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1. Connectome, Drosophila

Author

Bharioke, Arjun, Scheffer, Louis K., Chklovskii, Dmitri B., Meinertzhagen, Ian A., Mayerich, David, Section editor, Jaeger, Dieter, editor, and Jung, Ranu, editor

Published
2022
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2. A Connectome of the Male Drosophila Ventral Nerve Cord

Author

Takemura, Shin-ya, primary, Hayworth, Kenneth J, additional, Huang, Gary B, additional, Januszewski, Michal, additional, Lu, Zhiyuan, additional, Marin, Elizabeth C, additional, Preibisch, Stephan, additional, Xu, C Shan, additional, Bogovic, John, additional, Champion, Andrew S, additional, Cheong, Han SJ, additional, Costa, Marta, additional, Eichler, Katharina, additional, Katz, William, additional, Knecht, Christopher, additional, Li, Feng, additional, Morris, Billy J, additional, Ordish, Christopher, additional, Rivlin, Patricia K, additional, Schlegel, Philipp, additional, Shinomiya, Kazunori, additional, Stürner, Tomke, additional, Zhao, Ting, additional, Badalamente, Griffin, additional, Bailey, Dennis, additional, Brooks, Paul, additional, Canino, Brandon S, additional, Clements, Jody, additional, Cook, Michael, additional, Duclos, Octave, additional, Dunne, Christopher R, additional, Fairbanks, Kelli, additional, Fang, Siqi, additional, Finley-May, Samantha, additional, Francis, Audrey, additional, George, Reed, additional, Gkantia, Marina, additional, Harrington, Kyle, additional, Hopkins, Gary Patrick, additional, Hsu, Joseph, additional, Hubbard, Philip M, additional, Javier, Alexandre, additional, Kainmueller, Dagmar, additional, Korff, Wyatt, additional, Kovalyak, Julie, additional, Krzemiński, Dominik, additional, Lauchie, Shirley A, additional, Lohff, Alanna, additional, Maldonado, Charli, additional, Manley, Emily A, additional, Mooney, Caroline, additional, Neace, Erika, additional, Nichols, Matthew, additional, Ogundeyi, Omotara, additional, Okeoma, Nneoma, additional, Paterson, Tyler, additional, Phillips, Elliott, additional, Phillips, Emily M, additional, Ribeiro, Caitlin, additional, Ryan, Sean M, additional, Rymer, Jon Thomson, additional, Scott, Anne K, additional, Scott, Ashley L, additional, Shepherd, David, additional, Shinomiya, Aya, additional, Smith, Claire, additional, Smith, Natalie, additional, Suleiman, Alia, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Tamimi, Imaan FM, additional, Trautman, Eric T, additional, Umayam, Lowell, additional, Walsh, John J, additional, Yang, Tansy, additional, Rubin, Gerald M, additional, Scheffer, Louis K, additional, Funke, Jan, additional, Saalfeld, Stephan, additional, Hess, Harald F, additional, Plaza, Stephen M, additional, Card, Gwyneth M, additional, Jefferis, Gregory SXE, additional, and Berg, Stuart, additional

Published
2024
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3. Fully-Automatic Synapse Prediction and Validation on a Large Data Set

Author

Huang, Gary B., Scheffer, Louis K., and Plaza, Stephen M.

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Extracting a connectome from an electron microscopy (EM) data set requires identification of neurons and determination of synapses between neurons. As manual extraction of this information is very time-consuming, there has been extensive research effort to automatically segment the neurons to help guide and eventually replace manual tracing. Until recently, there has been comparatively less research on automatically detecting the actual synapses between neurons. This discrepancy can, in part, be attributed to several factors: obtaining neuronal shapes is a prerequisite first step in extracting a connectome, manual tracing is much more time-consuming than annotating synapses, and neuronal contact area can be used as a proxy for synapses in determining connections. However, recent research has demonstrated that contact area alone is not a sufficient predictor of synaptic connection. Moreover, as segmentation has improved, we have observed that synapse annotation is consuming a more significant fraction of overall reconstruction time. This ratio will only get worse as segmentation improves, gating overall possible speed-up. Therefore, we address this problem by developing algorithms that automatically detect pre-synaptic neurons and their post-synaptic partners. In particular, pre-synaptic structures are detected using a Deep and Wide Multiscale Recursive Network, and post-synaptic partners are detected using a MLP with features conditioned on the local segmentation. This work is novel because it requires minimal amount of training, leverages advances in image segmentation directly, and provides a complete solution for polyadic synapse detection. We further introduce novel metrics to evaluate our algorithm on connectomes of meaningful size. These metrics demonstrate that complete automatic prediction can be used to effectively characterize most connectivity correctly.

Published
2016

4. Large-scale EM Analysis of the Drosophila Antennal Lobe with Automatically Computed Synapse Point Clouds

Author

Zhao, Ting, Takemura, Shin-ya, Huang, Gary B., Horne, Jane Anne, Katz, William T., Shinomiya, Kazunori, Scheffer, Louis K., Meinertzhagen, Ian A., Rivlin, Patricia K., and Plaza, Stephen M.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

The promise of extracting connectomes and performing useful analysis on large electron microscopy (EM) datasets has been an elusive dream for many years. Tracing in even the smallest portions of neuropil requires copious human annotation, the rate-limiting step for generating a connectome. While a combination of improved imaging and automatic segmentation will lead to the analysis of increasingly large volumes, machines still fail to reach the quality of human tracers. Unfortunately, small errors in image segmentation can lead to catastrophic distortions of the connectome. In this paper, to analyze very large datasets, we explore different mechanisms that are less sensitive to errors in automation. Namely, we advocate and deploy extensive synapse detection on the entire antennal lobe (AL) neuropil in the brain of the fruit fly Drosophila, a region much larger than any densely annotated to date. The resulting synapse point cloud produced is invaluable for determining compartment boundaries in the AL and choosing specific regions for subsequent analysis. We introduce our methodology in this paper for region selection and show both manual and automatic synapse annotation results. Finally, we note the correspondence between image datasets obtained using the synaptic marker, antibody nc82, and our datasets enabling registration between light and EM image modalities.

Published
2015

5. Graphene Sails with Phased Array Optical Drive - Towards More Practical Interstellar Probes

Author

Scheffer, Louis K.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

A spacecraft pushed by radiation has the major advantage that the power source is not included in the accelerated mass, making it the preferred technique for reaching relativistic speeds. There are two main technical challenges. First, to get significant acceleration, the sail must be both extremely light weight and capable of operating at high intensities of the incident beam and the resulting high temperatures. Second, the transmitter must emit high power beams through huge apertures, many kilometers in diameter, in order to focus radiation on the sail across the long distances needed to achieve high final speeds. Existing proposals for the sail use carbon or aluminum films, but aluminum is limited by a low melting point, and both have low mechanical strength requiring either a distributed payload or complex rigging. We propose here a graphene sail, which offers high absorption per unit weight, high temperature operation, and the mechanical strength to support simple rigging to a lumped mass payload. For the transmitter, existing proposals use a compact high power source, and focus the energy with a large (hundreds to thousands of km) space-based lens. Existing optical drive proposals also require launch from the outer solar system, have severe pointing restrictions, and require difficult maneuvering of the beam source. Instead we propose an active Fresnel lens, allowing smaller apertures of less mass, easier pointing with fewer restrictions, and probe launch from the inner solar system. The technologies for both the sail and the transmitter are already under development for other reasons. Worked examples, physically smaller and less massive than those suggested so far, range from a 1kg payload launched to 10\% of the speed of light by a transmitter only 25 times the mass of ISS, to a larger system that can launch a 1000 kg payload to 50\% of the speed of light., Comment: 14 pages, 6 figures, 3 tables. V2 includes additional references

Published
2015

6. Automated Alignment of Imperfect EM Images for Neural Reconstruction

Author

Scheffer, Louis K., Karsh, Bill, and Vitaladevun, Shiv

Subjects
Quantitative Biology - Quantitative Methods
Abstract

The most established method of reconstructing neural circuits from animals involves slicing tissue very thin, then taking mosaics of electron microscope (EM) images. To trace neurons across different images and through different sections, these images must be accurately aligned, both with the others in the same section and to the sections above and below. Unfortunately, sectioning and imaging are not ideal processes - some of the problems that make alignment difficult include lens distortion, tissue shrinkage during imaging, tears and folds in the sectioned tissue, and dust and other artifacts. In addition the data sets are large (hundreds of thousands of images) and each image must be aligned with many neighbors, so the process must be automated and reliable. This paper discusses methods of dealing with these problems, with numeric results describing the accuracy of the resulting alignments., Comment: 23 pages, 10 figures

Published
2013

7. Investigating Nearby Exoplanets via Interstellar Radar

Author

Scheffer, Louis K.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Interstellar radar is a potential intermediate step between passive observation of exoplanets and interstellar exploratory missions. Compared to passive observation, it has the traditional advantages of radar astronomy. It can measure surface characteristics, determine spin rates and axes, provide extremely accurate ranges, construct maps of planets, distinguish liquid from solid surfaces, find rings and moons, and penetrate clouds. It can do this even for planets close to the parent star. Compared to interstellar travel or probes, it also offers significant advantages. The technology required to build such a radar already exists, radar can return results within a human lifetime, and a single facility can investigate thousands of planetary systems. The cost, although high, is within the reach of Earth's economy, so it is cheaper as well., Comment: 6 pages. no figures; Second version - found previous work and included it; report range for Earth size planets; change proposed polarization to circular

Published
2013
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8. A genetically specified connectomics approach applied to long-range feeding regulatory circuits

Author

Atasoy, Deniz, Betley, J Nicholas, Li, Wei-Ping, Su, Helen H, Sertel, Sinem M, Scheffer, Louis K, Simpson, Julie H, Fetter, Richard D, and Sternson, Scott M

Subjects
Neurosciences, Neurological, Amino Acid Sequence, Animals, Animals, Genetically Modified, Connectome, Drosophila melanogaster, Feeding Behavior, Male, Mice, Mice, 129 Strain, Mice, Inbred C57BL, Mice, Transgenic, Molecular Sequence Data, Nerve Net, Organ Culture Techniques, Photic Stimulation, Time Factors, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

Synaptic connectivity and molecular composition provide a blueprint for information processing in neural circuits. Detailed structural analysis of neural circuits requires nanometer resolution, which can be obtained with serial-section electron microscopy. However, this technique remains challenging for reconstructing molecularly defined synapses. We used a genetically encoded synaptic marker for electron microscopy (GESEM) based on intra-vesicular generation of electron-dense labeling in axonal boutons. This approach allowed the identification of synapses from Cre recombinase-expressing or GAL4-expressing neurons in the mouse and fly with excellent preservation of ultrastructure. We applied this tool to visualize long-range connectivity of AGRP and POMC neurons in the mouse, two molecularly defined hypothalamic populations that are important for feeding behavior. Combining selective ultrastructural reconstruction of neuropil with functional and viral circuit mapping, we characterized some basic features of circuit organization for axon projections of these cell types. Our findings demonstrate that GESEM labeling enables long-range connectomics with molecularly defined cell types.

Published
2014

9. Better Lunar Ranges with Fewer Photons - Resolving the Lunar Retro-reflectors

Author

Scheffer, Louis K.

Subjects
General Relativity and Quantum Cosmology
Abstract

Because of lunar librations, the retroreflectors left on the moon do not, in general, face directly at the Earth. Usually this is regarded as a disadvantage. It results in a spread of arrival times, because each cube that comprises the retroreflector is at a slightly different distance from the earth. However, we can turn this same effect into an advantage. Using pulses and detectors somewhat faster than those currently used for lunar ranging, we can resolve at least some of the structure of a retroreflector, at least when the libration angles are large. This additional structure in the transfer function means that a unique mm level fit can be obtained with many fewer photons. Fitting to the expected reflector transfer function in general requires fewer photons than straight averaging, and smoothly reduces to averaging in the cases where no structure can be resolved. The gains from resolving the reflectors are largest at large libration angles, exactly the case where averaging is most inefficient. In these cases the number of photons needed can be reduced by an order of magnitude or more. Analysis shows that angles for which the gain is very high happen several times each month, with the details depending on the exact librations. Experimental validation of this technique should be possible with existing SLR stations and mockups of the lunar reflectors., Comment: 12 pages; 11 eps figures

Published
2005

10. A Conventional Physics Explanation for the Anomalous Acceleration of Pioneer 10/11

Author

Scheffer, Louis K.

Subjects
General Relativity and Quantum Cosmology, Astrophysics
Abstract

Anderson, et al., find the measured trajectories of Pioneer 10 and 11 spacecraft deviate from the trajectories computed from known forces acting on them. This unmodelled acceleration can be accounted for by non-isotropic radiation of spacecraft heat. Various forms of non-isotropic radiation were proposed by Katz, Murphy, and Scheffer, but Anderson, et al. felt that none of these could explain the observed effect. This paper calculates the known effects in more detail and considers new sources of radiation, all based on spacecraft construction. These effects are then modelled over the duration of the experiment. The model provides a reasonable fit to the acceleration from its appearance at a heliocentric distance of 5 AU to the last measurement at 71 AU, but overpredicts by 9% the decrease in acceleration between intervals I and III of the Pioneer 10 observations. (For comparison, the two different measurements of the effect (SIGMA and CHASMP) themselves differ by 4% in interval III.) In any case, by accounting for the bulk of the acceleration, the proposed mechanism makes it much more likely that the entire effect can be explained without the need for new physics., Comment: LaTex; 5 pages, 2 figures, to be submitted to PRL

Published
2001

11. Conventional Forces can Explain the Anomalous Acceleration of Pioneer 10

Author

Scheffer, Louis K.

Subjects
General Relativity and Quantum Cosmology, Astrophysics
Abstract

Anderson, et al. find the measured trajectories of Pioneer 10 and 11 spacecraft deviate from the trajectories computed from known forces acting on them. This unmodelled acceleration (and the less well known, but similar, unmodelled torque) can be accounted for by non-isotropic radiation of spacecraft heat. Various forms of non-isotropic radiation were proposed by Katz, Murphy, and Scheffer, but Anderson, et al. felt that none of these could explain the observed effect. This paper calculates the known effects in more detail and considers new sources of radiation, all based on spacecraft construction. These effects are then modelled over the duration of the experiment. The model reproduces the acceleration from its appearance at a heliocentric distance of 5 AU to the last measurement at 71 AU to within 10 percent. However, it predicts a larger decrease in acceleration between intervals I and III of the Pioneer 10 observations than is observed. This is a 2 sigma discrepancy from the average of the three analyses (SIGMA, CHASMP, and Markwardt). A more complex (but more speculative) model provides a somewhat better fit. Radiation forces can also plausibly explain the previously unmodelled torques, including the spindown of Pioneer 10 that is directly proportional to spacecraft bus heat, and the slow but constant spin-up of Pioneer 11. In any case, by accounting for the bulk of the acceleration, the proposed mechanism makes it much more likely that the entire effect can be explained without the need for new physics., Comment: Final minor changes for publication - added explanation of acronyms, added to RTG asymmetry argument.. Was: 12 pages, 9 figures, major revision. Added discussion of gas leaks and spin history, a radiation based explanation of spin changes, and references to re-analysis of Markwardt. Fixed radio forces, tuned models. Was: 7 pages, 5 figures; added liklihood calculations in body and abstract per suggestion

Published
2001
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12. Support for a prosaic explanation for the anomalous acceleration of Pioneer 10 and 11

Author

Scheffer, Louis K.

Subjects
General Relativity and Quantum Cosmology
Abstract

Anderson, et al., find the measured trajectories of Pioneer 10 and 11 spacecraft deviate from the trajectories computed from known forces acting on them. This unmodelled acceleration can be accounted for by non-isotropic radiation of spacecraft heat. This explanation was first proposed by Murphy, but Anderson, et al. felt it could not explain the observed effect. This paper includes new calculations on the expected magnitude of this effect, based on the relative emissivities of the different sides of the spacecraft, as estimated from the known spacecraft construction. The calculations indicate the proposed effect can account for most, if not all, of the unmodelled acceleration., Comment: 3 pages, revtex4

Published
2001

13. Connectome, Drosophila

Author

Bharioke, Arjun, Scheffer, Louis K., Chklovskii, Dmitri B., Meinertzhagen, Ian A., Jaeger, Dieter, editor, and Jung, Ranu, editor

Published
2015
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14. Connectome, Drosophila

Author

Bharioke, Arjun, primary, Scheffer, Louis K., additional, Chklovskii, Dmitri B., additional, and Meinertzhagen, Ian A., additional

Published
2019
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16. Synaptic circuits and their variations within different columns in the visual system of Drosophila

Author

Takemura, Shin-ya, Xu, C. Shan, Lu, Zhiyuan, Rivlin, Patricia K., Parag, Toufiq, Olbris, Donald J., Plaza, Stephen, Zhao, Ting, Katz, William T., Umayam, Lowell, Weaver, Charlotte, Hess, Harald F., Horne, Jane Anne, Nunez-Iglesias, Juan, Aniceto, Roxanne, Chang, Lei-Ann, Lauchie, Shirley, Nasca, Ashley, Ogundeyi, Omotara, Sigmund, Christopher, Takemura, Satoko, Tran, Julie, Langille, Carlie, Le Lacheur, Kelsey, McLin, Sari, Shinomiya, Aya, Chklovskii, Dmitri B., Meinertzhagen, Ian A., and Scheffer, Louis K.

Published
2015

19. Overview

Author

Lavagno, Luciano, primary, Martin, Grant E., additional, Scheffer, Louis K., additional, and Markov, Igor L., additional

Published
2017
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26. En bloc preparation of Drosophila brains enables high-throughput FIB-SEM connectomics.

Author

Zhiyuan Lu, Shan Xu, C., Hayworth, Kenneth J., Song Pang, Kazunori Shinomiya, Plaza, Stephen M., Scheffer, Louis K., Rubin, Gerald M., Hess, Harald F., Rivlin, Patricia K., and Meinertzhagen, Ian A.

Subjects
DROSOPHILA, CENTRAL nervous system, FRUIT flies, NERVOUS system, CELL anatomy
Abstract

Deriving the detailed synaptic connections of an entire nervous system is the unrealized goal of the nascent field of connectomics. For the fruit fly Drosophila, in particular, we need to dissect the brain, connectives, and ventral nerve cord as a single continuous unit, fix and stain it, and undertake automated segmentation of neuron membranes. To achieve this, we designed a protocol using progressive lowering of temperature dehydration (PLT), a technique routinely used to preserve cellular structure and antigenicity. We combined PLT with low temperature en bloc staining (LTS) and recover fixed neurons as round profiles with darkly stained synapses, suitable for machine segmentation and automatic synapse detection. Here we report three different PLT-LTS methods designed to meet the requirements for FIBSEM imaging of the Drosophila brain. These requirements include: good preservation of ultrastructural detail, high level of en bloc staining, artifactfree microdissection, and smooth hot-knife cutting to reduce the brain to dimensions suited to FIB-SEM. In addition to PLT-LTS, we designed a jig to microdissect and pre-fix the fly’s delicate brain and central nervous system. Collectively these methods optimize morphological preservation, allow us to image the brain usually at 8 nm per voxel, and simultaneously speed the formerly slow rate of FIB-SEM imaging. [ABSTRACT FROM AUTHOR]

Published
2022
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27. A visual motion detection circuit suggested by Drosophila connectomics

Author

Takemura, Shin-ya, Bharioke, Arjun, Lu, Zhiyuan, Nern, Aljoscha, Vitaladevuni, Shiv, Rivlin, Patricia K., Katz, William T., Olbris, Donald J., Plaza, Stephen M., Winston, Philip, Zhao, Ting, Horne, Jane Anne, Fetter, Richard D., Takemura, Satoko, Blazek, Katerina, Chang, Lei-Ann, Ogundeyi, Omotara, Saunders, Mathew A., Shapiro, Victor, Sigmund, Christopher, Rubin, Gerald M., Scheffer, Louis K., Meinertzhagen, Ian A., and Chklovskii, Dmitri B.

Subjects
Neural circuitry -- Testing, Motion detectors -- Research, Electron microscopy -- Usage, Drosophila -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Animal behaviour arises from computations in neuronal circuits, but our understanding of these computations has been frustrated by the lack of detailed synaptic connection maps, or connectomes. For example, despite intensive investigations over half a century, the neuronal implementation of local motion detection in the insect visual system remains elusive. Here we develop a semi-automated pipeline using electron microscopy to reconstruct a connectome, containing 379 neurons and 8,637 chemical synaptic contacts, within the Drosophila optic medulla. By matching reconstructed neurons to examples from light microscopy, we assigned neurons to cell types and assembled a connectome of the repeating module of the medulla. Within this module, we identified cell types constituting a motion detection circuit, and showed that the connections onto individual motion-sensitive neurons in this circuit were consistent with their direction selectivity. Our results identify cellular targets for future functional investigations, and demonstrate that connectomes can provide key insights into neuronal computations., Vision in insects has been subject to intense behavioural (1),physiological (2) and anatomical (3) investigations, yet our understanding of its underlying neural computations is still far from complete. One such [...]

Published
2013
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32. Drosophila Connectome

Author

Bharioke, Arjun, primary, Scheffer, Louis K., additional, Chklovskii, Dmitri B., additional, and Meinertzhagen, Ian A., additional

Published
2013
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35. The connectome of the adult Drosophila mushroom body provides insights into function

Author

Li, Feng, primary, Lindsey, Jack W, additional, Marin, Elizabeth C, additional, Otto, Nils, additional, Dreher, Marisa, additional, Dempsey, Georgia, additional, Stark, Ildiko, additional, Bates, Alexander S, additional, Pleijzier, Markus William, additional, Schlegel, Philipp, additional, Nern, Aljoscha, additional, Takemura, Shin-ya, additional, Eckstein, Nils, additional, Yang, Tansy, additional, Francis, Audrey, additional, Braun, Amalia, additional, Parekh, Ruchi, additional, Costa, Marta, additional, Scheffer, Louis K, additional, Aso, Yoshinori, additional, Jefferis, Gregory SXE, additional, Abbott, Larry F, additional, Litwin-Kumar, Ashok, additional, Waddell, Scott, additional, and Rubin, Gerald M, additional

Published
2020
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36. Author response: The connectome of the adult Drosophila mushroom body provides insights into function

Author

Li, Feng, primary, Lindsey, Jack W, additional, Marin, Elizabeth C, additional, Otto, Nils, additional, Dreher, Marisa, additional, Dempsey, Georgia, additional, Stark, Ildiko, additional, Bates, Alexander S, additional, Pleijzier, Markus William, additional, Schlegel, Philipp, additional, Nern, Aljoscha, additional, Takemura, Shin-ya, additional, Eckstein, Nils, additional, Yang, Tansy, additional, Francis, Audrey, additional, Braun, Amalia, additional, Parekh, Ruchi, additional, Costa, Marta, additional, Scheffer, Louis K, additional, Aso, Yoshinori, additional, Jefferis, Gregory SXE, additional, Abbott, Larry F, additional, Litwin-Kumar, Ashok, additional, Waddell, Scott, additional, and Rubin, Gerald M, additional

Published
2020
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37. A connectome and analysis of the adult Drosophila central brain

Author

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

Published
2020
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38. Author response: A connectome and analysis of the adult Drosophila central brain

Author

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

Published
2020
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41. A Connectome and Analysis of the Adult Drosophila Central Brain

Author

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

Published
2020
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43. A connectome and analysis of the adult Drosophila central brain

Author

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

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 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

Published
2020

44. A Connectome of the Adult Drosophila Central Brain

Author

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

Published
2020
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48. Comparisons between the ON- and OFF-edge motion pathways in the Drosophila brain

Author

Shinomiya, Kazunori, primary, Huang, Gary, additional, Lu, Zhiyuan, additional, Parag, Toufiq, additional, Xu, C Shan, additional, Aniceto, Roxanne, additional, Ansari, Namra, additional, Cheatham, Natasha, additional, Lauchie, Shirley, additional, Neace, Erika, additional, Ogundeyi, Omotara, additional, Ordish, Christopher, additional, Peel, David, additional, Shinomiya, Aya, additional, Smith, Claire, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Rivlin, Patricia K, additional, Nern, Aljoscha, additional, Scheffer, Louis K, additional, Plaza, Stephen M, additional, and Meinertzhagen, Ian A, additional

Published
2019
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49. Author response: Comparisons between the ON- and OFF-edge motion pathways in the Drosophila brain

Author

Shinomiya, Kazunori, primary, Huang, Gary, additional, Lu, Zhiyuan, additional, Parag, Toufiq, additional, Xu, C Shan, additional, Aniceto, Roxanne, additional, Ansari, Namra, additional, Cheatham, Natasha, additional, Lauchie, Shirley, additional, Neace, Erika, additional, Ogundeyi, Omotara, additional, Ordish, Christopher, additional, Peel, David, additional, Shinomiya, Aya, additional, Smith, Claire, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Rivlin, Patricia K, additional, Nern, Aljoscha, additional, Scheffer, Louis K, additional, Plaza, Stephen M, additional, and Meinertzhagen, Ian A, additional

Published
2018
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