Revealing cell assemblies at multiple levels of granularity.

Abstract:

BACKGROUND:Current neuronal monitoring techniques, such as calcium imaging and multi-electrode arrays, enable recordings of spiking activity from hundreds of neurons simultaneously. Of primary importance in systems neuroscience is the identification of cell assemblies: groups of neurons that cooperate in some form within the recorded population. NEW METHOD:We introduce a simple, integrated framework for the detection of cell-assemblies from spiking data without a priori assumptions about the size or number of groups present. We define a biophysically-inspired measure to extract a directed functional connectivity matrix between both excitatory and inhibitory neurons based on their spiking history. The resulting network representation is analyzed using the Markov Stability framework, a graph theoretical method for community detection across scales, to reveal groups of neurons that are significantly related in the recorded time-series at different levels of granularity. RESULTS AND COMPARISON WITH EXISTING METHODS:Using synthetic spike-trains, including simulated data from leaky-integrate-and-fire networks, our method is able to identify important patterns in the data such as hierarchical structure that are missed by other standard methods. We further apply the method to experimental data from retinal ganglion cells of mouse and salamander, in which we identify cell-groups that correspond to known functional types, and to hippocampal recordings from rats exploring a linear track, where we detect place cells with high fidelity. CONCLUSIONS:We present a versatile method to detect neural assemblies in spiking data applicable across a spectrum of relevant scales that contributes to understanding spatio-temporal information gathered from systems neuroscience experiments.

journal_name

J Neurosci Methods

authors

Billeh YN,Schaub MT,Anastassiou CA,Barahona M,Koch C

doi

10.1016/j.jneumeth.2014.08.011

subject

Has Abstract

pub_date

2014-10-30 00:00:00

pages

92-106

eissn

0165-0270

issn

1872-678X

pii

S0165-0270(14)00295-7

journal_volume

236

pub_type

杂志文章
  • Iterative expert-in-the-loop classification of sleep PSG recordings using a hierarchical clustering.

    abstract:BACKGROUND:The classification of sleep signals is a subjective and time consuming task. A large number of automatic classifiers have been published in the past decade but a sleep community has no strong confidence to use them in clinical practice and still remains using a standard manual scoring according standardized ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2019.01.013

    authors: Gerla V,Kremen V,Macas M,Dudysova D,Mladek A,Sos P,Lhotska L

    更新日期:2019-04-01 00:00:00

  • The separation and quantification of aminochromes using high-pressure liquid chromatography with electrochemical detection.

    abstract::There is increasing evidence that oxidative stress plays an important role in the pathogenesis of many neurodegenerative diseases including Parkinson's disease (PD). In particular there is support for the participation of oxidized catecholamines in PD. Catecholamines are highly reactive and are readily oxidized to ami...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2004.08.010

    authors: Ochs SD,Westfall TC,Macarthur H

    更新日期:2005-03-30 00:00:00

  • Resolution-based spectral clustering for brain parcellation using functional MRI.

    abstract:BACKGROUND:Brain parcellation is important for exploiting neuroimaging data. Variability in physiology between individuals has led to the need for data-driven approaches to parcellation, with recent research focusing on simultaneously estimating and partitioning the network structure of the brain. NEW METHOD:We view d...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2020.108628

    authors: Dillon K,Wang YP

    更新日期:2020-04-01 00:00:00

  • Tracing of neuronal connections with cholera toxin subunit B: light and electron microscopic immunohistochemistry using monoclonal antibodies.

    abstract::Subunit B of cholera toxin was used as a tracer substance in the central nervous system after being injected into various brain regions, mainly somatosensory relay structures. The tracer was localized with an immunoperoxidase technique, using monoclonal antibodies raised in mouse hybridomas. This method, which is appl...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(88)90167-7

    authors: Ericson H,Blomqvist A

    更新日期:1988-07-01 00:00:00

  • Neurotransmitter receptor autoradiography in immunohistochemically identified neurons.

    abstract::A method for the simultaneous visualization of neurotransmitter receptor binding sites and immunohistochemically characterized cells is described using in vitro sections of rat striatum. The striatum provides a rich neurochemical environment in which to examine muscarinic acetylcholine receptor relations to peptide-re...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(85)90061-5

    authors: Ariano MA,Kenny SL

    更新日期:1985-10-01 00:00:00

  • Rabies virus-mediated connectivity tracing from single neurons.

    abstract::An understanding of how the brain processes information requires knowledge of its underlying wiring diagrams, as well as insights into the relationship between circuit architecture and physiological function. Notably, rabies virus based single-cell genetic manipulations that can facilitate an experimental link between...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章,评审

    doi:10.1016/j.jneumeth.2019.108365

    authors: Schwarz MK,Remy S

    更新日期:2019-09-01 00:00:00

  • Seizure states identification in experimental epilepsy using gabor atom analysis.

    abstract:BACKGROUND:Epileptic seizures evolve through several states, and in the process the brain signals may change dramatically. Signals from different states share similar features, making it difficult to distinguish them from a time series; the goal of this work is to build a classifier capable of identifying seizure state...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2014.12.001

    authors: Sotelo A,Guijarro ED,Trujillo L

    更新日期:2015-02-15 00:00:00

  • The multiscale entropy: Guidelines for use and interpretation in brain signal analysis.

    abstract:BACKGROUND:Multiscale entropy (MSE) estimates the predictability of a signal over multiple temporal scales. It has been recently applied to study brain signal variability, notably during aging. The grounds of its application and interpretation remain unclear and subject to debate. METHOD:We used both simulated and exp...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2016.09.004

    authors: Courtiol J,Perdikis D,Petkoski S,Müller V,Huys R,Sleimen-Malkoun R,Jirsa VK

    更新日期:2016-11-01 00:00:00

  • Unbiased and robust quantification of synchronization between spikes and local field potential.

    abstract:BACKGROUND:In neuroscience, relating the spiking activity of individual neurons to the local field potential (LFP) of neural ensembles is an increasingly useful approach for studying rhythmic neuronal synchronization. Many methods have been proposed to measure the strength of the association between spikes and rhythms ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2016.05.004

    authors: Li Z,Cui D,Li X

    更新日期:2016-08-30 00:00:00

  • A method to record changes in local neuronal discharge in response to infusion of small drug quantities in awake monkeys.

    abstract::A newly designed combination microelectrode-injection system is described which can be used to record electrophysiological responses of individual neurons in the primate brain to local administration of small quantities of drugs or other compounds. The assembly of the system is simple, and the materials used are inexp...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2004.03.015

    authors: Kliem MA,Wichmann T

    更新日期:2004-09-30 00:00:00

  • A computer program for sequencing and presenting complex sounds for auditory neuroimaging studies.

    abstract::This paper describes a computer program, named ASAP (audio sequencing and presentation), that runs on IBM PC compatible hardware with a Microsoft Windows operating system and has been specially designed for facilitating auditory neuroimaging studies. The program's main characteristics are: (1) the ability to generate ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(00)00249-1

    authors: Kieckhefer E,Kanwal JS

    更新日期:2000-08-15 00:00:00

  • Quantitation of multiple gene expression by in situ hybridization autoradiography: accurate normalization using Bayes classifier.

    abstract::In the method of in situ hybridization autoradiography, quantitative comparisons among multiple mRNA signals have proven difficult for many reasons, attributable both to technical factors (e.g. different probe specific activities) as well as to large differences in the patterns and levels of expression of different ge...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(99)00015-1

    authors: Zhao W,Truettner J,Schmidt-Kastner R,Belayev L,Ginsberg MD

    更新日期:1999-04-01 00:00:00

  • A double-labeled preparation for simultaneous measurement of [3H]-noradrenaline and [14C]-glutamic acid exocytosis from streptolysin-O (SLO)-perforated synaptosomes.

    abstract::We have developed a novel method to examine [3H]-noradrenaline and [14C]-glutamate release from the same sample of streptolysin-O (SLO) perforated rat cortical synaptosomes. Ca2+ -dependent [3H]-noradrenaline and [14C]-glutamate release was examined at different temperatures and was found to be greater at 30 degrees C...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(01)00350-8

    authors: McFadden SC,Bobich JA,Zheng Q

    更新日期:2001-05-30 00:00:00

  • Spike-train acquisition, analysis and real-time experimental control using a graphical programming language (LabView).

    abstract::A solution is described for the acquisition on a personal computer of standard pulses derived from neuronal discharge, measurement of neuronal discharge times, real-time control of stimulus delivery based on specified inter-pulse interval conditions in the neuronal spike train, and on-line display and analysis of the ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(95)00061-5

    authors: Nordstrom MA,Mapletoft EA,Miles TS

    更新日期:1995-11-01 00:00:00

  • Semantic-hierarchical model improves classification of spoken-word evoked electrocorticography.

    abstract::Classification of spoken word-evoked potentials is useful for both neuroscientific and clinical applications including brain-computer interfaces (BCIs). By evaluating whether adopting a biology-based structure improves a classifier's accuracy, we can investigate the importance of such structure in human brain circuitr...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2018.10.034

    authors: Na Y,Choi I,Jang DP,Kang JK,Woo J

    更新日期:2019-01-01 00:00:00

  • AutoSholl allows for automation of Sholl analysis independent of user tracing.

    abstract:BACKGROUND:Sholl analysis has been used to analyze neuronal morphometry and dendritic branching and complexity for many years. While the process has become semi-automated in recent years, existing software packages are still dependent on user tracing and hence are subject to observer bias, variability, and increased us...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2019.108529

    authors: Srinivasan A,Srinivasan A,Ferland RJ

    更新日期:2020-02-01 00:00:00

  • A new technique for measuring the temporal characteristics of the carbon fibre microelectrodes in in vivo voltammetry at millisecond time intervals.

    abstract::A common approach to test the time-response of carbon fibre microelectrodes entails the use of a flow injection system which allows delivery of a bolus of test compound in the flow stream to a detector electrode. The introduced bolus is distorted from its original form by convective and dispersive forces during the pe...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(98)00086-7

    authors: Yavich L

    更新日期:1998-10-01 00:00:00

  • Microscopic magnetic resonance elastography of traumatic brain injury model.

    abstract::Traumatic brain injury (TBI) is a major cause of death and disability for which there is no cure. One of the issues inhibiting clinical trial success is the lack of targeting specific patient populations due to inconsistencies between clinical diagnostic tools and underlying pathophysiology. The development of reliabl...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2011.08.019

    authors: Boulet T,Kelso ML,Othman SF

    更新日期:2011-10-15 00:00:00

  • A novel method for removal of deep brain stimulation artifact from electroencephalography.

    abstract:BACKGROUND:Deep brain stimulation (DBS) has treatment efficacy in neurological and psychiatric disorders such as Parkinson's disease and major depression. Electroencephalography (EEG) is a versatile neurophysiological tool that can be used to better understand DBS treatment mechanisms. DBS causes artifacts in EEG recor...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2014.09.002

    authors: Sun Y,Farzan F,Garcia Dominguez L,Barr MS,Giacobbe P,Lozano AM,Wong W,Daskalakis ZJ

    更新日期:2014-11-30 00:00:00

  • The grooming analysis algorithm discriminates between different levels of anxiety in rats: potential utility for neurobehavioural stress research.

    abstract::Stress has long been known to affect grooming in rodent species, altering both its activity measures and behavioural microstructure. Since stress disturbs a general pattern of self-grooming uninterrupted cephalocaudal progression, the grooming analysis algorithm (Kalueff and Tuohimaa, Brain Res. Protocols, 2004; 15: 1...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2004.10.001

    authors: Kalueff AV,Tuohimaa P

    更新日期:2005-04-30 00:00:00

  • Analysis of the growth cone turning assay for studying axon guidance.

    abstract::The "pipette" or "growth cone turning" assay is widely used for studying how axons respond to diffusible guidance cues in their environment. However, little quantitative analysis has been presented of the gradient shapes produced by this assay, or how they depend on parameters of the assay. Here we used confocal micro...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2008.01.014

    authors: Pujic Z,Giacomantonio CE,Unni D,Rosoff WJ,Goodhill GJ

    更新日期:2008-05-30 00:00:00

  • The use of c-fos as a metabolic marker in neuronal pathway tracing.

    abstract::The use of c-fos protein (Fos) immunocytochemistry as a metabolic marker for tracing neuroanatomical connections, seizure pathways and sites of action of neuroactive drugs is discussed in this report. Fos immunocytochemistry will be very useful for these purposes providing that a number of potential problems are recog...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章,评审

    doi:10.1016/0165-0270(89)90150-7

    authors: Dragunow M,Faull R

    更新日期:1989-09-01 00:00:00

  • An accurate method for the quantification of cytochrome C oxidase in tissue sections.

    abstract::Cytochrome oxidase (COX) is the enzyme that constitutes the last step of the mitochondrial electron transport chain for the production of ATP. Measurement of COX activity can be achieved by histochemistry, thus providing information about the metabolic status of the brain. Brain regions with high metabolism will prese...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2013.01.010

    authors: Melendez-Ferro M,Rice MW,Roberts RC,Perez-Costas E

    更新日期:2013-04-15 00:00:00

  • Geometric classification of brain network dynamics via conic derivative discriminants.

    abstract:BACKGROUND:Over the past decade, pattern decoding techniques have granted neuroscientists improved anatomical specificity in mapping neural representations associated with function and cognition. Dynamical patterns are of particular interest, as evidenced by the proliferation and success of frequency domain methods tha...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2018.06.019

    authors: Singh MF,Braver TS,Ching S

    更新日期:2018-10-01 00:00:00

  • Correction for the influence of background muscle activity on stretch reflex amplitudes.

    abstract::Background muscle activity (BGR) exerts a strong influence on stretch reflex amplitudes. While it is considered important to correct for this influence, which method best able to eliminate the effects of BGR remains unknown. We have therefore compared one previously described and one novel correction method which resp...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(93)90152-h

    authors: Bloem BR,van Dijk JG,Beckley DJ,Zwinderman AH,Remler MP,Roos RA

    更新日期:1993-02-01 00:00:00

  • A novel telemetry system for recording EEG in small animals.

    abstract::It has become increasingly evident that continuous EEG monitoring is necessary to observe the development of epilepsy in animals, and to determine the effect of drugs on spontaneous seizures. Telemetric recording systems have been increasingly used to monitor EEG in freely moving animals. One challenge faced by such s...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2011.07.018

    authors: Chang P,Hashemi KS,Walker MC

    更新日期:2011-09-30 00:00:00

  • Confocal microscopic estimation of GABAergic nerve terminals in the central nervous system.

    abstract::We describe a method for estimating the average proportion of GABAergic terminal area relative to total nerve terminal area with confocal microscopy. Nerve terminal regions were identified with dual colour immunofluorescence on Vibratome sections with an antibody to synaptophysin (SYN), and GABAergic processes, includ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(99)00163-6

    authors: Hiscock JJ,Murphy S,Willoughby JO

    更新日期:2000-01-31 00:00:00

  • A portable chamber for long-distance transport of surviving human brain slice preparations.

    abstract::Incubation chambers for surviving brain slice preparations are in most cases designed to be stationary. For investigations on human brain tissue resected for the treatment of brain tumor or epilepsy, portable incubation chambers are needed in addition to stationary ones to allow transport of the slices between laborat...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(96)00072-6

    authors: Köhling R,Lücke A,Straub H,Speckmann EJ

    更新日期:1996-08-01 00:00:00

  • A tungsten-in-glass iontophoresis assembly for studying input-output relationships in central neurons.

    abstract::A method is described for the production of an electrode capable of monitoring and modulating the input-output relationship of thalamic neurons. Tungsten-in-glass electrodes were manufactured with the ability to simultaneously record lateral geniculate nucleus action potentials and associated, retinally evoked S-poten...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(93)90126-c

    authors: Godwin DW

    更新日期:1993-09-01 00:00:00

  • Muscarinic receptor family interacting proteins: role in receptor function.

    abstract::G protein-coupled receptors constitute one of the most important families of membrane receptors through which cells respond to extracellular stimuli. Receptors of this superfamily likely function as signal transduction complexes. The identification and analysis of their components provide new insights into a better un...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2010.11.025

    authors: Borroto-Escuela DO,Correia PA,Romero-Fernandez W,Narvaez M,Fuxe K,Ciruela F,Garriga P

    更新日期:2011-02-15 00:00:00