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team science
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sharing science to speed discovery
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celebrating open science
team science
people & teams
discovery is a team effort
allenites
the people who make our work possible
advisors
their input shapes our science
board of directors
they help us fulfill our mission
shanahan foundation fellowship
at the interface of data and neuroscience
next generation leaders
fostering emerging leaders in bioscience
research
back to menu
overview
our approach
science at the scale of greatest impact
publications
explore our publications
open science
sharing science to speed discovery
science accelerators
brain science
building a blueprint of the brain
cell science
understanding how cells become organs
neural dynamics
revealing the brain’s hidden algorithms
immunology
creating the ultimate immune system reference
synthetic biology
seattle hub for synthetic biology
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brain science
building a complete, interactive blueprint of the brain's cells and connections to unlock how it all works
visit brain-map.org
brain science team
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The brain's complexity is staggering. Understanding it requires a blueprint. We're building one.

Imagine trying to understand a city without a map: no street grid, no neighborhood names, no guide to which utilities connect where. That's the challenge brain scientists have faced for decades. We're creating the maps that change everything.

Our Brain Science team produces three interlocking resources: cell type atlases that catalog every kind of brain cell across ages and species, connectomes that chart the brain's intricate wiring, and a knowledge platform that knits it all together with powerful analysis tools. Every dataset is freely shared, so discoveries made here fuel discoveries everywhere.

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Our brain cell atlases, connectomes, and open knowledge platform give scientists worldwide the reference tools they need to accelerate every corner of brain research.

meet our teams

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brain science management
leading institute-wide deciphering of mammalian brain cellular and circuit organization across development, evolution, and disease
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data and technology
driving breakthroughs in neuroscience through advanced computation, data management technologies and collaborative open data sharing
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connectomics
mapping the nervous system at cellular and synaptic resolution within and across brain regions
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human cell types
characterizing cellular diversity in the nervous system of humans and other mammals to study disease, evolution and brain function
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imaging
exploring the diversity of cell types in the brain using a variety of microscopy and image processing techniques
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integrated cell physiology
establishing connections between morphoelectric characteristics and transcriptomic-defined cell types
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neuroanatomy
investigating the neuroanatomical architecture of the brain at the population and single cell level
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molecular genetics
driving comprehensive molecular profiling of mouse brain cell types and developing advanced transgenic and viral tools
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research operations
driving large-scale scientific initiatives via strategic partnerships, streamlined communication, and efficient planning

brain science news

news
“Computational crystal ball” helps predict cell behavior
New technology could lead to better treatments for cancer by allowing scientists to perform virtual experiments
news
Mind trip: How psilocybin changes the brain
New research may help improve psychedelic therapy for neuropsychiatric disorders
news
Computer model predicts aspects of cognitive performance
The Allen Human Brain Atlas helped researchers design a model that looked at “intrinsic neural timescales”
By examining brain cell types and connections across species at a refined level and at the most comprehensive scale – we are working towards understanding the structure and function of the human brain itself.
Hongkui Zeng
Executive Vice President and Director, Brain Science
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featured publications

view all publications
publication / 2025
What makes the human brain special: from cellular function to clinical translation
Journal of Neurophysiology
publication / 2025
The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales
Communications Biology
publication / 2025
AAV delivery of full-length SYNGAP1 rescues epileptic and behavioral phenotypes in a mouse model of SYNGAP1-related disorders
Molecular Therapy: The Journal of the American Society of Gene Therapy
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access open tools, brain atlases, neuroscience databases, and more

science resources

brain science events

explore more events
event / May 11 - 14, 2026
2026 Computational Cell Types Workshop
In this hackathon-style workshop, attendees will be introduced to single cell- and spatial transcriptomic datasets from the Allen Institute and their collaborators, while working in teams to use these datasets for data analysis, tool creation, model development, and more.
event / July 23 - 24, 2026
Incorporating open connectomics data into teaching neuroscience
Join a community of undergraduate neuroscience educators at the Incorporating Open Connectomics data into teaching Neuroscience workshop on July 23 – July 24, 2026, hosted by the Allen Institute.
event / July 27 - 30, 2026
Coding with Allen Institute Data: A Python Workshop for Undergraduate Educators 2026
This workshop will introduce undergraduate neuroscience educators to working with Allen Institute open datasets using Python.
explore more events

brain science advisory council

David J. Anderson
California Institute of Technology
Paola Arlotta
Harvard University
Edward M. Callaway
Salk Institute for Biological Studies
Rosa Cossart
French National Institute of Health and Medical Research (Inserm)
Karl Deisseroth
Stanford University
Michael D. Ehlers
CSO & Venture Partner | Apple Tree Partners
Viren Jain
Google
Erich Jarvis
Rockefeller University
Botond Roska
Institute for Molecular and Clinical Ophthalmology Basel
Barbara Treutlein
Swiss Federal Institute of Technology in Zürich (ETH Zürich)
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brain science

Mapping every cell, connection, and circuit in the brain—openly shared with the world.

cell science

Decoding how cells become tissues, then programming that knowledge into powerful new research tools.

neural dynamics

Revealing the brain's hidden algorithms that transform neural activity into real-world behavior.

immunology

Creating the deepest open reference for the healthy human immune system ever built.

synthetic biology

Engineering cells to record their own histories, transforming how we understand disease over time.

research

Big questions, open answers, and science built to be shared.

education

Inspiring the next generation of scientists through open science resources.

impact

Our science is empowering researchers and advancing health worldwide.
advancing science through open, collaborative research
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