Improving data quality in neuronal population recordings

Harris, Kenneth D.; Quiroga, Rodrigo Quian; Freeman, Jeremy; Smith, Spencer L.

doi:10.1038/nn.4365

Cited by 232 publications

(246 citation statements)

References 145 publications

(174 reference statements)

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“…Maintaining access to all clusters and their cluster quality metrics, including those that likely correspond to multiunit spiking, has a number of important advantages. First, thresholds could be established by examining how known properties of a given set of units (such as the number and size of hippocampal place fields) vary as a function of cluster quality (Harris et al, 2016). Second, simple changes in inclusion thresholds can be used for direct assessment of whether cluster quality influences a specific finding.…”

Section: Discussionmentioning

confidence: 99%

“…Data collected from these devices comprise multiple channels of continuously sampled extracellular voltages. A key step in making these data interpretable is spike sorting, the process of detecting spiking events and assigning those events to single units corresponding to putative individual neurons (Einevoll et al, 2012; Harris et al, 2016; Lewicki, 1998; Muller, 1996; Quiroga, 2012). …”

Section: Introductionmentioning

confidence: 99%

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A Fully Automated Approach to Spike Sorting

Chung

Magland

Barnett

et al. 2017

Neuron

410

396

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Summary Understanding the detailed dynamics of neuronal networks will require the simultaneous measurement of spike trains from hundreds of neurons (or more). Currently, approaches to extracting spike times and labels from raw data are time consuming, lack standardization and involve manual intervention, making it difficult to maintain data provenance and assess the quality of scientific results. Here, we describe an automated clustering approach and associated software package that addresses these problems and provides novel cluster quality metrics. We show that our approach has accuracy comparable to or exceeding that achieved using manual or semi-manual techniques with desktop CPU runtimes faster than acquisition time for up to hundreds of electrodes. Moreover, a single choice of parameters in the algorithm is effective for a variety of electrode geometries and across multiple brain regions. This algorithm has the potential to enable reproducible and automated spike sorting of larger scale recordings than is currently possible.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Fully Automated Approach to Spike Sorting

Chung

Magland

Barnett

et al. 2017

Neuron

410

396

View full text Add to dashboard Cite

show abstract

“…To understand how brain represents, transforms and communicates information requires simultaneously monitoring distributed neural activity at brain-wide scale with single neuron resolution [2]. Extracellular electrical recording probes can detect spikes from individual neurons within milliseconds, however, their contact site numbers are limited and only a few dozen neurons per probe can be recorded [3,4].…”

mentioning

confidence: 99%

“…However, too many transmission wires and large form factor hardware make it impractical to use in freely moving rodents [5]. Optical approaches such as Ca 2+ imaging cover multiple areas across spatial scales, but cannot identify the precise timing of spikes of neuronal activity due to their low temporal resolution [2]. Simultaneously monitoring neural activities across multiple brain regions at neuronal scale with high temporal resolution is still challenging.…”

mentioning

confidence: 99%

Towards high-density recording of brain-wide neural activity

Liang

2018

Sci. China Mater.

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“…Past studies have approached separately those studies [141][142][143][144]. Very few methods cover these three problems but, Pnevmatikakis et al [145] is such a method and has the advantages of dealing with big datasets by running computations in the cloud, giving clean results by discarding artefacts.…”

Section: Preliminary Resultsmentioning

confidence: 99%

Imaging, manipulation and optogenetics in zebrafish

Favre-bulle¹

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This thesis investigates the advantages and limits of using laser light for illumination and micromanipulation of the nervous system deep in-vivo in zebrafish. Further interest in the study neuronal pathways and functions in zebrafish led to employ laser micro-manipulation for the stimulation of the systems of interest and the development of optogenetics system and light sheet microscopy for analyses of the processes. First I present the investigation of the interaction of light and brain tissue as we aim to quantify light scattered in zebrafish brain tissue with depth. This is of great importance for optogenetics as it uses light to control (turn on or off) neurons and the unwanted/scattered light out of the aimed region could significantly affect results of experiments. The measurements and model developed to predict light propagation through brain tissue and how much a focussed beam broadens and alters with depth are presented in details. Results show that illumination of individual neurons is possible at depth in the zebrafish brain, despite scattering that results from shallower neural tissue. This means that the approach presented allows for optogenetics manipulation of single neurons to be performed without optical correction for scattering. Secondly, I construct an optogenetics system where we employ advanced optics and novel algorithm to deliver versatile two dimensional illumination that can be used at any depth in the fish. I present an example of a problem that I have solved, and resulting optogenetics results that were obtained, using this new technology. In chapter 5, I was responsible for the improvements implemented on the optogenetics system and the different tests to show its performances. Lucy Heap has performed multiple experiments on that system and I present one example she performed and the results she got.In chapter 7, I performed the manipulation of free otolith in water. I with Alex Stilgoe performed scanning experiments of otolith on an optical trapping system that Alex Stilgoe built.We both performed the analysis of the experimental results. Alex Stilgoe performed the force modelisation with Ray optics methods and we compared it with experimental results. Statement of parts of the thesis submitted to qualify for the award of another degreeNone. I have special thanks to Shu, Swaantje and Lucy for our philosophical discussions, the sharing of our experiences in the good and bad moments of our PhDs and their support.Finally I have some friends that I would like to thank for their great support without necessarily realising it: Mari-wenn, Estelle and Arnaud.8 ABSTRACT

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Improving data quality in neuronal population recordings

Cited by 232 publications

References 145 publications

A Fully Automated Approach to Spike Sorting

A Fully Automated Approach to Spike Sorting

Towards high-density recording of brain-wide neural activity

Imaging, manipulation and optogenetics in zebrafish

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