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Human Cells imaged by the Allen Institute for Cell Science using AGAVE
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Publications

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Neurobiology of Disease

Spontaneous pathology in PS19 tauopathy mice progresses via brain networks

Oct 15, 2025

Denise M. O. Ramirez, Jennifer D. Whitesell, Nikhil Bhagwat, Talitha L. Thomas, Apoorva D. Ajay, Ariana Nawaby, Benoît Delatour, Sylvie Bay, Pierre LaFaye, Julie A. Harris, Julian P. Meeks, Marc I. Diamond

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Nature Communications

Data-driven fine-grained region discovery in the mouse brain with transformers

Oct 07, 2025

Alex J. Lee, Alma Dubuc, Michael Kunst, Shenqin Yao, Nicholas Lusk, Lydia Ng, Hongkui Zeng, Bosiljka Tasic, Reza Abbasi-Asl

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Journal of Neurophysiology

What makes the human brain special: from cellular function to clinical translation

Oct 01, 2025

Karen M. J. van Loo, Aniella Bak, Rebecca Hodge, Francesco Bedogni, Julian S. B. Ramirez, Samuel N. Emerson, Anke Höllig, Huibert D. Mansvelder, Natalia A. Goriounova, Jan-Marino Ramirez, Henner Koch

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Communications Biology

The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales

Sep 30, 2025

Kaitlin M. Stouffer, Xiaoyin Chen, Hongkui Zeng, Benjamin Charlier, Laurent Younes, Alain Trouvé, Michael I. Miller

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Nature

Arousal as a universal embedding for spatiotemporal brain dynamics

Sep 24, 2025

Ryan V. Raut, Zachary P. Rosenthal, Xiaodan Wang, Hanyang Miao, Zhanqi Zhang, Jin-Moo Lee, Marcus E. Raichle, Adam Q. Bauer, Steven L. Brunton, Bingni W. Brunton, J. Nathan Kutz

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Molecular Therapy: The Journal of the American Society of Gene Therapy

AAV delivery of full-length SYNGAP1 rescues epileptic and behavioral phenotypes in a mouse model of SYNGAP1-related disorders

Sep 23, 2025

Meagan A. Quinlan, Rong Guo, Andrew G. Clark, Emily M. Luber, Robert J. Christian, Refugio A. Martinez, Erin L. Groce, Jiatai Liu, Yemeserach M. Bishaw, Ravi Bhowmik, Elizabeth Liang, Melissa Reding, Kara Ronellenfitch, Vonn Wright, Kathryn M. Gudsnuk, Jennifer M. Leedy, John K. Mich, Bryan B. Gore, Tanya L. Daigle, Manuel E. Lopez, Ed S. Lein, Justin K. Ichida, Boaz P. Levi

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Cell

Imaging high-frequency voltage dynamics in multiple neuron classes of behaving mammals

Sep 04, 2025

Simon Haziza, Radosław Chrapkiewicz, Yanping Zhang, Vasily Kruzhilin, Jane Li, Jizhou Li, Geoffroy Delamare, Rachel Swanson, György Buzsáki, Madhuvanthi Kannan, Ganesh Vasan, Michael Z. Lin, Hongkui Zeng, Tanya L. Daigle, Mark J. Schnitzer

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Nature Neuroscience

Impaired capillary-venous drainage contributes to gliosis and demyelination in mouse white matter during aging

Sep 01, 2025

Stefan Stamenkovic, Franca Schmid, Gokce Gurler, Farzaneh Abolmaali, Nicolas A. Weitermann, Kevin T. Takasaki, Stephanie K. Bonney, Maria J. Sosa, Hannah C. Bennett, Yongsoo Kim, Jack Waters, Andy Y. Shih

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Nature Reviews. Neuroscience

Three-photon microscopy: an emerging technique for deep intravital brain imaging

Sep 01, 2025

Robert Prevedel, Júlia Ferrer Ortas, Jason N. D. Kerr, Jack Waters, Michael O. Breckwoldt, Benjamin Deneen, Michelle Monje, Stella J. Soyka, Varun Venkataramani

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Cell

Cholinergic neuronal activity promotes diffuse midline glioma growth through muscarinic signaling

Aug 21, 2025

Richard Drexler, Antonia Drinnenberg, Avishai Gavish, Belgin Yalçin, Kiarash Shamardani, Abigail E. Rogers, Rebecca Mancusi, Vrunda Trivedi, Kathryn R. Taylor, Yoon Seok Kim, Pamelyn J. Woo, Neeraj Soni, Minhui Su, Alexandre Ravel, Eva Tatlock, Alexandra Midler, Samuel H. Wu, Charu Ramakrishnan, Ritchie Chen, Alberto E. Ayala-Sarmiento, David Rincon Fernandez Pacheco, La'Akea Siverts, Tanya L. Daigle, Bosiljka Tasic, Hongkui Zeng, Joshua J. Breunig, Karl Deisseroth, Michelle Monje

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Alzheimer's & Dementia: The Journal of the Alzheimer's Association

An integrated view of the relationships between amyloid, tau, and inflammatory pathophysiology in Alzheimer’s disease

Aug 01, 2025

Amy F. T. Arnsten, Kelly Del Tredici, Nicolas R. Barthélemy, Mariano Gabitto, Christopher H. van Dyck, Edward Lein, Heiko Braak, Dibyadeep Datta

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Nature Neuroscience

The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex

Aug 01, 2025

Agnes L. Bodor, Casey M. Schneider-Mizell, Chi Zhang, Leila Elabbady, Alex Mallen, Andi Bergeson, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Rachel Dalley, Clare Gamlin, Emily Joyce, Daniel Kapner, Sam Kinn, Gayathri Mahalingam, Sharmishtaa Seshamani, Shelby Suckow, Marc Takeno, Russel Torres, Wenjing Yin, 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, Szi-Chieh Yu, William Wong, Jingpeng Wu, Brendan Celii, Luke Campagnola, Stephanie C. Seeman, Tim Jarsky, Naixin Ren, Anton Arkhipov, Jacob Reimer, H. Sebastian Seung, R. Clay Reid, Forrest Collman, Nuno Maçarico da Costa

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Neuron

Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration

Jul 15, 2025

Melissa E. Murray, Colin Smith, Vilas Menon, C. Dirk Keene, Ed Lein, Michael Hawrylycz, Adriano Aguzzi, Brett Benedetti, Katja Brose, Kelsey Caetano-Anolles, Maria Inmaculada Cobos Sillero, John F. Crary, Philip L. De Jager, Arline Faustin, Margaret E. Flanagan, Ozgun Gokce, Seth G. N. Grant, Lea T. Grinberg, David A. Gutman, Elizabeth M. C. Hillman, Zhi Huang, David J. Irwin, David T. Jones, Alifiya Kapasi, Celeste M. Karch, Walter T. Kukull, Tammaryn Lashley, Edward B. Lee, Thomas Lehner, Laura Parkkinen, Maria Pedersen, Dominique Pritchett, Matthew H. Rutledge, Julie A. Schneider, William W. Seeley, Claire E. Shepherd, Tara L. Spires-Jones, Judith A. Steen, Margaret Sutherland, Sanja Vickovic, Bin Zhang, David J. Stewart, Michael J. Keiser, Jacob W. Vogel, Brittany N. Dugger, Hemali Phatnani

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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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Cell Reports

Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque

Jun 24, 2025

Emily Kussick, Nelson Johansen, Naz Taskin, Ananya Chowdhury, Meagan A. Quinlan, Alex Fraser, Andrew G. Clark, Brooke Wynalda, Refugio Martinez, Erin L. Groce, Melissa Reding, Elizabeth Liang, Lyudmila Shulga, Cindy Huang, Tamara Casper, Michael Clark, Windy Ho, Yuan Gao, Cindy T. J. van Velthoven, Cassandra Sobieski, Rebecca Ferrer, Melissa R. Berg, Britni C. Curtis, Chris English, Jesse C. Day, Michal G. Fortuna, Nicholas Donadio, Dakota Newman, Shenqin Yao, Anish Bhaswanth Chakka, Jeff Goldy, Amy Torkelson, Junitta B. Guzman, Rushil Chakrabarty, Beagen Nguy, Nathan Guilford, Trangthanh H. Pham, Vonn Wright, Kara Ronellenfitch, Robyn Naidoo, Jaimie Kenney, Ali Williford, Charu Ramakrishnan, Antonia Drinnenberg, Kathryn Gudsnuk, Bargavi Thyagarajan, Kimberly A. Smith, Nick Dee, Karl Deisseroth, Hongkui Zeng, Zizhen Yao, Bosiljka Tasic, Boaz P. Levi, Rebecca Hodge, Trygve E. Bakken, Ed S. Lein, Jonathan T. Ting, Tanya L. Daigle

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Cell Genomics

Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex

Jun 11, 2025

Nelson J. Johansen, Niklas Kempynck, Nathan R. Zemke, Saroja Somasundaram, Seppe De Winter, Marcus Hooper, Deepanjali Dwivedi, Ruchi Lohia, Fabien Wehbe, Bocheng Li, Darina Abaffyová, Ethan J. Armand, Julie De Man, Eren Can Ekşi, Nikolai Hecker, Gert Hulselmans, Vasilis Konstantakos, David Mauduit, John K. Mich, Gabriele Partel, Tanya L. Daigle, Boaz P. Levi, Kai Zhang, Yoshiaki Tanaka, Jesse Gillis, Jonathan T. Ting, Yoav Ben-Simon, Jeremy Miller, Joseph R. Ecker, Bing Ren, Stein Aerts, Ed S. Lein, Bosiljka Tasic, Trygve E. Bakken

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Cell

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

May 29, 2025

Yoav Ben-Simon, Marcus Hooper, Sujatha Narayan, Tanya L. Daigle, Deepanjali Dwivedi, Sharon W. Way, Aaron Oster, David A. Stafford, John K. Mich, Michael J. Taormina, Refugio A. Martinez, Ximena Opitz-Araya, Jada R. Roth, Jason R. Alexander, Shona Allen, Adam Amster, Joel Arbuckle, Angela Ayala, Pamela M. Baker, Trygve E. Bakken, Tyler Barcelli, Stuard Barta, Jacqueline Bendrick, Darren Bertagnolli, Cameron Bielstein, Prajal Bishwakarma, Jessica Bowlus, Gabriella Boyer, Krissy Brouner, Brittny Casian, Tamara Casper, Anish B. Chakka, Rushil Chakrabarty, Rebecca K. Chance, Sakshi Chavan, Michael Clark, Kaity Colbert, Forrest Collman, Scott Daniel, Maxwell Departee, Peter DiValentin, Nicholas Donadio, Nadezhda Dotson, Tom Egdorf, Tim Fliss, Mariano Gabitto, Jazmin Garcia, Amanda Gary, Molly Gasperini, Jessica Gloe, Jeff Goldy, Bryan B. Gore, Lucas Graybuck, Noah Greisman, Francoise Haeseleer, Carliana Halterman, Zeb Haradon, Samantha D. Hastings, Olivia Helback, Windy Ho, Dirk Hockemeyer, Cindy Huang, Sydney Huff, Avery Hunker, Nelson Johansen, Danielle Jones, Zoe Juneau, Brian Kalmbach, Madhav Kannan, Shannon Khem, Emily Kussick, Rana Kutsal, Rachael Larsen, Changkyu Lee, Angus Y. Lee, Madison Leibly, Garreck H. Lenz, Su Li, Elizabeth Liang, Nicholas Lusk, Zachary Madigan, Jessica Malloy, Jocelin Malone, Rachel McCue, Jose Melchor, Tyler Mollenkopf, Skyler Moosman, Elyse Morin, Dakota Newman, Lydia Ng, Kiet Ngo, Victoria Omstead, Sven Otto, Alana Oyama, Nick Pena, Trangthanh Pham, Elliot Phillips, Christina A. Pom, Lydia Potekhina, Shea Ransford, Patrick L. Ray, Dean Rette, Cade Reynoldson, Christine Rimorin, Dana Rocha, Augustin Ruiz, Raymond E. A. Sanchez, Lane Sawyer, Adriana Sedeno-Cortes, Joshua P. Sevigny, Nadiya Shapovalova, Noah Shepard, Lyudmila Shulga, Ana R. Sigler, La'Akea Siverts, Sherif Soliman, Saroja Somasundaram, Brian Staats, Kaiya Stewart, Eric Szelenyi, Michael Tieu, Cameron Trader, Alex Tran, Cindy T. J. van Velthoven, Miranda Walker, Yimin Wang, Natalie Weed, Morgan Wirthlin, Toren Wood, Brooke Wynalda, Zizhen Yao, Thomas Zhou, Jeanelle Ariza, Nick Dee, Melissa Reding, Kara Ronellenfitch, Shoaib Mufti, Susan M. Sunkin, Kimberly A. Smith, Luke Esposito, Jack Waters, Bargavi Thyagarajan, Shenqin Yao, Ed S. Lein, Hongkui Zeng, Boaz P. Levi, John Ngai, Jonathan T. Ting, Bosiljka Tasic

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