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people

R. Clay Reid

Investigator, Sr. Connectomics

teams /
Allenite

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.

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news
Scientists complete largest wiring diagram and functional map of the brain to date
The MICrONS Project is considered the most complicated neuroscience experiment ever attempted
video
Revealing the largest wiring diagram and functional map of the brain through MICrONS
Scientists have created the largest wiring diagram and functional map of an animal brain
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Attempting the impossible: A 20-year journey to learn the language of the brain
In what is considered the most complicated neuroscience experiment ever attempted, scientists from the Allen Institute and global collaborators have...

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featured publications

publication / 2025
The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex
Nature Neuroscience
publication / 2025
An unsupervised map of excitatory neuron dendritic morphology in the mouse visual cortex
Nature Communications
publication / 2025
CAVE: Connectome Annotation Versioning Engine
Nature Methods
publication / 2025
NEURD offers automated proofreading and feature extraction for connectomics
Nature
publication / 2025
Inhibitory specificity from a connectomic census of mouse visual cortex
Nature
publication / 2025
Functional connectomics reveals general wiring rule in mouse visual cortex
Nature
publication / 2025
Perisomatic ultrastructure efficiently classifies cells in mouse cortex
Nature
publication / 2025
Foundation model of neural activity predicts response to new stimulus types
Nature
publication / 2024
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues
eLife
publication / 2022
Oligodendrocyte precursor cells ingest axons in the mouse neocortex
Proceedings of the National Academy of Sciences of the United States of America
publication / 2022
Binary and analog variation of synapses between cortical pyramidal neurons
eLife
publication / 2022
A scalable and modular automated pipeline for stitching of large electron microscopy datasets
eLife
publication / 2022
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues
Nature Methods
publication / 2022
Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity
Cell
publication / 2021
Structure and function of axo-axonic inhibition
eLife
publication / 2021
Laminar distribution and arbor density of two functional classes of thalamic inputs to primary visual cortex
Cell Reports
publication / 2021
Autoencoder networks extract latent variables and encode these variables in their connectomes
Neural Networks: The Official Journal of the International Neural Network Society
publication / 2021
Chromatic micromaps in primary visual cortex
Nature Communications
publication / 2021
Survey of spiking in the mouse visual system reveals functional hierarchy
Nature
publication / 2021
Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice
eLife
publication / 2020
A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy
Nature Communications
publication / 2020
The Mind of a Mouse
Cell
publication / 2020
Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics
eNeuro
publication / 2020
A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex
Nature Neuroscience
publication / 2018
Transport and trapping of nanosheets via hydrodynamic forces and curvature-induced capillary quadrupolar interactions
Journal of Colloid and Interface Science
publication / 2018
Visual physiology of the layer 4 cortical circuit in silico
PLoS computational biology
publication / 2018
Nontoxic, double-deletion-mutant rabies viral vectors for retrograde targeting of projection neurons
Nature Neuroscience
publication / 2018
Mouse color and wavelength-specific luminance contrast sensitivity are non-uniform across visual space
eLife
publication / 2018
Large-scale neuroanatomy using LASSO: Loop-based Automated Serial Sectioning Operation
PloS One
publication / 2017
Spatial Organization of Chromatic Pathways in the Mouse Dorsal Lateral Geniculate Nucleus
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
publication / 2016
A Comparison of Visual Response Properties in the Lateral Geniculate Nucleus and Primary Visual Cortex of Awake and Anesthetized Mice
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
publication / 2016
Inferring cortical function in the mouse visual system through large-scale systems neuroscience
Proceedings of the National Academy of Sciences of the United States of America
publication / 2016
Anatomy and function of an excitatory network in the visual cortex
Nature
publication / 2015
Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance
Neuron
publication / 2014
Removable cranial windows for long-term imaging in awake mice
Nature Protocols
publication / 2014
A mouse model of higher visual cortical function
Current Opinion in Neurobiology
publication / 2013
The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience
Scientific and statistical database management: International Conference, SSDBM ...: proceedings. International Conference on Scientific and Statistical Database Management
publication
Connectomics of predicted Sst transcriptomic types in mouse visual cortex
Nature
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