Literature DB >> 32617751

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

Jasper Wouters1, Fabian Kloosterman2,3,4, Alexander Bertrand5.   

Abstract

Spike sorting is the process of retrieving the spike times of individual neurons that are present in an extracellular neural recording. Over the last decades, many spike sorting algorithms have been published. In an effort to guide a user towards a specific spike sorting algorithm, given a specific recording setting (i.e., brain region and recording device), we provide an open-source graphical tool for the generation of hybrid ground-truth data in Python. Hybrid ground-truth data is a data-driven modelling paradigm in which spikes from a single unit are moved to a different location on the recording probe, thereby generating a virtual unit of which the spike times are known. The tool enables a user to efficiently generate hybrid ground-truth datasets and make informed decisions between spike sorting algorithms, fine-tune the algorithm parameters towards the used recording setting, or get a deeper understanding of those algorithms.

Keywords:  GUI; Hybrid ground truth; Spike sorting; Validation

Mesh:

Year:  2021        PMID: 32617751     DOI: 10.1007/s12021-020-09474-8

Source DB:  PubMed          Journal:  Neuroinformatics        ISSN: 1539-2791


  24 in total

1.  Superparamagnetic clustering of data.

Authors: 
Journal:  Phys Rev Lett       Date:  1996-04-29       Impact factor: 9.161

2.  ViSAPy: a Python tool for biophysics-based generation of virtual spiking activity for evaluation of spike-sorting algorithms.

Authors:  Espen Hagen; Torbjørn V Ness; Amir Khosrowshahi; Christina Sørensen; Marianne Fyhn; Torkel Hafting; Felix Franke; Gaute T Einevoll
Journal:  J Neurosci Methods       Date:  2015-02-04       Impact factor: 2.390

Review 3.  The NEURON simulation environment.

Authors:  M L Hines; N T Carnevale
Journal:  Neural Comput       Date:  1997-08-15       Impact factor: 2.026

4.  A detailed and fast model of extracellular recordings.

Authors:  Luis A Camuñas-Mesa; Rodrigo Quian Quiroga
Journal:  Neural Comput       Date:  2013-03-07       Impact factor: 2.026

5.  Simultaneously Excitatory and Inhibitory Effects of Transcranial Alternating Current Stimulation Revealed Using Selective Pulse-Train Stimulation in the Rat Motor Cortex.

Authors:  Ahmad Khatoun; Boateng Asamoah; Myles Mc Laughlin
Journal:  J Neurosci       Date:  2017-08-28       Impact factor: 6.167

6.  Fully integrated silicon probes for high-density recording of neural activity.

Authors:  James J Jun; Nicholas A Steinmetz; Joshua H Siegle; Daniel J Denman; Marius Bauza; Brian Barbarits; Albert K Lee; Costas A Anastassiou; Alexandru Andrei; Çağatay Aydın; Mladen Barbic; Timothy J Blanche; Vincent Bonin; João Couto; Barundeb Dutta; Sergey L Gratiy; Diego A Gutnisky; Michael Häusser; Bill Karsh; Peter Ledochowitsch; Carolina Mora Lopez; Catalin Mitelut; Silke Musa; Michael Okun; Marius Pachitariu; Jan Putzeys; P Dylan Rich; Cyrille Rossant; Wei-Lung Sun; Karel Svoboda; Matteo Carandini; Kenneth D Harris; Christof Koch; John O'Keefe; Timothy D Harris
Journal:  Nature       Date:  2017-11-08       Impact factor: 49.962

Review 7.  Continuing progress of spike sorting in the era of big data.

Authors:  David Carlson; Lawrence Carin
Journal:  Curr Opin Neurobiol       Date:  2019-03-08       Impact factor: 6.627

Review 8.  Towards reliable spike-train recordings from thousands of neurons with multielectrodes.

Authors:  Gaute T Einevoll; Felix Franke; Espen Hagen; Christophe Pouzat; Kenneth D Harris
Journal:  Curr Opin Neurobiol       Date:  2011-10-22       Impact factor: 6.627

9.  Bayes optimal template matching for spike sorting - combining fisher discriminant analysis with optimal filtering.

Authors:  Felix Franke; Rodrigo Quian Quiroga; Andreas Hierlemann; Klaus Obermayer
Journal:  J Comput Neurosci       Date:  2015-02-05       Impact factor: 1.621

10.  A Fully Automated Approach to Spike Sorting.

Authors:  Jason E Chung; Jeremy F Magland; Alex H Barnett; Vanessa M Tolosa; Angela C Tooker; Kye Y Lee; Kedar G Shah; Sarah H Felix; Loren M Frank; Leslie F Greengard
Journal:  Neuron       Date:  2017-09-13       Impact factor: 17.173

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  3 in total

Review 1.  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

2.  MEArec: A Fast and Customizable Testbench Simulator for Ground-truth Extracellular Spiking Activity.

Authors:  Alessio Paolo Buccino; Gaute Tomas Einevoll
Journal:  Neuroinformatics       Date:  2021-01

3.  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

  3 in total

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