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We explore the brain’s circuits and activity

Discovering how information processed by networks of neurons generates our thoughts, emotions, and actions

Our Mission

From individual neurons to the whole brain, we work to reveal how the brain interprets environments to make decisions.

Learn about our team

Our approach

Innovative methods and groundbreaking discoveries to deepen our understanding of the brain, while paving the way for new treatments for brain disorders.

Scientists at the Neural Dynamics accelerator at Allen Institute analyze and trace the path of signaling in neural circuits cascading across the whole brain and body.

Our approach is focused on how the parts of the brain work together to produce behavior. Teams of researchers develop next-generation neurotechnologies that capture rich data that are shared with the wider scientific community.  

Open Science

We are doing science in the open. Our data and tools are openly available to the community.

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Collaborative Process

We work in a coordinated manner to address complex and deep scientific challenges, leveraging the joint strengths and expertise of diverse scientists and technical staff.​

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Platforms accelerate our work

Mesoscale Anatomy

This platform builds on turn-key lightsheet microscopes to image mouse brains at high resolution and throughput. Analysis of the resulting volumetric images, including registration to standard brain coordinates and segmentation and counting of individual neurons, is fully automated.

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SLAP2

This platform uses a two-photon microscope SLAP2 that records patterns of synaptic input and output in individual neurons at hundreds to thousands of frames per second in mice performing complex behaviors, using a flexible scan system that combines a digital micromirror device (DMD) with a high-speed scanner.

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Scientific Instrumentation & Process Engineering

The Scientific Instrumentation and Process Engineering (SIPE) team is a shared engineering resource within the Allen Institute, focused on enabling and scaling cutting-edge bioscience through integrated hardware and software systems.

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Surgery

This team performs a variety of surgical procedures, including stereotaxic injections and implanting chronic cranial windows and Neuropixels probes.

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Multi-Neuropixels Electrophysiology

This platform implements pioneering technology for highly reproducible, targeted, brain-wide, cell-type-specific electrophysiology to record neural activity from defined neuron types across the brain. Analysis and quality control of the electrophysiology data are fully automated.

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Brain-Wide Anatomy at Synaptic Resolution

This platform combines innovative histology, ExA-SPIM microscopy, image handling, and machine learning to map the morphology and molecular identity of individual neurons across the whole brain at high throughput.

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Fiber Photometry

This platform enables optical measurement of neural activity and neurotransmitter release in populations of neurons to study neural circuit dynamics in behaving animals.

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Behavior

The Behavior platform uses advanced technology to implement a standardized, modular, multi-task virtual reality gymnasium for mice, with the goal to study brain function across different behaviors at scale.

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Projects

Team-based research efforts, with the primary goal of answering a foundational scientific question to make discoveries.

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Information Foraging

We study the biological mechanisms that enable animals to learn the structure of their world through free exploration. To do this, we collect long-term, uninterrupted records of the natural behavior, brain activity, and network connectivity of mice while they repeatedly interact with odors in their environment.

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Behavior and Motor Control

We are developing and using genetic, electrophysiological, optical, and behavioral approaches to investigate how the brain adaptively controls behavior. The team focuses on understanding the descending circuits that control the execution of actions and how they change when actions are reinforced and refined.

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Brain-Wide Circuit Dynamics

We are using large-scale electrophysiology to study how distributed brain regions coordinate their spiking activity to guide behavior in changing environments.

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Get Involved

Upcoming events

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AIND-UW CNC Hackacollabathon

We are excited to announce the next Hackacollabathon, co-hosted by the Allen Institute / Neural Dynamics (AIND) and the UW Computational Neuroscience Center (CNC). This event brings together researchers from the Allen Institute and UW to collaboratively explore new datasets collected in Neural Dynamics.

The event will feature work from the Dynamic Routing project. The team has been conducting large-scale, brain-wide Neuropixels recordings in mice performing a sensory switching task in which animals flexibly attend to either auditory or visual stimuli to receive rewards. This dataset gives insight into how information is processed across the brain during flexible, goal-directed behavior. Read more about the project here.

Event format:

  • Short science talks from the Dynamic Routing team
  • Hands-on tutorial introducing the dataset and analysis tools
  • Open hacking time to explore the data individually or in small groups

We will provide access to the data and code through Code Ocean – registration is free but required. Lunch will also be provided! Please join us if you are interested in analyzing large-scale, neural datasets in a collaborative environment. Python experience expected (NumPy, SciPy, matplotlib, pandas).  

For questions, contact Su-YeeLee (suyee.lee@alleninstitute.org) or Saskia de Vries (saskiad@alleninstitute.org).

Event details

Summer Workshop on the Dynamic Brain 2026

The 2026 Summer Workshop on the Dynamic Brain is an intensive, project-based residential course with a focus on the neurobiology of sensory processing, coding, and neural population dynamics. This program is intended for researchers at the graduate and postdoctoral level with an interest in developing the intersection of their scientific knowledge and their computational skills.

Applications are due February 1, 2026.

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Event details