A scalable and modular automated pipeline for stitching of large electron microscopy datasets

Autor: Gayathri Mahalingam, Russel Torres, Daniel Kapner, Eric T Trautman, Tim Fliss, Shamishtaa Seshamani, Eric Perlman, Rob Young, Samuel Kinn, JoAnn Buchanan, Marc M Takeno, Wenjing Yin, Daniel J Bumbarger, Ryder P Gwinn, Julie Nyhus, Ed Lein, Steven J Smith, R Clay Reid, Khaled A Khairy, Stephan Saalfeld, Forrest Collman, Nuno Macarico da Costa

Publikováno v: eLife, Vol 11 (2022)

Serial-section electron microscopy (ssEM) is the method of choice for studying macroscopic biological samples at extremely high resolution in three dimensions. In the nervous system, nanometer-scale images are necessary to reconstruct dense neural wi

Externí odkaz: https://doaj.org/article/bd5f8cd87b2346a0937e74c351b6c225

Stimulus novelty uncovers coding diversity in visual cortical circuits

Autor: Marina Garrett, Peter Groblewski, Alex Piet, Doug Ollerenshaw, Farzaneh Najafi, Iryna Yavorska, Adam Amster, Corbett Bennett, Michael Buice, Shiella Caldejon, Linzy Casal, Florence D’Orazi, Scott Daniel, Saskia EJ de Vries, Daniel Kapner, Justin Kiggins, Jerome Lecoq, Peter Ledochowitsch, Sahar Manavi, Nicholas Mei, Christopher B. Morrison, Sarah Naylor, Natalia Orlova, Jed Perkins, Nick Ponvert, Clark Roll, Sam Seid, Derric Williams, Allison Williford, Ruweida Ahmed, Daniel Amine, Yazan Billeh, Chris Bowman, Nicholas Cain, Andrew Cho, Tim Dawe, Max Departee, Marie Desoto, David Feng, Sam Gale, Emily Gelfand, Nile Gradis, Conor Grasso, Nicole Hancock, Brian Hu, Ross Hytnen, Xiaoxuan Jia, Tye Johnson, India Kato, Sara Kivikas, Leonard Kuan, Quinn L’Heureux, Sophie Lambert, Arielle Leon, Elizabeth Liang, Fuhui Long, Kyla Mace, Ildefons Magrans de Abril, Chris Mochizuki, Chelsea Nayan, Katherine North, Lydia Ng, Gabriel Koch Ocker, Michael Oliver, Paul Rhoads, Kara Ronellenfitch, Kathryn Schelonka, Josh Sevigny, David Sullivan, Ben Sutton, Jackie Swapp, Thuyanh K Nguyen, Xana Waughman, Joshua Wilkes, Michael Wang, Colin Farrell, Wayne Wakeman, Hongkui Zeng, John Phillips, Stefan Mihalas, Anton Arkhipov, Christof Koch, Shawn R Olsen

The detection of novel stimuli is critical to learn and survive in a dynamic environment. Though novel stimuli powerfully affect brain activity, their impact on specific cell types and circuits is not well understood. Disinhibition is one candidate m

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::eb95f8c91aba00c999a8c19cdb0d2cff
https://doi.org/10.1101/2023.02.14.528085

Author response: A scalable and modular automated pipeline for stitching of large electron microscopy datasets

Autor: Russel Torres, Gayathri Mahalingam, Daniel Kapner, Eric T Trautman, Tim Fliss, Shamishtaa Seshamani, Eric Perlman, Rob Young, Samuel Kinn, JoAnn Buchanan, Marc M Takeno, Wenjing Yin, Daniel J Bumbarger, Ryder P Gwinn, Julie Nyhus, Ed Lein, Steven J Smith, R Clay Reid, Khaled A Khairy, Stephan Saalfeld, Forrest Collman, Nuno Macarico da Costa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::47a22edb567e7f8343ad353cbbd46ba8
https://doi.org/10.7554/elife.76534.sa2

Functional connectomics spanning multiple areas of mouse visual cortex

Autor: Russel Torres, Kai Kuehner, Wenjing Yin, Saumil S. Patel, Chris Xu, Emmanouil Froudarakis, Grace Williams, Amy L. R. Sterling, Nicholas L. Turner, Daniel J. Bumbarger, Anthony Ramos, Andreas S. Tolias, Zheng H Tan, Fei Ye, J. Alexander Bae, Brendan Celii, Szi-chieh Yu, Runzhe Yang, Jingpeng Wu, Oluwaseun Ogedengbe, Merlin Moore, Gayathri Mahalingam, Kyle Willie, Xaq Pitkow, Sarah Williams, Christos Papadopoulos, Sven Dorkenwald, Daniel Kapner, Sam Kinn, Ran Lu, Dimitri Yatsenko, Leila Elabbady, Fabian H. Sinz, Selden Koolman, Agnes L. Bodor, Ben Silverman, Nico Kemnitz, Chris S. Jordan, Sergiy Popovych, Elanine Miranda, Cameron Smith, Akhilesh Halageri, Paul G. Fahey, Tianyu Wang, William Silversmith, Sarah McReynolds, Ryan Willie, Eric Mitchell, Jacob Reimer, JoAnn Buchanan, Edgar Y. Walker, Barak Nehoran, Thomas Macrina, Zhen Jia, H. Sebastian Seung, William Wong, Stelios Papadopoulos, James Hebditch, Derrick Brittain, Casey M Schneider-Mizell, Nuno Maçarico da Costa, Manuel Castro, Forrest Collman, R. Clay Reid, Shanka Subhra Mondal, Marc Takeno, Kai Li, Tim P. Fliss, Jay Gager, Taliah Muhammad, Shang Mu, Clare Gamlin, Shelby Suckow, Erick Cobos, Mahaly Baptiste, Kisuk Lee

To understand the brain we must relate neurons’ functional responses to the circuit architecture that shapes them. Here, we present a large functional connectomics dataset with dense calcium imaging of a millimeter scale volume. We recorded activit

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::78e52d00cad2815c9dd88338701089fe
https://doi.org/10.1101/2021.07.28.454025