This paper presents the Brain Cell Atlas, a comprehensive reference atlas of brain cells assembled from 70 human and 103 mouse studies. The atlas integrates over 26.3 million cells or nuclei across major developmental stages and brain regions, including both healthy and diseased tissues. Using machine learning, the atlas provides a consensus cell type annotation and identifies novel cell types, such as putative neural progenitor cells and a PCDH9high microglia subpopulation. The study demonstrates the gene regulatory differences of this microglia subpopulation between the hippocampus and prefrontal cortex and elucidates its cell-cell communication network. The Brain Cell Atlas serves as a valuable resource for studying brain cells and functions within the Human Cell Atlas.
