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Registration workflows for the creation of INCF digital atlas hubs

Filed under:

Jyl Boline (Informed Minds), Brian Avants (University of Pennsylvania), Richard Baldock (MRC Human Genetics Unit and IGMM), Rembrandt Bakker (Radboud University), Albert Burger (MRC Human Genetics Unit and Heriot-Watt University), James Gee (University of Pennsylvania), Christian Haselgrove (University of Massachusetts Medical Center), Andreas Hess (Institute of Experimental and Clinical Pharmacology and Toxicology), Luis Ibanez (Kitware Inc.), Stephen Larson (University of California), Piotr Majka (Nencki Institute of Experimental Biology), Yuko Okamura-Oho (Brain Research Network and RIKEN Advanced Science Institute), Seth Ruffins (Broad CIRM Center, USC), Ilya Zaslavsky (San Diego Supercomputer Center, University of California)

The International Neuroinformatics Coordinating Facility (INCF, 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
 *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.
The INCF DA program is developing registration workflows and integrating them with the Digital Atlasing Infrastructure (DAI), which will aid in the creation of new atlas hubs. An example is shown here with the ViBrism gene expression dataset.
Preferred presentation format: Poster
Topic: Digital atlasing

Filed under:
Andrew Davison
Andrew Davison says:
May 11, 2012 02:29 PM
Very important work. Abstract mentions a figure, but this seems to have gone missing.