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01-04-2023 | Magnetic Resonance Imaging | Research

Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System

Authors: Johanna Perens, Casper Gravesen Salinas, Urmas Roostalu, Jacob Lercke Skytte, Carsten Gundlach, Jacob Hecksher-Sørensen, Anders Bjorholm Dahl, Tim B. Dyrby

Published in: Neuroinformatics | Issue 2/2023

Abstract

Magnetic resonance imaging (MRI) and light-sheet fluorescence microscopy (LSFM) are technologies that enable non-disruptive 3-dimensional imaging of whole mouse brains. A combination of complementary information from both modalities is desirable for studying neuroscience in general, disease progression and drug efficacy. Although both technologies rely on atlas mapping for quantitative analyses, the translation of LSFM recorded data to MRI templates has been complicated by the morphological changes inflicted by tissue clearing and the enormous size of the raw data sets. Consequently, there is an unmet need for tools that will facilitate fast and accurate translation of LSFM recorded brains to in vivo, non-distorted templates. In this study, we have developed a bidirectional multimodal atlas framework that includes brain templates based on both imaging modalities, region delineations from the Allen’s Common Coordinate Framework, and a skull-derived stereotaxic coordinate system. The framework also provides algorithms for bidirectional transformation of results obtained using either MR or LSFM (iDISCO cleared) mouse brain imaging while the coordinate system enables users to easily assign in vivo coordinates across the different brain templates.

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Title: Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System
Authors: Johanna Perens
Casper Gravesen Salinas
Urmas Roostalu
Jacob Lercke Skytte
Carsten Gundlach
Jacob Hecksher-Sørensen
Anders Bjorholm Dahl
Tim B. Dyrby
Publication date: 01-04-2023
Publisher: Springer US
Keywords: Magnetic Resonance Imaging
Magnetic Resonance Imaging
Published in: Neuroinformatics / Issue 2/2023
Print ISSN: 1539-2791
Electronic ISSN: 1559-0089
DOI: https://doi.org/10.1007/s12021-023-09623-9

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Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System

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