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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Acknowledgements
We would like to thank Hanne Duus Lautsen and Mette Musfelth Nebbelunde for their skillful assistance in the lab.
Funding
The work was funded by Gubra ApS and Innovation Fund Denmark, grant number 8053-00121B.
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Johanna Perens, Casper Gravesen Salinas, Urmas Roostalu, Jacob Lercke Skytte, Tim B. Dyrby and Carsten Gundlach designed and performed the experiments. Johanna Perens, Tim B. Dyrby, Anders Bjorholm Dahl and Jacob Hecksher-Sørensen wrote the manuscript. All authors reviewed the manuscript.
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Conflict of interest
Johanna Perens, Casper Gravesen Salinas, Urmas Roostalu, Jacob Lercke Skytte, and Jacob Hecksher-Sørensen are currently employed at Gubra ApS and own shares of Gubra ApS.
Competing interests
Johanna Perens, Casper Gravesen Salinas, Urmas Roostalu, Jacob Lercke Skytte and Jacob Hecksher-Sørensen are employees at Gubra and own shares in Gubra.
Ethics Approval
Animal experiments were conducted in compliance with internationally accepted principles for the use of laboratory animals and approved by the Danish Animal Experiments Inspectorate (license #2013-15-2934-00784).
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Perens, J., Salinas, C.G., Roostalu, U. et al. Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System. Neuroinform 21, 269–286 (2023). https://doi.org/10.1007/s12021-023-09623-9
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DOI: https://doi.org/10.1007/s12021-023-09623-9