Journal
NATURE METHODS
Volume 19, Issue 1, Pages 111-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41592-021-01334-w
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Funding
- Southeast University through the SEU-ALLEN Joint Center, Institute of Brain and Intelligence
- National Science Foundation of China (NSFC) [61871411]
- University Synergy Innovation Program of Anhui Province [GXXT-2019-008, GXXT-2021-001]
- NSFC [32071367]
- NSFC-Guangdong Joint Fund [U20A6005]
- Fundamental Research Funds for the Central Universities [2242021k30046]
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The study introduces a cross-modal registration method, mBrainAligner, for aligning whole mouse brain images to the standard Allen Common Coordinate Framework atlas. Researchers then built a mouse brain atlas for the fluorescence micro-optical sectioning tomography modality, enabling further research on single-cell mapping and neuron types.
Recent whole-brain mapping projects are collecting large-scale three-dimensional images using modalities such as serial two-photon tomography, fluorescence micro-optical sectioning tomography, light-sheet fluorescence microscopy, volumetric imaging with synchronous on-the-fly scan and readout or magnetic resonance imaging. Registration of these multi-dimensional whole-brain images onto a standard atlas is essential for characterizing neuron types and constructing brain wiring diagrams. However, cross-modal image registration is challenging due to intrinsic variations of brain anatomy and artifacts resulting from different sample preparation methods and imaging modalities. We introduce a cross-modal registration method, mBrainAligner, which uses coherent landmark mapping and deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas. We build a brain atlas for the fluorescence micro-optical sectioning tomography modality to facilitate single-cell mapping, and used our method to generate a whole-brain map of three-dimensional single-neuron morphology and neuron cell types. mBrainAligner is a cross-modal registration platform for whole mouse brains imaged with different modalities. In addition, a fluorescence micro-optical sectioning tomography-based mouse brain atlas has been generated.
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