Team Science Projects

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.

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.

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.

Neural Dynamics in Multi-Regional Circuits with Thalamus in the Middle

We are uncovering how neural signals are transmitted from subcortical brain regions via the thalamus to modulate cortical activity and thereby influence behavior.

Cell Types & Learning

We are combining longitudinal in vivo calcium imaging with spatial transcriptomics to investigate how specific cell types restructure their activity during novelty processing and task learning.

Dynamic Routing

We are studying task-switching behaviors in mice to determine how the brain controls the flow of its own activity and how neuronal circuits are reconfigured to dynamically route information for different tasks.

OpenScope

OpenScope provides access to cutting-edge neurophysiological methods to scientists across the world. Similar to astronomical observatories, scientists propose experiments that are then executed at the Allen Institute.

Single-Cell Computation

Our goal is to investigate the computations performed by individual neurons of different types, based on measuring synaptic input and firing output.

Brain-Wide Neuromodulation

We are studying the molecular and anatomical subclasses of neuromodulator neurons and exploring how networks use neuromodulators to drive learning and decision making.

Credit Assignment During Learning

We are using optical connection-mapping techniques and brain computer interface (BCI) in the context of a learning task to ask how the brain updates its synapses to support behavioral learning without interfering with existing skills or memories.

Platforms accelerate our work

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.

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.

Surgery

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

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.

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.

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.

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.