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preprint / 2024
SHIELD: Skull-shaped hemispheric implants enabling large-scale electrophysiology datasets in the mouse brain
bioRxiv
Neural Dynamics

Corbett Bennett, Ben Ouellette, Tamina Ramirez, Alex Cahoon, Hannah Cabasco, Yoni Browning, Anna Lakunina, Galen F. Lynch, Ethan McBride, Hannah Belski, Ryan Gillis, Conor Grasso, Robert Howard, Tye Johnson, Henry Loeffler, Heston Smith, David Sullivan, Allison Williford, Shiella Caldejon, Severine Durand, Samuel Gale, Alan Guthrie, Vivian Ha, Warren Han, Ben Hardcastle, Chris Mochizuki, Arjun Sridhar, Lucas Suarez, Jackie Swapp, Joshua Wilkes, Joshua H. Siegle, Colin Farrell, Peter A. Groblewski, Shawn R. Olsen

10.1101/2023.11.12.566771
Neural Dynamics
publication / 2024
Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
eLife
Brain Science
MindScope

Aixin Zhang, Lei Jin, Shenqin Yao, Makoto Matsuyama, Cindy T. J. van Velthoven, Heather Anne Sullivan, Na Sun, Manolis Kellis, Bosiljka Tasic, Ian Wickersham, Xiaoyin Chen

10.7554/elife.87866
AIBS First Author, AIBS Last Author, Brain Science
publication / 2024
Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy
Nature Protocols
Cell Science

Benjamin W. Gregor, Mackenzie E. Coston, Ellen M. Adams, Joy Arakaki, Antoine Borensztejn, Thao P. Do, Margaret A. Fuqua, Amanda Haupt, Melissa C. Hendershott, Winnie Leung, Irina A. Mueller, Aditya Nath, Angelique M. Nelson, Susanne M. Rafelski, Emmanuel E. Sanchez, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Winfried Wiegraebe, Brian P. Whitney, Calysta Yan, Ruwanthi N. Gunawardane, Nathalie Gaudreault

10.1038/s41596-023-00912-w
Cell Science, Scientific, Technical Tools
publication / 2024
Beyond expectations: residual dynamic mode decomposition and variance for stochastic dynamical systems
Nonlinear Dynamics
Shanahan

Matthew J. Colbrook, Qin Li, Ryan V. Raut, Alex Townsend

publication / 2024
Brain-wide neural activity underlying memory-guided movement
Cell
Neural Dynamics

Susu Chen, Yi Liu, Ziyue Aiden Wang, Jennifer Colonell, Liu D. Liu, Han Hou, Nai-Wen Tien, Tim Wang, Timothy Harris, Shaul Druckmann, Nuo Li, Karel Svoboda

10.1016/j.cell.2023.12.035
Neural Dynamics
publication / 2024
Community-developed checklists for publishing images and image analyses
Nature Methods
Cell Science

Christopher Schmied, Michael S. Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T. Carvalho, Catalin Chiritescu, Jana Christopher, Beth A. Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G. Martins, Aastha Mathur, Kota Miura, Paula Montero Llopis, Roland Nitschke, Alison North, Adam C. Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T. Scott, Arne Seitz, Olaf Selchow, Ved P. Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Douglas Taatjes, Christian Tischer, Helena Klara Jambor

10.1038/s41592-023-01987-9
Cell Science, External Collaboration, Newsletter, Opinion, Perspective
publication / 2024
Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses
Nature Neuroscience
Brain Science
MindScope

Lei Jin, Heather A. Sullivan, Mulangma Zhu, Thomas K. Lavin, Makoto Matsuyama, Xin Fu, Nicholas E. Lea, Ran Xu, YuanYuan Hou, Luca Rutigliani, Maxwell Pruner, Kelsey R. Babcock, Jacque Pak Kan Ip, Ming Hu, Tanya L. Daigle, Hongkui Zeng, Mriganka Sur, Guoping Feng, Ian R. Wickersham

10.1038/s41593-023-01545-8
Brain Science
publication / 2024
Publisher Correction: Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses
Nature Neuroscience
Brain Science

Lei Jin, Heather A. Sullivan, Mulangma Zhu, Thomas K. Lavin, Makoto Matsuyama, Xin Fu, Nicholas E. Lea, Ran Xu, YuanYuan Hou, Luca Rutigliani, Maxwell Pruner, Kelsey R. Babcock, Jacque Pak Kan Ip, Ming Hu, Tanya L. Daigle, Hongkui Zeng, Mriganka Sur, Guoping Feng, Ian R. Wickersham

publication / 2024
Understanding metric-related pitfalls in image analysis validation
Nature Methods
Cell Science

Annika Reinke, Minu D. Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A. Emre Kavur, Tim Rädsch, Carole H. Sudre, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M. Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A. Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp-Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Erik Meijering, Bjoern Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Michael A. Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I. Sánchez, Shravya Shetty, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Ziv R. Yaniv, Paul F. Jäger, Lena Maier-Hein

10.1038/s41592-023-02150-0
Cell Science, External Collaboration, Newsletter, Opinion, Perspective
publication / 2024
Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex
Nature
Brain Science

Nathan R. Zemke, Ethan J. Armand, Wenliang Wang, Seoyeon Lee, Jingtian Zhou, Yang Eric Li, Hanqing Liu, Wei Tian, Joseph R. Nery, Rosa G. Castanon, Anna Bartlett, Julia K. Osteen, Daofeng Li, Xiaoyu Zhuo, Vincent Xu, Lei Chang, Keyi Dong, Hannah S. Indralingam, Jonathan A. Rink, Yang Xie, Michael Miller, Fenna M. Krienen, Qiangge Zhang, Naz Taskin, Jonathan Ting, Guoping Feng, Steven A. McCarroll, Edward M. Callaway, Ting Wang, Ed S. Lein, M. Margarita Behrens, Joseph R. Ecker, Bing Ren

publication / 2024
Backward masking in mice requires visual cortex
Nature Neuroscience
Brain and Consciousness
Brain Science
MindScope

Samuel D. Gale, Chelsea Strawder, Corbett Bennett, Stefan Mihalas, Christof Koch, Shawn R. Olsen

10.1038/s41593-023-01488-0
#consciousness, MindScope Program
publication / 2024
Comparison of the connectivity of the posterior intralaminar thalamic nucleus and peripeduncular nucleus in rats and mice
Frontiers in Neural Circuits
Brain Science
MindScope

Hui-Ru Cai, Sheng-Qiang Chen, Xiao-Jun Xiang, Xue-Qin Zhang, Run-Zhe Ma, Ge Zhu, Song-Lin Ding

10.3389/fncir.2024.1384621
AIBS Last Author, Brain Science
publication / 2024
Development of a high-throughput image cytometric screening method as a research tool for immunophenotypic characterization of patient samples from clinical studies
Journal of Immunological Methods
Immunology

Samir Patel, James I. McDonald, Hamza Mohammed, Vaishnavi Parthasarathy, Veronica Hernandez, Tyanna Stuckey, Allen H. Lin, Srinivas Koushik Gundimeda, Bo Lin, Julian Reading, Leo Li-Ying Chan

publication / 2024
Editorial: 15 years of frontiers in neuroanatomy: the circuits behind the visual cortex
Frontiers in Neuroanatomy
Brain Science
MindScope

Toru Takahata, Song-Lin Ding

10.3389/fnana.2024.1507122
Brain Science
publication / 2024
Hierarchical Bayesian inference to model continuous phenotypical progression in Alzheimer's Disease
bioRxiv
Shanahan

Anamika Agrawal, Victoria Mallett Rachleff, Kyle J. Travaglini, Shubhabrata Mukherjee, Paul Crane, Michael Hawrylycz, C. Dirk Keene, Ed Lein, Gonzalo E. Mena, Mariano I. Gabitto

publication / 2024
Information-Theoretic Tools to Understand Distributed Source Coding in Neuroscience
IEEE Journal on Selected Areas in Information Theory
Shanahan

Ariel K. Feldman, Praveen Venkatesh, Douglas J. Weber, Pulkit Grover

publication / 2024
PhysiCell Studio: a graphical tool to make agent-based modeling more accessible
GigaByte (Hong Kong, China)
Cell Science

Randy Heiland, Daniel Bergman, Blair Lyons, Grant Waldow, Julie Cass, Heber Lima da Rocha, Marco Ruscone, Vincent Noël, Paul Macklin

10.46471/gigabyte.128
Cell Science, External Collaboration, Scientific, Technical
publication / 2024
Taste for discovery: a conversation with neuroscientist Serge Charpak
Neurophotonics
Brain Science
MindScope

Jérôme Lecoq

10.1117/1.nph.11.1.010401
MindScope Program
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