TY - JOUR
T1 - Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System
AU - Perens, Johanna
AU - Salinas, Casper Gravesen
AU - Roostalu, Urmas
AU - Skytte, Jacob Lercke
AU - Gundlach, Carsten
AU - Hecksher-Sørensen, Jacob
AU - Dahl, Anders Bjorholm
AU - Dyrby, Tim B
N1 - © 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
PY - 2023/4
Y1 - 2023/4
N2 - 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.
AB - 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.
KW - Animals
KW - Brain Mapping/methods
KW - Brain/diagnostic imaging
KW - Imaging, Three-Dimensional/methods
KW - Magnetic Resonance Imaging/methods
KW - Mice
KW - Skull/diagnostic imaging
KW - Light sheet fluorescence microscopy
KW - Brain atlas
KW - Multimodal imaging
KW - Whole brain imaging
KW - Magnetic resonance imaging
KW - Crossmodal registration
UR - http://www.scopus.com/inward/record.url?scp=85148434878&partnerID=8YFLogxK
U2 - 10.1007/s12021-023-09623-9
DO - 10.1007/s12021-023-09623-9
M3 - Journal article
C2 - 36809643
SN - 1539-2791
VL - 21
SP - 269
EP - 286
JO - Neuroinformatics
JF - Neuroinformatics
IS - 2
ER -