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
- Qingming Luo
2025-07-02
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 level 1–4 . However, such atlases are unavailable 5 . 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.