Spike sorting with hidden Markov models

Herbst, Joshua A.; Gammeter, Stephan; Ferrero, David M.; Hahnloser, Richard H. R.

doi:10.1016/j.jneumeth.2008.06.011

Cited by 42 publications

(43 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Quantification of these variations, especially when consecutive transmission events partially overlap in time, requires decomposing the transmission event into these three subcomponents. This task is unfortunately outside the scope of classical spike-sorting algorithms, where the waveforms are assumed to not overlap and remain constant in shape [an exception to the first assumption was presented by Herbst et al (2008), still requiring substantial computational resources]. Therefore, a dedicated fitting procedure was developed in MATLAB (MathWorks).…”

Section: Discussionmentioning

confidence: 99%

The Calyx of Held Develops Adult-Like Dynamics and Reliability by Hearing Onset in the MouseIn Vivo

Sonntag¹,

Englitz²,

Typlt³

et al. 2011

J. Neurosci.

View full text Add to dashboard Cite

The development of the auditory system has received increasing attention since the mechanisms of patterned, spontaneous activity in prehearing mammals were discovered. This early activity originates in the cochlea and is assumed to be of importance for the establishment and refinement of synaptic connections in the auditory system. In the present study we investigate synaptic transmission and its interplay with spontaneous discharges in the developing auditory system. We used the calyx of Held as a model system, where this question can be investigated in vivo over a broad range of ages [postnatal day 8 (P8)-P28]. To precisely quantify the timing and reliability of synaptic transmission, we developed a novel fitting approach which decomposes the extracellularly recorded signal into its presynaptic and postsynaptic components. In prehearing mice, we found signal transmission to be unreliable, with high variability in the transmission delay and in the amplitude of postsynaptic components. These timing and amplitude changes were strongly correlated with the preceding activity. Around hearing onset (P12-P14), the properties of signal transmission converged to the adult-like state which was characterized by high transmission reliability as well as high consistency in timing and amplitude. Although activity-dependent depression was still found in action potentials, EPSP depression no longer played a prominent role. In conclusion, the maturation of synaptic transmission at the calyx of Held seems to be precisely timed to achieve its adult potential by the time acoustically evoked signal processing commences.

show abstract

Section: Discussionmentioning

confidence: 99%

The Calyx of Held Develops Adult-Like Dynamics and Reliability by Hearing Onset in the MouseIn Vivo

Sonntag¹,

Englitz²,

Typlt³

et al. 2011

J. Neurosci.

View full text Add to dashboard Cite

show abstract

“…The clustering can be performed in a variety of feature spaces spanned by features such as peak or valley amplitude, principal components, or wavelet coefficients. In addition to these commercial or widely used tools, new algorithms for performing spike sorting continue to be developed [5][6][7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

“…Considered as a state-of-the-art spike sorting algorithm [11], Wave clus has been reported to be the second most highly cited spike sorting algorithm in the literature [21].…”

Section: Introductionmentioning

confidence: 99%

Taller Peaks: an improved spike detection algorithm that simultaneously reduces type I and type II errors for Wave{\_}clus

Okatan¹

2017

Turk J Elec Eng & Comp Sci

View full text Add to dashboard Cite

Abstract:Wave clus is an unsupervised spike detection and sorting algorithm that has been used in dozens of experimental studies as a spike sorting tool. It is often used as a benchmark for comparing the performance of new spike sorting algorithms. For these reasons, the spike detection performance of Wave clus is important for both experimental and computational studies that involve spike sorting. Two measures of spike detection performance are the number of false positive detections (type I error) and the number of missed spikes (type II error). Here, a new spike detection algorithm is proposed that reduces the number of misses and false positives of Wave clus in a widely used simulated data set across the entire range of commonly used detection thresholds. The algorithm accepts a spike if its amplitude is larger than the amplitude of its two immediate neighbors, where an immediate neighbor is the nearest peak of the same polarity within ± 1 refractory period. The simultaneous reduction that is achieved in the number of false positives and misses is important for experimental and computational studies that use Wave clus as a spike sorting tool or as a benchmark. A software patch that incorporates the algorithm into Wave clus as an optional spike detection algorithm is provided.

show abstract

“…This study aims for the online estimation of the discharge rate of each train, despite these interferences and despite unknown action potential shapes (although a rough initial shape is necessary). It uses some of the concepts proposed in [8] and [9], where the information carried by spike trains is encoded by action potentials waveforms and decoded offline using a Viterbi algorithm. Like [10] and [11], it tackles the online problem, but it also uses tools from reliability theory to handle the regularity of the trains.…”

Section: Introductionmentioning

confidence: 99%

Sequential Decoding of Intramuscular EMG Signals via Estimation of a Markov Model

Monsifrot

Carpentier

Aoustin

et al. 2014

IEEE Trans. Neural Syst. Rehabil. Eng.

View full text Add to dashboard Cite

Abstract-This paper addresses the sequential decoding of intramuscular single-channel EMG signals to extract the activity of individual motor neurons. A hidden Markov model is derived from the physiological generation of the EMG signal. The EMG signal is described as a sum of several action potentials (wavelet) trains, embedded in noise. For each train, the time interval between wavelets is modeled by a process that parameters are linked to the muscular activity. The parameters of this process are estimated sequentially by a Bayes filter, along with the firing instants. The method was tested on some simulated signals and an experimental one, from which the rates of detection and classification of action potentials were above 95% with respect to the reference decomposition. The method works sequentially in time, and is the first to address the problem of intramuscular EMG decomposition online. It has potential applications for manmachine interfacing based on motor neuron activities.

show abstract

Spike sorting with hidden Markov models

Cited by 42 publications

References 36 publications

The Calyx of Held Develops Adult-Like Dynamics and Reliability by Hearing Onset in the MouseIn Vivo

The Calyx of Held Develops Adult-Like Dynamics and Reliability by Hearing Onset in the MouseIn Vivo

Taller Peaks: an improved spike detection algorithm that simultaneously reduces type I and type II errors for Wave{\_}clus

Sequential Decoding of Intramuscular EMG Signals via Estimation of a Markov Model

Contact Info

Product

Resources

About