This paper details the creation of a comprehensive, molecularly-defined, and spatially-resolved cell atlas of the entire adult mouse brain using Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) technology. Researchers imaged over 1,100 genes in approximately 10 million cells, integrating this data with single-cell RNA sequencing to identify more than 5,000 transcriptionally distinct cell clusters and over 300 major cell types. The atlas was registered to the Allen Mouse Brain Common Coordinate Framework, allowing for the systematic quantification of cell-type composition and organization across various brain regions. This work also identified spatial modules, spatial gradients, and inferred cell-type-specific interactions, including potential molecular (ligand-receptor) bases for these interactions, thereby offering profound insights into the brain's cellular architecture and a foundation for future functional investigations.
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