Literature DB >> 30856552

Continuing progress of spike sorting in the era of big data.

David Carlson1, Lawrence Carin2.   

Abstract

Engineering efforts are currently attempting to build devices capable of collecting neural activity from one million neurons in the brain. Part of this effort focuses on developing dense multiple-electrode arrays, which require post-processing via 'spike sorting' to extract neural spike trains from the raw signal. Gathering information at this scale will facilitate fascinating science, but these dreams are only realizable if the spike sorting procedure and data pipeline are computationally scalable, at or superior to hand processing, and scientifically reproducible. These challenges are all being amplified as the data scale continues to increase. In this review, recent efforts to attack these challenges are discussed, which have primarily focused on increasing accuracy and reliability while being computationally scalable. These goals are addressed by adding additional stages to the data processing pipeline and using divide-and-conquer algorithmic approaches. These recent developments should prove useful to most research groups regardless of data scale, not just for cutting-edge devices.
Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.

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Year:  2019        PMID: 30856552      PMCID: PMC7702194          DOI: 10.1016/j.conb.2019.02.007

Source DB:  PubMed          Journal:  Curr Opin Neurobiol        ISSN: 0959-4388            Impact factor:   6.627


  45 in total

Review 1.  A review of methods for spike sorting: the detection and classification of neural action potentials.

Authors:  M S Lewicki
Journal:  Network       Date:  1998-11       Impact factor: 1.273

Review 2.  Recent progress in multi-electrode spike sorting methods.

Authors:  Baptiste Lefebvre; Pierre Yger; Olivier Marre
Journal:  J Physiol Paris       Date:  2017-03-02

3.  Realistic simulation of extracellular recordings.

Authors:  Juan Martinez; Carlos Pedreira; Matias J Ison; Rodrigo Quian Quiroga
Journal:  J Neurosci Methods       Date:  2009-08-22       Impact factor: 2.390

4.  A Sordid Affair: Spike Sorting and Data Reproducibility.

Authors:  Heidi Y Febinger; Alan D Dorval; John D Rolston
Journal:  Neurosurgery       Date:  2018-03-01       Impact factor: 4.654

5.  A unified framework and method for automatic neural spike identification.

Authors:  Chaitanya Ekanadham; Daniel Tranchina; Eero P Simoncelli
Journal:  J Neurosci Methods       Date:  2013-10-30       Impact factor: 2.390

6.  Nanofabricated Neural Probes for Dense 3-D Recordings of Brain Activity.

Authors:  Gustavo Rios; Evgueniy V Lubenov; Derrick Chi; Michael L Roukes; Athanassios G Siapas
Journal:  Nano Lett       Date:  2016-10-21       Impact factor: 11.189

Review 7.  Challenges and opportunities for large-scale electrophysiology with Neuropixels probes.

Authors:  Nicholas A Steinmetz; Christof Koch; Kenneth D Harris; Matteo Carandini
Journal:  Curr Opin Neurobiol       Date:  2018-02-13       Impact factor: 6.627

8.  A model-based spike sorting algorithm for removing correlation artifacts in multi-neuron recordings.

Authors:  Jonathan W Pillow; Jonathon Shlens; E J Chichilnisky; Eero P Simoncelli
Journal:  PLoS One       Date:  2013-05-03       Impact factor: 3.240

9.  Sorting Overlapping Spike Waveforms from Electrode and Tetrode Recordings.

Authors:  Yasamin Mokri; Rodrigo F Salazar; Baldwin Goodell; Jonathan Baker; Charles M Gray; Shih-Cheng Yen
Journal:  Front Neuroinform       Date:  2017-08-17       Impact factor: 4.081

10.  A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo.

Authors:  Pierre Yger; Giulia Lb Spampinato; Elric Esposito; Baptiste Lefebvre; Stéphane Deny; Christophe Gardella; Marcel Stimberg; Florian Jetter; Guenther Zeck; Serge Picaud; Jens Duebel; Olivier Marre
Journal:  Elife       Date:  2018-03-20       Impact factor: 8.140

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  6 in total

1.  SHYBRID: A Graphical Tool for Generating Hybrid Ground-Truth Spiking Data for Evaluating Spike Sorting Performance.

Authors:  Jasper Wouters; Fabian Kloosterman; Alexander Bertrand
Journal:  Neuroinformatics       Date:  2021-01

2.  Evaluation and resolution of many challenges of neural spike sorting: a new sorter.

Authors:  Nathan J Hall; David J Herzfeld; Stephen G Lisberger
Journal:  J Neurophysiol       Date:  2021-11-17       Impact factor: 2.714

Review 3.  From End to End: Gaining, Sorting, and Employing High-Density Neural Single Unit Recordings.

Authors:  Réka Barbara Bod; János Rokai; Domokos Meszéna; Richárd Fiáth; István Ulbert; Gergely Márton
Journal:  Front Neuroinform       Date:  2022-06-13       Impact factor: 3.739

4.  SpikeForest, reproducible web-facing ground-truth validation of automated neural spike sorters.

Authors:  Jeremy Magland; James J Jun; Elizabeth Lovero; Alexander J Morley; Cole Lincoln Hurwitz; Alessio Paolo Buccino; Samuel Garcia; Alex H Barnett
Journal:  Elife       Date:  2020-05-19       Impact factor: 8.140

Review 5.  Functional Characterization of Human Pluripotent Stem Cell-Derived Models of the Brain with Microelectrode Arrays.

Authors:  Anssi Pelkonen; Cristiana Pistono; Pamela Klecki; Mireia Gómez-Budia; Antonios Dougalis; Henna Konttinen; Iveta Stanová; Ilkka Fagerlund; Ville Leinonen; Paula Korhonen; Tarja Malm
Journal:  Cells       Date:  2021-12-29       Impact factor: 6.600

6.  SpikeInterface, a unified framework for spike sorting.

Authors:  Alessio P Buccino; Cole L Hurwitz; Samuel Garcia; Jeremy Magland; Joshua H Siegle; Roger Hurwitz; Matthias H Hennig
Journal:  Elife       Date:  2020-11-10       Impact factor: 8.140

  6 in total

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