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people

Karel Svoboda

Executive Vice President and Director, Neural Dynamics

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Leadership
Allenite

Karel Svoboda is the Vice President and Executive Director of the Allen Institute for Neural Dynamics. Before joinig the Allen Institute, he was a Senior Group Leader at HHMI’s Janelia Research Campus. Svoboda’s work is at the intersection of neuronal biophysics and cognition. His goal is to identify core principles underlying information processing in mammalian neural circuits at the level of the whole brain. Svoboda has developed several widely-used methods to interrogate neural structure and function in intact brains. Notable contributions include microscopy methods to image synapses over times of weeks in the intact brain during learning; engineered sensitive fluorescent protein sensors for noninvasive imaging of neural activity; microscopes with very large fields of view that enable imaging multiple brain regions with single neuron resolution. Svoboda is an advocate for open and reproducible science. He is a founder of the Neurodata Without Borders and ScanImage projects.

Svoboda was born in Prague, then part of Czechoslovakia, and grew up in West Germany. He graduated from Cornell University with a BA in Physics (1988) and from Harvard University with a PhD in Biophysics (1994). He was a member of technical staff at Bell Laboratories (until 1997) and a principal investigator at Cold Spring Harbor Laboratory (until 2006). Svoboda was awarded the Society for Neuroscience Young Investigator Award (2004) and the Brain Prize from the Lundbeck Foundation (2015). He is a member of the National Academy of Sciences (USA).

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featured events

event / October 25 - 29, 2026
2026 Lake Conference – Comparative and Evolutionary Neurobiology
Join the Allen Institute and Circuit Neuroscience Basel for the Lake Conference in Seattle, Washington this October.

featured stories

news
Neuropixels Opto sheds new light into deepest regions of the brain
A single tool measures and manipulates brain cell communication and democratizes advanced neuroscience
news
Karel Svoboda and Jay Shendure elected to National Academy of Medicine
The honor recognizes leaders who have demonstrated outstanding achievement and made lasting contributions to the advancement of the medical sciences,...
news
Scientists use Open Ephys GUI to study how psychedelics affect the brain
Software co-created by the Allen Institute is helping scientists better understand psilocybin, which could lead to new treatments for neuropsychiatric disorders like depression

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featured publications

publication / 2025
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues
eLife
preprint / 2025
Glutamate indicators with increased sensitivity and tailored deactivation rates
publication / 2024
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues
eLife
publication / 2023
Compression strategies for large-scale electrophysiology data
Journal of Neural Engineering
publication / 2023
Predictive and robust gene selection for spatial transcriptomics
Nature Communications
publication / 2023
Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator
Neuron
publication / 2022
Next-generation brain observatories
Neuron
publication / 2022
The Neurodata Without Borders ecosystem for neurophysiological data science
eLife
publication / 2022
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues
Nature Methods
publication / 2020
The Mind of a Mouse
Cell
publication / 2019
Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
Science (New York, N.Y.)
publication / 2018
Distinct descending motor cortex pathways and their roles in movement
Nature
publication / 2018
Shared and distinct transcriptomic cell types across neocortical areas
Nature
publication / 2017
Fully integrated silicon probes for high-density recording of neural activity
Nature
publication / 2015
Neurodata Without Borders: Creating a Common Data Format for Neurophysiology
Neuron
publication / 2012
A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing
Nature Neuroscience
publication / 2012
A Cre-dependent GCaMP3 reporter mouse for neuronal imaging in vivo
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
publication / 2009
A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale
PLoS computational biology
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