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Registration workflows for the creation of INCF digital atlas hubs

Jyl Boline1*, Brian Avants2, Richard Baldock3, Rembrandt Bakker4, Albert Burger5, James Gee2, Christian Haselgrove6, Andreas Hess7, Luis Ibanez8, Stephen Larson9, Piotr Majka10, Yuko Okamura-Oho11, Seth Ruffins12 and Ilya Zaslavsky13
  • 1 Informed Minds, United States
  • 2 University of Pennsylvania, United States
  • 3 MRC Human Genetics Unit and IGMM, United Kingdom
  • 4 Radboud University, Netherlands
  • 5 MRC Human Genetics Unit and Heriot-Watt University, United Kingdom
  • 6 University of Massachusetts Medical Center, United States
  • 7 Institute of Experimental and Clinical Pharmacology and Toxicology, Germany
  • 8 Kitware Inc., United Arab Emirates
  • 9 University of California, United States
  • 10 Nencki Institute of Experimental Biology, Poland
  • 11 Brain Research Network and RIKEN Advanced Science Institute, Japan
  • 12 Broad CIRM Center, USC, United States
  • 13 San Diego Supercomputer Center, University of California, United States

The International Neuroinformatics Coordinating Facility (INCF, http://incf.org/ ) Digital Atlasing Program is making strides towards the goal of making multidimensional data of the rodent brain more widely accessible and usable to the research community via a digital atlasing framework (Hawrylycz et al, 2011, PLoS Comput Biol 7[2]: e1001065. doi:10.1371/journal.pcbi.1001065). The approach employs standard spatial reference systems (principally Waxholm Space, WHS) with supporting data sharing infrastructure (Digital Atlasing Infrastructure, DAI). The current efforts of the group are on further development of this framework through these two areas, each of which is the main working area of a Task Force. The WHS task force creates and improves methods for people to bring their data into this framework, while the DAI task force concentrates on improving and expanding the DAI. A current focus on integrating image registration workflows to the underlying infrastructure requires contributions from both these groups, and crosses into the related areas of metadata, provenance, and ontologies. The workflows are being developed around specific data sharing use cases (see figure). At this time, the use cases focus on 2D brain slice images (some sparsely, others highly sampled) of various modalities. The goal is to create tools, recommendations, and standard operating procedures to aid in the registration of data to a known standard atlas space and creation of new atlas hubs. Atlas hubs register their data to a spatial reference system, publish their data and services with INCF Central and share their data via web services. With workflows that allow the creation of new atlas hubs such as one for ViBrism (illustrated in the figure), new datasets (here, a large unique microarray gene expression) will be able to be queried and compared to the data in other atlas hubs, such as EMAGE and Allen Brain Atlas. Project areas for the group include:

*Registration fiducials and landmarks
*Standards for registration transformations
*Data management and handling
*Metadata
*Provenance
*Hub in a Box
*WHS for the rat
*PONS pan mammalian delineations of WHS dataset

These areas are integrated with DAI or are needed to integrate other components with DAI. This program welcomes input from the community, and requests expert recommendations in several of the project areas outside the original scope of this program. Please contact any of the authors for further information.

Keywords: digital atlasing, Waxholm Space, registration workflows, metadata, data sharing

Conference: 5th INCF Congress of Neuroinformatics, Munich, Germany, 10 Sep - 12 Sep, 2012.

Presentation Type: Poster

Topic: Neuroinformatics

Citation: Boline J, Avants B, Baldock R, Bakker R, Burger A, Gee J, Haselgrove C, Hess A, Ibanez L, Larson S, Majka P, Okamura-Oho Y, Ruffins S and Zaslavsky I (2014). Registration workflows for the creation of INCF digital atlas hubs. Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2014.08.00130

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Received: 21 Mar 2013; Published Online: 27 Feb 2014.

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