Joshua H. Siegle

3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data

3D-MAESTRO automates processing of large-scale volumetric brain microscopy data, enabling scalable and reproducible analysis of mouse brain structures.

A Population Coupling Model Identifies Reduced Propagation from V1 to Higher Visual Areas During Locomotion

The paper introduces a population-level GLM (pop-GLM) to detect cross-population coupling, showing reduced V1 to higher visual area connectivity during locomotion.

Map of spiking activity underlying change detection in the mouse visual system

The paper presents a database of spiking activity in the mouse visual system during an image change detection task, revealing task-specific coding patterns across brain regions.

Neuropixels Opto: Combining high-resolution electrophysiology and optogenetics

The paper introduces Neuropixels Opto probes that combine high-resolution electrophysiology with optogenetics for spatially addressable neuronal manipulation and recording.

Topographic structure and function of locus coeruleus norepinephrine neurons

The paper identifies topographic organization in locus coeruleus norepinephrine neurons, linking their morphology, gene expression, and activity to specific brain regions and learning-related behaviors.

Relative timing and coupling of neural population bursts in large-scale recordings from multiple neuron populations

The paper develops a method to analyze the relative timing and coupling of neural population bursts across brain regions in mice, finding consistent and variable patterns of activity.

Efficient and reproducible pipelines for spike sorting large-scale electrophysiology data

The paper presents scalable spike sorting pipelines and benchmarking tools for large-scale electrophysiology data, showing Kilosort4 outperforms Kilosort2.5 and 7x compression has minimal impact on performance.

Foundry-fabricated dual-color nanophotonic neural probes for photostimulation and electrophysiological recording

This paper presents a nanophotonic neural probe with dual-color photostimulation and electrophysiological recording capabilities, demonstrating dense emitter integration for targeted circuit manipulation.

Deciphering neuronal variability across states reveals dynamic sensory encoding

The paper analyzes neuronal variability across brain states to understand how factors like internal dynamics, behavior, and stimuli influence sensory processing over time.

SHIELD: Skull-shaped hemispheric implants enabling large-scale-electrophysiology datasets in the mouse brain

SHIELD enables large-scale electrophysiological recordings in mice by providing a skull-shaped implant for repeated multi-probe insertions across brain regions.

A unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior

The paper introduces ONIX, a system for long-duration neural recordings during natural behavior in mice, enabling high-throughput data acquisition with minimal behavioral impact.

Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings

This paper introduces NP Ultra, a high-density electrode that improves neuronal recording yield, detection, and cell type classification in mice.

Uncovering circuit mechanisms of current sinksand sources with biophysical simulations ofprimary visual cortex

The paper uses biophysical simulations of mouse primary visual cortex to show that current sinks and sources are shaped by both synaptic weights and dendritic placement, with distinct contributions from thalamocortical inputs and cortical feedback.

Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment

Pinpoint is a web-based tool for planning and automating multi-probe electrophysiology and injection procedures in 3D space, improving efficiency and reproducibility.

Compression strategies for large-scale electrophysiology data

This paper evaluates compression strategies for electrophysiology data, finding that lossy compression can significantly reduce file sizes without affecting spike sorting accuracy.

Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex

The paper links in vitro, in vivo, and in silico cell classes in mouse visual cortex using computational modeling and optotagging experiments to identify distinct clusters with specific properties.

A survey of neurophysiological differentiation across mouse visual brain areas and timescales

This paper uses Neuropixels recordings to analyze neurophysiological differentiation (ND) in mouse visual brain areas across timescales, finding higher ND for naturalistic stimuli and successful detection trials.

Removing independent noise in systems neuroscience data using DeepInterpolation

DeepInterpolation improves signal-to-noise ratio in neuroscience data without sacrificing resolution, enhancing detection of neuronal activity across multiple modalities.

Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

This study compares neuronal responses in visual cortex using electrophysiology and two-photon imaging in awake mice, finding differences in responsiveness and selectivity and exploring data transformations to reconcile them.

Geometry of inter-areal interactions in mouse visual cortex

The paper studies how interactions between mouse visual cortical areas change over time using functional connectivity analysis of neural activity data.

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.

Multi-regional module-based signal transmission in mouse visual cortex

The paper tracks spiking activity across six levels of the mouse visual hierarchy to identify two multi-regional communication modules with distinct signal flow and functional roles.

SpikeInterface, a unified framework for spike sorting

SpikeInterface provides a unified framework to run, compare, and benchmark spike sorting algorithms, reducing manual curation and enabling comprehensive benchmarking of automated methods.

CellExplorer: a graphical user interface and standardized pipeline for visualizing and characterizing single neuron features

CellExplorer provides a framework for visualizing and characterizing single neuron features through standardized processing and a graphical interface.

Systematic Integration of Structural and Functional Data into Multi-Scale Models of Mouse Primary Visual Cortex

The paper develops a multi-scale model of mouse primary visual cortex integrating structural and functional data to identify cell-class specific connectivity rules.

Does the neuronal noise in cortex help generalization?

The paper analyzes neuronal variability in the cortex and finds that its distribution resembles deep learning noise, suggesting it may aid generalization during learning.

High-density extracellular probes reveal dendritic backpropagation and facilitate neuron classification

The paper uses high-density extracellular recordings to classify neurons by brain region and identify dendritic backpropagation through waveform analysis.