Recent progress in multi-electrode spike sorting methods

Lefebvre, Baptiste; Yger, Pierre; Marre, Olivier

doi:10.1101/086991

Cited by 6 publications

(8 citation statements)

References 58 publications

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“…The proposed method with different strategies to estimate the number of neurons as shown in II-C2 is compared. Since the existing literatures [44], [45] have reported that the maximal number of neurons detected by extracellular electrodes is between 8 and 10, an initial range of the estimated number of neurons is set between 2 and 10 in this paper. The reduced dimension, m 0 , is assigned to 3 at the initialization stage in 5) 2( 4) 2( 5) 2(4) 2( 5) 4( 5) 2(4) our method.…”

Section: B Numerical Simulations On the Synthetic Datasetmentioning

confidence: 99%

A Unified Optimization Model of Feature Extraction and Clustering for Spike Sorting

Huang

Liu

Ling

2021

IEEE Trans. Neural Syst. Rehabil. Eng.

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Spike sorting technologies support neuroscientists to access the neural activity with single-neuron or single-actionpotential resolutions. However, conventional spike sorting technologies perform the feature extraction and the clustering separately after the spikes are well detected. It not only induces many redundant processes, but it also yields a lower accuracy and an unstable result especially when noises and/or overlapping spikes exist in the dataset. To address these issues, this paper proposes a unified optimization model integrating the feature extraction and the clustering for spike sorting. Unlike the widely used combination strategies, i.e., performing the principal component analysis (PCA) for spike feature extraction and the K-means (KM) for clustering in sequence, interestingly, this paper finds the solution of the proposed unified model by iteratively performing PCA and KM-like procedures. Subsequently, by embedding the K-means++ strategy in KM-like initializing and a comparison updating rule in the solving process, the proposed model can well handle the noises and overlapping interference as well as enjoy a high accuracy and a low computational complexity. Finally, an automatic spike sorting method is derived after taking the best of the clustering validity indices into the proposed model. The extensive numerical simulation results on both synthetic and realworld datasets confirm that our proposed method outperforms the related state-of-the-art approaches.

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Section: B Numerical Simulations On the Synthetic Datasetmentioning

confidence: 99%

A Unified Optimization Model of Feature Extraction and Clustering for Spike Sorting

Huang

Liu

Ling

2021

IEEE Trans. Neural Syst. Rehabil. Eng.

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“…In addition, large amplitude spikes could potentially overshadow low-amplitude ones. Recent development of a new spike sorting algorithm for multi-electrode arrays has partially resolved the issues associated with temporally overlapping spikes, on the condition that these spike waveforms are sufficiently different on the detection electrode (Lefebvre et al, 2016;Pachitariu et al, 2016).…”

Section: Limitationsmentioning

confidence: 99%

Electrophysiological monitoring of inhibition in mammalian species, from rodents to humans

Peyrache

Destexhe

2019

Neurobiology of Disease

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GABAergic interneurons constitute a highly diverse family of neurons that play a critical role in cortical functions. Due to their prominent role in cortical network dynamics, genetic, developmental, or other dysfunctions in GABAergic neurons have been linked to neurological disorders such as epilepsy. Thus it is crucial to investigate the interaction of these various neurons and to develop methods to specifically and directly monitor inhibitory activity in vivo. While research in small mammals has benefited from a wealth of recent technological development, bridging the gap to large mammals and humans remains a challenge. This is of particular interest since single neuron monitoring with intracranial electrodes in epileptic patients is developing quickly, opening new avenues for understanding the role of different cell types in epilepsy. Here we review currently available techniques that monitor inhibitory activity in the brain and the respective validations in rodents. Finally, we discuss the future developments of these techniques and how knowledge from animal research can be translated to the study of neuronal circuit dynamics in the human brain.

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“…These devices enable access to hundreds of neurons distributed across multiple brain regions, densely sampling the extracellular field; this means that each neuron is detected on multiple channels of a probe. This additional resolution in sampling is expected to aid analysis and is currently being used by novel algorithms [14][15][16][17] .…”

Section: Introduction Extracellular Recordingsmentioning

confidence: 99%

Recording from the same neuron with high-density CMOS probes and patch-clamp: a ground-truth dataset and an experiment in collaboration

Marques-Smith

Neto

Lopes³

et al. 2018

Preprint

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We built a rig to perform patch-clamp and extracellular recordings from the same neuron in vivo. In this setup, the axes of two micromanipulators are precisely aligned and their relative position tracked in real-time, allowing us to accurately target patch-clamp recordings to neurons near an extracellular probe. We used this setup to generate a publicly-available dataset where a cortical neuron's spiking activity is recorded in patch-clamp next to a dense CMOS Neuropixels probe. "Ground-truth" datasets of this kind are rare but valuable to the neuroscience community, as they power the development and improvement of spike-sorting and analysis algorithms, tethering them to empirical observations. In this article, we describe our approach and report exploratory and descriptive analysis on the resulting dataset. We study the detectability of patch-clamp spikes on the extracellular probe, within-unit reliability of spike features and spatiotemporal dynamics of the action potential waveform. We open discussion and collaboration on this dataset through an online repository, with a view to producing follow-up publications. PrologueOur efforts to record from the same neuron in vivo using patch-clamp and dense extracellular probes have resulted in three outputs: a publicly-available dataset (http://bit.ly/paired_recs), a manuscript, and a code repository (http://bit.ly/paired_git). Together, these three components form the publication arising from the experiments we have performed. The role of the dataset is to be downloaded and re-used. The role of the manuscript is to describe the experimental methods through which we acquired the dataset, explain it and showcase which types of questions it can be used to address. The repository has two roles: first, promoting reproducibility and error correction.By making our analysis and figure-generation code freely-available, we wish to make our analysis procedures clear and enable the reader to reproduce our results from the raw data, alerting us to any potential mistakes. Second, the repository will form a living, dynamic and interactive component of the publication: a forum for open collaboration on this dataset. Any interested scientists can contribute to it, joining us in detailed exploration of these recordings with a view to producing follow-up publications in which they will be credited for their input.Why did we opt to publish this way? The first reason is that the very nature of the project we here describe -recording the same neuron with patch-clamp and extracellular probes -invites an open science and open source approach. This is because the primary use of this type of "ground truth" validation data is to aid the development of new sorting and analysis algorithms, as well as to benchmark and improve existing ones. The second reason is that despite being conceptually very simple, this project generated a large and complex dataset that can be tackled in many ways and used to address different types of question. Some of these questions are beyond the reach of our analytical...

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Recent progress in multi-electrode spike sorting methods

Cited by 6 publications

References 58 publications

A Unified Optimization Model of Feature Extraction and Clustering for Spike Sorting

A Unified Optimization Model of Feature Extraction and Clustering for Spike Sorting

Electrophysiological monitoring of inhibition in mammalian species, from rodents to humans

Recording from the same neuron with high-density CMOS probes and patch-clamp: a ground-truth dataset and an experiment in collaboration

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