Photoacoustic Tomography with Temporal Encoding Reconstruction (PATTERN) for cross-modal individual analysis of the whole brain

Yuwen Chen, Haoyu Yang, Yan Luo, Yijun Niu, Muzhou Yu, Shanjun Deng, Xuanhao Wang, Handi Deng, Haichao Chen, Lixia Gao, Xinjian Li, Pingyong Xu, Fudong Xue, Jing Miao, Song-Hai Shi, Yi Zhong, Cheng Ma () and Bo Lei ()
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Yuwen Chen: Tsinghua University
Haoyu Yang: Tsinghua University
Yan Luo: Tsinghua University
Yijun Niu: Tsinghua University
Muzhou Yu: Xi’an Jiaotong University
Shanjun Deng: Sun Yat-sen University
Xuanhao Wang: Zhejiang Laboratory
Handi Deng: Tsinghua University
Haichao Chen: Tsinghua University
Lixia Gao: Zhejiang University
Xinjian Li: Zhejiang University
Pingyong Xu: Chinese Academy of Sciences
Fudong Xue: Chinese Academy of Sciences
Jing Miao: Canterbury School
Song-Hai Shi: Tsinghua University
Yi Zhong: Tsinghua University
Cheng Ma: Tsinghua University
Bo Lei: Tsinghua University

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: Abstract Cross-modal analysis of the same whole brain is an ideal strategy to uncover brain function and dysfunction. However, it remains challenging due to the slow speed and destructiveness of traditional whole-brain optical imaging techniques. Here we develop a new platform, termed Photoacoustic Tomography with Temporal Encoding Reconstruction (PATTERN), for non-destructive, high-speed, 3D imaging of ex vivo rodent, ferret, and non-human primate brains. Using an optimally designed image acquisition scheme and an accompanying machine-learning algorithm, PATTERN extracts signals of genetically-encoded probes from photobleaching-based temporal modulation and enables reliable visualization of neural projection in the whole central nervous system with 3D isotropic resolution. Without structural and biological perturbation to the sample, PATTERN can be combined with other whole-brain imaging modalities to acquire the whole-brain image with both high resolution and morphological fidelity. Furthermore, cross-modal transcriptome analysis of an individual brain is achieved by PATTERN imaging. Together, PATTERN provides a compatible and versatile strategy for brain-wide cross-modal analysis at the individual level.

Date: 2024
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DOI: 10.1038/s41467-024-48393-z

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