SpikeDeeptector: a deep-learning based method for detection of neural spiking activity

AECuration: automated event curation for spike sorting

Objective. This paper discusses a novel method for automating the curation of neural spike events detected from neural recordings using spike sorting methods. Spike sorting seeks to identify isolated neural events from extracellular recordings. This is critical for interpretation of electrophysiology recordings in neuroscience studies. Spike sorting analysis is vulnerable to errors because of non-neural events, such as experimental artifacts or electrical interference. To improve the specificity of spike sorting results, a manual postprocessing curation is typically used to examine the detected events and identify neural spikes based on their specific features. However, this manual curation process is subjective, prone to human errors and not scalable, especially for large datasets.Approach. To address these challenges, we introduce AECuration, a novel automatic curation method based on an autoencoder model trained on features of simulated extracellular spike waveforms. Using reconstruction error as a performance metric, our method classifies neural and non-neural events in experimental electrophysiology datasets.Main results. This paper demonstrates that AECuration can classify neural events with 97.46% accuracy on synthetic datasets. Moreover, our method can improve the sensitivity of different spike sorting pipelines on datasets with ground-truth recordings by up to 20%. The ratio of clustered units with low interspike interval violation rates is improved from 55.3% to 85.5% as demonstrated using our in-house experimental dataset.Significance. AEcuration is a time-domain evaluation method that automates the analysis of extracellular recordings based on learned time-domain features. Once trained on a synthetic dataset, this method can be applied to real extracellular datasets without the need for re-training. This highlights the generalizability of AECuration. It can be readily integrated with existing spike sorting pipelines as a preprocessing filtering or a postprocessing curation step to improve the overall accuracy and efficiency.

Deep learning-based spike sorting: a survey

Objective.Deep learning is increasingly permeating neuroscience, leading to a rise in signal-processing applications for extracellular recordings. These signals capture the activity of small neuronal populations, necessitating 'spike sorting' to assign action potentials (spikes) to their underlying neurons. With the rise in publications delving into new methodologies and techniques for deep learning-based spike sorting, it is crucial to synthesise these findings critically. This survey provides an in-depth evaluation of the approaches, methodologies and outcomes presented in recent articles, shedding light on the current state-of-the-art.Approach.Twenty-four articles published until December 2023 on deep learning-based spike sorting have been examined. The proposed methods are divided into three sub-problems of spike sorting: spike detection, feature extraction and classification. Moreover, integrated systems, i.e. models that detect spikes and extract features or do classification within a single network, are included.Main results.Although most algorithms have been developed for single-channel recordings, models utilising multi-channel data have already shown promising results, with efficient hardware implementations running quantised models on application-specific integrated circuits and field programmable gate arrays. Convolutional neural networks have been used extensively for spike detection and classification as the data can be processed spatiotemporally while maintaining low-parameter models and increasing generalisation and efficiency. Autoencoders have been mainly utilised for dimensionality reduction, enabling subsequent clustering with standard methods. Also, integrated systems have shown great potential in solving the spike sorting problem from end to end.Significance.This survey explores recent articles on deep learning-based spike sorting and highlights the capabilities of deep neural networks in overcoming associated challenges, but also highlights potential biases of certain models. Serving as a resource for both newcomers and seasoned researchers in the field, this work provides insights into the latest advancements and may inspire future model development.

Technical survey of end-to-end signal processing in BCIs using invasive MEAs

Modern brain-computer interfaces and neural implants allow interaction between the tissue, the user and the environment, where people suffer from neurodegenerative diseases or injuries.This interaction can be achieved by using penetrating/invasive microelectrodes for extracellular recordings and stimulation, such as Utah or Michigan arrays. The application-specific signal processing of the extracellular recording enables the detection of interactions and enables user interaction. For example, it allows to read out movement intentions from recordings of brain signals for controlling a prosthesis or an exoskeleton. To enable this, computationally complex algorithms are used in research that cannot be executed on-chip or on embedded systems. Therefore, an optimization of the end-to-end processing pipeline, from the signal condition on the electrode array over the analog pre-processing to spike-sorting and finally the neural decoding process, is necessary for hardware inference in order to enable a local signal processing in real-time and to enable a compact system for achieving a high comfort level. This paper presents a survey of system architectures and algorithms for end-to-end signal processing pipelines of neural activity on the hardware of such neural devices, including (i) on-chip signal pre-processing, (ii) spike-sorting on-chip or on embedded hardware and (iii) neural decoding on workstations. A particular focus for the hardware implementation is on low-power electronic design and artifact-robust algorithms with low computational effort and very short latency. For this, current challenges and possible solutions with support of novel machine learning techniques are presented in brief. In addition, we describe our future vision for next-generation BCIs.

Bridging Minds and Machines: The Recent Advances of Brain-Computer Interfaces in Neurological and Neurosurgical Applications

Brain-computer interfaces (BCIs), a remarkable technological advancement in neurology and neurosurgery, mark a significant leap since the inception of electroencephalography in 1924. These interfaces effectively convert central nervous system signals into commands for external devices, offering revolutionary benefits to patients with severe communication and motor impairments due to a myriad of neurological conditions like stroke, spinal cord injuries, and neurodegenerative disorders. BCIs enable these individuals to communicate and interact with their environment, using their brain signals to operate interfaces for communication and environmental control. This technology is especially crucial for those completely locked in, providing a communication lifeline where other methods fall short. The advantages of BCIs are profound, offering autonomy and an improved quality of life for patients with severe disabilities. They allow for direct interaction with various devices and prostheses, bypassing damaged or nonfunctional neural pathways. However, challenges persist, including the complexity of accurately interpreting brain signals, the need for individual calibration, and ensuring reliable, long-term use. Additionally, ethical considerations arise regarding autonomy, consent, and the potential for dependence on technology. Despite these challenges, BCIs represent a transformative development in neurotechnology, promising enhanced patient outcomes and a deeper understanding of brain-machine interfaces.

A fully automatic multichannel neural spike sorting algorithm with spike reduction and positional feature

Objective: The sorting of neural spike data recorded by multichannel and high channel neural probes such as Neuropixels, especially in real-time, remains a significant technical challenge. Most neural spike sorting algorithms focus on sorting neural spikes post-hoc for high sorting accuracy-but reducing the processing delay for fast sorting, potentially even live sorting, is generally not possible with these algorithms.Approach: Here we report our Graph nEtwork Multichannel sorting (GEMsort) algorithm, which is largely based on graph network, to allow rapid neural spike sorting for multiple neural recording channels. This was accomplished by two innovations: In GEMsort, duplicated neural spikes recorded from multiple channels were eliminated from duplicate channels by only selecting the highest amplitude neural spike in any channel for subsequent processing. In addition, the channel from which the representative neural spike was recorded was used as an additional feature to differentiate between neural spikes recorded from different neurons having similar temporal features.Main results: Synthetic and experimentally recorded multichannel neural recordings were used to evaluate the sorting performance of GEMsort. The sorting results of GEMsort were also compared with two other state-of-the-art sorting algorithms (Kilosort and Mountainsort) in sorting time and sorting agreements.Significance: GEMsort allows rapidly sort neural spikes and is highly suitable to be implemented with digital circuitry for high processing speed and channel scalability.

Deep-Learning-Based Automated Anomaly Detection of EEGs in Intensive Care Units

An intensive care unit (ICU) is a special ward in the hospital for patients who require intensive care. It is equipped with many instruments monitoring patients' vital signs and supported by the medical staff. However, continuous monitoring demands a massive workload of medical care. To ease the burden, we aim to develop an automatic detection model to monitor when brain anomalies occur. In this study, we focus on electroencephalography (EEG), which monitors the brain electroactivity of patients continuously. It is mainly for the diagnosis of brain malfunction. We propose the gated-recurrent-unit-based (GRU-based) model for detecting brain anomalies; it predicts whether the spike or sharp wave happens within a short time window. Based on the banana montage setting, the proposed model exploits characteristics of multiple channels simultaneously to detect anomalies. It is trained, validated, and tested on separated EEG data and achieves more than 90% testing performance on sensitivity, specificity, and balanced accuracy. The proposed anomaly detection model detects the existence of a spike or sharp wave precisely; it will notify the ICU medical staff, who can provide immediate follow-up treatment. Consequently, it can reduce the medical workload in the ICU significantly.

Cellular nucleus image-based smarter microscope system for single cell analysis

Cell imaging technology is undoubtedly a powerful tool for studying single-cell heterogeneity due to its non-invasive and visual advantages. It covers microscope hardware, software, and image analysis techniques, which are hindered by low throughput owing to abundant hands-on time and expertise. Herein, a cellular nucleus image-based smarter microscope system for single-cell analysis is reported to achieve high-throughput analysis and high-content detection of cells. By combining the hardware of an automatic fluorescence microscope and multi-object recognition/acquisition software, we have achieved more advanced process automation with the assistance of Robotic Process Automation (RPA), which realizes a high-throughput collection of single-cell images. Automated acquisition of single-cell images has benefits beyond ease and throughout and can lead to uniform standard and higher quality images. We further constructed a single-cell image database-based convolutional neural network (Efficient Convolutional Neural Network, E-CNN) exceeding 20618 single-cell nucleus images. Computational analysis of large and complex data sets enhances the content and efficiency of single-cell analysis with the assistance of Artificial Intelligence (AI), which breaks through the super-resolution microscope's hardware limitation, such as specialized light sources with specific wavelengths, advanced optical components, and high-performance graphics cards. Our system can identify single-cell nucleus images that cannot be artificially distinguished with an accuracy of 95.3%. Overall, we build an ordinary microscope into a high-throughput analysis and high-content smarter microscope system, making it a candidate tool for Imaging cytology.

ConTraNet: A hybrid network for improving the classification of EEG and EMG signals with limited training data

OBJECTIVE

Bio-Signals such as electroencephalography (EEG) and electromyography (EMG) are widely used for the rehabilitation of physically disabled people and for the characterization of cognitive impairments. Successful decoding of these bio-signals is however non-trivial because of the time-varying and non-stationary characteristics. Furthermore, existence of short- and long-range dependencies in these time-series signal makes the decoding even more challenging. State-of-the-art studies proposed Convolutional Neural Networks (CNNs) based architectures for the classification of these bio-signals, which are proven useful to learn spatial representations. However, CNNs because of the fixed size convolutional kernels and shared weights pay only uniform attention and are also suboptimal in learning short-long term dependencies, simultaneously, which could be pivotal in decoding EEG and EMG signals. Therefore, it is important to address these limitations of CNNs. To learn short- and long-range dependencies simultaneously and to pay more attention to more relevant part of the input signal, Transformer neural network-based architectures can play a significant role. Nonetheless, it requires a large corpus of training data. However, EEG and EMG decoding studies produce limited amount of the data. Therefore, using standalone transformers neural networks produce ordinary results. In this study, we ask a question whether we can fix the limitations of CNN and transformer neural networks and provide a robust and generalized model that can simultaneously learn spatial patterns, long-short term dependencies, pay variable amount of attention to time-varying non-stationary input signal with limited training data.

APPROACH

In this work, we introduce a novel single hybrid model called ConTraNet, which is based on CNN and Transformer architectures that contains the strengths of both CNN and Transformer neural networks. ConTraNet uses a CNN block to introduce inductive bias in the model and learn local dependencies, whereas the Transformer block uses the self-attention mechanism to learn the short- and long-range or global dependencies in the signal and learn to pay different attention to different parts of the signals.

MAIN RESULTS

We evaluated and compared the ConTraNet with state-of-the-art methods on four publicly available datasets (BCI Competition IV dataset 2b, Physionet MI-EEG dataset, Mendeley sEMG dataset, Mendeley sEMG V1 dataset) which belong to EEG-HMI and EMG-HMI paradigms. ConTraNet outperformed its counterparts in all the different category tasks (2-class, 3-class, 4-class, 7-class, and 10-class decoding tasks).

SIGNIFICANCE

With limited training data ConTraNet significantly improves classification performance on four publicly available datasets for 2, 3, 4, 7, and 10-classes compared to its counterparts.

Graph neural networks in EEG spike detection

OBJECTIVE

This study develops new machine learning architectures that are more adept at detecting interictal epileptiform discharges (IEDs) in scalp EEG. A comparison of results using the average precision (AP) metric is made with the proposed models on two datasets obtained from Baptist Hospital of Miami and Temple University Hospital.

METHODS

Applying graph neural networks (GNNs) on functional connectivity (FC) maps of different frequency sub-bands to yield a novel architecture we call FC-GNN. Attention mechanism is applied on a complete graph to let the neural network select its important edges, hence bypassing the extraction of features, a model we refer to as CA-GNN.

RESULTS

On the Baptist Hospital dataset, the results were as follows: Vanilla Self-Attention →0.9029±0.0431, Hierarchical Attention →0.8546±0.0587, Vanilla Visual Geometry Group (VGG) →0.92±0.0618, Satelight →0.9219±0.046, FC-GNN →0.9731±0.0187, and CA-GNN →0.9788±0.0125. In the same order, the results on the Temple University Hospital dataset are 0.9692, 0.9113, 0.97, 0.9575, 0.963, and 0.9879.

CONCLUSION

Based on the good results they yield, GNNs prove to have a strong potential in detecting epileptogenic activity.

SIGNIFICANCE

This study opens the door for the discovery of the powerful role played by GNNs in capturing IEDs, which is an essential step for identifying the epileptogenic networks of the affected brain and hence improving the prospects for more accurate 3D source localization.

DualSort: online spike sorting with a running neural network

Objective.Spike sorting, i.e. the detection and separation of measured action potentials from different extracellularly recorded neurons, remains one of the bottlenecks in deciphering the brain. In recent years, the application of neural networks (NNs) for spike sorting has garnered significant attention. Most methods focus on specific sub-problems within the conventional spike sorting pipeline, such as spike detection or feature extraction, and attempt to solve them with complex network architectures. This paper presents DualSort, a simple NN that gets combined with downstream post-processing for real-time spike sorting. It shows high efficiency, low complexity, and requires a comparatively small amount of human interaction.Approach.Synthetic and experimentally obtained extracellular single-channel recordings were utilized to train and evaluate the proposed NN. For training, spike waveforms were labeled with respect to their associated neuron and position in the signal, allowing the detection and categorization of spikes in unison. DualSort classifies a single spike multiple times in succession, as it runs over the signal in a step-by-step manner and uses a post-processing algorithm that transmits the network output into spike trains. Main results.With the used datasets, DualSort was able to detect and distinguish different spike waveforms and separate them from background activity. The post-processing algorithm significantly strengthened the overall performance of the model, making the system more robust as a whole. Although DualSort is an end-to-end solution that efficiently transforms filtered signals into spike trains, it competes with contemporary state-of-the-art technologies that exclusively target single sub-problems in the conventional spike sorting pipeline.Significance.This work demonstrates that even under high noise levels, complex NNs are not necessary by any means to achieve high performance in spike detection and sorting. The utilization of data augmentation on a limited quantity of spikes could substantially decrease hand-labeling compared to other studies. Furthermore, the proposed framework can be utilized without human interaction when combined with an unsupervised technique that provides pseudo labels for DualSort. Due to the low complexity of our network, it works efficiently and enables real-time processing on basic hardware. The proposed approach is not limited to spike sorting, as it may also be used to process different signals, such as electroencephalogram (EEG), which needs to be investigated in future research.

The Application of Deep Learning to Electroencephalograms, Magnetic Resonance Imaging, and Implants for the Detection of Epileptic Seizures: A Narrative Review

Epilepsy is a neurological disorder characterized by recurrent seizures affecting millions worldwide. Medically intractable seizures in epilepsy patients are not only detrimental to the quality of life but also pose a significant threat to their safety. Outcomes of epilepsy therapy can be improved by early detection and intervention during the interictal window period. Electroencephalography is the primary diagnostic tool for epilepsy, but accurate interpretation of seizure activity is challenging and highly time-consuming. Machine learning (ML) and deep learning (DL) algorithms enable us to analyze complex EEG data, which can not only help us diagnose but also locate epileptogenic zones and predict medical and surgical treatment outcomes. DL models such as convolutional neural networks (CNNs), inspired by visual processing, can be used to classify EEG activity. By applying preprocessing techniques, signal quality can be enhanced by denoising and artifact removal. DL can also be incorporated into the analysis of magnetic resonance imaging (MRI) data, which can help in the localization of epileptogenic zones in the brain. Proper detection of these zones can help in good neurosurgical outcomes. Recent advancements in DL have facilitated the implementation of these systems in neural implants and wearable devices, allowing for real-time seizure detection. This has the potential to transform the management of drug-refractory epilepsy. This review explores the application of ML and DL techniques to Electroencephalograms (EEGs), MRI, and wearable devices for epileptic seizure detection. This review briefly explains the fundamentals of both artificial intelligence (AI) and DL, highlighting these systems' potential advantages and undeniable limitations.

A deep learning network based on CNN and sliding window LSTM for spike sorting

Spike sorting plays an essential role to obtain electrophysiological activity of single neuron in the fields of neural signal decoding. With the development of electrode array, large numbers of spikes are recorded simultaneously, which rises the need for accurate automatic and generalization algorithms. Hence, this paper proposes a spike sorting model with convolutional neural network (CNN) and a spike classification model with combination of CNN and Long-Short Term Memory (LSTM). The recall rate of our detector could reach 94.40% in low noise level dataset. Although the recall declined with the increasing noise level, our model still presented higher feasibility and better robustness than other models. In addition, the results of our classification model presented an accuracy of greater than 99% in simulated data and an average accuracy of about 95% in experimental data, suggesting our classifier outperforms the current "WMsorting" and other deep learning models. Moreover, the performance of our whole algorithm was evaluated through simulated data and the results shows that the accuracy of spike sorting reached about 97%. It is noteworthy to say that, this proposed algorithm could be used to achieve accurate and robust automated spike detection and spike classification.

Edge computing on TPU for brain implant signal analysis

The ever-increasing number of recording sites of silicon-based probes imposes a great challenge for detecting and evaluating single-unit activities in an accurate and efficient manner. Currently separate solutions are available for high precision offline evaluation and separate solutions for embedded systems where computational resources are more limited. We propose a deep learning-based spike sorting system, that utilizes both unsupervised and supervised paradigms to learn a general feature embedding space and detect neural activity in raw data as well as predict the feature vectors for sorting. The unsupervised component uses contrastive learning to extract features from individual waveforms, while the supervised component is based on the MobileNetV2 architecture. One of the key advantages of our system is that it can be trained on multiple, diverse datasets simultaneously, resulting in greater generalizability than previous deep learning-based models. We demonstrate that the proposed model does not only reaches the accuracy of current state-of-art offline spike sorting methods but has the unique potential to run on edge Tensor Processing Units (TPUs), specialized chips designed for artificial intelligence and edge computing. We compare our model performance with state of art solutions on paired datasets as well as on hybrid recordings as well. The herein demonstrated system paves the way to the integration of deep learning-based spike sorting algorithms into wearable electronic devices, which will be a crucial element of high-end brain-computer interfaces.

From End to End: Gaining, Sorting, and Employing High-Density Neural Single Unit Recordings

The meaning behind neural single unit activity has constantly been a challenge, so it will persist in the foreseeable future. As one of the most sourced strategies, detecting neural activity in high-resolution neural sensor recordings and then attributing them to their corresponding source neurons correctly, namely the process of spike sorting, has been prevailing so far. Support from ever-improving recording techniques and sophisticated algorithms for extracting worthwhile information and abundance in clustering procedures turned spike sorting into an indispensable tool in electrophysiological analysis. This review attempts to illustrate that in all stages of spike sorting algorithms, the past 5 years innovations' brought about concepts, results, and questions worth sharing with even the non-expert user community. By thoroughly inspecting latest innovations in the field of neural sensors, recording procedures, and various spike sorting strategies, a skeletonization of relevant knowledge lays here, with an initiative to get one step closer to the original objective: deciphering and building in the sense of neural transcript.

Fast parametric curve matching (FPCM) for automatic spike detection

Epilepsy is a widely spread neurological disease, whose treatment often requires resection of the pathological cortical tissue. Interictal spike analysis observed in the non-invasively collected EEG or MEG data offers a way to localize epileptogenic cortical structures for surgery planning purposes. While a plethora of automatic spike detection techniques have been developed each with its own assumptions and limitations, non of them is ideal and the best results are achieved when the output of several automatic spike detectors are combined. This is especially true in the low signal-to-noise ratio conditions. To this end we propose a novel biomimetic approach for automatic spike detection based on a constrained mixed spline machinery that we dub as fast parametric curve matching (FPCM). Using the peak-wave shape parametrization, the constrained parametric morphological model is constructed and convolved with the observed multichannel data to very efficiently determine mixed spline parameters corresponding to each time-point in the dataset. Then the logical predicates that directly map to the expected interictal event morphology allow us to accomplish the spike detection task. The results of simulations mimicking typical low SNR scenario show the robustness and high ROC AUC values of the FPCM method as compared to the spike detection performed by the means of more conventional approaches such as wavelet decomposition, template matching or simple amplitude thresholding. Applied to the real MEG and EEG data from the human patients and to ECoG data from the rat, the FPCM technique demonstrates reliable detection of the interictal events and localization of epileptogenic zones concordant with independent conclusions made by the epileptologist. Since the FPCM is computationally light, tolerant to high amplitude artifacts and flexible to accommodate verbalized descriptions of the arbitrary target morphology, it may complement the existing arsenal of means for analysis of noisy interictal datasets.

Enhancing the decoding accuracy of EEG signals by the introduction of anchored-STFT and adversarial data augmentation method

Brain-computer interfaces (BCIs) enable communication between humans and machines by translating brain activity into control commands. Electroencephalography (EEG) signals are one of the most used brain signals in non-invasive BCI applications but are often contaminated with noise. Therefore, it is possible that meaningful patterns for classifying EEG signals are deeply hidden. State-of-the-art deep-learning algorithms are successful in learning hidden, meaningful patterns. However, the quality and the quantity of the presented inputs are pivotal. Here, we propose a feature extraction method called anchored Short Time Fourier Transform (anchored-STFT), which is an advanced version of STFT, as it minimizes the trade-off between temporal and spectral resolution presented by STFT. In addition, we propose a data augmentation method derived from l2-norm fast gradient sign method (FGSM), called gradient norm adversarial augmentation (GNAA). GNAA is not only an augmentation method but is also used to harness adversarial inputs in EEG data, which not only improves the classification accuracy but also enhances the robustness of the classifier. In addition, we also propose a CNN architecture, namely Skip-Net, for the classification of EEG signals. The proposed pipeline outperforms the current state-of-the-art methods and yields classification accuracies of 90.7% on BCI competition II dataset III and 89.5%, 81.8%, 76.0% and 85.4%, 69.1%, 80.9% on different data distributions of BCI Competition IV dataset 2b and 2a, respectively.

The impact of reducing signal acquisition specifications on neuronal spike sorting

Measuring electrical potentials in the extracellular space of the brain is a popular technique because it can detect action potentials from putative individual neurons. Electrophysiology is undergoing a transformation where the number of recording channels, and thus number of neurons detected, is growing at a dramatic rate. This rapid scaling is paving the way for both new discoveries and commercial applications; however, as the number of channels increases there will be an increasing need to make these systems more power efficient. One area ripe for optimization are the signal acquisition specifications needed to detect and sort action potentials (i.e., "spikes") to putative single neuron sources. In this work, we take existing recordings collected using Intan hardware and modify them in a way that corresponds to reduced recording performance. The accuracy of these degraded recordings to spike sort using MountainSort4 is evaluated by comparing against expert labels. We show that despite reducing signal specifications by a factor of 2 or more, spike sorting accuracy does not change substantially. Specifically, reducing both sample rate and bit depth from 30 kHz and 16 bits to 12 kHz and 12 bits resulted in a 3% drop in spike sorting accuracy. Our results suggest that current neural acquisition systems are over-specified. These results may inform the design of next generation neural acquisition systems enabling higher channel count systems.

Using multielectrode arrays to investigate neurodegenerative effects of the amyloid-beta peptide

BACKGROUND

Multielectrode arrays are widely used to analyze the effects of potentially toxic compounds, as well as to evaluate neuroprotective agents upon the activity of neural networks in short- and long-term cultures. Multielectrode arrays provide a way of non-destructive analysis of spontaneous and evoked neuronal activity, allowing to model neurodegenerative diseases in vitro. Here, we provide an overview on how these devices are currently used in research on the amyloid-β peptide and its role in Alzheimer's disease, the most common neurodegenerative disorder.

MAIN BODY

Most of the studies analysed here indicate fast responses of neuronal cultures towards aggregated forms of amyloid-β, leading to increases of spike frequency and impairments of long-term potentiation. This in turn suggests that this peptide might play a crucial role in causing the typical neuronal dysfunction observed in patients with Alzheimer's disease.

CONCLUSIONS

Although the number of studies using multielectrode arrays to examine the effect of the amyloid-β peptide onto neural cultures or whole compartments is currently limited, they still show how this technique can be used to not only investigate the interneuronal communication in neural networks, but also making it possible to examine the effects onto synaptic currents. This makes multielectrode arrays a powerful tool in future research on neurodegenerative diseases.

Inferring entire spiking activity from local field potentials

Extracellular recordings are typically analysed by separating them into two distinct signals: local field potentials (LFPs) and spikes. Previous studies have shown that spikes, in the form of single-unit activity (SUA) or multiunit activity (MUA), can be inferred solely from LFPs with moderately good accuracy. SUA and MUA are typically extracted via threshold-based technique which may not be reliable when the recordings exhibit a low signal-to-noise ratio (SNR). Another type of spiking activity, referred to as entire spiking activity (ESA), can be extracted by a threshold-less, fast, and automated technique and has led to better performance in several tasks. However, its relationship with the LFPs has not been investigated. In this study, we aim to address this issue by inferring ESA from LFPs intracortically recorded from the motor cortex area of three monkeys performing different tasks. Results from long-term recording sessions and across subjects revealed that ESA can be inferred from LFPs with good accuracy. On average, the inference performance of ESA was consistently and significantly higher than those of SUA and MUA. In addition, local motor potential (LMP) was found to be the most predictive feature. The overall results indicate that LFPs contain substantial information about spiking activity, particularly ESA. This could be useful for understanding LFP-spike relationship and for the development of LFP-based BMIs.

BECT Spike Detection Based on Novel EEG Sequence Features and LSTM Algorithms

The benign epilepsy with spinous waves in the central temporal region (BECT) is the one of the most common epileptic syndromes in children, that seriously threaten the nervous system development of children. The most obvious feature of BECT is the existence of a large number of electroencephalogram (EEG) spikes in the Rolandic area during the interictal period, that is an important basis to assist neurologists in BECT diagnosis. With this regard, the paper proposes a novel BECT spike detection algorithm based on time domain EEG sequence features and the long short-term memory (LSTM) neural network. Three time domain sequence features, that can obviously characterize the spikes of BECT, are extracted for EEG representation. The synthetic minority oversampling technique (SMOTE) is applied to address the spike imbalance issue in EEGs, and the bi-directional LSTM (BiLSTM) is trained for spike detection. The algorithm is evaluated using the EEG data of 15 BECT patients recorded from the Children's Hospital, Zhejiang University School of Medicine (CHZU). The experiment shows that the proposed algorithm can obtained an average of 88.54% F1 score, 92.04% sensitivity, and 85.75% precision, that generally outperforms several state-of-the-art spike detection methods.

Duplicate Detection of Spike Events: A Relevant Problem in Human Single-Unit Recordings

Single-unit recordings in the brain of behaving human subjects provide a unique opportunity to advance our understanding of neural mechanisms of cognition. These recordings are exclusively performed in medical centers during diagnostic or therapeutic procedures. The presence of medical instruments along with other aspects of the hospital environment limit the control of electrical noise compared to animal laboratory environments. Here, we highlight the problem of an increased occurrence of simultaneous spike events on different recording channels in human single-unit recordings. Most of these simultaneous events were detected in clusters previously labeled as artifacts and showed similar waveforms. These events may result from common external noise sources or from different micro-electrodes recording activity from the same neuron. To address the problem of duplicate recorded events, we introduce an open-source algorithm to identify these artificial spike events based on their synchronicity and waveform similarity. Applying our method to a comprehensive dataset of human single-unit recordings, we demonstrate that our algorithm can substantially increase the data quality of these recordings. Given our findings, we argue that future studies of single-unit activity recorded under noisy conditions should employ algorithms of this kind to improve data quality.

An Accurate and Robust Method for Spike Sorting Based on Convolutional Neural Networks

In the fields of neuroscience and biomedical signal processing, spike sorting is a crucial step to extract the information of single neurons from extracellular recordings. In this paper, we propose a novel deep learning approach based on one-dimensional convolutional neural networks (1D-CNNs) to implement accurate and robust spike sorting. The results of the simulated data demonstrated that the clustering accuracy in most datasets was greater than 99%, despite the multiple levels of noise and various degrees of overlapped spikes. Moreover, the proposed method performed significantly better than the state-of-the-art method named “WMsorting” and a deep-learning-based multilayer perceptron (MLP) model. In addition, the experimental data recorded from the primary visual cortex of a macaque monkey were used to evaluate the proposed method in a practical application. It was shown that the method could successfully isolate most spikes of different neurons (ranging from two to five) by training the 1D-CNN model with a small number of manually labeled spikes. Considering the above, the deep learning method proposed in this paper is of great advantage for spike sorting with high accuracy and strong robustness. It lays the foundation for application in more challenging works, such as distinguishing overlapped spikes and the simultaneous sorting of multichannel recordings.

A neural network for online spike classification that improves decoding accuracy

Separating neural signals from noise can improve brain-computer interface performance and stability. However, most algorithms for separating neural action potentials from noise are not suitable for use in real time and have shown mixed effects on decoding performance. With the goal of removing noise that impedes online decoding, we sought to automate the intuition of human spike-sorters to operate in real time with an easily tunable parameter governing the stringency with which spike waveforms are classified. We trained an artificial neural network with one hidden layer on neural waveforms that were hand-labeled as either spikes or noise. The network output was a likelihood metric for each waveform it classified, and we tuned the network's stringency by varying the minimum likelihood value for a waveform to be considered a spike. Using the network's labels to exclude noise waveforms, we decoded remembered target location during a memory-guided saccade task from electrode arrays implanted in prefrontal cortex of rhesus macaque monkeys. The network classified waveforms in real time, and its classifications were qualitatively similar to those of a human spike-sorter. Compared with decoding with threshold crossings, in most sessions we improved decoding performance by removing waveforms with low spike likelihood values. Furthermore, decoding with our network's classifications became more beneficial as time since array implantation increased. Our classifier serves as a feasible preprocessing step, with little risk of harm, that could be applied to both off-line neural data analyses and online decoding.NEW & NOTEWORTHY Although there are many spike-sorting methods that isolate well-defined single units, these methods typically involve human intervention and have inconsistent effects on decoding. We used human classified neural waveforms as training data to create an artificial neural network that could be tuned to separate spikes from noise that impaired decoding. We found that this network operated in real time and was suitable for both off-line data processing and online decoding.

Deep Learning-Based Template Matching Spike Classification for Extracellular Recordings

We propose a deep learning-based spike sorting method for extracellular recordings. For analysis of extracellular single unit activity, the process of detecting and classifying action potentials called “spike sorting” has become essential. This is achieved through distinguishing the morphological differences of the spikes from each neuron, which arises from the differences of the surrounding environment and characteristics of the neurons. However, cases of high structural similarity and noise make the task difficult. And for manual spike sorting, it requires professional knowledge along with extensive time cost and suffers from human bias. We propose a deep learning-based spike sorting method on extracellular recordings from a single electrode that is efficient, robust to noise, and accurate. In circumstances where labelled data does not exist, we created pseudo-labels through principal component analysis and K-means clustering to be used for multi-layer perceptron training and built high performing spike classification model. When tested, our model outperformed conventional methods by 2.1% on simulation data of various noise levels, by 6.0% on simulation data of various clusters count, and by 1.7% on in-vivo data. As a result, we showed that the deep learning-based classification can classify spikes from extracellular recordings, even showing high classification accuracy on spikes that are difficult even for manual classification.