Unsupervised spike detection and sorting with wavelets and superparamagnetic clustering

This study introduces a new method for detecting and sorting spikes from multiunit recordings. The method combines the wavelet transform, which localizes distinctive spike features, with superparamagnetic clustering, which allows automatic classification of the data without assumptions such as low variance or gaussian distributions. Moreover, an improved method for setting amplitude thresholds for spike detection is proposed. We describe several criteria for implementation that render the algorithm unsupervised and fast. The algorithm is compared to other conventional methods using several simulated data sets whose characteristics closely resemble those of in vivo recordings. For these data sets, we found that the proposed algorithm outperformed conventional methods

A scalable 32 channel neural recording and real-time FPGA based spike sorting system

This demo presents a scalable a 32-channel neural recording platform with real-time, on-node spike sorting ca- pability. The hardware consists of: an Intan RHD2132 neural amplifier; a low power Igloo ® nano FPGA; and an FX3 USB 3.0 controller. Graphical User Interfaces for controlling the system, displaying real-time data, and template generation with a modified form of WaveClus are demonstrated

Analyzing and clustering neural data

This thesis aims to analyze neural data in an overall effort by the Charles Stark Draper Laboratory to determine an underlying pattern in brain activity in healthy individuals versus patients with a brain degenerative disorder. The neural data comes from ECoG (electrocorticography) applied to either humans or primates. Each ECoG array has electrodes that measure voltage variations which neuroscientists claim correlates to neurons transmitting signals to one another. ECoG differs from the less invasive technique of EEG (electroencephalography) in that EEG electrodes are placed above a patients scalp while ECoG involves drilling small holes in the skull to allow electrodes to be closer to the brain. Because of this ECoG boasts an exceptionally high signal-to-noise ratio and less susceptibility to artifacts than EEG [6]. While wearing the ECoG caps, the patients are asked to perform a range of different tasks. The tasks performed by patients are partitioned into different levels of mental stress i.e. how much concentration is presumably required. The specific dataset used in this thesis is derived from cognitive behavior experiments performed on primates at MGH (Massachusetts General Hospital). The content of this thesis can be thought of as a pipelined process. First the data is collected from the ECoG electrodes, then the data is pre-processed via signal processing techniques and finally the data is clustered via unsupervised learning techniques. For both the pre-processing and the clustering steps, different techniques are applied and then compared against one another. The focus of this thesis is to evaluate clustering techniques when applied to neural data. For the pre-processing step, two types of bandpass filters, a Butterworth Filter and a Chebyshev Filter were applied. For the clustering step three techniques were applied to the data, K-means Clustering, Spectral Clustering and Self-Tuning Spectral Clustering. We conclude that for pre-processing the results from both filters are very similar and thus either filter is sufficient. For clustering we conclude that K- means has the lowest amount of overlap between clusters. K-means is also the most time-efficient of the three techniques and is thus the ideal choice for this application.2016-10-27T00:00:00

Spike Clustering and Neuron Tracking over Successive Time Windows

This paper introduces a new methodology for tracking signals from individual neurons over time in multiunit extracellular recordings. The core of our strategy relies upon an extension of a traditional mixture model approach, with parameter optimization via expectation-maximimization (EM), to incorporate clustering results from the preceding time period in a Bayesian manner. EM initialization is also achieved by utilizing these prior clustering results. After clustering, we match the current and prior clusters to track persisting neurons. Applications of this spike sorting method to recordings from macaque parietal cortex show that it provides significantly more consistent clustering and tracking results

Feature Analysis for Discrimination of Motor Unit Action Potentials

© 2018 IEEE. In electrophysiological signal processing for intramuscular electromyography data (nEMG), single motor unit activity is of great interest. The changes of action potential (MUAP) morphology, motor unit (MU) activation, and recruitment provide the most informative part to study the nature causality in neuromuscular disorders. In practice, for a single nEMG recording, more than one motor unit activities (in the surrounding area of a needle electrode) are usually collected. Such a fact makes the MUAP discrimination that separates single unit activities a crucial task. Most neurology laboratories worldwide still recruit specialists who spend hours to manually or semi-automatically sort MUAPs. From a machine learning perspective, this task is analogous to the clustering-based classification problem in which the number of classes and other class information are unfortunately missing. In this paper, we present a feature analysis strategy to help better utilize unsupervised (i.e., totally automated) methods for MUAP discrimination. To that end, we extract a large pool of features from each MUAP. Then we select the top ranked candidates using clusterability scores as selection criteria. We found spectrograms of wavelet decomposition as a top-ranking feature, highly correlated to the motor unit reference and was more separable than existing features. Using a correlation-based clustering technique, we demonstrate the sorting performance with this feature set. Compared with the reference produced by human experts, our method obtained a comparable result (e.g., equivalent number of classes was found, identical MUAP morphology in each pair of corresponding MU class, and similar histograms of MUs). Taking the manual labels as references, our method got a much higher sensitivity and accuracy than the compared unsupervised sorting method. We obtained a similar result in MUAP classification to the reference

Mechanisms of Feedback in the Visual System

Feedback is an ubiquitous feature of neural systems though there is little consensus on the roles of mechanisms involved with feedback. We set up an in vivo preparation to study and characterize an accessible and isolated feedback loop within the visual system of the leopard frog, Rana pipiens. We recorded extracellularly within the nucleus isthmi, a nucleus providing direct topographic feedback to the optic tectum, a nucleus that receives the vast majority of retinal output. The optic tectum and nucleus isthmi of the amphibian are homologous structures to the superior colliculus and parabigeminal nucleus in mammals, respectively. We formulated a novel threshold for detecting neuronal spikes within a low signal-to-noise environment, as exists in the nucleus isthmi due to its high density of small neuronal cell bodies. Combining this threshold with a recently developed spike sorting procedure enabled us to extract simultaneous recordings from up to 7 neurons at a time from a single extracellular electrode. We then stimulated the frog using computer driven dynamic spatiotemporal visual stimuli to characterize the responses of the nucleus isthmi neurons. We found that the responses display surprisingly long time courses to simple visual stimuli. Furthermore, we found that when stimulated with complex contextual stimuli the response of the nucleus isthmi is quite counter-intuitive. When a stimulus is presented outside of the classical receptive field along with a stimulus within the receptive field, the response is actually higher than the response to just a stimulus within the classical receptive field. Finally, we compared the responses of all of the simultaneously recorded neurons and, together with data from in vitro experiments within the nucleus isthmi, conclude that the nucleus isthmi of the frog is composed of just one electrophysiological population of cells

Efficient Approximation of Action Potentials with High-Order Shape Preservation in Unsupervised Spike Sorting

This paper presents a novel approximation unit added to the conventional spike processing chain which provides an appreciable reduction of complexity of the high-hardware cost feature extractors. The use of the Taylor polynomial is proposed and modelled employing its cascaded derivatives to non-uniformly capture the essential samples in each spike for reliable feature extraction and sorting. Inclusion of the approximation unit can provide 3X compression (i.e. from 66 to 22 samples) to the spike waveforms while preserving their shapes. Detailed spike waveform sequences based on in-vivo measurements have been generated using a customized neural simulator for performance assessment of the approximation unit tested on six published feature extractors. For noise levels σN between 0.05 and 0.3 and groups of 3 spikes in each channel, all the feature extractors provide almost same sorting performance before and after approximation. The overall implementation cost when including the approximation unit and feature extraction shows a large reduction (i.e. up to 8.7X) in the hardware costly and more accurate feature extractors, offering a substantial improvement in feature extraction design