
Karel Svoboda, Ph.D.
Bio:
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).
News & Events
Announcing the Allen Institute for Neural Dynamics, a new neuroscience division of the Allen Institute
Lake Conference - Neural Coding & Dynamics 2025
The World's Observatory of the Mind | OpenScope
Projects launch to map brain connections in mouse and macaque
Scientific Overview | ExA-SPIM
Lab Notes | Cracking the code of addiction
Announcing the Allen Institute for Neural Dynamics, a new neuroscience division of the Allen Institute
Lake Conference - Neural Coding & Dynamics 2025
The World's Observatory of the Mind | OpenScope
Publications
eLife
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues
Aug 28, 2024
Adam Glaser, Jayaram Chandrashekar, Sonya Vasquez, Cameron Arshadi, Naveen Ouellette, Xiaoyun Jiang, Judith Baka, Gabor Kovacs, Micah Woodard, Sharmishtaa Seshamani, Kevin Cao, Nathan Clack, Andrew Recknagel, Anna Grim, Pooja Balaram, Emily Turschak, Marcus Hooper, Alan Liddell, John Rohde, Ayana Hellevik, Kevin Takasaki, Lindsey Erion Barner, Molly Logsdon, Chris Chronopoulos, Saskia de Vries, Jonathan Ting, Steve Perlmutter, Brian Kalmbach, Nikolai Dembrow, Bosiljka Tasic, R. Clay Reid, David Feng, Karel Svoboda
Read MoreJournal of Neural Engineering
Compression strategies for large-scale electrophysiology data
Sep 18, 2023
Alessio P. Buccino, Olivier Winter, David Bryant, David Feng, Karel Svoboda, Joshua H. Siegle
Read MoreNature Communications
Predictive and robust gene selection for spatial transcriptomics
Apr 12, 2023
Ian Covert, Rohan Gala, Tim Wang, Karel Svoboda, Uygar Sümbül, Su-In Lee
Read MoreNeuron
Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator
Mar 28, 2023
Ahmed S. Abdelfattah, Jihong Zheng, Amrita Singh, Yi-Chieh Huang, Daniel Reep, Getahun Tsegaye, Arthur Tsang, Benjamin J. Arthur, Monika Rehorova, Carl V. L. Olson, Yichun Shuai, Lixia Zhang, Tian-Ming Fu, Daniel E. Milkie, Maria V. Moya, Timothy D. Weber, Andrew L. Lemire, Christopher A. Baker, Natalie Falco, Qinsi Zheng, Jonathan B. Grimm, Mighten C. Yip, Deepika Walpita, Martin Chase, Luke Campagnola, Gabe J. Murphy, Allan M. Wong, Craig R. Forest, Jerome Mertz, Michael N. Economo, Glenn C. Turner, Minoru Koyama, Bei-Jung Lin, Eric Betzig, Ondrej Novak, Luke D. Lavis, Karel Svoboda, Wyatt Korff, Tsai-Wen Chen, Eric R. Schreiter, Jeremy P. Hasseman, Ilya Kolb
Read MoreNeuron
Next-generation brain observatories
Oct 11, 2022
Christof Koch, Karel Svoboda, Amy Bernard, Michele A. Basso, Anne K. Churchland, Adrienne L. Fairhall, Peter A. Groblewski, Jérôme A. Lecoq, Zachary F. Mainen, Mackenzie W. Mathis, Shawn R. Olsen, John W. Phillips, Alexandre Pouget, Shreya Saxena, Josh H. Siegle, Anthony M. Zador
Read MoreeLife
The Neurodata Without Borders ecosystem for neurophysiological data science
Oct 04, 2022
Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin K. Dichter, Satrajit Ghosh, Lawrence Niu, Pamela Baker, Ivan Soltesz, Lydia Ng, Karel Svoboda, Loren Frank, Kristofer E. Bouchard
Read MoreNature Methods
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues
May 01, 2022
Adam K. Glaser, Kevin W. Bishop, Lindsey A. Barner, Etsuo A. Susaki, Shimpei I. Kubota, Gan Gao, Robert B. Serafin, Pooja Balaram, Emily Turschak, Philip R. Nicovich, Hoyin Lai, Luciano A. G. Lucas, Yating Yi, Eva K. Nichols, Hongyi Huang, Nicholas P. Reder, Jasmine J. Wilson, Ramya Sivakumar, Elya Shamskhou, Caleb R. Stoltzfus, Xing Wei, Andrew K. Hempton, Marko Pende, Prayag Murawala, Hans-Ulrich Dodt, Takato Imaizumi, Jay Shendure, Brian J. Beliveau, Michael Y. Gerner, Li Xin, Hu Zhao, Lawrence D. True, R. Clay Reid, Jayaram Chandrashekar, Hiroki R. Ueda, Karel Svoboda, Jonathan T. C. Liu
Read MoreCell
The Mind of a Mouse
Sep 17, 2020
Larry F. Abbott, Davi D. Bock, Edward M. Callaway, Winfried Denk, Catherine Dulac, Adrienne L. Fairhall, Ila Fiete, Kristen M. Harris, Moritz Helmstaedter, Viren Jain, Narayanan Kasthuri, Yann LeCun, Jeff W. Lichtman, Peter B. Littlewood, Liqun Luo, John H. R. Maunsell, R. Clay Reid, Bruce R. Rosen, Gerald M. Rubin, Terrence J. Sejnowski, H. Sebastian Seung, Karel Svoboda, David W. Tank, Doris Tsao, David C. Van Essen
Read MoreScience (New York, N.Y.)
Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
Aug 16, 2019
Ahmed S. Abdelfattah, Takashi Kawashima, Amrita Singh, Ondrej Novak, Hui Liu, Yichun Shuai, Yi-Chieh Huang, Luke Campagnola, Stephanie C. Seeman, Jianing Yu, Jihong Zheng, Jonathan B. Grimm, Ronak Patel, Johannes Friedrich, Brett D. Mensh, Liam Paninski, John J. Macklin, Gabe J. Murphy, Kaspar Podgorski, Bei-Jung Lin, Tsai-Wen Chen, Glenn C. Turner, Zhe Liu, Minoru Koyama, Karel Svoboda, Misha B. Ahrens, Luke D. Lavis, Eric R. Schreiter
Read MoreNature
Shared and distinct transcriptomic cell types across neocortical areas
Nov 01, 2018
Bosiljka Tasic, Zizhen Yao, Lucas T. Graybuck, Kimberly A. Smith, Thuc Nghi Nguyen, Darren Bertagnolli, Jeff Goldy, Emma Garren, Michael N. Economo, Sarada Viswanathan, Osnat Penn, Trygve Bakken, Vilas Menon, Jeremy Miller, Olivia Fong, Karla E. Hirokawa, Kanan Lathia, Christine Rimorin, Michael Tieu, Rachael Larsen, Tamara Casper, Eliza Barkan, Matthew Kroll, Sheana Parry, Nadiya V. Shapovalova, Daniel Hirschstein, Julie Pendergraft, Heather A. Sullivan, Tae Kyung Kim, Aaron Szafer, Nick Dee, Peter Groblewski, Ian Wickersham, Ali Cetin, Julie A. Harris, Boaz P. Levi, Susan M. Sunkin, Linda Madisen, Tanya L. Daigle, Loren Looger, Amy Bernard, John Phillips, Ed Lein, Michael Hawrylycz, Karel Svoboda, Allan R. Jones, Christof Koch, Hongkui Zeng
Read MoreNature
Distinct descending motor cortex pathways and their roles in movement
Nov 01, 2018
Michael N. Economo, Sarada Viswanathan, Bosiljka Tasic, Erhan Bas, Johan Winnubst, Vilas Menon, Lucas T. Graybuck, Thuc Nghi Nguyen, Kimberly A. Smith, Zizhen Yao, Lihua Wang, Charles R. Gerfen, Jayaram Chandrashekar, Hongkui Zeng, Loren L. Looger, Karel Svoboda
Read MoreNature
Fully integrated silicon probes for high-density recording of neural activity
Nov 08, 2017
James J. Jun, Nicholas A. Steinmetz, Joshua H. Siegle, Daniel J. Denman, Marius Bauza, Brian Barbarits, Albert K. Lee, Costas A. Anastassiou, Alexandru Andrei, Çağatay Aydın, Mladen Barbic, Timothy J. Blanche, Vincent Bonin, João Couto, Barundeb Dutta, Sergey L. Gratiy, Diego A. Gutnisky, Michael Häusser, Bill Karsh, Peter Ledochowitsch, Carolina Mora Lopez, Catalin Mitelut, Silke Musa, Michael Okun, Marius Pachitariu, Jan Putzeys, P. Dylan Rich, Cyrille Rossant, Wei-Lung Sun, Karel Svoboda, Matteo Carandini, Kenneth D. Harris, Christof Koch, John O'Keefe, Timothy D. Harris
Read MoreNeuron
Neurodata Without Borders: Creating a Common Data Format for Neurophysiology
Nov 18, 2015
Jeffery L. Teeters, Keith Godfrey, Rob Young, Chinh Dang, Claudia Friedsam, Barry Wark, Hiroki Asari, Simon Peron, Nuo Li, Adrien Peyrache, Gennady Denisov, Joshua H. Siegle, Shawn R. Olsen, Christopher Martin, Miyoung Chun, Shreejoy Tripathy, Timothy J. Blanche, Kenneth Harris, György Buzsáki, Christof Koch, Markus Meister, Karel Svoboda, Friedrich T. Sommer
Read MoreNature Neuroscience
A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing
Mar 25, 2012
Linda Madisen, Tianyi Mao, Henner Koch, Jia-min Zhuo, Antal Berenyi, Shigeyoshi Fujisawa, Yun-Wei A. Hsu, Alfredo J. Garcia, Xuan Gu, Sebastien Zanella, Jolene Kidney, Hong Gu, Yimei Mao, Bryan M. Hooks, Edward S. Boyden, György Buzsáki, Jan Marino Ramirez, Allan R. Jones, Karel Svoboda, Xue Han, Eric E. Turner, Hongkui Zeng
Read MoreThe Journal of Neuroscience: The Official Journal of the Society for Neuroscience
A Cre-dependent GCaMP3 reporter mouse for neuronal imaging in vivo
Feb 29, 2012
Hatim A. Zariwala, Bart G. Borghuis, Tycho M. Hoogland, Linda Madisen, Lin Tian, Chris I. De Zeeuw, Hongkui Zeng, Loren L. Looger, Karel Svoboda, Tsai-Wen Chen
Read MorePLoS computational biology
A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale
Mar 01, 2009
Jason W. Bohland, Caizhi Wu, Helen Barbas, Hemant Bokil, Mihail Bota, Hans C. Breiter, Hollis T. Cline, John C. Doyle, Peter J. Freed, Ralph J. Greenspan, Suzanne N. Haber, Michael Hawrylycz, Daniel G. Herrera, Claus C. Hilgetag, Z. Josh Huang, Allan Jones, Edward G. Jones, Harvey J. Karten, David Kleinfeld, Rolf Kötter, Henry A. Lester, John M. Lin, Brett D. Mensh, Shawn Mikula, Jaak Panksepp, Joseph L. Price, Joseph Safdieh, Clifford B. Saper, Nicholas D. Schiff, Jeremy D. Schmahmann, Bruce W. Stillman, Karel Svoboda, Larry W. Swanson, Arthur W. Toga, David C. Van Essen, James D. Watson, Partha P. Mitra
Read More