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Growing the INCF Digital Atlasing Infrastructure

Jyl Boline1*, Richard Baldock2, Rembrandt Bakker3, Albert Burger4, 5, James Gee6, Christian Haselgrove7, Mike Hawrylycz8, Andreas Hess9, G. Allan Johnson10, Piotr Majka11, Lydia L. Ng8, Yuko Okamura-Oho12, Seth W. Rufffins13 and Ilya Zaslavsky14
  • 1 Informed Minds Inc, United States
  • 2 University of Edinburgh, MRC Human Genetics Unit and IGMM, United Kingdom
  • 3 Radboud University, Netherlands
  • 4 University of Edinburgh, MRC Human Genetics Unit, United Kingdom
  • 5 Heriot-Watt University, United Kingdom
  • 6 University of Pennsylvania, United States
  • 7 University of Massachusetts Medical School, United States
  • 8 Allen Institute for Brain Science, United States
  • 9 Universität Erlangen, Institute of Experimental and Clinical Pharmacology and Toxicology, Germany
  • 10 Duke, Duke Center for In Vivo Microscopy,, United States
  • 11 Nencki Institute of Experimental Biology, Poland
  • 12 Brain Research Network and RIKEN Advanced Science Institute, Japan
  • 13 University of Southern California, Broad CIRM Center, United States
  • 14 University of California, San Diego Supercomputer Center, United States

Digital brain atlases are essential tools in neuroscience research. They function as references and analytical tools, and provide stable integration frameworks as a basis for investigations of normal and abnormal brain structure and function. Thus, the aim of the International Neuroinformatics Coordinating Facility (INCF, http://incf.org/) Digital Atlasing Program (http://incf.org/programs/atlasing) has been using digital atlases as the basis of a framework for data sharing. We have created a prototype framework for this purpose, related recommendations, standards, and documentation to make the rapidly growing collection of multi-dimensional data of the rodent brain widely accessible and usable to the research community. The framework consists of a canonical atlas space (Waxholm Space, WHS) and a hub-based distributed INCF Digital Atlasing Infrastructure (DAI). The current framework is primarily for the adult C57BL/6J mouse, but we are in the process of expanding it to the rat.

Recently, work has revolved around creating greater access to DAI for neuroscientists via query tools (e.g. WIB, WHSlookup, the Atlasing Portal, and the atlasing wiki) and facilitating their ability to bring new data into this framework via registration tools (e.g. Jibber, JAWs, and high throughput 2D image registration tools), improving reliability and access to this data as well as certain components of the infrastructure (e.g. hardware, versioning and URIs, creating and updating registrations between key atlases including the new Allen Brain Atlas), and developing WHS for the rat (Wistar and Sprague-Dawley).

Tying 2D image registration workflows to DAI has been a main focus of the program, which crosses into areas dealing with metadata, provenance, and ontologies. Other supporting project areas include registration fiducials, standards, metadata, provenance, and data management and handling.

Usability, visibility, and the ability to collaborate with other related projects are key to the success of this program. To this end, the program welcomes input from the community, and requests expert recommendations in our project areas. Please contact any of the authors for further information.

For an overview and access to tools, visit the Atlasing Portal at http://incf-dev.crbs.ucsd.edu/atlasportal/catalog/main/home.page. For more information about Program activities and projects, visit the INCF wiki at http://wiki.incf.org/mediawiki/index.php/Digital_Brain_Atlasing. For access to the code repository, see https://code.google.com/p/incf-dai/.

Acknowledgements

This work was conducted within the DAI and WHS Task Forces of the INCF Digital Atlasing Program.

Keywords: mouse brain, rat brain, infrastructure, image registration, workflows

Conference: Neuroinformatics 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014.

Presentation Type: Poster, not to be considered for oral presentation

Topic: Digital atlasing

Citation: Boline J, Baldock R, Bakker R, Burger A, Gee J, Haselgrove C, Hawrylycz M, Hess A, Johnson G, Majka P, Ng LL, Okamura-Oho Y, Rufffins SW and Zaslavsky I (2014). Growing the INCF Digital Atlasing Infrastructure. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014. doi: 10.3389/conf.fninf.2014.18.00039

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Received: 04 Apr 2014; Published Online: 04 Jun 2014.

* Correspondence: Dr. Jyl Boline, Informed Minds Inc, Wilton Manors, FL, 33305, United States, jylboline@informedminds.info