Understanding how brain circuitry and activity drive behavior, learning and decision-making
Understanding how brain circuitry and activity drive behavior, learning and decision-making

The Allen Institute for Neural Dynamics explores the brain’s activity, at the level of individual neurons and the whole brain, to reveal how we interpret our environments to make decisions. We aim to discover how neural signaling – and changes in that signaling – allow the brain to perform complex but fundamental computations and drive flexible behaviors. Our experiments and openly shared resources will shed light on behavior, memory, how we handle uncertainty and risk, how humans and other animals chase rewards – and how some or all of these complicated cognitive functions go awry in neuropsychiatric disorders such as depression, ADHD or addiction. 

News at the Allen Institute for Neural Dynamics


Look in the labs | Neural Dynamics

September 13, 2022

Scientists are 3D imaging whole mouse brains in high resolution to learn how different brain regions connect and communicate.

Press Release

Announcing the Allen Institute for Neural Dynamics, a new neuroscience division of the Allen Institute

November 4, 2021

New Institute will study how the brain’s circuitry and activity give rise to complex behavior, decision making and memory

Projects and platforms

Work at the Allen Institute for Neural Dynamics will take the form of exciting discovery projects utilizing data generation platforms built with next generation neurotechnologies. 


The electrophysiology platform combines high-density neural probes, optogenetic manipulations, and precise anatomy-guided targeting to enhance our understanding of how information flows throughout the brain. The platform focuses on scaling up our ability to record spikes from living brains, while also finding ways to link spike trains to the genetically defined cell types that generate them. Large-scale recordings are carried out in the context of naturalistic behaviors that engage diverse neural circuits. The platform generates rich multimodal datasets that will be released to the public, as well as computational tools for extracting meaning from neural data. 

Multiscale Molecular Anatomy

The multi-scale molecular anatomy platform generates comprehensive descriptions of neuronal types and examine connectivity at various scales in defined cell types. Using large-scale microscopy methods, the platform identifies projection neuron types, based on the structure of single neurons combined with spatial transcriptomics (morphomolecular cell types) and super-resolution immunofluorescence of postsynaptic targets. Analysis of the wiring in the mouse brain will create foundational data sets to examine complex behaviors at the level of defined neuronal types.

Optical Physiology

The optical physiology platform enables measurement and manipulation of in vivo neural dynamics across spatial scales ranging from individual synapses to brain-spanning circuits. The platform focuses on studying neural communication by monitoring neurotransmitters, neuromodulators, and membrane potential, at the millisecond timescales required to keep up with fast neural computations. The platform is developing technologies for sophisticated two-photon microscopy and multiplexed photometry. 


The instrumentation department develops and maintains technology to support the scientific mission of the Allen Institute for Neural Dynamics. Our practice integrates hardware and software related to experimental control, animal behavior data acquisition and storage across the various platforms. We aim to develop specialized tools enabling cutting-edge research and to share these tools widely in the spirit of open science.