Karel Svoboda

Measuring neuronal input-output operations in vivo with random access projection microscopy

This paper introduces SLAP2, a high-speed microscope for measuring submicron synapses and dendritic voltage in behaving mice, revealing nonlinear input-output amplification in neurons.

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.

GIAnT: a Glutamate Imaging Analysis Toolbox

GIAnT is a toolbox for analyzing glutamate imaging data that corrects motion, identifies active synapses, and improves signal quality.

Spike inference from calcium imaging data acquired with GCaMP8 indicators

This study evaluates and optimizes spike inference methods for GCaMP8 calcium imaging data, showing improved detection of high-frequency spikes and real-time activity.

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.

Functional reorganization of motor cortex connectivity during learning

This study shows how rapid learning in mice involves structured changes in motor cortex connectivity, rerouting preparatory activity to control a conditioned neuron.

Glutamate indicators with increased sensitivity and tailored deactivation rates

The paper develops two variants of a glutamate indicator with enhanced sensitivity and tailored deactivation rates for studying synaptic transmission in vivo.

Neural dynamics outside task-coding dimensions drive decision trajectories through transient amplification

The paper shows that neural activity in non-task-coding dimensions can drive behavior through transient amplification, challenging the assumption that only task-relevant dimensions are behaviorally significant.

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.

Exploring the correspondence between gene expressionand thalamic nuclei using the THALMANAC resource

The paper introduces THALMANAC, a resource for analyzing single-cell transcriptomic data of the thalamus, revealing gene expression patterns that support and refine thalamic nucleus parcellation.

Brain-wide representations of prior information in mouse decision-making

Mice infer stimulus-side priors from recent choices; prior signals are decodable pre-stimulus in 24.0% to 30.2% of 242 brain regions, including early visual and motor areas.

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.

A common computational and neural anomaly across mouse models of autism

The paper shows that mice with ASD-related mutations exhibit similar computational and neural anomalies in prior updating during decision-making.

Reproducibility of in-vivo electrophysiological measurements in mice

This study evaluates the reproducibility of electrophysiological measurements across ten labs using standardized protocols and finds that variability in electrode targeting and statistical methods affects reproducibility.

A brainstem map of orofacial rhythms

The paper maps brainstem neural activity related to breathing, licking, and swallowing in mice, revealing coordinated rhythms and a premotor network involved in orofacial movements.

Sub-threshold neuronal activity and the dynamical regime of cerebral cortex

The paper evaluates whether the cerebral cortex operates in a fluctuation-driven regime by analyzing spiking and sub-threshold membrane potentials in different cortical areas.

Brain-wide neural activity underlying memory-guided movement

The paper records brain-wide neural activity in mice during a memory-guided task, showing distributed coding of choice and action across brain regions.

Connectivity underlying motor cortex activity during naturalistic goal-directed behavior

The paper maps functional connectivity in the motor cortex of mice during naturalistic reward-seeking behavior, revealing columnar architecture and hub neurons that influence neighboring cells.

Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species

The paper develops AAV-based genetic tools to specifically target astrocytes and oligodendrocytes across species, revealing functional roles in reward-dependent acetylcholine responses.

Feedforward amplification in recurrent networks underliesparadoxical neural coding

The paper shows that feedforward amplification in recurrent neural networks explains paradoxical neural coding in motor cortex, where early low-selectivity activity influences behavior more than late high-selectivity activity.

Not everything, not everywhere, not all at once: a study of brain-wide encoding of movement

This study maps movement-related activity across the brain in mice, finding systematic differences in signal strength and encoding structures across regions.

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.

Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator

The paper identifies a mutation that enhances the sensitivity of a fluorescent voltage indicator, improving its ability to detect both spiking and subthreshold voltage signals in multiple organisms.

Fast and sensitive GCaMP calcium indicators for imaging neural populations

The paper develops fast and sensitive GCaMP indicators for neural activity imaging, achieving ultra-fast kinetics and high sensitivity.

Data architecture for a large-scale neuroscience collaboration

The paper describes a modular data architecture for a neuroscience collaboration, enabling data contribution, access, and analysis across multiple labs.

BCI learning phenomena can be explained by gradient-based optimization

This study shows that two BCI learning phenomena can be explained by gradient-based optimization, without requiring special mechanisms.

Statistically unbiased prediction enables accurate denoising of voltage imaging data

SUPPORT is a self-supervised method that denoises voltage imaging data by leveraging spatiotemporal dependencies, preserving dynamics without requiring action potential information.

Brain-wide measurement of synaptic protein turnover reveals localized plasticity during learning

The paper develops DELTA, a method to measure brain-wide synaptic protein turnover at single-synapse resolution, revealing localized plasticity in hippocampal CA1 during learning.

Brain mechanism of foraging: reward-dependentsynaptic plasticity or neural integration of values?

This study compares two models of action value encoding in foraging behavior and finds the synaptic model more robust based on experimental predictions.