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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 84,296 bioRxiv papers from 362,950 authors.

Most downloaded bioRxiv papers, all time

in category neuroscience

14,714 results found. For more information, click each entry to expand.

21: High-performance GFP-based calcium indicators for imaging activity in neuronal populations and microcompartments
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Posted to bioRxiv 03 Oct 2018

High-performance GFP-based calcium indicators for imaging activity in neuronal populations and microcompartments
11,201 downloads neuroscience

Hod Dana, Yi Sun, Boaz Mohar, Brad Hulse, Jeremy P Hasseman, Getahun Tsegaye, Arthur Tsang, Allan Wong, Ronak Patel, John J Macklin, Yang Chen, Arthur Konnerth, Vivek Jayaraman, Loren L. Looger, Eric R. Schreiter, Karel Svoboda, Douglas S. Kim

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics, and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and tracking large populations of neurons using 2-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

22: A suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality
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Posted to bioRxiv 25 Nov 2017

A suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality
10,757 downloads neuroscience

Tanya L. Daigle, Linda Madisen, Travis A. Hage, Matthew T. Valley, Ulf Knoblich, Rylan S. Larsen, Marc M Takeno, Lawrence Huang, Hong Gu, Rachael Larsen, Maya Mills, Alice Bosma-Moody, La’Akea Siverts, Miranda Walker, Lucas T. Graybuck, Zizhen Yao, Olivia Fong, Emma Garren, Garreck Lenz, Mariya Chavarha, Julie Pendergraft, James Harrington, Karla E Hirokawa, Julie A Harris, Medea McGraw, Douglas R. Ollerenshaw, Kimberly Smith, Christopher A. Baker, Jonathan T Ting, Susan M. Sunkin, Jerome Lecoq, Michael Z. Lin, Edward S Boyden, Gabe J. Murphy, Nuno Maçarico da Costa, Jack Waters, Lu Li, Bosiljka Tasic, Hongkui Zeng

Modern genetic approaches are powerful in providing access to diverse types of neurons within the mammalian brain and greatly facilitating the study of their function. We here report a large set of driver and reporter transgenic mouse lines, including 23 new driver lines targeting a variety of cortical and subcortical cell populations and 26 new reporter lines expressing an array of molecular tools. In particular, we describe the TIGRE2.0 transgenic platform and introduce Cre-dependent reporter lines that enable optical physiology, optogenetics, and sparse labeling of genetically-defined cell populations. TIGRE2.0 reporters broke the barrier in transgene expression level of single-copy targeted-insertion transgenesis in a wide range of neuronal types, along with additional advantage of a simplified breeding strategy compared to our first-generation TIGRE lines. These novel transgenic lines greatly expand the repertoire of high-precision genetic tools available to effectively identify, monitor, and manipulate distinct cell types in the mouse brain.

23: Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
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Posted to bioRxiv 06 Oct 2018

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
10,561 downloads neuroscience

Ahmed S. Abdelfattah, Takashi Kawashima, Amrita Singh, Ondrej Novak, Hui Liu, Yichun Shuai, Yi-Chieh Huang, Jonathan B. Grimm, Ronak Patel, Johannes Friedrich, Brett D. Mensh, Liam Paninski, John J Macklin, Kaspar Podgorski, Bei-Jung Lin, Tsai-Wen Chen, Glenn C. Turner, Zhe Liu, Minoru Koyama, Karel Svoboda, Misha B. Ahrens, Luke D. Lavis, Eric R. Schreiter

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, Voltron, that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 minutes of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

24: Widespread and targeted gene expression by systemic AAV vectors: Production, purification, and administration
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Posted to bioRxiv 11 Jan 2018

Widespread and targeted gene expression by systemic AAV vectors: Production, purification, and administration
9,839 downloads neuroscience

Rosemary C Challis, Sripriya Ravindra Kumar, Ken Y Chan, Collin Challis, Min J Jang, Pradeep S Rajendran, John D Tompkins, Kalyanam Shivkumar, Benjamin E. Deverman, Viviana Gradinaru

We recently developed novel AAV capsids for efficient and noninvasive gene transfer across the central and peripheral nervous systems. In this protocol, we describe how to produce and systemically administer AAV-PHP viruses to label and/or genetically manipulate cells in the mouse nervous system and organs including the heart. The procedure comprises three separate stages: AAV production, intravenous delivery, and evaluation of transgene expression. The protocol spans eight days, excluding the time required to assess gene expression, and can be readily adopted by laboratories with standard molecular and cell culture capabilities. We provide guidelines for experimental design and choosing the capsid, cargo, and viral dose appropriate for the experimental aims. The procedures outlined here are adaptable to diverse biomedical applications, from anatomical and functional mapping to gene expression, silencing, and editing.

25: Kilosort: realtime spike-sorting for extracellular electrophysiology with hundreds of channels
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Posted to bioRxiv 30 Jun 2016

Kilosort: realtime spike-sorting for extracellular electrophysiology with hundreds of channels
9,797 downloads neuroscience

Marius Pachitariu, Nicholas Steinmetz, Shabnam Kadir, Matteo Carandini, Harris Kenneth D.

Advances in silicon probe technology mean that in vivo electrophysiological recordings from hundreds of channels will soon become commonplace. To interpret these recordings we need fast, scalable and accurate methods for spike sorting, whose output requires minimal time for manual curation. Here we introduce Kilosort, a spike sorting framework that meets these criteria, and show that it allows rapid and accurate sorting of large-scale in vivo data. Kilosort models the recorded voltage as a sum of template waveforms triggered on the spike times, allowing overlapping spikes to be identified and resolved. Rapid processing is achieved thanks to a novel low-dimensional approximation for the spatiotemporal distribution of each template, and to batch-based optimization on GPUs. A novel post-clustering merging step based on the continuity of the templates substantially reduces the requirement for subsequent manual curation operations. We compare Kilosort to an established algorithm on data obtained from 384-channel electrodes, and show superior performance, at much reduced processing times. Data from 384-channel electrode arrays can be processed in approximately realtime. Kilosort is an important step towards fully automated spike sorting of multichannel electrode recordings, and is freely available github.com/cortex-lab/Kilosort.

26: Molecular architecture of the mouse nervous system
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Posted to bioRxiv 05 Apr 2018

Molecular architecture of the mouse nervous system
9,678 downloads neuroscience

Amit Zeisel, Hannah Hochgerner, Peter Lönnerberg, Anna Johnsson, Fatima Memic, Job van der Zwan, Martin Häring, Emelie Braun, Lars Borm, Gioele La Manno, Simone Codeluppi, Alessandro Furlan, Nathan Skene, Kenneth D. Harris, Jens Hjerling Leffler, Ernest Arenas, Patrik Ernfors, Ulrika Marklund, Sten Linnarsson

The mammalian nervous system executes complex behaviors controlled by specialised, precisely positioned and interacting cell types. Here, we used RNA sequencing of half a million single cells to create a detailed census of cell types in the mouse nervous system. We mapped cell types spatially and derived a hierarchical, data-driven taxonomy. Neurons were the most diverse, and were grouped by developmental anatomical units, and by the expression of neurotransmitters and neuropeptides. Neuronal diversity was driven by genes encoding cell identity, synaptic connectivity, neurotransmission and membrane conductance. We discovered several distinct, regionally restricted, astrocytes types, which obeyed developmental boundaries and correlated with the spatial distribution of key glutamate and glycine neurotransmitters. In contrast, oligodendrocytes showed a loss of regional identity, followed by a secondary diversi cation. The resource presented here lays a solid foundation for understanding the molecular architecture of the mammalian nervous system, and enables genetic manipulation of specific cell types.

27: A Single-Cell Atlas of Cell Types, States, and Other Transcriptional Patterns from Nine Regions of the Adult Mouse Brain
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Posted to bioRxiv 10 Apr 2018

A Single-Cell Atlas of Cell Types, States, and Other Transcriptional Patterns from Nine Regions of the Adult Mouse Brain
9,577 downloads neuroscience

Arpiar Saunders, Evan Macosko, Alec Wysoker, Melissa Goldman, Fenna Krienen, Heather de Rivera, Elizabeth Bien, Matthew Baum, Shuyu Wang, Aleks Goeva, James Nemesh, Nolan Kamitaki, Sara Brumbaugh, David Kulp, Steven A. McCarroll

The mammalian brain is composed of diverse, specialized cell populations, few of which we fully understand. To more systematically ascertain and learn from cellular specializations in the brain, we used Drop-seq to perform single-cell RNA sequencing of 690,000 cells sampled from nine regions of the adult mouse brain: frontal and posterior cortex (156,000 and 99,000 cells, respectively), hippocampus (113,000), thalamus (89,000), cerebellum (26,000), and all of the basal ganglia - the striatum (77,000), globus pallidus externus/nucleus basalis (66,000), entopeduncular/subthalamic nuclei (19,000), and the substantia nigra/ventral tegmental area (44,000). We developed computational approaches to distinguish biological from technical signals in single-cell data, then identified 565 transcriptionally distinct groups of cells, which we annotate and present through interactive online software we developed for visualizing and re-analyzing these data (DropViz). Comparison of cell classes and types across regions revealed features of brain organization. These included a neuronal gene-expression module for synthesizing axonal and presynaptic components; widely shared patterns in the combinatorial co-deployment of voltage-gated ion channels by diverse neuronal populations; functional distinctions among cells of the brain vasculature; and specialization of glutamatergic neurons across cortical regions to a degree not observed in other neuronal or non-neuronal populations. We describe systematic neuronal classifications for two complex, understudied regions of the basal ganglia, the globus pallidus externus and substantia nigra reticulata. In the striatum, where neuron types have been intensely researched, our data reveal a previously undescribed population of striatal spiny projection neurons (SPNs) comprising 4% of SPNs. The adult mouse brain cell atlas can serve as a reference for analyses of development, disease, and evolution.

28: The "sewing machine" for minimally invasive neural recording
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Posted to bioRxiv 14 Mar 2019

The "sewing machine" for minimally invasive neural recording
9,445 downloads neuroscience

Timothy L Hanson, Camilo A Diaz-Botia, Viktor Kharazia, Michel M Maharbiz, Philip N Sabes

We present a system for scalable and customizable recording and stimulation of neural activity. In large animals and humans, the current benchmark for high spatial and temporal resolution neural interfaces are fixed arrays of wire or silicon electrodes inserted into the parenchyma of the brain. However, probes that are large and stiff enough to penetrate the brain have been shown to cause acute and chronic damage and inflammation, which limits their longevity, stability, and yield. One approach to this problem is to separate the requirements of the insertion device, which should to be as stiff as possible, with the implanted device, which should be as small and flexible as possible. Here, we demonstrate the feasibility and scalability of this approach with a system incorporating fine and flexible thin-film polymer probes, a fine and stiff insertion needle, and a robotic insertion machine. Together the system permits rapid and precise implantation of probes, each individually targeted to avoid observable vasculature and to attain diverse anatomical targets. As an initial demonstration of this system, we implanted arrays of electrodes in rat somatosensory cortex, recorded extracellular action potentials from them, and obtained histological images of the tissue response. This approach points the way toward a new generation of scaleable, stable, and safe neural interfaces, both for the basic scientific study of brain function and for clinical applications.

29: Nested oscillatory dynamics in cortical organoids model early human brain network development
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Posted to bioRxiv 29 Jun 2018

Nested oscillatory dynamics in cortical organoids model early human brain network development
9,100 downloads neuroscience

Cleber A. Trujillo, Richard Gao, Priscilla D. Negraes, Isaac A. Chaim, Alain Domissy, Matthieu Vandenberghe, Anna Devor, Gene W Yeo, Bradley Voytek, Alysson R. Muotri

Structural and transcriptional changes during early brain maturation follow fixed developmental programs defined by genetics. However, whether this is true for functional network activity remains unknown, primarily due to experimental inaccessibility of the initial stages of the living human brain. Here, we analyzed cortical organoids that spontaneously developed periodic and regular oscillatory network events that are dependent on glutamatergic and GABAergic signaling. These nested oscillations exhibit cross-frequency coupling, proposed to coordinate neuronal computation and communication. As evidence of potential network maturation, oscillatory activity subsequently transitioned to more spatiotemporally irregular patterns, capturing features observed in preterm human electroencephalography (EEG). These results show that the development of structured network activity in the human neocortex may follow stable genetic programming, even in the absence of external or subcortical inputs. Our model provides novel opportunities for investigating and manipulating the role of network activity in the developing human cortex.

30: Automated Reconstruction of a Serial-Section EM Drosophila Brain with Flood-Filling Networks and Local Realignment
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Posted to bioRxiv 11 Apr 2019

Automated Reconstruction of a Serial-Section EM Drosophila Brain with Flood-Filling Networks and Local Realignment
9,058 downloads neuroscience

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

Reconstruction of neural circuitry at single-synapse resolution is an attractive 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.

31: A Connectome of the Adult Drosophila Central Brain
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Posted to bioRxiv 21 Jan 2020

A Connectome of the Adult Drosophila Central Brain
8,768 downloads neuroscience

C. Shan Xu, Michal Januszewski, Zhiyuan Lu, Shin-ya Takemura, Kenneth J. Hayworth, Gary Huang, Kazunori Shinomiya, Jeremy Maitin-Shepard, David Ackerman, Stuart Berg, Tim Blakely, John A Bogovic, Jody Clements, Tom Dolafi, Philip Hubbard, Dagmar Kainmueller, William Katz, Takashi Kawase, Khaled A. Khairy, Laramie Leavitt, Peter H. Li, Larry Lindsey, Nicole L. Neubarth, Donald J. Olbris, Hideo Otsuna, Eric T. Troutman, Lowell Umayam, Ting Zhao, Masayoshi Ito, Jens Goldammer, Tanya Wolff, Robert Svirskas, Philipp Schlegel, Erika R. 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 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, Kei Ito, Stephan Saalfeld, Reed George, Ian A. Meinertzhagen, Gerald M Rubin, Harald F. Hess, Louis K. Scheffer, Viren Jain, Stephen M. Plaza

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.

32: High-dimensional geometry of population responses in visual cortex
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Posted to bioRxiv 22 Jul 2018

High-dimensional geometry of population responses in visual cortex
8,636 downloads neuroscience

Carsen Stringer, Marius Pachitariu, Nicholas A. Steinmetz, Matteo Carandini, Kenneth D. Harris

A neuronal population encodes information most efficiently when its activity is uncorrelated and high-dimensional, and most robustly when its activity is correlated and lower-dimensional. Here, we analyzed the correlation structure of natural image coding, in large visual cortical populations recorded from awake mice. Evoked population activity was high dimensional, with correlations obeying an unexpected power-law: the n-th principal component variance scaled as 1/n. This was not inherited from the 1/f spectrum of natural images, because it persisted after stimulus whitening. We proved mathematically that the variance spectrum must decay at least this fast if a population code is smooth, i.e. if small changes in input cannot dominate population activity. The theory also predicts larger power-law exponents for lower-dimensional stimulus ensembles, which we validated experimentally. These results suggest that coding smoothness represents a fundamental constraint governing correlations in neural population codes.

33: A neural algorithm for a fundamental computing problem
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Posted to bioRxiv 25 Aug 2017

A neural algorithm for a fundamental computing problem
8,405 downloads neuroscience

Sanjoy Dasgupta, Charles F Stevens, Saket Navlakha

Similarity search, such as identifying similar images in a database or similar documents on the Web, is a fundamental computing problem faced by many large-scale information retrieval systems. We discovered that the fly's olfactory circuit solves this problem using a novel variant of a traditional computer science algorithm (called locality-sensitive hashing). The fly's circuit assigns similar neural activity patterns to similar input stimuli (odors), so that behaviors learned from one odor can be applied when a similar odor is experienced. The fly's algorithm, however, uses three new computational ingredients that depart from traditional approaches. We show that these ingredients can be translated to improve the performance of similarity search compared to traditional algorithms when evaluated on several benchmark datasets. Overall, this perspective helps illuminate the logic supporting an important sensory function (olfaction), and it provides a conceptually new algorithm for solving a fundamental computational problem.

34: Modern machine learning outperforms GLMs at predicting spikes
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Posted to bioRxiv 24 Feb 2017

Modern machine learning outperforms GLMs at predicting spikes
8,211 downloads neuroscience

Ari S. Benjamin, Hugo L. Fernandes, Tucker Tomlinson, Pavan Ramkumar, Chris VerSteeg, Raeed Chowdhury, Lee Miller, Konrad Paul Kording

Neuroscience has long focused on finding encoding models that effectively ask "what predicts neural spiking?" and generalized linear models (GLMs) are a typical approach. It is often unknown how much of explainable neural activity is captured, or missed, when fitting a GLM. Here we compared the predictive performance of GLMs to three leading machine learning methods: feedforward neural networks, gradient boosted trees (using XGBoost), and stacked ensembles that combine the predictions of several methods. We predicted spike counts in macaque motor (M1) and somatosensory (S1) cortices from standard representations of reaching kinematics, and in rat hippocampal cells from open field location and orientation. In general, the modern methods (particularly XGBoost and the ensemble) produced more accurate spike predictions and were less sensitive to the preprocessing of features. This discrepancy in performance suggests that standard feature sets may often relate to neural activity in a nonlinear manner not captured by GLMs. Encoding models built with machine learning techniques, which can be largely automated, more accurately predict spikes and can offer meaningful benchmarks for simpler models.

35: A computational toolbox and step-by-step tutorial for the analysis of neuronal population dynamics in calcium imaging data
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Posted to bioRxiv 28 Jan 2017

A computational toolbox and step-by-step tutorial for the analysis of neuronal population dynamics in calcium imaging data
8,183 downloads neuroscience

Sebastián A. Romano, Verónica Pérez-Schuster, Adrien Jouary, Alessia Candeo, Jonathan Boulanger-Weill, Germán Sumbre

The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a tutorial for the use of a comprehensive computational toolbox for the analysis of neuronal population activity imaging. It consists of tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. They are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets, and provide a case study to explain its implementation.

36: Inferring single-trial neural population dynamics using sequential auto-encoders
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Posted to bioRxiv 20 Jun 2017

Inferring single-trial neural population dynamics using sequential auto-encoders
8,164 downloads neuroscience

Chethan Pandarinath, Daniel J. O’Shea, Jasmine Collins, Rafal Jozefowicz, Sergey D. Stavisky, Jonathan C Kao, Eric M. Trautmann, Matthew T. Kaufman, Stephen I. Ryu, Leigh R. Hochberg, Jaimie M. Henderson, Krishna V. Shenoy, L. F. Abbott, David Sussillo

Neuroscience is experiencing a data revolution in which simultaneous recording of many hundreds or thousands of neurons is revealing structure in population activity that is not apparent from single-neuron responses. This structure is typically extracted from trial-averaged data. Single-trial analyses are challenging due to incomplete sampling of the neural population, trial-to-trial variability, and fluctuations in action potential timing. Here we introduce Latent Factor Analysis via Dynamical Systems (LFADS), a deep learning method to infer latent dynamics from single-trial neural spiking data. LFADS uses a nonlinear dynamical system (a recurrent neural network) to infer the dynamics underlying observed population activity and to extract ‘de-noised’ single-trial firing rates from neural spiking data. We apply LFADS to a variety of monkey and human motor cortical datasets, demonstrating its ability to predict observed behavioral variables with unprecedented accuracy, extract precise estimates of neural dynamics on single trials, infer perturbations to those dynamics that correlate with behavioral choices, and combine data from non-overlapping recording sessions (spanning months) to improve inference of underlying dynamics. In summary, LFADS leverages all observations of a neural population's activity to accurately model its dynamics on single trials, opening the door to a detailed understanding of the role of dynamics in performing computation and ultimately driving behavior.

37: Empirical assessment of published effect sizes and power in the recent cognitive neuroscience and psychology literature
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Posted to bioRxiv 25 Aug 2016

Empirical assessment of published effect sizes and power in the recent cognitive neuroscience and psychology literature
8,063 downloads neuroscience

Denes Szucs, John PA Ioannidis

We have empirically assessed the distribution of published effect sizes and estimated power by extracting more than 100,000 statistical records from about 10,000 cognitive neuroscience and psychology papers published during the past 5 years. The reported median effect size was d=0.93 (inter-quartile range: 0.64-1.46) for nominally statistically significant results and d=0.24 (0.11-0.42) for non-significant results. Median power to detect small, medium and large effects was 0.12, 0.44 and 0.73, reflecting no improvement through the past half-century. Power was lowest for cognitive neuroscience journals. 14% of papers reported some statistically significant results, although the respective F statistic and degrees of freedom proved that these were non-significant; p value errors positively correlated with journal impact factors. False report probability is likely to exceed 50% for the whole literature. In light of our findings the recently reported low replication success in psychology is realistic and worse performance may be expected for cognitive neuroscience.

38: A Critique of Pure Learning: What Artificial Neural Networks can Learn from Animal Brains
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Posted to bioRxiv 20 Mar 2019

A Critique of Pure Learning: What Artificial Neural Networks can Learn from Animal Brains
7,972 downloads neuroscience

Anthony M Zador

Over the last decade, artificial neural networks (ANNs), have undergone a revolution, catalyzed in large part by better tools for supervised learning. However, training such networks requires enormous data sets of labeled examples, whereas young animals (including humans) typically learn with few or no labeled examples. This stark contrast with biological learning has led many in the ANN community posit that instead of supervised paradigms, animals must rely instead primarily on unsupervised learning, leading the search for better unsupervised algorithms. Here we argue that much of an animal's behavioral repertoire is not the result of clever learning algorithms--supervised or unsupervised--but arises instead from behavior programs already present at birth. These programs arise through evolution, are encoded in the genome, and emerge as a consequence of wiring up the brain. Specifically, animals are born with highly structured brain connectivity, which enables them learn very rapidly. Recognizing the importance of the highly structured connectivity suggests a path toward building ANNs capable of rapid learning.

39: A Complete Electron Microscopy Volume Of The Brain Of Adult Drosophila melanogaster
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Posted to bioRxiv 22 May 2017

A Complete Electron Microscopy Volume Of The Brain Of Adult Drosophila melanogaster
7,826 downloads neuroscience

Zhihao Zheng, J. Scott Lauritzen, Eric Perlman, Camenzind G. Robinson, Matthew Nichols, Daniel Milkie, Omar Torrens, John Price, Corey B. Fisher, Nadiya Sharifi, Steven A. Calle-Schuler, Lucia Kmecova, Iqbal J. Ali, Bill Karsh, Eric T. Trautman, John A Bogovic, Philipp Hanslovsky, Gregory S. X. E. Jefferis, Michael Kazhdan, Khaled Khairy, Stephan Saalfeld, Richard Fetter, Davi Bock

Drosophila melanogaster has a rich repertoire of innate and learned behaviors. Its 100,000-neuron brain is a large but tractable target for comprehensive neural circuit mapping. Only electron microscopy (EM) enables complete, unbiased mapping of synaptic connectivity; however, the fly brain is too large for conventional EM. We developed a custom high-throughput EM platform and imaged the entire brain of an adult female fly. We validated the dataset by tracing brain-spanning circuitry involving the mushroom body (MB), intensively studied for its role in learning. Here we describe the complete set of olfactory inputs to the MB; find a new cell type providing driving input to Kenyon cells (the intrinsic MB neurons); identify neurons postsynaptic to Kenyon cell dendrites; and find that axonal arbors providing input to the MB calyx are more tightly clustered than previously indicated by light-level data. This freely available EM dataset will significantly accelerate Drosophila neuroscience.

40: Enhancer viruses and a transgenic platform for combinatorial cell subclass-specific labeling
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Posted to bioRxiv 20 Jan 2019

Enhancer viruses and a transgenic platform for combinatorial cell subclass-specific labeling
7,786 downloads neuroscience

Lucas T. Graybuck, Tanya L. Daigle, Adriana E. Sedeño-Cortés, Miranda Walker, Brian E. Kalmbach, Garreck H. Lenz, Thuc Nghi Nguyen, Emma Garren, Tae Kyung Kim, La’ Akea Siverts, Jacqueline L. Bendrick, Thomas Zhou, Marty Mortrud, Shenqin Yao, Ali H. Cetin, Rachael Larsen, Luke Esposito, Bryan Gore, Eric Szelenyi, Elyse Morin, John K. Mich, Nick Dee, Jeff Goldy, Kimberly Smith, Zizhen Yao, Viviana Gradinaru, Susan M. Sunkin, Ed S. Lein, Boaz Levi, Jonathan T Ting, Hongkui Zeng, Bosiljka Tasic

The rapid pace of cell type identification by new single-cell analysis methods has not been met with efficient experimental access to the newly discovered types. To enable flexible and efficient access to specific neural populations in the mouse cortex, we collected chromatin accessibility data from individual cells and clustered the single-cell data to identify enhancers specific for cell classes and subclasses. When cloned into adeno-associated viruses (AAVs) and delivered to the brain by retro-orbital injections, these enhancers drive transgene expression in specific cell subclasses in the cortex. We characterize several enhancer viruses in detail to show that they result in labeling of different projection neuron subclasses in mouse cortex, and that one of them can be used to label the homologous projection neuron subclass in human cortical slices. To enable the combinatorial labeling of more than one cell type by enhancer viruses, we developed a three-color Cre-, Flp- and Nigri- recombinase dependent reporter mouse line, Ai213. The delivery of three enhancer viruses driving these recombinases via a single retroorbital injection into a single Ai213 transgenic mouse results in labeling of three different neuronal classes/subclasses in the same brain tissue. This approach combines unprecedented flexibility with specificity for investigation of cell types in the mouse brain and beyond. ### Competing Interest Statement The authors have declared no competing interest.

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