Molecularly defined cellular atlas of the entire mouse brain with isotropic single-cell resolution

This repository provides the data necessary to reproduce the results presented in the article "Molecularly defined cellular atlas of the entire mouse brain with isotropic single-cell resolution", including whole-brain spatial location information of 20 distinct neuron types. This dataset contains spatial coordinate data regarding the whole-brain distribution of 20 distinct neuron types, formatted as SWC files — a standard format for representing neuronal morphologies. Detailed specifications of the SWC files are as follows: Each line corresponds to information of a single soma point; columns 3–5 represent the spatial coordinates of the soma, which have been uniformly registered to the Common Coordinate Framework version 3 (CCFv3). Specifically, column 3 denotes the left-right(LR) axis, column 4 the dorsal-ventral(DV) axis, and column 5 the anterior-posterior (AP) axis. For each neuron type, 3 independent data samples are provided. In addition, we have developed a Distance Parameter Dataset to characterize neuronal distribution in the mouse brain. This dataset introduces a novel distance-based parameter (replacing traditional density metrics) to describe neuronal sparsity/density at fine spatial scales and analyze neuronal organizational patterns. The entire mouse brain is partitioned into a 10 µm × 10 µm × 10 µm 3D grid, with each grid serving as a computational unit characterized by a 19-dimensional parameter vector (representing distance parameters of 19 neuron types). Due to the large data volume, this Distance Parameter Dataset cannot be uploaded to the current repository and is instead available for download on our website https://atlas.brainsmatics.cn/MiCAM/.