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An automatic spike sorting algorithm based on adaptive spike detection and a mixture of skew-t distributions.

ABSTRACT: Developing high-density electrodes for recording large ensembles of neurons provides a unique opportunity for understanding the mechanism of the neuronal circuits. Nevertheless, the change of brain tissue around chronically implanted neural electrodes usually causes spike wave-shape distortion and raises the crucial issue of spike sorting with an unstable structure. The automatic spike sorting algorithms have been developed to extract spikes from these big extracellular data. However, due to the spike wave-shape instability, there have been a lack of robust spike detection procedures and clustering to overcome the spike loss problem. Here, we develop an automatic spike sorting algorithm based on adaptive spike detection and a mixture of skew-t distributions to address these distortions and instabilities. The adaptive detection procedure applies to the detected spikes, consists of multi-point alignment and statistical filtering for removing mistakenly detected spikes. The detected spikes are clustered based on the mixture of skew-t distributions to deal with non-symmetrical clusters and spike loss problems. The proposed algorithm improves the performance of the spike sorting in both terms of precision and recall, over a broad range of signal-to-noise ratios. Furthermore, the proposed algorithm has been validated on different datasets and demonstrates a general solution to precise spike sorting, in vitro and in vivo.

SUBMITTER: Toosi R

PROVIDER: S-EPMC8260722 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:High-density microelectrode arrays can be used to record extracellular action potentials from hundreds to thousands of neurons simultaneously. Efficient spike sorters must be developed to cope with such large data volumes. Most existing spike sorting methods for single electrodes or small multielectrodes, however, suffer from the "curse of dimensionality" and cannot be directly applied to recordings with hundreds of electrodes. This holds particularly true for the standard reference spike sorting algorithm, principal component analysis-based feature extraction, followed by k-means or expectation maximization clustering, against which most spike sorters are evaluated. We present a spike sorting algorithm that circumvents the dimensionality problem by sorting local groups of electrodes independently with classical spike sorting approaches. It is scalable to any number of recording electrodes and well suited for parallel computing. The combination of data prewhitening before the principal component analysis-based extraction and a parameter-free clustering algorithm obviated the need for parameter adjustments. We evaluated its performance using surrogate data in which we systematically varied spike amplitudes and spike rates and that were generated by inserting template spikes into the voltage traces of real recordings. In a direct comparison, our algorithm could compete with existing state-of-the-art spike sorters in terms of sensitivity and precision, while parameter adjustment or manual cluster curation was not required. NEW & NOTEWORTHY We present an automatic spike sorting algorithm that combines three strategies to scale classical spike sorting techniques for high-density microelectrode arrays: 1) splitting the recording electrodes into small groups and sorting them independently; 2) clustering a subset of spikes and classifying the rest to limit computation time; and 3) prewhitening the spike waveforms to enable the use of parameter-free clustering. Finally, we combined these strategies into an automatic spike sorter that is competitive with state-of-the-art spike sorters.

Project description:BACKGROUND: Understanding how neurons contribute to perception, motor functions and cognition requires the reliable detection of spiking activity of individual neurons during a number of different experimental conditions. An important problem in computational neuroscience is thus to develop algorithms to automatically detect and sort the spiking activity of individual neurons from extracellular recordings. While many algorithms for spike sorting exist, the problem of accurate and fast online sorting still remains a challenging issue. RESULTS: Here we present a novel software tool, called FSPS (Fuzzy SPike Sorting), which is designed to optimize: (i) fast and accurate detection, (ii) offline sorting and (iii) online classification of neuronal spikes with very limited or null human intervention. The method is based on a combination of Singular Value Decomposition for fast and highly accurate pre-processing of spike shapes, unsupervised Fuzzy C-mean, high-resolution alignment of extracted spike waveforms, optimal selection of the number of features to retain, automatic identification the number of clusters, and quantitative quality assessment of resulting clusters independent on their size. After being trained on a short testing data stream, the method can reliably perform supervised online classification and monitoring of single neuron activity. The generalized procedure has been implemented in our FSPS spike sorting software (available free for non-commercial academic applications at the address: http://www.spikesorting.com) using LabVIEW (National Instruments, USA). We evaluated the performance of our algorithm both on benchmark simulated datasets with different levels of background noise and on real extracellular recordings from premotor cortex of Macaque monkeys. The results of these tests showed an excellent accuracy in discriminating low-amplitude and overlapping spikes under strong background noise. The performance of our method is competitive with respect to other robust spike sorting algorithms. CONCLUSIONS: This new software provides neuroscience laboratories with a new tool for fast and robust online classification of single neuron activity. This feature could become crucial in situations when online spike detection from multiple electrodes is paramount, such as in human clinical recordings or in brain-computer interfaces.

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An automatic spike sorting algorithm based on adaptive spike detection and a mixture of skew-t distributions.

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