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Currently indexing 88,562 bioRxiv papers from 379,808 authors.

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Results 81 through 100 out of 15425

in category neuroscience


81: Spike sorting for large, dense electrode arrays

Cyrille Rossant, Shabnam Kadir et al.

4,929 downloads (posted 16 Feb 2015)

Developments in microfabrication technology have enabled the production of neural electrode arrays with hundreds of closely-spaced recording sites, and electrodes with thousands of sites are currently under development. These probes will in principle allow the simultaneous recording of very large numbers of neurons. However, use of this technology requires the development of techniques for decoding the spike times of the recorded neurons, from the raw data captured from the probes. There currently exists no practical solution to this problem of “spike sorting” for large, dense electrode arrays. Here, we present a set of novel tools to solve this problem, implemented in a suite of practical, user-friendly, open-source software. We validate these methods on data from rat cortex, demonstrating error rates as low as 5%.


82: Ultra fast tissue staining with chemical tags

Johannes Kohl, Julian Ng et al.

4,915 downloads (posted 19 May 2014)

Genetically encoded fluorescent proteins and immunostainings are widely used to detect cellular or sub-cellular structures in thick biological samples. However, each approach suffers from limitations, including low signal and limited spectral flexibility or slow speed, poor penetration and high background, respectively. Here we overcome these limitations by using transgenically expressed chemical tags for rapid, even and low-background labeling of thick biological tissues. We construct a platform of widely applicable tr...


83: Neural Population Control via Deep Image Synthesis

Pouya Bashivan, Kohitij Kar et al.

4,909 downloads (posted 04 Nov 2018)

Particular deep artificial neural networks (ANNs) are today's most accurate models of the primate brain's ventral visual stream. Here we report that, using a targeted ANN-driven image synthesis method, new luminous power patterns (i.e. images) can be applied to the primate retinae to predictably push the spiking activity of targeted V4 neural sites beyond naturally occurring levels. More importantly, this method, while not yet perfect, already achieves unprecedented independent control of the activity state of entire po...


84: The Dreem Headband as an Alternative to Polysomnography for EEG Signal Acquisition and Sleep Staging

Pierrick J Arnal, Valentin Thorey et al.

4,858 downloads (posted 10 Jun 2019)

Despite the central role of sleep in our lives and the high prevalence of sleep disorders, sleep is still poorly understood. The development of ambulatory technologies capable of monitoring brain activity during sleep longitudinally is critical to advancing sleep science and facilitating the diagnosis of sleep disorders. We introduced the Dreem headband (DH) as an affordable, comfortable, and user-friendly alternative to polysomnography (PSG). The purpose of this study was to assess the signal acquisition of the DH and ...


85: A guide to robust statistical methods in neuroscience

Rand R. Wilcox, Guillaume A. Rousselet

4,847 downloads (posted 20 Jun 2017)

There is a vast array of new and improved methods for comparing groups and studying associations that offer the potential for substantially increasing power, providing improved control over the probability of a Type I error, and yielding a deeper and more nuanced under- standing of neuroscience data. These new techniques effectively deal with four insights into when and why conventional methods can be unsatisfactory. But for the non-statistician, the vast array of new and improved techniques for comparing groups and stu...


86: Distinct descending motor cortex pathways and their roles in movement

Michael N Economo, Sarada Viswanathan et al.

4,815 downloads (posted 05 Dec 2017)

Activity in motor cortex predicts specific movements, seconds before they are initiated. This preparatory activity has been observed in L5 descending "pyramidal tract" (PT) neurons. A key question is how preparatory activity can be maintained without causing movement, and how preparatory activity is eventually converted to a motor command to trigger appropriate movements. We used single cell transcriptional profiling and axonal reconstructions to identify two types of PT neuron. Both types share projections to multiple ...


87: Probing variability in a cognitive map using manifold inference from neural dynamics

Ryan J. Low, Sam Lewallen et al.

4,768 downloads (posted 16 Sep 2018)

Hippocampal neurons fire selectively in local behavioral contexts such as the position in an environment or phase of a task, and are thought to form a cognitive map of task-relevant variables. However, their activity varies over repeated behavioral conditions, such as different runs through the same position or repeated trials. Although widely observed across the brain, such variability is not well understood, and could reflect noise or structure, such as the encoding of additional cognitive information. Here, we introd...


88: Spatial organization of the somatosensory cortex revealed by cyclic smFISH

Simone Codeluppi, Lars Borm et al.

4,717 downloads (posted 04 Mar 2018)

The global efforts towards the creation of a molecular census of the brain using single-cell transcriptomics is generating a large catalog of molecularly defined cell types lacking spatial information. Thus, new methods are needed to map a large number of cell-specific markers simultaneously on large tissue areas. Here, we developed a cyclic single molecule fluorescence in situ hybridization methodology and defined the cellular organization of the somatosensory cortex using markers identified by single-cell transcriptom...


89: Aged blood inhibits hippocampal neurogenesis and activates microglia through VCAM1 at the blood-brain barrier

Hanadie Yousef, Cathrin J Czupalla et al.

4,698 downloads (posted 03 Jan 2018)

An aged circulatory environment can promote brain dysfunction and we hypothesized that the blood-brain barrier (BBB) mediates at least some of these effects. We observe brain endothelial cells (BECs) in the aged mouse hippocampus express an inflammatory transcriptional profile with focal upregulation of Vascular Cell Adhesion Molecule 1 (VCAM1), a protein that facilitates vascular-immune cell interactions. Concomitantly, the shed, soluble form of VCAM1 is prominently increased in the aged circulation of humans and mice,...


90: Tractography-based connectomes are dominated by false-positive connections

Klaus H. Maier-Hein, Peter Neher et al.

4,676 downloads (posted 07 Nov 2016)

Fiber tractography based on non-invasive diffusion imaging is at the heart of connectivity studies of the human brain. To date, the approach has not been systematically validated in ground truth studies. Based on a simulated human brain dataset with ground truth white matter tracts, we organized an open international tractography challenge, which resulted in 96 distinct submissions from 20 research groups. While most state-of-the-art algorithms reconstructed 90% of ground truth bundles to at least some extent, on averag...


91: A genetically encoded fluorescent sensor for in vivo imaging of GABA

Jonathan S. Marvin, Yoshiteru Shimoda et al.

4,647 downloads (posted 14 May 2018)

Current techniques for monitoring GABA, the primary inhibitory neurotransmitter in vertebrates, cannot follow ephemeral transients in intact neural circuits. We applied the design principles used to create iGluSnFR, a fluorescent reporter of synaptic glutamate, to develop a GABA sensor using a protein derived from a previously unsequenced Pseudomonas fluorescens strain. Structure-guided mutagenesis and library screening led to a usable iGABASnFR (maximum DeltaF/F ~ 2.5, Kd ~ 9 micromolar, good specificity, adequate kine...


92: Distributed correlates of visually-guided behavior across the mouse brain

Nicholas A. Steinmetz, Peter Zatka-Haas et al.

4,643 downloads (posted 20 Nov 2018)

Behavior arises from neuronal activity, but it is not known how the active neurons are distributed across brain regions and how their activity unfolds in time. Here, we used high-density Neuropixels probes to record from ~30,000 neurons in mice performing a visual contrast discrimination task. The task activated 60% of the neurons, involving nearly all 42 recorded brain regions, well beyond the regions activated by passive visual stimulation. However, neurons selective for choice (left vs. right) were rare, and found mo...


93: High precision coding in visual cortex

Carsen Stringer, Michalis Michaelos et al.

4,606 downloads (posted 21 Jun 2019)

Single neurons in visual cortex provide unreliable measurements of visual features due to their high trial-to-trial variability. It is not known if this “noise” extends its effects over large neural populations to impair the global encoding of stimuli. We recorded simultaneously from ∼20,000 neurons in mouse primary visual cortex (V1) and found that the neural populations had discrimination thresholds of ∼0.34° in an orientation decoding task. These thresholds were nearly 100 times smaller than those reported behavioral...



Michael Powell, Mahan Hosseini et al.

4,600 downloads (posted 03 Oct 2016)

Machine learning is a powerful set of techniques that has enhanced the abilities of neuroscientists to interpret information collected through EEG, fMRI, and MEG data. With these powerful techniques comes the danger of overfitting of hyper-parameters which can render results invalid, and cause a failure to generalize beyond the data set. We refer to this problem as ‘over-hyping’ and show that it is pernicious despite commonly used precautions. In particular, over-hyping occurs when an analysis is run repeatedly with sli...


95: Population imaging of neural activity in awake behaving mice in multiple brain regions

Kiryl D Piatkevich, Seth Bensussen et al.

4,484 downloads (posted 23 Apr 2019)

A longstanding goal in neuroscience has been to image membrane voltage, with high temporal precision and sensitivity, in awake behaving mammals. Here, we report a genetically encoded voltage indicator, SomArchon, which exhibits millisecond response times and compatibility with optogenetic control, and which increases the sensitivity, signal-to-noise ratio, and number of neurons observable, by manyfold over previous reagents. SomArchon only requires conventional one-photon microscopy to achieve these high performance cha...


96: Filter-banks and artificial intelligence in seizure detection using electroencephalograms

M. A. Pinto-Orellana, F. R. Cerqueira

4,483 downloads (posted 03 Feb 2017)

Epilepsy is the most typical neurological disease in the world, and it implies an expensive and specialized diagnosis process based on electroencephalograms and video recordings. We developed a method that only requires the brainwave provided by the difference between two standard-located electrodes. Our proposed technique separates the original signal using a filter array with three different types of filters, and then extracts several features based on information theory and statistical information. In our study, we f...


97: Fixed versus mixed RSA: Explaining visual representations by fixed and mixed feature sets from shallow and deep computational models

Seyed-Mahdi Khaligh-Razavi, Linda Henriksson et al.

4,460 downloads (posted 03 Oct 2014)

Studies of the primate visual system have begun to test a wide range of complex computational object-vision models. Realistic models have many parameters, which in practice cannot be fitted using the limited amounts of brain-activity data typically available. Task performance optimization (e.g. using backpropagation to train neural networks) provides major constraints for fitting parameters and discovering nonlinear representational features appropriate for the task (e.g. object classification). Model representations ca...


98: Real-time spike sorting platform for high-density extracellular probes with ground-truth validation and drift correction

James J. Jun, Catalin Mitelut et al.

4,452 downloads (posted 19 Jan 2017)

Electrical recordings from a large array of electrodes give us access to neural population activity with single-cell, single-spike resolution. These recordings contain extracellular spikes which must be correctly detected and assigned to individual neurons. Despite numerous spike-sorting techniques developed in the past, a lack of high-quality ground-truth datasets hinders the validation of spike-sorting approaches. Furthermore, existing approaches requiring manual corrections are not scalable for hours of recordings ex...


99: Single-cell in situ transcriptomic map of astrocyte cortical layer diversity

Omer Ali Bayraktar, Theresa Bartels et al.

4,437 downloads (posted 03 Oct 2018)

During organogenesis, patterns and gradients of gene expression underlie organization and diversified cell specification to generate complex tissue architecture. While the cerebral cortex is organized into six excitatory neuronal layers, it is unclear whether glial cells are diversified to mimic neuronal laminae or show distinct layering. To determine the molecular architecture of the mammalian cortex, we developed a high- content pipeline that can quantify single-cell gene expression in situ. The Large-area Spatial Tra...


100: CaImAn: An open source tool for scalable Calcium Imaging data Analysis

Andrea Giovannucci, Johannes Friedrich et al.

4,427 downloads (posted 05 Jun 2018)

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. Here we present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration ...