WAXHOLM SPACE - MOUSE BRAIN SPATIAL COORDINATE SYSTEM

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Waxholm space (WHS) is a conceptual construct that arose from the first meeting of the Neuroinformatics Coordinating Facility (INCF) advisory board held in Waxholm, Sweden in September 2008. Waxholm space will provide a mouse brain spatial coordinate system that will serve as a reference target for spatial normalization of experimental results attained by the research community. Wide utility will be achieved by incorporation of a comprehensive set of volume image sets acquired on each of seven mice. Those will consist of the following: 1) 3D MR Microscopy images at the highest spatial resolution yet attained (21.5 ¿m) acquired with three different imaging protocols to highlight the widest range of tissue contrast and morphologic structure [1]; 2) Volume Nissl images at 5¿m x 5¿m x 20 ¿m on the same brain reconstructed with minimal distortion and high fidelity [2] and registered to the MR data; 3) a collection of 33 labels derived in the intact specimen on the MR data and transferred to the reconstructed Nissl volume[3, 4]. These data will provide researchers three methods for entering WHS; 1) registration of 3D volume MR images into the target MR reference; 2) registration of conventional histology into the target Nissl; 3) registration of labels into the target labels. SPECIFIC AIMS: We propose here several of the critical milestones necessary to establish WHS: Phase I Completion Feb 1, 2009, We will: -- acquire the canonical dataset on an adult male C57BL/6 mouse; MR data with T1,T2, and T2* weighting at 21.5 ¿m; b) Nissl sections @ 5¿m x 5¿m x 20 ¿m on the same specimen. -- register the MR and Nissl volume and co-align those to a standardized orientation as will be defined by consensus by members of the INCF panel. -- provide and validate labels for at least 33 anatomical structures and validate the ontology of these structures to accepted standards. -- place the canonical data set and the documentation defining WHS on at least one publicly accessible web site with suitable search, imaging, analysis and commenting tools- all of which will be freely available to the neuroscience community. -- define the orientation and best practices for acquisition of future data to facilitate mapping into WHS. Phase II Completion August 1, 2009, we will: -- expand the canonical data set by adding 6 additional data sets with identical acquisition parameters i.e. 3 MR data sets, complete volumetric Nissl data, and labels. -- register all the data to provide a probabilistic atlas -- lace all the data on the freely accessible server. Phase III, We will: -- register representative atlases from at least three other sources to WHS starting initially with the Allen Brain Atlas -- establish the tools and pipelines necessary for registration for MR, Nissl, and labels and validate their use. References 1. Johnson, G.A., et al., NeuroImage, 2007. 37(1): p. 82-89. 2. Bertrand, L. and J. Nissanov, Front Neuroinformatics, 2008. 2: p. 3. 3. Ali, A.A., et al., Neuroimage, 2005. 27(2): p. 425-35. 4. Badea, A., et al., NeuroImage, 2007. 37(3): p. 683-693.