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1. A connectome and analysis of the adult Drosophila central brain

Author

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

Subjects
connectome, brain regions, cell types, graph properties, connectome reconstuction methods, synapse detecton, Medicine, Science, Biology (General), QH301-705.5
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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3. Automated Reconstruction of a Serial-Section EM Drosophila Brain With Flood-Filling Networks and Local Realignment

Author

Davi D. Bock, Laramie Leavitt, Eric Perlman, István Taisz, Feng Li, Larry Lindsey, Michał Januszewski, Peter H. Li, Jeremy Maitin-Shepard, Gregory S.X.E. Jefferis, Alexander Shakeel Bates, Michael D. Tyka, Matthew Nichols, Viren Jain, Zhihao Zheng, and Tim Blakely

Subjects
business.industry, Computer science, Key (cryptography), Volume (computing), Pairwise sequence alignment, Image content, Segmentation, Computer vision, Serial section, Artificial intelligence, Tracing, business, Skeletonization
Abstract

Reconstruction of neural circuitry at single-synapse resolution is a key target for improving understanding of the nervous system in health and disease. Serial section transmission electron microscopy (ssTEM) is among the most prolific imaging methods employed in pursuit of such reconstructions. We demonstrate how Flood-Filling Networks (FFNs) can be used to computationally segment a forty-teravoxel whole-brain Drosophila ssTEM volume. To compensate for data irregularities and imperfect global alignment, FFNs were combined with procedures that locally re-align serial sections as well as dynamically adjust and synthesize image content. The proposed approach produced a largely merger-free segmentation of the entire ssTEM Drosophila brain, which we make freely available. As compared to manual tracing using an efficient skeletonization strategy, the segmentation enabled circuit reconstruction and analysis workflows that were an order of magnitude faster.

Published
2021
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4. A connectome and analysis of the adult Drosophila central brain

Author

Temour Tokhi, Tom Dolafi, Nneoma Okeoma, Tanya Wolff, Philip M Hubbard, Kazunori Shinomiya, Madelaine K Robertson, Gerald M. Rubin, Gregory S.X.E. Jefferis, Christopher J Knecht, Laramie Leavitt, Alia Suleiman, Satoko Takemura, Christopher Ordish, Jody Clements, Ian A. Meinertzhagen, Alexander Shakeel Bates, Takashi Kawase, Samantha Finley, Nicholas Padilla, Jackie Swift, C. Shan Xu, Stuart Berg, Tyler Paterson, Ashley L Scott, Erika Neace, Shirley Lauchie, Sean M Ryan, Emily M Joyce, Shin-ya Takemura, Tim Blakely, Michael A Cook, Christopher Patrick, Bryon Eubanks, Audrey Francis, Robert Svirskas, William T. Katz, Eric T. Trautman, Caroline Mooney, Ting Zhao, Nicole A Kirk, Megan Sammons, Brandon S Canino, Reed A. George, Louis K. Scheffer, Jolanta A. Borycz, Jon Thomson Rymer, Natasha Cheatham, Dagmar Kainmueller, Gary B. Huang, Khaled Khairy, Nicole Neubarth, Elliott E Phillips, John A. Bogovic, Neha Rampally, Larry Lindsey, Viren Jain, David G. Ackerman, Jane Anne Horne, Kelli Fairbanks, Lowell Umayam, Jens Goldammer, Emily M Phillips, Donald J. Olbris, Feng Li, Emily A Manley, Philipp Schlegel, Hideo Otsuna, Marta Costa, Stephen M. Plaza, Omotara Ogundeyi, Samantha Ballinger, Charli Maldonado, Kelsey Smith, Gary Patrick Hopkins, Vivek Jayaraman, Emily Tenshaw, Julie Kovalyak, Peter H. Li, Tansy Yang, Masayoshi Ito, Miatta Ndama, Claire Smith, Michał Januszewski, Alanna Lohff, SungJin Kim, Anne K Scott, Kei Ito, Iris Talebi, Jeremy Maitlin-Shepard, Nora Forknall, Marisa Dreher, Harald F. Hess, Sari McLin, Patricia K. Rivlin, Dennis A Bailey, Kenneth J. Hayworth, Octave Duclos, Caitlin Ribeiro, John J. Walsh, Zhiyuan Lu, Dorota Tarnogorska, Ruchi Parekh, Aya Shinomiya, Stephan Saalfeld, Margaret A Sobeski, Natalie L Smith, Chelsea X Alvarado, Scheffer, Louis K [0000-0002-3289-6564], Xu, C Shan [0000-0002-8564-7836], Januszewski, Michal [0000-0002-3480-2744], Lu, Zhiyuan [0000-0002-4128-9774], Takemura, Shin-ya [0000-0003-2400-6426], Huang, Gary B [0000-0002-9606-3510], Shinomiya, Kazunori [0000-0003-0262-6421], Maitlin-Shepard, Jeremy [0000-0001-8453-7961], Hubbard, Philip M [0000-0002-6746-5035], Katz, William T [0000-0002-9417-6212], Ackerman, David [0000-0003-0172-6594], Blakely, Tim [0000-0003-0995-5471], Bogovic, John [0000-0002-4829-9457], Kainmueller, Dagmar [0000-0002-9830-2415], Khairy, Khaled A [0000-0002-9274-5928], Li, Peter H [0000-0001-6193-4454], Trautman, Eric T [0000-0001-8588-0569], Bates, Alexander S [0000-0002-1195-0445], Goldammer, Jens [0000-0002-5623-8339], Wolff, Tanya [0000-0002-8681-1749], Svirskas, Robert [0000-0001-8374-6008], Schlegel, Philipp [0000-0002-5633-1314], Knecht, Christopher J [0000-0002-5663-5967], Alvarado, Chelsea X [0000-0002-5973-7512], Bailey, Dennis A [0000-0002-4675-8373], Borycz, Jolanta A [0000-0002-4402-9230], Canino, Brandon S [0000-0002-8454-865X], Cook, Michael [0000-0002-7892-6845], Dreher, Marisa [0000-0002-0041-9229], Eubanks, Bryon [0000-0002-9288-2009], Fairbanks, Kelli [0000-0002-6601-4830], Finley, Samantha [0000-0002-8086-206X], Forknall, Nora [0000-0003-2139-7599], Francis, Audrey [0000-0003-1974-7174], Joyce, Emily M [0000-0001-5794-6321], Kovalyak, Julie [0000-0001-7864-7734], Lauchie, Shirley A [0000-0001-8223-9522], Lohff, Alanna [0000-0002-1242-1836], McLin, Sari [0000-0002-9120-1136], Patrick, Christopher M [0000-0001-8830-1892], Phillips, Elliott E [0000-0002-4918-2058], Phillips, Emily M [0000-0001-7615-301X], Robertson, Madelaine K [0000-0002-1764-0245], Rymer, Jon Thomson [0000-0002-4271-6774], Ryan, Sean M [0000-0002-8879-6108], Sammons, Megan [0000-0003-4516-5928], Shinomiya, Aya [0000-0002-6358-9567], Smith, Natalie L [0000-0002-8271-9873], Swift, Jackie [0000-0003-1321-8183], Takemura, Satoko [0000-0002-2863-0050], Talebi, Iris [0000-0002-0173-8053], Tarnogorska, Dorota [0000-0002-7063-6165], Walsh, John J [0000-0002-7176-4708], Yang, Tansy [0000-0003-1131-0410], Horne, Jane Anne [0000-0001-9673-2692], Parekh, Ruchi [0000-0002-8060-2807], Jayaraman, Vivek [0000-0003-3680-7378], Costa, Marta [0000-0001-5948-3092], Jefferis, Gregory SXE [0000-0002-0587-9355], Ito, Kei [0000-0002-7274-5533], Saalfeld, Stephan [0000-0002-4106-1761], Rubin, Gerald M [0000-0001-8762-8703], Hess, Harald F [0000-0003-3000-1533], Plaza, Stephen M [0000-0001-7425-8555], Apollo - University of Cambridge Repository, Takemura, Shin-Ya [0000-0003-2400-6426], and Jefferis, Gregory Sxe [0000-0002-0587-9355]

Subjects
Male, Computer science, computational biology, 0302 clinical medicine, Drosophila Proteins, Research article, Biology (General), Neurons, Cognitive science, 0303 health sciences, biology, D. melanogaster, General Neuroscience, connectome, Brain, systems biology, graph properties, General Medicine, Human brain, Drosophila melanogaster, medicine.anatomical_structure, Connectome, Medicine, Drosophila, Female, synapse detecton, Insight, Function and Dysfunction of the Nervous System, cell types, Research Article, Computational and Systems Biology, brain regions, Connectomes, QH301-705.5, Ubiquitin-Protein Ligases, Science, connectome reconstuction methods, Small mammal, Central region, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, medicine, Animals, 030304 developmental biology, General Immunology and Microbiology, biology.organism_classification, synapse detection, Synapses, 030217 neurology & neurosurgery, Neuroscience
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., eLife digest Animal brains of all sizes, from the smallest to the largest, work in broadly similar ways. Studying the brain of any one animal in depth can thus reveal the general principles behind the workings of all brains. The fruit fly Drosophila is a popular choice for such research. With about 100,000 neurons – compared to some 86 billion in humans – the fly brain is small enough to study at the level of individual cells. But it nevertheless supports a range of complex behaviors, including navigation, courtship and learning. Thanks to decades of research, scientists now have a good understanding of which parts of the fruit fly brain support particular behaviors. But exactly how they do this is often unclear. This is because previous studies showing the connections between cells only covered small areas of the brain. This is like trying to understand a novel when all you can see is a few isolated paragraphs. To solve this problem, Scheffer, Xu, Januszewski, Lu, Takemura, Hayworth, Huang, Shinomiya et al. prepared the first complete map of the entire central region of the fruit fly brain. The central brain consists of approximately 25,000 neurons and around 20 million connections. To prepare the map – or connectome – the brain was cut into very thin 8nm slices and photographed with an electron microscope. A three-dimensional map of the neurons and connections in the brain was then reconstructed from these images using machine learning algorithms. Finally, Scheffer et al. used the new connectome to obtain further insights into the circuits that support specific fruit fly behaviors. The central brain connectome is freely available online for anyone to access. When used in combination with existing methods, the map will make it easier to understand how the fly brain works, and how and why it can fail to work correctly. Many of these findings will likely apply to larger brains, including our own. In the long run, studying the fly connectome may therefore lead to a better understanding of the human brain and its disorders. Performing a similar analysis on the brain of a small mammal, by scaling up the methods here, will be a likely next step along this path.

Published
2020

5. Author response: A connectome and analysis of the adult Drosophila central brain

Author

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

Subjects
biology, Connectome, Drosophila (subgenus), biology.organism_classification, Neuroscience
Published
2020
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6. 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
Full Text
View/download PDF

7. Automated Reconstruction of a Serial-Section EM Drosophila Brain with Flood-Filling Networks and Local Realignment

Author

István Taisz, Michał Januszewski, Michael D. Tyka, Gregory S.X.E. Jefferis, Jeremy Maitin-Shepard, Viren Jain, Alexander Shakeel Bates, Eric Perlman, Zhihao Zheng, Laramie Leavitt, Feng Li, Matthew Nichols, Larry Lindsey, Tim Blakely, Peter H. Li, and Davi D. Bock

Subjects
0303 health sciences, Computer science, business.industry, Volume (computing), Serial section, Skeletonization, 03 medical and health sciences, 0302 clinical medicine, Transmission electron microscopy, Segmentation, Computer vision, Artificial intelligence, business, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

Reconstruction of neural circuitry at single-synapse resolution is a key target for improving understanding of the nervous system in health and disease. Serial section transmission electron microscopy (ssTEM) is among the most prolific imaging methods employed in pursuit of such reconstructions. We demonstrate how Flood-Filling Networks (FFNs) can be used to computationally segment a forty-teravoxel whole-brain Drosophila ssTEM volume. To compensate for data irregularities and imperfect global alignment, FFNs were combined with procedures that locally re-align serial sections as well as dynamically adjust and synthesize image content. The proposed approach produced a largely merger-free segmentation of the entire ssTEM Drosophila brain, which we make freely available. As compared to manual tracing using an efficient skeletonization strategy, the segmentation enabled circuit reconstruction and analysis workflows that were an order of magnitude faster.

Published
2019
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8. High-precision automated reconstruction of neurons with flood-filling networks

Author

Art Pope, Tim Blakely, Peter H. Li, Michał Januszewski, Viren Jain, Jeremy Maitin-Shepard, Larry Lindsey, Winfried Denk, Michael D. Tyka, and Jörgen Kornfeld

Subjects
0301 basic medicine, Male, Neurite, Computer science, Tracing, Machine learning, computer.software_genre, Biochemistry, Convolutional neural network, Machine Learning, 03 medical and health sciences, Mice, 0302 clinical medicine, Imaging, Three-Dimensional, Path length, Microscopy, Electron, Transmission, Biological neural network, Image Processing, Computer-Assisted, Neurites, Animals, Segmentation, Molecular Biology, Zebra finch, TRACE (psycholinguistics), Neurons, Computational neuroscience, business.industry, Brain, Cell Biology, Data set, 030104 developmental biology, Test set, Drosophila, Artificial intelligence, Finches, Nerve Net, business, Algorithm, computer, 030217 neurology & neurosurgery, Algorithms, Biotechnology
Abstract

Reconstruction of neural circuits from volume electron microscopy data requires the tracing of cells in their entirety, including all their neurites. Automated approaches have been developed for tracing, but their error rates are too high to generate reliable circuit diagrams without extensive human proofreading. We present flood-filling networks, a method for automated segmentation that, similar to most previous efforts, uses convolutional neural networks, but contains in addition a recurrent pathway that allows the iterative optimization and extension of individual neuronal processes. We used flood-filling networks to trace neurons in a dataset obtained by serial block-face electron microscopy of a zebra finch brain. Using our method, we achieved a mean error-free neurite path length of 1.1 mm, and we observed only four mergers in a test set with a path length of 97 mm. The performance of flood-filling networks was an order of magnitude better than that of previous approaches applied to this dataset, although with substantially increased computational costs.

Published
2018

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