Molecularly defined cellular atlas of the entire mouse brain with isotropic single-cell resolution
Authors: Mengting Zhao, Jiandong Zhou, Tao Jiang, Miao Ren, Chuhao Dou, Lingyi Cai, Shengda Bao, Xueyan Jia, Zhaoyang Meng, Feifang Tang, Zhao Feng, Jing Yuan, Xiaoquan Yang, Hui Gong, Qingming Luo*, Xiangning Li*, Anan Li*
* Correspondence author: (Q. L.), (X. L.) and (A. L.)

Overview
This repository provides all the data and code necessary to reproduce the results presented in the article, including whole-brain spatial location information of 20 distinct neuron types, 19-dimensional neuron distance-based parameter vectors for each 10 µm × 10 µm × 10 µm unit in the 3D grid of the entire mouse brain, and complete analysis code.

Data Access Repository
Spatial Location Information Dataset
Here, we provide download access to spatial coordinate data of whole-brain distributions for 20 distinct neuron types. The data is formatted as SWC files, a standard format widely used for representing neuronal morphologies. For each neuron type, there are 3 sets of data available. The downloadable files are listed as follows:


Distance Parameter Dataset
Due to the limitations of traditional density calculation methods, which cannot accurately depict the sparsity and density of neuronal distributions in three-dimensional spaces and are severely hampered by the prevalence of zero values, affecting subsequent analyses, we propose a novel parameter based on neuronal distances. This parameter is intended to replace traditional density metrics and is designed to characterize the distribution of neurons within the spatial domains of the mouse brain, meeting the need for describing neuronal sparsity and density on finer spatial scales and analyzing the organizational patterns of neurons in the mouse brain at more detailed levels. We partitioned the entire mouse brain into a 3D grid of 10 µm × 10 µm × 10 µm, with each grid serving as a computational unit characterized by a 19-dimensional parameter vector representing the distance parameters of 19 neuron types. Downloadable files available here:


Code Access Repository
Codes

Test data used in the code