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R. Clay Reid

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R. Clay Reid, M.D., Ph.D.

Senior Investigator

Brain Science

Bio:

R. Clay Reid joined the Allen Institute in 2012 to study how information is encoded and processed in neural networks of the visual system, using behavior, anatomy and physiology. Prior to joining the Allen Institute, Reid served as Professor of Neurobiology at Harvard Medical School, where he had been on the faculty for fifteen years. Reid is a recognized authority on how the brain processes and makes sense of visual information, and has approached these topics from a variety of methods including electrophysiology, imaging, and quantitative analysis. Most recently he has used a combination of imaging and anatomical approaches to investigate how the structure of neural connections relates to functional brain circuitry. He has helped to pioneer new methods for recording increasingly large groups of neurons simultaneously in order to study information processing in neuronal populations. A recipient of the Klingenstein Fellowship in 1993 and the Society for Neuroscience Young Investigator Award in 2001, Reid has long been regarded as a pioneering leader in the field. Reid holds B.S. degrees in Mathematics and in Physics and Philosophy from Yale University, a Ph.D. from the Rockefeller University, and an M.D. from Cornell University Medical College.

News & Events

Four different kinds of brain cells are shown in high resolution. A large green neuron in the center is surrounded by different kinds of brain cells in purple, gold and pink.

News

Brain scientists unveil wiring diagram containing 200,000 cells and nearly half billion connections in tiny piece of a mouse's brain

07.29.2021

Detailed map captures 3D shapes of neurons and their synapses in stunning detail and is open to community for neuroscience and machine learning...

News

Projects launch to map brain connections in mouse and macaque

09.26.2023

NIH BRAIN Initiative-funded research will lay the groundwork to map entire brains in incredible detail

Proceedings of the National Academy of Sciences of the United States of America

Oligodendrocyte precursor cells ingest axons in the mouse neocortex

Nov 29, 2022

Neurons in the developing brain undergo extensive structural refinement as nascent circuits adopt their mature form. This physical transformation of...

eLife

Binary and analog variation of synapses between cortical pyramidal neurons

Nov 16, 2022

Learning from experience depends at least in part on changes in neuronal connections. We present the largest map of connectivity to date between...

eLife

A scalable and modular automated pipeline for stitching of large electron microscopy datasets

Jul 26, 2022

Serial-section electron microscopy (ssEM) is the method of choice for studying macroscopic biological samples at extremely high resolution in three...

Nature Methods

A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues

May 01, 2022

Light-sheet microscopy has emerged as the preferred means for high-throughput volumetric imaging of cleared tissues. However, there is a need for a...

Cell

Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity

Mar 17, 2022

We assembled a semi-automated reconstruction of L2/3 mouse primary visual cortex from ∼250 × 140 × 90 μm3 of electron microscopic images,...

eLife

Structure and function of axo-axonic inhibition

Dec 01, 2021

Inhibitory neurons in mammalian cortex exhibit diverse physiological, morphological, molecular, and connectivity signatures. While considerable work...

Cell Reports

Laminar distribution and arbor density of two functional classes of thalamic inputs to primary visual cortex

Oct 12, 2021

Motion/direction-sensitive and location-sensitive neurons are the two major functional types in mouse visual thalamus that project to the primary...

Neural Networks: The Official Journal of the International Neural Network Society

Autoencoder networks extract latent variables and encode these variables in their connectomes

Sep 01, 2021

Advances in electron microscopy and data processing techniques are leading to increasingly large and complete microscale connectomes. At the same...

Nature Communications

Chromatic micromaps in primary visual cortex

Apr 19, 2021

The clustering of neurons with similar response properties is a conspicuous feature of neocortex. In primary visual cortex (V1), maps of several...

Nature

Survey of spiking in the mouse visual system reveals functional hierarchy

Apr 01, 2021

The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically1. However, direct observation of...

eLife

Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice

Mar 08, 2021

Fluorescent calcium indicators are often used to investigate neural dynamics, but the relationship between fluorescence and action potentials (APs)...

Nature Communications

A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy

Oct 02, 2020

Electron microscopy (EM) is widely used for studying cellular structure and network connectivity in the brain. We have built a parallel imaging...

Cell

The Mind of a Mouse

Sep 17, 2020

Large scientific projects in genomics and astronomy are influential not because they answer any single question but because they enable investigation...

Nature Neuroscience

A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex

Jan 01, 2020

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the...

Journal of Colloid and Interface Science

Transport and trapping of nanosheets via hydrodynamic forces and curvature-induced capillary quadrupolar interactions

Dec 01, 2018

HYPOTHESIS: The manipulation of nanosheets on a fluid-fluid interface remains a significant challenge. At this interface, hydrodynamic forces can be...

PLoS computational biology

Visual physiology of the layer 4 cortical circuit in silico

Nov 01, 2018

Despite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex, quantitative...

Nature Neuroscience

Nontoxic, double-deletion-mutant rabies viral vectors for retrograde targeting of projection neurons

Apr 01, 2018

Recombinant rabies viral vectors have proven useful for applications including retrograde targeting of projection neurons and monosynaptic tracing,...

eLife

Mouse color and wavelength-specific luminance contrast sensitivity are non-uniform across visual space

Jan 10, 2018

Mammalian visual behaviors, as well as responses in the neural systems underlying these behaviors, are driven by luminance and color contrast. With...

PloS One

Large-scale neuroanatomy using LASSO: Loop-based Automated Serial Sectioning Operation

Jan 01, 2018

Serial section transmission electron microscopy (ssTEM) is the most promising tool for investigating the three-dimensional anatomy of the brain with...

The Journal of Neuroscience: The Official Journal of the Society for Neuroscience

Spatial Organization of Chromatic Pathways in the Mouse Dorsal Lateral Geniculate Nucleus

Feb 01, 2017

In both dichromats and trichromats, cone opsin signals are maintained independently in cones and combined at the bipolar and retinal ganglion cell...

The Journal of Neuroscience: The Official Journal of the Society for Neuroscience

A Comparison of Visual Response Properties in the Lateral Geniculate Nucleus and Primary Visual Cortex of Awake and Anesthetized Mice

Nov 30, 2016

The cerebral cortex of the mouse has become one of the most important systems for studying information processing and the neural correlates of...

Proceedings of the National Academy of Sciences of the United States of America

Inferring cortical function in the mouse visual system through large-scale systems neuroscience

Jul 05, 2016

The scientific mission of the Project MindScope is to understand neocortex, the part of the mammalian brain that gives rise to perception, memory,...

Nature

Anatomy and function of an excitatory network in the visual cortex

Apr 21, 2016

Circuits in the cerebral cortex consist of thousands of neurons connected by millions of synapses. A precise understanding of these local networks...

Neuron

Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance

Mar 04, 2015

An increasingly powerful approach for studying brain circuits relies on targeting genetically encoded sensors and effectors to specific cell types....

Nature Protocols

Removable cranial windows for long-term imaging in awake mice

Nov 01, 2014

Cranial window implants in head-fixed rodents are becoming a preparation of choice for stable optical access to large areas of the cortex over...

Current Opinion in Neurobiology

A mouse model of higher visual cortical function

Feb 01, 2014

During sensory experience, the retina transmits a diverse array of signals to the brain, which must be parsed to generate meaningful percepts that can...

Scientific and statistical database management: International Conference, SSDBM ...: proceedings. International Conference on Scientific and Statistical Database Management

The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience

Jan 01, 2013

We describe a scalable database cluster for the spatial analysis and annotation of high-throughput brain imaging data, initially for 3-d electron...

eNeuro

Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics

Serial section electron microscopy (ssEM), a technique where volumes of tissue can be anatomically reconstructed by imaging consecutive tissue slices,...

R. Clay Reid, M.D., Ph.D.

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