A Cell Atlas for the Mouse Brain

Summary

The document presents a dynamically generated 3D cell atlas of the whole mouse brain built from Allen Brain Atlas Nissl images, gene expression markers, and selected literature values. The authors estimate volumetric cell densities, generate 3D positions for cells across 737 brain regions, and classify them into excitatory and inhibitory neurons as well as astrocytes, oligodendrocytes, and microglia. The workflow uses image realignment, thresholding, overlap correction, and acceptance-rejection sampling to populate brain regions with cells, then validates the resulting regional counts and densities against published data and an automated point-detection approach. The atlas is designed as a public, expandable resource that can incorporate new markers, data sources, and future connectivity information.

Keywords

• mouse brain

• cell atlas

• 3D reconstruction

• cell density

• neurons

• glia

• astrocytes

• oligodendrocytes

• microglia

• excitatory neurons

• inhibitory neurons

• Allen Mouse Brain Atlas

• Nissl staining

• gene expression

• validation

Main claims

The study presents the first 3D whole mouse brain cell atlas with region by region estimates for major neuronal and glial cell types

Existing literature provides neuron counts for only a small fraction of mouse brain regions and reported values often differ substantially, motivating a data driven atlas that integrates multiple sources

The atlas reconstructs cell positions and densities for excitatory and inhibitory neurons, astrocytes, oligodendrocytes, and microglia across all 737 Allen Mouse Brain Atlas regions

The atlas is dynamic and can be refined as new staining, transcriptomic, and anatomical data become available

Whole brain scale analysis reveals nonuniform cellular organization, including extreme enrichment of cerebellar granule cell regions and relatively uniform glial distributions

Comparison with literature and automated counting shows generally good agreement while also highlighting persistent uncertainty in some regions such as the cerebellum