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discovery is a team effort
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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
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our approach
science at the scale of greatest impact
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explore our publications
open science
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building a blueprint of the brain
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revealing the brain’s hidden algorithms
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neural dynamics
Revealing the brain's hidden algorithms—how circuits, cells, and molecules combine to create behavior
explore neural dynamics
neural dynamics team
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Every decision, every habit, every learned skill starts with patterns of activity in your brain.

We can observe behavior: what a person or animal does in any given moment. What we can't easily see is the cascading neural activity in the brain that produced it. Bridging that gap is the defining challenge of neuroscience, and it requires studying all the pieces of the brain at once.

We study how animals make flexible, real-world decisions like foraging for resources while minimizing effort and avoiding danger. These kinds of behaviors recruit almost every major brain system. By recording neural activity across the whole brain and building mathematical models that tie it to behavior, we're discovering the algorithms that let the brain learn, generalize, and adapt. With this powerful new perspective, our open datasets and tools will seed an entirely new generation of neuroscience.

Blue glowing neural network nodes and interconnected pathways on dark background
By connecting behavior to brain activity at unprecedented scale, we're building the knowledge base that will shape clinical and academic brain research for decades to come.

reasearch projects

Cell Types & Learning
‍
Investigating how specific brain cell types change their activity during novelty and learning using calcium imaging and spatial transcriptomics.

Dynamic Routing
Studying how the brain flexibly reroutes neural activity during task-switching in mice.

OpenScope
A shared neuroscience platform where global researchers propose experiments that are executed using advanced tools at the Allen Institute.

Single-Cell Computation
Exploring how individual neurons compute by tracking synaptic inputs and outputs at single-synapse resolution in living brains.

Brain-Wide Neuromodulation
Examining how different neuromodulator neuron types influence learning and decision-making across brain networks.

Credit Assignment During Learning
Using brain-computer interfaces and optical mapping to understand how the brain updates synapses during learning without disrupting existing knowledge.

‍

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A group of Neural Dynamics researchers collaborating at Allen Institute.

neural dynamics news

news
Neuropixels Opto sheds new light into deepest regions of the brain
A single tool measures and manipulates brain cell communication and democratizes advanced neuroscience
news
Scientists develop new way to “listen in” on the brain’s hidden language
Paradigm-shifting technology is changing how researchers do neuroscience
news
Allen Institute scientists igniting curiosity of young minds
Students at the University of Puget sound are gaining valuable real-world insight and training using the Allen Institute's cutting edge resources and...
Sculpted by evolution, the brain’s amazing, complex neural circuits produce our behavior within the world. We aim to discover how information processed by networks of neurons generates our thoughts, emotions and actions.
Karel Svoboda
Executive Vice President and Director, Neural Dynamics
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neural dynamics publications

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publication / 2025
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues
eLife
preprint / 2025
Glutamate indicators with increased sensitivity and tailored deactivation rates
preprint / 2025
Adaptation, not prediction, drives neuronal spiking responses in mammalian sensory cortex
Next
1 / 9
view all publications
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access open tools, brain atlases, neuroscience databases, and more

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neural dynamics events

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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.
event / September 15–16, 2026
Emerging connectomics of thalamus and striatum workshop
Join us for a hands-on opportunity to learn how to use volumetric electron microscopy (EM) data and address biological questions central to the thalamus and striatum at the Emerging Connectomics of the Thalamus and Striatum Workshop, hosted at by the Allen Institute.
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neural dynamics scientific advisory council

Anne K. Churchland
University of California, Los Angeles
Roshan Cools
Radboud University Medical Center
Peter Dayan
Max Planck Institute
Adrienne Fairhall
University of Washington
Tirin Moore
Stanford University / Howard Hughes Medical Institute
Tom Mrsic-Flogel
Sainsbury Wellcome Centre
Liam Paninski
Columbia University
Bernardo Sabatini
Harvard University / Howard Hughes Medical Institute
Fan Wang
Massachusetts Institute of Technology
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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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