Forrest Collman
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Articles by Forrest Collman
Hippocampal CA3 connectomics reveals a gradient of mossy fiber inputs and selective feedforward inhibition onto pyramidal cells
Abstract The mossy fiber (MF) connections to pyramidal cells in hippocampal CA3 are thought to participate in pattern separation, pattern completion and memory encoding, yet no large-scale neuronal wiring diagram exists for these connections. We assembled a 3D electron microscopy volume (~1 × 1 × 0.1 mm3) from mouse hippocampal CA3.
Connecting single-cell transcriptomes to projectomes in the mouse visual cortex
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Abstract The mammalian brain consists of diverse neuron types with various functions. Recent single-cell RNA sequencing approaches have led to a whole-brain taxonomy of transcriptomically defined cell types1. Patch-seq experiments augment these cell-type descriptions by linking transcriptomic profiles with local morphological and electrophysiological properties2,3,4,5,6,7. However, linking transcriptomic identities to long-range axonal projections remains a major unresolved challenge.
By Staci A. Sorensen, Nathan Gouwens, Yun Wang, Matt Mallory, Agata Budzillo, Rachel Dalley, Brian Lee Verified, Olga Gliko, Hsien-Chi Kuo, Xiuli Kuang, Rusty Mann, Leila Ahmadinia, Lauren Alfiler, Fahimeh Baftizadeh, Katherine Baker, Darren Bertagnolli, Kris Bickley, Phil Bohn, Jasmine Bomben, Chris Bowman, Gabriella Boyer, Krissy Brouner, Alex Cahoon, Natalie Chen, Chao Chen, Kai Chen, Maggie M. Chvilicek, Forrest Collman, Tanya L. Daigle, Tim Dawes, Nick Dee, Maxwell Departee, Tom Egdorf, Laila El-Hifnawi, Luke Esposito, Colin Farrell, Clare R. Gamlin, Amanda Gary, Jeff Goldy, Hong Gu, Kristen Hadley, Mike Hawrylycz, Alex Henry, Karla E. Hirokawa, Zili Huang, Katelyn Johnson, Zoe Juneau, Lisa Kim Verified, Lauren Kruse, Changkyu Lee, Phil Lesnar, Yaoyao Li, Elizabeth Liang, Katie Link, Michelle Maxwell, Delissa McMillen, Alice Mukora, Thomas Ochoa, Daniel Park, Lydia Potekhina, Shea Ransford, Melissa Reding, Augustin Ruiz, David Sandman, Lyudmila Shulga, La’Akea Siverts, Kimberly Smith, Josef Sulc, Susan M. Sunkin, Michael Tieu, Jonathan T. Ting, Jessica Trinh, Sara Vargas, Miranda Walker, Adrian A. Wanner, Jack Waters, Grace Williams, Julia Wilson, Wei Xiong, Ed Lein, Jim Berg, Brian E. Kalmbach, Shenqin Yao, Hui Gong, Qingming Luo, Quanxin Wang, Lydia Ng, Uygar Sumbul, Zizhen Yao, Tim Jarsky, Bosiljka Tasic, Hongkui Zeng, Sarah Bannick, Dillan Brown, Rebecca de Frates, Rachel Enstrom, Andrew Glomb, Olena Gerasymchuk, Dijon Hill, Sara Kebede, Arielle L. Leon, Quinn Lheureux, Medea McGraw, Lindsay Ng, Aaron Oldre, Christina Alice Pom, Zoran Popovich, Ram Rajanbabu, Martin Schroedter, Josh Sevigny, Cliff R. Slaughterbeck, Michelle Stoecklin, Ramel Velasco, Dave Vumbaco, Micheal Wang, Mirah Wells
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Nature
Verified
A central somatotopic map of the fly leg supports spatially targeted grooming
Keywords neural circuits connectomics somatosensation Drosophila sensorimotor somatotopy neuroscience Get full text access Log in, subscribe or purchase for full access. References 1. Mountcastle, V.B. The Sensory Hand: Neural Mechanisms of Somatic Sensation Harvard University Press, 2005 2. Sherrington, C.S. Decerebrate Rigidity, and Reflex Coordination of Movements J. Physiol. 1898; 22:319-332 3. Stein, P.S.G. ∙ Grossman, M.L. Central program for scratch reflex in turtle J. Comp. Physiol.
Author Correction: Foundation model of neural activity predicts response to new stimulus types
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Correction to: Nature https://doi.org/10.1038/s41586-025-08829-y Published online 9 April 2025 To ensure accurate documentation of the implemented models, we clarify several architectural details in the Methods describing the Conv-LSTM and CvT-LSTM architectures. These clarifications are limited to the Methods description and do not affect the results or conclusions.
By Eric Wang, Paul G. Fahey, Zhuokun Ding, Stelios Papadopoulos, Kayla Ponder, Marissa A Weis, Andersen Chang, Taliah Muhammad, Saumil S. Patel, Zhiwei Ding, Dat Q Tran, Jiakun Fu, Casey M. Schneider-Mizell, R. Clay Reid, Forrest Collman, Katrin Franke, Alexander S. Ecker, Jacob Reimer, Xaq Pitkow, Fabian Sinz, Andreas S. Tolias
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Nature
Verified
The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex - Nature Neuroscience
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Abstract Despite significant progress in characterizing neocortical cell types, a complete understanding of the synaptic connections of individual excitatory cells remains elusive. This study investigates the connectivity of mouse visual cortex thick tufted layer 5 pyramidal cells, also known as extratelencephalic neurons (L5-ETns), using a 1 mm3 publicly available electron microscopy dataset.
By Agnes L Bodor, Casey M. Schneider-Mizell, JoAnn Buchanan, Rachel Dalley, Emily Joyce, Gayathri Mahalingam, Marc Takeno, Russel Miguel Torres, J. Alexander Bae, Nico Kemnitz, Kai Li, Eric Mitchell, Shanka Subhra Mondal, Barak Nehoran, Szi-chieh Yu, Tim Jarsky, Jacob Reimer, H. Sebastian Seung, R. Clay Reid, Forrest Collman, Andi Bergeson
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Nature
Verified
A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types
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Keywords epigenetics transcriptomics enhancer cell type neocortex AAV transgenic recombinase mouse human Introduction To understand how the brain works, we need to establish the structure-function relationships between the units that comprise it and the outputs of its activity.1 One approach is to gain experimental access to each building block (e.g., a cell type) and manipulate it to observe effects on an animal’s physiology and behavior.2,3,4 Historically, the definition of building blocks...
By Yoav Ben-Simon, Marcus J. Hooper, Sujatha Narayan, Tanya L. Daigle, Deepanjali Dwivedi, Sharon Way, Aaron Oster Verified, David Stafford, John K. Mich, Michael J. Taormina, Refugio Martinez, Jada Roth, Jason Alexander, Shona Allen, Adam Amster, Angela Ayala, Pamela Baker, Trygve E. Bakken, Jacqueline L. Bendrick, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Anish B. Chakka, Rushil Chakrabarty, Rebecca Chance, Sakshi Salil Chavan, michael CLARK, Forrest Collman, Scott Daniel, Nicholas Donadio, Nadezhda Dotson, Mariano I. Gabitto, Jazmin Garcia, Amanda Gary, Molly J Gasperini, Jessica Gloe, Jeff Goldy, Bryan B. Gore, Lucas T. Graybuck, Françoise Haeseleer, Zeb Haradon, Samantha Hastings, Windy Ho, Dirk Hockemeyer, Cindy Huang, Avery C. Hunker, Nelson Johansen, Danielle Jones, Brian E. Kalmbach, Emily Kussick, Changkyu Lee, Angus Y. Lee, Su Li, Elizabeth Liang, Nicholas A. Lusk, Jessica Malloy, Jocelin Malone, José Melchor, Elyse L. Morin, Dakota Newman, Lydia Ng, Kiet A. Ngo, Sven Otto, Nick Pena, Trangthanh Pham, Patrick Ray, Augustin Ruiz, Raymond Sanchez, Adriana E. Sedeño-Cortés, Noah Shepard, Lyudmila Shulga, Sherif Soliman, Saroja Somasundaram, Brian Staats, Eric R. Szelenyi, Michael Tieu, Alex Tran, Miranda Walker, Yimin Wang Verified, Natalie Weed, Morgan Wirthlin, Brooke Wynalda, Zizhen Yao, Thomas Zhou, Jeanelle Ariza, Nick Dee, Melissa Reding, Kara Ronellenfitch, Shoaib Mufti, Susan M. Sunkin, Kimberly Smith, Luke Esposito, Jack Waters, Bargavi Thyagarajan, Shenqin Yao, Ed Lein, Hongkui Zeng, Boaz P. Levi, John Ngai, Jonathan T. Ting, Bosiljka Tasic, Ximena Opitz-Araya, Joel Arbuckle, Tyler Barcelli, Stuard Barta, Cameron Bielstein, Prajal Bishwakarma, Jessica Bowlus, Gabriella Boyer, Brittny Casian, Kaity Colbert, Maxwell Departee, Peter DiValentin, Tom Egdorf, Tim Fliss, Noah Greisman, Carliana Halterman, Olivia Helback, Sydney Huff, Zoe Juneau, Madhav Kannan, Shannon Khem, Rana Kutsal, Rachael Larsen, Madison Leibly, Garreck H. Lenz, Zachary Madigan, Rachel McCue, Tyler Mollenkopf, Skyler Moosman, Victoria Omstead, Alana Oyama, Christina A. Pom, Lydia Potekhina, Shea Ransford, Dean Rette, Cade Reynoldson, Christine Rimorin, Dana Rocha, Joshua P. Sevigny, Nadiya Shapovalova, Ana R. Sigler, La’Akea Siverts, Kaiya Stewart, Cameron Trader, Toren Wood
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Cell Press
Verified
Author Correction: Inhibitory specificity from a connectomic census of mouse visual cortex - Nature
Correction to: Nature https://doi.org/10.1038/s41586-024-07780-8 Published online 9 April 2025 In the version of the article initially published, in the “Sublaminar inhibitory specificity” section, the following reference was missing: Jézéquel, J. et al. Cadherins orchestrate specific patterns of perisomatic inhibition onto distinct pyramidal cell populations. Nat. Commun. https://doi.org/10.1038/s41467-025-59635-z (2025). It has now been added as ref. 46 in the HTML and PDF versions of the article.
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Foundation model of neural activity predicts response to new stimulus types - Nature
Abstract The complexity of neural circuits makes it challenging to decipher the brain’s algorithms of intelligence. Recent breakthroughs in deep learning have produced models that accurately simulate brain activity, enhancing our understanding of the brain’s computational objectives and neural coding. However, it is difficult for such models to generalize beyond their training distribution, limiting their utility.
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Integrating multimodal data to understand cortical circuit architecture and function - Nature Neuroscience
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Abstract In recent years there has been a tremendous growth in new technologies that allow large-scale investigation of different characteristics of the nervous system at an unprecedented level of detail. There is a growing trend to use combinations of these new techniques to determine direct links between different modalities.
By Anton Arkhipov, Saskia de Vries, Trygve E. Bakken, Amy Bernard, Michael Buice, Forrest Collman, Marina E. Garrett, Nathan Gouwens, Michael J. Hawrylycz, Rebecca D. Hodge, Tim Jarsky, Brian E. Kalmbach, Jérôme Lecoq, Ed Lein, Boaz P. Levi, Stefan Mihalas, Shawn Olsen, Clay Reid, Joshua H. Siegle, Staci A. Sorensen, Bosiljka Tasic, Cindy van Velthoven, Shenqin Yao, Zizhen Yao, Christof Koch
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Nature
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Neuronal wiring diagram of an adult brain - Nature
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Abstract Connections between neurons can be mapped by acquiring and analysing electron microscopic brain images. In recent years, this approach has been applied to chunks of brains to reconstruct local connectivity maps that are highly informative1,2,3,4,5,6, but nevertheless inadequate for understanding brain function more globally.
By Philipp Schlegel, Szi-chieh Yu, Albert Lin, Marta Costa, Katharina Eichler, Jay Gager, Krzysztof Kruk, Eric Perlman, Runzhe Yang, Thomas Macrina, J. Alexander Bae, Barak Nehoran, Eric Mitchell, Jingpeng Wu, Alexander Bates, Nils Eckstein, Jan Funke, Forrest Collman, Davi D. Bock, H. Sebastian Seung, Mala Murthy
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Nature
Verified
Connectomic reconstruction of a female Drosophila ventral nerve cord - Nature
Abstract A deep understanding of how the brain controls behaviour requires mapping neural circuits down to the muscles that they control. Here, we apply automated tools to segment neurons and identify synapses in an electron microscopy dataset of an adult female Drosophila melanogaster ventral nerve cord (VNC)1, which functions like the vertebrate spinal cord to sense and control the body. We find that the fly VNC contains roughly 45 million synapses and 14,600 neuronal cell bodies.
Synaptic architecture of leg and wing premotor control networks in Drosophila - Nature
Abstract Animal movement is controlled by motor neurons (MNs), which project out of the central nervous system to activate muscles1. MN activity is coordinated by complex premotor networks that facilitate the contribution of individual muscles to many different behaviours2,3,4,5,6. Here we use connectomics7 to analyse the wiring logic of premotor circuits controlling the Drosophila leg and wing.
Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses
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Structure and function of axo-axonic inhibition
Abstract Inhibitory neurons in mammalian cortex exhibit diverse physiological, morphological, molecular, and connectivity signatures. While considerable work has measured the average connectivity of several interneuron classes, there remains a fundamental lack of understanding of the connectivity distribution of distinct inhibitory cell types with synaptic resolution, how it relates to properties of target cells, and how it affects function.
Oligodendrocyte precursor cells prune axons in the mouse neocortex
Oligodendrocyte precursor cells prune axons in the mouse neocortex JoAnn Buchanan, Leila Elabbady, Forrest Collman, Nikolas L. Jorstad, Trygve E. Bakken, Carolyn Ott, Jenna Glatzer, Adam A. Bleckert, Agnes L. Bodor, Derrick Brittan, Daniel J. Bumbarger, Gayathri Mahalingam, Sharmishtaa Seshamani, Casey Schneider-Mizell, Marc M. Takeno, Russel Torres, Wenjing Yin, Rebecca D. Hodge, Manuel Castro, Sven Dorkenwald, Dodam Ih, Chris S.
Chandelier cell anatomy and function reveal a variably distributed but common signal
Chandelier cell anatomy and function reveal a variably distributed but common signal Casey M. Schneider-Mizell, Agnes L. Bodor, Forrest Collman, Derrick Brittain, Adam A. Bleckert, Sven Dorkenwald, Nicholas L. Turner, Thomas Macrina, Kisuk Lee, Ran Lu, Jingpeng Wu, Jun Zhuang, Anirban Nandi, Brian Hu, JoAnn Buchanan, Marc M. Takeno, Russel Torres, Gayathri Mahalingam, Daniel J. Bumbarger, Yang Li, Tom Chartrand, Nico Kemnitz, William M.
Transcriptomic evidence for dense peptidergic neuromodulation networks in mouse cortex
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