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Unraveling the Complexity of the Mammalian Brain 

By Brian Cama, Jenny Burns, Jake Siegel, and Peter Kim

To understand the brain in health and disease, we must first understand its parts: the cells.

Mapping the whole mouse brain

This is a view of the whole mouse brain colored by region. The mouse brain has around 100 million cells.

These cells can be grouped by what genes are active in them—also called the “gene expression profile.”

Each color here represents a group or type of cells with a specific set of genes that are active. The size of the colored areas represents the number of cells of that type that has a particular gene expression profile.

Cell location is also vital for understanding the brain. Here, each color represents a specific cell type, and they’re organized based on where in the brain they are found.

All of this rich complexity has been discovered and documented by scientists. Led by the Allen Institute, they produced the first complete cell type atlas of a mammalian brain (the mouse) and uncovered astonishing diversity.

This is a landmark achievement. We now know how many cell types there are in the brain, where they’re distributed; and for a particular brain region, its cell type composition.
— Hongkui Zeng, Ph.D.

Executive Vice President and Director, Allen Institute for Brain Science 

Over six years, hundreds of scientists across North America built the atlas and discovered over 5,000 brain cell types.

Each colored region that lights up reflects where those cell types exist in the brain.

Scientists used advanced, single-cell genomics and spatial mapping technologies to reveal this complex and rich cellular landscape.

Some teams mapped precisely where those cells were in the brain.

Others uncovered what genes were turned on in each cell, and what molecules controlled the switch.

This massive, high-quality dataset is freely available to the neuroscience community. Scientists around the world can reference this atlas to advance research in brain health and disease.

The findings were published in ten studies in a special issue of Nature.
Million Cells

Over 32 million cells analyzed

Cell Types

More than 5,300 cell types identified


More than 1,100 genes spatially located

Researchers believe they’ve uncovered the true cell type organization of the mammalian brain because independent transcriptomic, epigenomic, and spatial datasets all align and support this conclusion.
The data and insights generated from the research open up a new chapter in our understanding of the mammalian brain.
This project was funded by the NIH’s Brain Research Through Advancing Innovative Neurotechnologies® (BRAIN) Initiative, or The BRAIN Initiative®

Scientific Collaborators

Harvard University
Salk Institute
Broad Institute
University of California San Diego
University of California, Berkeley

Produced By

Jake Siegel
Peter Kim
Steven Hurd
Jenny Burns
Brian Cama
Cindy van Velthoven, Ph.D.
Delissa McMillen, M.S., M.B.A.
Amy Torkelson
Katelyn James
Erik Dinnel

Science Programs at Allen Institute