Simultaneous paired intracellular and tetrode recordings for evaluating the performance of spike sorting algorithms

1999 ◽  
Vol 26-27 ◽  
pp. 1061-1068 ◽  
Author(s):  
M. Wehr ◽  
J.S. Pezaris ◽  
M. Sahani
2021 ◽  
Author(s):  
Helat A. Hussein ◽  
Subhi R. M. Zeebaree ◽  
Mohammed A. M. Sadeeq ◽  
Hanan M. Shukur ◽  
Ahmed Alkhayyat ◽  
...  

2012 ◽  
Vol 211 (1) ◽  
pp. 58-65 ◽  
Author(s):  
Carlos Pedreira ◽  
Juan Martinez ◽  
Matias J. Ison ◽  
Rodrigo Quian Quiroga

Neuroscience ◽  
2019 ◽  
Vol 414 ◽  
pp. 168-185 ◽  
Author(s):  
Jeyathevy Sukiban ◽  
Nicole Voges ◽  
Till A. Dembek ◽  
Robin Pauli ◽  
Veerle Visser-Vandewalle ◽  
...  

2018 ◽  
Vol 120 (4) ◽  
pp. 1859-1871 ◽  
Author(s):  
Fernando J. Chaure ◽  
Hernan G. Rey ◽  
Rodrigo Quian Quiroga

The most widely used spike-sorting algorithms are semiautomatic in practice, requiring manual tuning of the automatic solution to achieve good performance. In this work, we propose a new fully automatic spike-sorting algorithm that can capture multiple clusters of different sizes and densities. In addition, we introduce an improved feature selection method, by using a variable number of wavelet coefficients, based on the degree of non-Gaussianity of their distributions. We evaluated the performance of the proposed algorithm with real and simulated data. With real data from single-channel recordings, in ~95% of the cases the new algorithm replicated, in an unsupervised way, the solutions obtained by expert sorters, who manually optimized the solution of a previous semiautomatic algorithm. This was done while maintaining a low number of false positives. With simulated data from single-channel and tetrode recordings, the new algorithm was able to correctly detect many more neurons compared with previous implementations and also compared with recently introduced algorithms, while significantly reducing the number of false positives. In addition, the proposed algorithm showed good performance when tested with real tetrode recordings. NEW & NOTEWORTHY We propose a new fully automatic spike-sorting algorithm, including several steps that allow the selection of multiple clusters of different sizes and densities. Moreover, it defines the dimensionality of the feature space in an unsupervised way. We evaluated the performance of the algorithm with real and simulated data, from both single-channel and tetrode recordings. The proposed algorithm was able to outperform manual sorting from experts and other recent unsupervised algorithms.


2012 ◽  
Vol 203 (2) ◽  
pp. 369-376 ◽  
Author(s):  
Jiri Wild ◽  
Zoltan Prekopcsak ◽  
Tomas Sieger ◽  
Daniel Novak ◽  
Robert Jech

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Jeremy Magland ◽  
James J Jun ◽  
Elizabeth Lovero ◽  
Alexander J Morley ◽  
Cole Lincoln Hurwitz ◽  
...  

Spike sorting is a crucial step in electrophysiological studies of neuronal activity. While many spike sorting packages are available, there is little consensus about which are most accurate under different experimental conditions. SpikeForest is an open-source and reproducible software suite that benchmarks the performance of automated spike sorting algorithms across an extensive, curated database of ground-truth electrophysiological recordings, displaying results interactively on a continuously-updating website. With contributions from eleven laboratories, our database currently comprises 650 recordings (1.3 TB total size) with around 35,000 ground-truth units. These data include paired intracellular/extracellular recordings and state-of-the-art simulated recordings. Ten of the most popular spike sorting codes are wrapped in a Python package and evaluated on a compute cluster using an automated pipeline. SpikeForest documents community progress in automated spike sorting, and guides neuroscientists to an optimal choice of sorter and parameters for a wide range of probes and brain regions.


2019 ◽  
Author(s):  
Jasper Wouters ◽  
Fabian Kloosterman ◽  
Alexander Bertrand

AbstractSpike 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.


Sign in / Sign up

Export Citation Format

Share Document