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Bringing Data into the INCF Digital Atlas-based Sharing Framework

Jyl Boline1*, Richard Baldock2, Rembrandt Bakker3, Janis Breeze4, Albert Burger5, James Gee6, Christian Haselgrove7, Mike Hawrylycz8, Andreas Hess9, Luis Ibanez10, G. Allan Johnson11, Stephen Larson12, Lydia Ng8, Yuko Okamura-Oho13, Seth Ruffins14, Fons Verbeek15 and Ilya Zaslavsky16
  • 1 Informed Minds, United States
  • 2 MRC Human Genetics Unit, United Kingdom
  • 3 Radboud University, Netherlands
  • 4 INCF, Sweden
  • 5 Heriot-Watt University, United Kingdom
  • 6 University of Pennsylvania, United States
  • 7 University of Massachusetts Medical Center, United States
  • 8 Allen Institute for Brain Science, United States
  • 9 Institute of Experimental and Clinical Pharmacology and Toxicology, Germany
  • 10 Kitware, Inc., United States
  • 11 Duke University, Center for In Vivo Microscopy, United States
  • 12 University of California, San Diego, United States
  • 13 RIKEN Advanced Science Institute, Japan
  • 14 California Institute of Technology, Biological Imaging Center, United States
  • 15 Leiden Institute of Advanced Computer Science, Netherlands
  • 16 University of California, San Diego, San Diego Supercomputer Center, United States

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.

Keywords: computational neuroscience, digital atlasing

Conference: 4th INCF Congress of Neuroinformatics, Boston, United States, 4 Sep - 6 Sep, 2011.

Presentation Type: Poster Presentation

Topic: Computational neuroscience

Citation: Boline J, Baldock R, Bakker R, Breeze J, Burger A, Gee J, Haselgrove C, Hawrylycz M, Hess A, Ibanez L, Johnson G, Larson S, Ng L, Okamura-Oho Y, Ruffins S, Verbeek F and Zaslavsky I (2011). Bringing Data into the INCF Digital Atlas-based Sharing Framework. Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2011.08.00072

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Received: 17 Oct 2011; Published Online: 19 Oct 2011.

* Correspondence: Dr. Jyl Boline, Informed Minds, Wilton Manors, United States, jylboline@informedminds.info