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1. A Connectome and Analysis of the Adult Drosophila Central Brain

Author

C. Shan Xu, Jackie Swift, Miatta Ndama, Philipp Schlegel, SungJin Kim, Khaled Khairy, Christopher Ordish, Omotara Ogundeyi, Kelli Fairbanks, Kenneth J. Hayworth, Samantha Finley, Natasha Cheatham, Nora Forknall, Laramie Leavitt, Temour Tokhi, Nicole A Kirk, Shin-ya Takemura, Nneoma Okeoma, Robert Svirskas, Kazunori Shinomiya, Madelaine K Robertson, Caitlin Ribeiro, Christopher J Knecht, Emily M Joyce, Margaret A Sobeski, Ruchi Parekh, Alia Suleiman, Shirley Lauchie, Sean M Ryan, Iris Talebi, Harald F. Hess, Christopher Patrick, William T. Katz, Stephen M. Plaza, Dagmar Kainmueller, Feng Li, Natalie L Smith, Michał Januszewski, Satoko Takemura, Chelsea X Alvarado, Michael A Cook, Sari McLin, Tom Dolafi, Hideo Otsuna, Jeremy Maitin-Shepard, Kei Ito, Viren Jain, Donald J. Olbris, Tanya Wolff, Takashi Kawase, Tyler Paterson, Patricia K. Rivlin, Jolanta A. Borycz, Ashley L Scott, Claire Smith, Nicholas Padilla, Gary Patrick Hopkins, Vivek Jayaraman, Emily Tenshaw, Zhiyuan Lu, Stuart Berg, Dorota Tarnogorska, Samantha Ballinger, Audrey Francis, Julie Kovalyak, Ting Zhao, Anne K Scott, Alanna Lohff, Caroline Mooney, Brandon S Canino, Gary B. Huang, Jon Thomson Rymer, Marisa Dreher, Jody Clements, Nicole Neubarth, Larry Lindsey, John A. Bogovic, David G. Ackerman, Jane Anne Horne, Louis K. Scheffer, Elliott E Phillips, Lowell Umayam, Jens Goldammer, Eric T. Trautman, Emily A Manley, Charli Maldonado, Peter H. Li, Octave Duclos, John J. Walsh, Stephan Saalfeld, Reed A. George, Gerald M. Rubin, Philip M Hubbard, Ian A. Meinertzhagen, Emily M Phillips, Masayoshi Ito, Erika Neace, Kelsey Smith, Bryon Eubanks, Neha Rampally, Tim Blakely, Tansy Yang, Dennis A Bailey, Megan Sammons, and Aya Shinomiya

Subjects
0303 health sciences, Cell type, biology, Computer science, biology.organism_classification, Synapse, 03 medical and health sciences, 0302 clinical medicine, Connectome, Biological neural network, Drosophila melanogaster, Function and Dysfunction of the Nervous System, Neuroscience, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly’s brain.

Published
2020
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2. A Connectome of the Adult Drosophila Central Brain

Author

Audrey Francis, Ting Zhao, Feng Li, Megan Sammons, Madelaine K Robertson, SungJin Kim, Tyler Paterson, Philipp Schlegel, Chelsea X Alvarado, Viren Jain, Brandon S Canino, Omotara Ogundeyi, Nora Forknall, Dagmar Kainmueller, Tansy Yang, Natasha Cheatham, Neha Rampally, Caitlin Ribeiro, Kimothy L. Smith, Emily M Phillips, Ruchi Parekh, Jackie Swift, Donald J. Olbris, Takashi Kawase, Jon Thomson Rymer, Zhiyuan Lu, Nicholas Padilla, Christopher Ordish, Dorota Tarnogorska, Nicole Neubarth, Aya Shinomiya, Miatta Ndama, Samantha Finley, Stuart Berg, Erika Neace, Bryon Eubanks, John A. Bogovic, David G. Ackerman, Robert Svirskas, Sari McLin, Emily A Manley, Jane Anne Horne, Michael A Cook, Samantha Ballinger, Michał Januszewski, Jeremy Maitin-Shepard, Caroline Mooney, Nicole A Kirk, Shin-ya Takemura, Iris Talebi, Temour Tokhi, Kei K. Ito, Khaled Khairy, Stephen M. Plaza, Julie Kovalyak, Patricia K. Rivlin, Emily M Joyce, Kelli Fairbanks, Philip M Hubbard, Charli Maldonado, Nneoma Okeoma, Hideo Otsuna, Laurence F. Lindsey, Tim Blakely, Gerald M. Rubin, Alanna Lohff, William T. Katz, Anne K Scott, Mutsumi Ito, Peter H. Li, Ian A. Meinertzhagen, Natalie L Smith, Gary B. Huang, Dennis A Bailey, Reed A. George, Kenneth J. Hayworth, Tom Dolafi, Marisa Dreher, Tanya Wolff, Kazunori Shinomiya, Harald F. Hess, E.T. Troutman, Christopher J Knecht, Gary Patrick Hopkins, Alia Suleiman, Vivek Jayaraman, Emily Tenshaw, Octave Duclos, John J. Walsh, Stephan Saalfeld, Louis K. Scheffer, Elliott E Phillips, Lowell Umayam, Jens Goldammer, Sobeski, Jody Clements, Ashley L Scott, Shirley Lauchie, Sean M Ryan, Christopher Patrick, Jolanta A. Borycz, Claire Smith, C.S. Xu, and Laramie Leavitt

Subjects
Cell type, Computer science, Cell, Machine learning, computer.software_genre, Synapse, 03 medical and health sciences, 0302 clinical medicine, medicine, Biological neural network, 030304 developmental biology, Structure (mathematical logic), 0303 health sciences, biology, business.industry, Motor control, biology.organism_classification, Associative learning, medicine.anatomical_structure, Mushroom bodies, Identity (object-oriented programming), Connectome, Artificial intelligence, Drosophila melanogaster, Function and Dysfunction of the Nervous System, business, computer, 030217 neurology & neurosurgery
Abstract

The neural circuits responsible for behavior remain largely unknown. Previous efforts have reconstructed the complete circuits of small animals, with hundreds of neurons, and selected circuits for larger animals. Here we (the FlyEM project at Janelia and collaborators at Google) summarize new methods and present the complete circuitry of a large fraction of the brain of a much more complex animal, the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses, and proofread such large data sets; new methods that define cell types based on connectivity in addition to morphology; and new methods to simplify access to a large and evolving data set. From the resulting data we derive a better definition of computational compartments and their connections; an exhaustive atlas of cell examples and types, many of them novel; detailed circuits for most of the central brain; and exploration of the statistics and structure of different brain compartments, and the brain as a whole. We make the data public, with a web site and resources specifically designed to make it easy to explore, for all levels of expertise from the expert to the merely curious. The public availability of these data, and the simplified means to access it, dramatically reduces the effort needed to answer typical circuit questions, such as the identity of upstream and downstream neural partners, the circuitry of brain regions, and to link the neurons defined by our analysis with genetic reagents that can be used to study their functions.Note: In the next few weeks, we will release a series of papers with more involved discussions. One paper will detail the hemibrain reconstruction with more extensive analysis and interpretation made possible by this dense connectome. Another paper will explore the central complex, a brain region involved in navigation, motor control, and sleep. A final paper will present insights from the mushroom body, a center of multimodal associative learning in the fly brain.

Published
2020
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