High-resolution in vivo Wistar rodent brain atlas based on T1 weighted image

Su Huang; Zhongkang Lu; Weimin Huang; Sankar Seramani; Boominathan Ramasamy; Sakthivel Sekar; Cuntai Guan; Kishore Bhakoo

doi:10.1117/12.2216067

29 March 2016 High-resolution in vivo Wistar rodent brain atlas based on T1 weighted image

Su Huang, Zhongkang Lu, Weimin Huang, Sankar Seramani, Boominathan Ramasamy, Sakthivel Sekar, Cuntai Guan, Kishore Bhakoo

Author Affiliations +

Proceedings Volume 9788, Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging; 978825 (2016) https://doi.org/10.1117/12.2216067
Event: SPIE Medical Imaging, 2016, San Diego, California, United States

Abstract

Image based atlases for rats brain have a significant impact on pre-clinical research. In this project we acquired T1-weighted images from Wistar rodent brains with fine 59μm isotropical resolution for generation of the atlas template image. By applying post-process procedures using a semi-automatic brain extraction method, we delineated the brain tissues from source data. Furthermore, we applied a symmetric group-wise normalization method to generate an optimized template of T1 image of rodent brain, then aligned our template to the Waxholm Space. In addition, we defined several simple and explicit landmarks to corresponding our template with the well known Paxinos stereotaxic reference system. Anchoring at the origin of the Waxholm Space, we applied piece-wise linear transformation method to map the voxels of the template into the coordinates system in Paxinos' stereotoxic coordinates to facilitate the labelling task. We also cross-referenced our data with both published rodent brain atlas and image atlases available online, methodologically labelling the template to produce a Wistar brain atlas identifying more than 130 structures. Particular attention was paid to the cortex and cerebellum, as these areas encompass the most researched aspects of brain functions. Moreover, we adopted the structure hierarchy and naming nomenclature common to various atlases, so that the names and hierarchy structure presented in the atlas are readily recognised for easy use. It is believed the atlas will present a useful tool in rodent brain functional and pharmaceutical studies.

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Su Huang, Zhongkang Lu, Weimin Huang, Sankar Seramani, Boominathan Ramasamy, Sakthivel Sekar, Cuntai Guan, and Kishore Bhakoo "High-resolution in vivo Wistar rodent brain atlas based on T1 weighted image", Proc. SPIE 9788, Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging, 978825 (29 March 2016); https://doi.org/10.1117/12.2216067

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