A mouse brain stereotaxic topographic atlas with isotropic 1-μm resolution
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.
Article Details
Authors (35)
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