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Understanding the complexities of the brain

The Allen Institute for Brain Science is focused on understanding the complexities of the brain by mapping its cells and cell types with unprecedented precision and scale.

By building a detailed “parts list” of the mammalian brain and understanding how each part functions within an integrated whole, science can better–and more quickly–develop life-changing therapies and treatments for debilitating brain diseases.

How many cell types are there? What is their form, function, and how do they connect? By answering these foundational questions we can better understand human brain development, evolution, and disease. Established in 2003, the Allen Institute for Brain Science is our oldest scientific division.

Our advanced technologies, biological principles, and experimental models create fundamental, catalytic maps of brain structure and function that deepen our understanding of brain disease and illuminate a path forward.

Ed Lein Headshot

Brain Science Data Tools & Research Highlights 

We’re defining and analyzing the different cells that make up the mammalian brain to better understand how our brains work, how they develop, and what goes wrong in disease. Using a big, team, and open science approach, we share our discoveries, data, and resources with the broader scientific community to catalyze breakthroughs.

All of our tools, including brain atlases, databases, and more, are publicly available online at

Asian female researcher at a computer analyzing data on two computer monitors

Our Approach

By cataloguing and genetically profiling cell types of the brain with incredible precision and detail, we can improve our fundamental understanding of brain development, evolution, and disease.

We do this through advanced single-cell molecular analysis techniques, such as single-cell RNA sequencing and electrophysiology, combined with cutting-edge imaging technologies that provide a comprehensive view of how our brains are organized; what their cellular makeup is; how those cells connect, develop, and function; and the complex relationship between these factors.

Using a team science approach, we are exploring the mammalian brain at a molecular level and sharing our insights with the world.


Learn more about our teams.

Facilitating the integration of best practices in scientific research and development with innovative business approaches to further accelerate operational efficiency

Building web products including visualization applications, knowledge graph and an integrated data framework to enable advanced search and discovery of brain data

Mapping and characterizing microcircuits in the mouse visual cortex

Working to develop prospective and retrospective techniques to characterize adult human neocortical cell types.

The Imaging Department explores the diversity of cell types in the brain using a variety of microscopy and image processing techniques, including confocal microscopy, brightfield microscopy, 2- and 3-photon imaging, spatial transcriptomics, and light-sheet microscopy in cleared tissue.


Leading an effort toward comprehensive molecular analysis of cell type identity in the mouse brain. Building state-of-the-art transgenic and viral tools for experimental access to these cell types.

Investigating the cellular and circuit mechanisms underlying changes in cortical physiology with behavior

Coming soon!!!

Learn more about our other Scientific Divisions.

Allen Institute for Cell Science

The Allen Institute for Cell Science is focused on exploring and understanding human cells — the incredibly complex building blocks of our bodies.

Learn More

Allen Institute for Immunology

The Allen Institute for Immunology works to understand the delicate balancing act of the human immune system—how it works when we’re healthy, and what goes wrong in disease.

Learn More