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Publications

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eLife

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

Jun 30, 2025

Adam Glaser, Jayaram Chandrashekar, Sonya Vasquez, Cameron Arshadi, Rajvi Javeri, Naveen Ouellette, Xiaoyun Jiang, Judith Baka, Gabor Kovacs, Micah Woodard, Shamishtaa 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 EJ de Vries, Jonathan T Ting, Steven Perlmutter, Brian E Kalmbach, Nikolai Dembrow, Bosiljka Tasic, R Clay Reid, David Feng, Karel Svoboda, Melike Lakadamyali, John R Huguenard

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Nature Methods

CAVE: Connectome Annotation Versioning Engine

Apr 09, 2025

Sven Dorkenwald, Casey M. Schneider-Mizell, Derrick Brittain, Akhilesh Halageri, Chris Jordan, Nico Kemnitz, Manual A. Castro, William Silversmith, Jeremy Maitin-Shephard, Jakob Troidl, Hanspeter Pfister, Valentin Gillet, Daniel Xenes, J. Alexander Bae, Agnes L. Bodor, JoAnn Buchanan, Daniel J. Bumbarger, Leila Elabbady, Zhen Jia, Daniel Kapner, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Wenjing Yin, Szi-Chieh Yu, R. Clay Reid, Nuno Maçarico da Costa, H. Sebastian Seung, Forrest Collman

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Nature Communications

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

Apr 09, 2025

Marissa A. Weis, Stelios Papadopoulos, Laura Hansel, Timo Lüddecke, Brendan Celii, Paul G. Fahey, Eric Y. Wang, J. Alexander Bae, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Forrest Collman, Nuno Maçarico da Costa, Sven Dorkenwald, Leila Elabbady, Akhilesh Halageri, Zhen Jia, Chris Jordan, Dan Kapner, Nico Kemnitz, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, R. Clay Reid, Casey M. Schneider-Mizell, H. Sebastian Seung, William Silversmith, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Wenjing Yin, Szi-Chieh Yu, Jacob Reimer, Philipp Berens, Andreas S. Tolias, Alexander S. Ecker

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Translational Psychiatry

Layer-specific input to medial prefrontal cortex is linked to stress susceptibility

Apr 09, 2025

Sabahaddin Taha Solakoğlu, Şefik Evren Erdener, Olga Gliko, Alp Can, Uygar Sümbül, Emine Eren-Koçak

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Nature

Perisomatic ultrastructure efficiently classifies cells in mouse cortex

Apr 01, 2025

Leila Elabbady, Sharmishtaa Seshamani, Shang Mu, Gayathri Mahalingam, Casey M. Schneider-Mizell, Agnes L. Bodor, J. Alexander Bae, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Sven Dorkenwald, Akhilesh Halageri, Zhen Jia, Chris Jordan, Dan Kapner, Nico Kemnitz, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Eric Mitchell, Shanka Subhra Mondal, Barak Nehoran, Sergiy Popovych, William Silversmith, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Wenjing Yin, Szi-Chieh Yu, H. Sebastian Seung, R. Clay Reid, Nuno Maçarico da Costa, Forrest Collman

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Nature

Foundation model of neural activity predicts response to new stimulus types

Apr 01, 2025

Eric Y. Wang, Paul G. Fahey, Zhuokun Ding, Stelios Papadopoulos, Kayla Ponder, Marissa A. Weis, Andersen Chang, Taliah Muhammad, Saumil Patel, Zhiwei Ding, Dat Tran, Jiakun Fu, Casey M. Schneider-Mizell, MICrONS Consortium, R. Clay Reid, Forrest Collman, Nuno Maçarico da Costa, Katrin Franke, Alexander S. Ecker, Jacob Reimer, Xaq Pitkow, Fabian H. Sinz, Andreas S. Tolias

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Nature

Functional connectomics reveals general wiring rule in mouse visual cortex

Apr 01, 2025

Zhuokun Ding, Paul G. Fahey, Stelios Papadopoulos, Eric Y. Wang, Brendan Celii, Christos Papadopoulos, Andersen Chang, Alexander B. Kunin, Dat Tran, Jiakun Fu, Zhiwei Ding, Saumil Patel, Lydia Ntanavara, Rachel Froebe, Kayla Ponder, Taliah Muhammad, J. Alexander Bae, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Erick Cobos, Sven Dorkenwald, Leila Elabbady, Akhilesh Halageri, Zhen Jia, Chris Jordan, Dan Kapner, Nico Kemnitz, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, Casey M. Schneider-Mizell, William Silversmith, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Wenjing Yin, Szi-Chieh Yu, Dimitri Yatsenko, Emmanouil Froudarakis, Fabian Sinz, Krešimir Josić, Robert Rosenbaum, H. Sebastian Seung, Forrest Collman, Nuno Maçarico da Costa, R. Clay Reid, Edgar Y. Walker, Xaq Pitkow, Jacob Reimer, Andreas S. Tolias

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Nature

Connectomics of predicted Sst transcriptomic types in mouse visual cortex

Apr 01, 2025

Clare R. Gamlin, Casey M. Schneider-Mizell, Matthew Mallory, Leila Elabbady, Nathan Gouwens, Grace Williams, Alice Mukora, Rachel Dalley, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Emily Joyce, Daniel Kapner, Sam Kinn, Gayathri Mahalingam, Sharmishtaa Seshamani, Marc Takeno, Russel Torres, Wenjing Yin, Philip R. Nicovich, J. Alexander Bae, Manuel A. Castro, Sven Dorkenwald, Akhilesh Halageri, Zhen Jia, Chris Jordan, Nico Kemnitz, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, William Silversmith, Nicholas L. Turner, William Wong, Jingpeng Wu, Szi-Chieh Yu, Jim Berg, Tim Jarsky, Brian Lee, H. Sebastian Seung, Hongkui Zeng, R. Clay Reid, Forrest Collman, Nuno Maçarico da Costa, Staci A. Sorensen

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Nature

Inhibitory specificity from a connectomic census of mouse visual cortex

Apr 01, 2025

Casey M. Schneider-Mizell, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Leila Elabbady, Clare Gamlin, Daniel Kapner, Sam Kinn, Gayathri Mahalingam, Sharmishtaa Seshamani, Shelby Suckow, Marc Takeno, Russel Torres, Wenjing Yin, Sven Dorkenwald, J. Alexander Bae, Manuel A. Castro, Akhilesh Halageri, Zhen Jia, Chris Jordan, Nico Kemnitz, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, William Silversmith, Nicholas L. Turner, William Wong, Jingpeng Wu, Jacob Reimer, Andreas S. Tolias, H. Sebastian Seung, R. Clay Reid, Forrest Collman, Nuno Maçarico da Costa

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Nature

NEURD offers automated proofreading and feature extraction for connectomics

Apr 01, 2025

Brendan Celii, Stelios Papadopoulos, Zhuokun Ding, Paul G. Fahey, Eric Wang, Christos Papadopoulos, Alexander B. Kunin, Saumil Patel, J. Alexander Bae, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Erick Cobos, Sven Dorkenwald, Leila Elabbady, Akhilesh Halageri, Zhen Jia, Chris Jordan, Dan Kapner, Nico Kemnitz, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, Casey M. Schneider-Mizell, William Silversmith, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Szi-Chieh Yu, Wenjing Yin, Daniel Xenes, Lindsey M. Kitchell, Patricia K. Rivlin, Victoria A. Rose, Caitlyn A. Bishop, Brock Wester, Emmanouil Froudarakis, Edgar Y. Walker, Fabian Sinz, H. Sebastian Seung, Forrest Collman, Nuno Maçarico da Costa, R. Clay Reid, Xaq Pitkow, Andreas S. Tolias, Jacob Reimer

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Nature Neuroscience

Integrating multimodal data to understand cortical circuit architecture and function

Apr 01, 2025

Anton Arkhipov, Nuno da Costa, Saskia de Vries, Trygve Bakken, Corbett Bennett, Amy Bernard, Jim Berg, Michael Buice, Forrest Collman, Tanya Daigle, Marina Garrett, Nathan Gouwens, Peter A. Groblewski, Julie Harris, Michael Hawrylycz, Rebecca Hodge, Tim Jarsky, Brian Kalmbach, Jerome Lecoq, Brian Lee, Ed Lein, Boaz Levi, Stefan Mihalas, Lydia Ng, Shawn Olsen, Clay Reid, Joshua H. Siegle, Staci Sorensen, Bosiljka Tasic, Carol Thompson, Jonathan T. Ting, Cindy van Velthoven, Shenqin Yao, Zizhen Yao, Christof Koch, Hongkui Zeng

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Nature Methods

Connectivity of single neurons classifies cell subtypes in mouse brains

Apr 01, 2025

Lijuan Liu, Zhixi Yun, Linus Manubens-Gil, Hanbo Chen, Feng Xiong, Hongwei Dong, Hongkui Zeng, Michael Hawrylycz, Giorgio A. Ascoli, Hanchuan Peng

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Nature Methods

Enabling global image data sharing in the life sciences

Mar 28, 2025

Peter Bajcsy, Sreenivas Bhattiprolu, Katy Börner, Beth A. Cimini, Lucy Collinson, Jan Ellenberg, Reto Fiolka, Maryellen Giger, Wojtek Goscinski, Matthew Hartley, Nathan Hotaling, Rick Horwitz, Florian Jug, Isabel Kemmer, Anna Kreshuk, Emma Lundberg, Aastha Mathur, Kedar Narayan, Shuichi Onami, Anne L. Plant, Fred Prior, Jason R. Swedlow, Adam Taylor, Antje Keppler

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The Journal of Neuroscience: The Official Journal of the Society for Neuroscience

VIP-to-SST Cell Circuit Motif Shows Differential Short-Term Plasticity across Sensory Areas of Mouse Cortex

Mar 26, 2025

Jenifer Rachel, Martin Möck, Tanya L. Daigle, Bosiljka Tasic, Mirko Witte, Jochen F. Staiger

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Preprint

Glutamate indicators with increased sensitivity and tailored deactivation rates

Mar 24, 2025

Abhi Aggarwal, Adrian Negrean, Yang Chen, Rishyashring Iyer, Daniel Reep, Anyi Liu, Anirudh Palutla, Michael E. Xie, Bryan J. MacLennan, Kenta M. Hagihara, Lucas W. Kinsey, Julianna L. Sun, Pantong Yao, Jihong Zheng, Arthur Tsang, Getahun Tsegaye, Yonghai Zhang, Ronak H. Patel, Benjamin J. Arthur, Julien Hiblot, Philipp Leippe, Miroslaw Tarnawski, Jonathan S. Marvin, Jason D. Vevea, Srinivas C. Turaga, Alison G. Tebo, Matteo Carandini, L. F. Rossi, David Kleinfeld, Arthur Konnerth, Karel Svoboda, Glenn C. Turner, Jeremy Hasseman, Kaspar Podgorski

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Science Translational Medicine

Interneuron-specific dual-AAV SCN1A gene replacement corrects epileptic phenotypes in mouse models of Dravet syndrome

Mar 19, 2025

John K. Mich, Jiyun Ryu, Aguan D. Wei, Bryan B. Gore, Rong Guo, Angela M. Bard, Refugio A. Martinez, Emily M. Luber, Jiatai Liu, Yemeserach M. Bishaw, Robert J. Christian, Luiz M. Oliveira, Nicole Miranda, Jan-Marino Ramirez, Jonathan T. Ting, Ed S. Lein, Boaz P. Levi, Franck K. Kalume

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Molecular Therapy. Methods & Clinical Development

A versatile cell line for establishing potency of cell type-specific AAV transgenes

Mar 13, 2025

Refugio A. Martinez, Yemeserach M. Bishaw, Meagan A. Quinlan, Erin L. Groce, Bryan B. Gore, Ed S. Lein, John K. Mich, Boaz P. Levi

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Royal Society Open Science

Provide proactive reproducible analysis transparency with every publication

Mar 05, 2025

Paul Meijer, Nicole Howard, Jessica Liang, Autumn Kelsey, Sathya Subramanian, Ed Johnson, Paul Mariz, James Harvey, Madeline Ambrose, Vitalii Tereshchenko, Aldan Beaubien, Neelima Inala, Yousef Aggoune, Stark Pister, Anne Vetto, Melissa Kinsey, Tom Bumol, Ananda Goldrath, Xiaojun Li, Troy Torgerson, Peter Skene, Lauren Okada, Christian La France, Zach Thomson, Lucas Graybuck

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Science Programs at Allen Institute