-based sharing framework that includes a common space for the adult C57BL/6J mouse called Waxholm Space (doi:10.1016/j.neuroimage.2010.06.067), and an atlas hub based distributed INCF Digital Atlasing Infrastructure. The initial vision, perceived challenges and results of this effort are discussed in Hawrylycz et al, 2009, Nature Precedings doi:10.1038/npre.2009.4000.1, and a recent position paper (Hawrylycz et al, 2011, PLoS Comput Biol 7[2]: e1001065. doi:10.1371/journal.pcbi.1001065).
Since the basic atlas sharing framework has now been established, the main efforts of these groups are on making it easier for the community to bring their data into this framework and on improving the reliability and access to this data.
The primary goal of the WHS Task Force is to make it easier for researchers to register their data to WHS. This includes creating recommendations, standard operating procedures, and easier access to appropriate tools, and workflows. In addition, recommended fiducials and landmarks for certain data types will also be used to aid in registration and to help validate registration between the current atlases registered to WHS. This group is also working on standards for registration transformations that will enable easy sharing of mapped data in WHS.
The DAI Task Force is continuing to develop and improve DAI with a focus on creating and improving standards, atlas hubs, and lowering the barrier of creating atlas hubs by moving towards a “hub in a box” model.
In addition, members of the task forces are linking software tools to this atlasing framework. These include the Scalable Brain Atlas (SBA, http://scalablebrainatlas.incf.org, the Whole Brain Catalog (WBC, http://wholebraincatalog.org, and the Mouse BIRN Atlasing Toolkit (MBAT, http://mbat.loni.ucla.edu. These tools are able to access to information and data from the distributed atlas hubs, while each includes its own set of unique functions. The design of this framework allows any tool to take advantage of this atlasing framework, for more information see http://atlasing.incf.org.
This program continues to be a community effort that thrives from involvement by the wider scientific community. A satellite workshop around the Society for Neuroscience 2011 meeting is planned with a focus on the registration of data to WHS, all are welcome to attend.
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