R. Clay Reid

Scaling up polarization-sensitive optical coherence tomography to image the whole macaque brain

This paper develops a scalable PS-OCT system for whole-brain imaging in rhesus macaques, achieving high-resolution volumetric data with multi-terabyte datasets.

A retinotopic wiring principle of the human brain

The paper shows that structural connectivity in the human visual cortex preserves retinotopic organization, revealing a retinotopic wiring principle and systematic perceptual asymmetries in early visual cortex connectivity.

Heterogeneity of white matter structure in the human brain

The paper characterizes the 3D organization of large axons in human white matter, revealing distinct architectural patterns across different brain regions.

Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues

The paper introduces ExA-SPIM, a microscope that enables high-resolution imaging of large tissue samples without sectioning, demonstrating its use on mouse brains and human white matter.

Hebb's Vision: The Structural Underpinnings of Hebbian Assemblies

The paper identifies neural assemblies consistent with Hebb's theory using a novel dataset linking optical physiology to connectivity, finding they are structurally integrated but not defined by strong monosynaptic connections.

CAVE: Connectome Annotation Versioning Engine

CAVE enables reproducible connectome analysis in large-scale datasets during ongoing annotation and proofreading.

NEURD offers automated proofreading and feature extraction for connectomics

NEURD automates proofreading and feature extraction from connectomics data to improve accuracy and accessibility of neural morphology analyses.

Functional connectomics spanning multiple areas of mouse visual cortex

The paper presents a functional connectomics dataset of mouse visual cortex, combining calcium imaging with EM reconstruction to study neural circuits and their connectivity.

Functional connectomics reveals general wiring rule in mouse visual cortex

Functionally similar neurons in mouse visual cortex connect preferentially across layers and areas, including feedback, and feature tuning, not receptive-field position, predicts synapses beyond axon-dendrite proximity.

An unsupervised map of excitatory neurons' dendritic morphology in the mouse visual cortex

The paper uses graph-based machine learning to analyze dendritic morphology of excitatory neurons in mouse visual cortex, finding a continuous morphological landscape rather than discrete types.

A scalable and modular computational pipeline for axonal connectomics: automated tracing and assembly of axons across serial sections

The paper introduces a computational pipeline for automated tracing and assembly of axons across serial sections, validated on centimeter-scale data for orientation analysis and proofreading.

Microscale visualization of cellular features in adult macaque visual cortex

The paper visualizes dense distributions of immunolabeled proteins in adult macaque visual cortex using expansion microscopy and light sheet imaging, enabling multimodal atlas creation.

The Synaptic Architecture of Layer 5 Thick Tufted Excitatory Neurons in the Visual Cortex of Mice

The paper investigates the synaptic connectivity of thick tufted layer 5 pyramidal neurons in the mouse visual cortex, revealing their local inhibitory and long-range excitatory connections.

Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types

The paper predicts MET-type identities from EM data and shows they have distinct connectivity patterns and synapse targets.

Foundation model of neural activity predicts response to new stimulus types and anatomy

This paper trains a foundation model on neural activity data to predict responses to new stimuli and anatomical features, showing strong generalization across mice and tasks.

Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex

Electron microscopy of 1352 neurons in a mouse visual cortex column reveals widespread cell-type-specific inhibition, a basket-cell-targeting disinhibitory class, and interneuron motif groups sharing excitatory targets.

Binary and analog variation of synapses between cortical pyramidal neurons

The paper maps synaptic connectivity between cortical pyramidal neurons and shows synapse size is modeled by a combination of binary and analog variables.

A Scalable and Modular Automated Pipeline for Stitching of Large Electron Microscopy Datasets

The paper presents a scalable pipeline for assembling large electron microscopy datasets into 3D volumes, achieving high throughput and modular design for efficient processing.

Perisomatic Features Enable Efficient and Dataset Wide Cell-Type Classifications Across Large-Scale Electron Microscopy Volumes

The paper uses electron microscopy data to classify cell types in the neocortex based on perisomatic features, showing that these features are sufficient for accurate classification even in large datasets.

Motion/direction-sensitive thalamic neurons project extensively to the middle layers of primary visual cortex

The paper shows motion/direction-sensitive thalamic neurons project more to middle layers of V1 than previously thought, challenging existing views on thalamocortical organization.

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

The paper uses autoencoder networks to show that regularization can resolve ambiguity in connectivity weights, allowing latent variable extraction through nonlinear dimensionality reduction.

Petascale neural circuit reconstruction: automated methods

Cloud-run convolutional nets aligned 19,939 serial EM sections of mouse visual cortex despite cracks and folds, segmented neurons and detected 523 million synapses; code and the reconstruction are public.

Oligodendrocyte precursor cells prune axons in the mouse neocortex

The paper identifies oligodendrocyte precursor cells (OPCs) as major contributors to axon pruning in the mouse neocortex through phagocytic activity.

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

The paper characterizes the relationship between spiking activity and fluorescence signals in GCaMP6-expressing neurons, finding GCaMP6s has better single-spike detection than GCaMP6f.

A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas

The paper presents a dataset and analysis of spiking activity across multiple mouse visual areas, revealing that functional connectivity mirrors anatomical hierarchy.

Multiscale and multimodal reconstruction of cortical structure and function

The paper presents a semi-automated reconstruction of mouse primary visual cortex from electron microscopy data, revealing structural and functional relationships in cortical circuits.

A Petascale Automated Imaging Pipeline for Mapping Neuronal Circuits with High-throughput Transmission Electron Microscopy

The paper describes a high-throughput transmission electron microscopy pipeline for imaging neuronal circuits, achieving petascale data acquisition of mouse neocortex.

Chandelier cell anatomy and function reveal a variably distributed but common signal

The paper maps chandelier cell synapses onto pyramidal neurons and finds variability in synaptic input correlated with target neuron features, while showing functional correlation with arousal state.

EASE: EM-Assisted Source Extraction from calcium imaging data

The paper introduces EASE, a method that matches calcium imaging signals to EM-derived cell segments in mouse visual cortex, enabling dendritic functional analysis and denoising.

The spatial structure of feedforward information in mouse primary visual cortex

The paper maps the functional and structural properties of feedforward projections from the LGN to V1 in mice, revealing differences in receptive fields and depth-dependent biases between location-sensitive and motion-sensitive axons.