A mouse brain stereotaxic topographic atlas with isotropic 1-μm resolution

Zhao Feng, Xiangning Li, Yue Luo, Xin Liu, Ben Long, Tao Jiang, Xueyan Jia, Xiaowei Chen, Jie Luo, Xiaokang Chai, Zhen Wang, Miao Ren, Xin Lu, Gang Yao, Mengting Zhao, Yuxin Li, Zhixiang Liu, Hong Ni, Chuhao Dou, Shengda Bao, Shicheng Yang, Zoutao Zhang, Jiandong Zhou, Lingyi Cai, Qi Zhang, Ayizuohere Tudi, Chaozhen Tan, Zhengchao Xu, Siqi Chen, Wenxiang Ding, Wenjuan Shi, Anan Li, Hong-wei Dong (), Hui Gong () and Qingming Luo ()
Additional contact information
Zhao Feng: Hainan University
Xiangning Li: Hainan University
Yue Luo: Huazhong University of Science and Technology
Xin Liu: Huazhong University of Science and Technology
Ben Long: Huazhong University of Science and Technology
Tao Jiang: JITRI
Xueyan Jia: JITRI
Xiaowei Chen: JITRI
Jie Luo: JITRI
Xiaokang Chai: Huazhong University of Science and Technology
Zhen Wang: Huazhong University of Science and Technology
Miao Ren: Hainan University
Xin Lu: Huazhong University of Science and Technology
Gang Yao: Huazhong University of Science and Technology
Mengting Zhao: Hainan University
Yuxin Li: Huazhong University of Science and Technology
Zhixiang Liu: Huazhong University of Science and Technology
Hong Ni: Huazhong University of Science and Technology
Chuhao Dou: Huazhong University of Science and Technology
Shengda Bao: Huazhong University of Science and Technology
Shicheng Yang: Hainan University
Zoutao Zhang: Huazhong University of Science and Technology
Jiandong Zhou: Huazhong University of Science and Technology
Lingyi Cai: Huazhong University of Science and Technology
Qi Zhang: Huazhong University of Science and Technology
Ayizuohere Tudi: Huazhong University of Science and Technology
Chaozhen Tan: Huazhong University of Science and Technology
Zhengchao Xu: Huazhong University of Science and Technology
Siqi Chen: Huazhong University of Science and Technology
Wenxiang Ding: Huazhong University of Science and Technology
Wenjuan Shi: Huazhong University of Science and Technology
Anan Li: JITRI
Hong-wei Dong: University of California Los Angeles
Hui Gong: JITRI
Qingming Luo: Hainan University

Nature, 2025, vol. 645, issue 8080, 448-456

Abstract: Abstract Multi-omics studies, represented by connectomes and spatial transcriptomes, have entered the era of single-cell resolution, necessitating a reference brain atlas with spatial localization capability at the single-cell level1–4. However, such atlases are unavailable5. Here we present a whole mouse brain dataset of Nissl-based cytoarchitecture with isotropic 1-μm resolution, achieved through continuous micro-optical sectioning tomography. By integrating multi-modal images, we constructed a three-dimensional reference atlas of the mouse brain, providing the three-dimensional topographies of 916 structures and enabling arbitrary-angle slice image generation at 1-μm resolution. We developed an informatics-based platform for visualizing and sharing of the atlas images, offering services such as brain slice registration, neuronal circuit mapping and intelligent stereotaxic surgery planning. This atlas is interoperable with widely used stereotaxic atlases, supporting cross-atlas navigation of corresponding coronal planes in two dimensions and spatial mapping across atlas spaces in three dimensions. By facilitating the data analysis and visualization for large brain mapping projects, our atlas promises to be a versatile brainsmatics tool for studying the whole brain at single-cell level.

Date: 2025
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DOI: 10.1038/s41586-025-09211-8

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