Department of Neurobiology & Biophysics

Brain-wide circuits for perception, cognition, and action

We study how distributed circuits turn sensations into decisions, using large-scale electrophysiology, calcium imaging, and optogenetics. Our work aims to reveal the biological mechanisms of thought at a brain-wide scale.

Behind this text: 141 neurons recorded simultaneously, 90 s of a real Neuropixels recording from our lab. Each mark is one spike; rows are sorted by depth along the probe.

What we do

Our core research questions

Each panel below is real data from the lab and the collaborations we are part of.

Behavior

How do we choose our actions based on what we see?

Mice report what they saw by turning a wheel, which gives us hundreds of precisely measured choices per session, quantified with psychophysical modeling.
Neuropixels

What neurons across the brain contribute to vision and decision-making?

With next-generation probes we record thousands of channels simultaneously, from cortex to hindbrain.
Cortex-wide imaging

What are the brain dynamics that give rise to behavior?

Activity crosses the cortex in coordinated patterns, including waves that sweep and rotate, which we measure with imaging and electrophysiology.
Circuits

What circuits underlie brain-wide computation and dynamics?

High-precision anatomical approaches and optogenetic manipulations of brain activity tell us which projections actually carry a signal, and what happens without them.

Cortical imaging

Mouse brain activity over the cortical surface

An example cortex-wide calcium recording, running in real time, visualizing activity from both hemispheres of dorsal cortex at 35 frames per second.

Subject ZYE_0092, 2 June 2025. The trace below the image is mean fluorescence across the frame - click or drag along it to jump to that moment.

dorsal cortex · dF/F 0.00 s

141 neurons · ordered by depth 0.0–8.0 s

Electrophysiology

Large-scale measurement at single-spike resolution

Every dot is one action potential from one neuron. Rows run from the top of the probe down into the brain, so a vertical streak represents many cells firing together.

Spikes shown 0 Population rate 0.0 spikes/s

A single recording, sorted with Kilosort. The trace below the raster is population firing rate - click or drag along it to move the window, or use the arrow keys.

141 neurons not enough? Click!

Publications

Recent work

2026Brain-wide topographic coordination of rotating wavesYe, Ladd, MacKenzie, Kolich, Li, Birman, Bull, Daigle, Tasic, Zeng, SteinmetzScience

2026Large-scale electrophysiology at single-spike resolutionSiegle, SteinmetzNat Rev Neurosci PDF

2026Prefrontal to ventral tegmental area dynamics drive contingency degradationHjort, Garrett, Gordon, Ancell, Trzeciak, Lu, Bruchas, Witten, Steinmetz, StuberNature PDF

2026The midbrain reticular formation in contextual control of perceptual decisionsShaker, Schroeter, Birman, SteinmetzNeuron PDF

2025A brain-wide map of neural activity during complex behaviourThe International Brain Laboratory, ..., Birman, Roth, Steinmetz, et al.Nature

2025Benchmarking Probabilistic Time Series Forecasting Models on Neural ActivityLu, Li, Ladd, Matveev, Deole, Shea-Brown, Kutz, SteinmetzarXiv

2025Brain-wide representations of prior information in mouse decision-makingFindling, Hubert, The International Brain Laboratory, ..., Birman, Roth, Steinmetz, et al.Nature

2025Global and local origins of trial-to-trial spike count variability in visual cortexLi*, Lu*, Ladd, Matveev, Shea-Brown^, Steinmetz^bioRxiv

All 70 publications · Google Scholar · ORCID

People

Our team

Nick SteinmetzPrincipal Investigator

Kim MillerResearch Scientist

Fabiola Duarte OrtizPostdoctoral Scientist

Aditya DeolePostdoctoral Scientist

Edward YanPostdoctoral Scientist, CIHR Fellow

Saghar MirbagheriPhD Student

Anna LiPhD Student, NIH F31 Fellow

Nancy MackenziePhD Student

Xander LaddPhD Student

Rachel YinUndergraduate Scientist, Goldwater Scholar

Alice GettigUndergraduate Scientist

Zhorzh ZelenkovUndergraduate Scientist

Annie WuUndergraduate Scientist

Kimmie ShenoyUndergraduate Scientist

Ian McFaddenUndergraduate Scientist, summer

Allison LinHigh-School Summer Student

Bersabel BahruHigh-School Summer Student, BRIGHT-UP

Plus 30 alumni · All current and alumni

News

Lab news

Updates on papers, awards, and more.

August 2026

Saghar Mirbagheri successfully defends PhD thesis!

On "Prediction Content Shapes Population Representations in Mouse Primary Visual Cortex".

July 2026

Anna Li successfully defends PhD thesis!

On "Causal and distributed mechanisms of cortical computation".

June 2026

Brain-wide topographic coordination of rotating waves

Ye et al., Science.

All news

Open science

Shared data and code

Everything below is public. We encourage and support re-analysis and re-use of our work.

Datasets

Brain-wide rotating waves — cortex-wide imaging and NeuropixelsYe et al., Science, 2026
Midbrain reticular formation recordings — context-dependent visual decisionsShaker et al., Neuron, 2026
Neuropixels Ultra waveforms — browse or downloadYe et al., Neuron, 2025
IBL brain-wide map — 699 recordings, NWB on DANDIInternational Brain Laboratory, Nature, 2025
Olfactory Pavlovian conditioning — ephys + 2POttenheimer et al., eLife, 2023
Neuropixels 2.0 with imposed brain motionSteinmetz et al., Science, 2021
Visual discrimination recordings — also in NWB and ONESteinmetz et al., Nature, 2019

Software

Pinpoint — plan probe insertions
SlidingRP — refractory-period contamination metric
widefield — analyze cortex-wide imaging data
allenCCF — work with the Allen atlas
Alyx — experiment database

We are hiring postdocs and taking rotation students.

How to join the lab