ElecFeX is a user-friendly toolbox for efficient feature extraction from single-cell electrophysiological recordings.

Characterizing neurons by their electrophysiological phenotypes is essential for understanding the neural basis of behavioral and cognitive functions. Technological developments have enabled the collection of hundreds of neural recordings; this calls for new tools capable of performing feature extraction efficiently. To address the urgent need for a powerful and accessible tool, we developed ElecFeX, an open-source MATLAB-based toolbox that (1) has an intuitive graphical user interface, (2) provides customizable measurements for a wide range of electrophysiological features, (3) processes large-size datasets effortlessly via batch analysis, and (4) yields formatted output for further analysis. We implemented ElecFeX on a diverse set of neural recordings; demonstrated its functionality, versatility, and efficiency in capturing electrical features; and established its significance in distinguishing neuronal subgroups across brain regions and species. ElecFeX is thus presented as a user-friendly toolbox to benefit the neuroscience community by minimizing the time required for extracting features from their electrophysiological datasets.

MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures.

Microelectrode array (MEA) recordings are commonly used to compare firing and burst rates in neuronal cultures. MEA recordings can also reveal microscale functional connectivity, topology, and network dynamics-patterns seen in brain networks across spatial scales. Network topology is frequently characterized in neuroimaging with graph theoretical metrics. However, few computational tools exist for analyzing microscale functional brain networks from MEA recordings. Here, we present a MATLAB MEA network analysis pipeline (MEA-NAP) for raw voltage time-series acquired from single- or multi-well MEAs. Applications to 3D human cerebral organoids or 2D human-derived or murine cultures reveal differences in network development, including topology, node cartography, and dimensionality. MEA-NAP incorporates multi-unit template-based spike detection, probabilistic thresholding for determining significant functional connections, and normalization techniques for comparing networks. MEA-NAP can identify network-level effects of pharmacologic perturbation and/or disease-causing mutations and, thus, can provide a translational platform for revealing mechanistic insights and screening new therapeutic approaches.

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.

CropQuant-Air: an AI-powered system to enable phenotypic analysis of yield- and performance-related traits using wheat canopy imagery collected by low-cost drones.

As one of the most consumed stable foods around the world, wheat plays a crucial role in ensuring global food security. The ability to quantify key yield components under complex field conditions can help breeders and researchers assess wheat's yield performance effectively. Nevertheless, it is still challenging to conduct large-scale phenotyping to analyse canopy-level wheat spikes and relevant performance traits, in the field and in an automated manner. Here, we present CropQuant-Air, an AI-powered software system that combines state-of-the-art deep learning (DL) models and image processing algorithms to enable the detection of wheat spikes and phenotypic analysis using wheat canopy images acquired by low-cost drones. The system includes the YOLACT-Plot model for plot segmentation, an optimised YOLOv7 model for quantifying the spike number per m2 (SNpM2) trait, and performance-related trait analysis using spectral and texture features at the canopy level. Besides using our labelled dataset for model training, we also employed the Global Wheat Head Detection dataset to incorporate varietal features into the DL models, facilitating us to perform reliable yield-based analysis from hundreds of varieties selected from main wheat production regions in China. Finally, we employed the SNpM2 and performance traits to develop a yield classification model using the Extreme Gradient Boosting (XGBoost) ensemble and obtained significant positive correlations between the computational analysis results and manual scoring, indicating the reliability of CropQuant-Air. To ensure that our work could reach wider researchers, we created a graphical user interface for CropQuant-Air, so that non-expert users could readily use our work. We believe that our work represents valuable advances in yield-based field phenotyping and phenotypic analysis, providing useful and reliable toolkits to enable breeders, researchers, growers, and farmers to assess crop-yield performance in a cost-effective approach.

Improving multi-scale detection layers in the deep learning network for wheat spike detection based on interpretive analysis.

BACKGROUND: Detecting and counting wheat spikes is essential for predicting and measuring wheat yield. However, current wheat spike detection researches often directly apply the new network structure. There are few studies that can combine the prior knowledge of wheat spike size characteristics to design a suitable wheat spike detection model. It remains unclear whether the complex detection layers of the network play their intended role. RESULTS: This study proposes an interpretive analysis method for quantitatively evaluating the role of three-scale detection layers in a deep learning-based wheat spike detection model. The attention scores in each detection layer of the YOLOv5 network are calculated using the Gradient-weighted Class Activation Mapping (Grad-CAM) algorithm, which compares the prior labeled wheat spike bounding boxes with the attention areas of the network. By refining the multi-scale detection layers using the attention scores, a better wheat spike detection network is obtained. The experiments on the Global Wheat Head Detection (GWHD) dataset show that the large-scale detection layer performs poorly, while the medium-scale detection layer performs best among the three-scale detection layers. Consequently, the large-scale detection layer is removed, a micro-scale detection layer is added, and the feature extraction ability in the medium-scale detection layer is enhanced. The refined model increases the detection accuracy and reduces the network complexity by decreasing the network parameters. CONCLUSION: The proposed interpretive analysis method to evaluate the contribution of different detection layers in the wheat spike detection network and provide a correct network improvement scheme. The findings of this study will offer a useful reference for future applications of deep network refinement in this field.

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.

Firing-rate-modulated spike detection and neural decoding co-design.

Objective. Translational efforts on spike-signal-based implantable brain-machine interfaces (BMIs) are increasingly aiming to minimise bandwidth while maintaining decoding performance. Developing these BMIs requires advances in neuroscience and electronic technology, as well as using low-complexity spike detection algorithms and high-performance machine learning models. While some state-of-the-art BMI systems jointly design spike detection algorithms and machine learning models, it remains unclear how the detection performance affects decoding.Approach. We propose the co-design of the neural decoder with an ultra-low complexity spike detection algorithm. The detection algorithm is designed to attain a target firing rate, which the decoder uses to modulate the input features preserving statistical invariance in long term (over several months).Main results. We demonstrate a multiplication-free fixed-point spike detection algorithm with an average detection accuracy of 97% across different noise levels on a synthetic dataset and the lowest hardware complexity among studies we have seen. By co-designing the system to incorporate statistically invariant features, we observe significantly improved long-term stability, with decoding accuracy degrading by less than 10% after 80 days of operation. Our analysis also reveals a nonlinear relationship between spike detection and decoding performance. Increasing the detection sensitivity improves decoding accuracy and long-term stability, which means the activity of more neurons is beneficial despite the detection of more noise. Reducing the spike detection sensitivity still provides acceptable decoding accuracy whilst reducing the bandwidth by at least 30%.Significance. Our findings regarding the relationship between spike detection and decoding performance can provide guidance on setting the threshold for spike detection rather than relying on training or trial-and-error. The trade-off between data bandwidth and decoding performance can be effectively managed using appropriate spike detection settings. We demonstrate improved decoding performance by maintaining statistical invariance of input features. We believe this approach can motivate further research focused on improving decoding performance through the manipulation of data itself (based on a hypothesis) rather than using more complex decoding models.

An improved BECT spike detection method with functional brain network features based on PLV.

Background: Children with benign childhood epilepsy with centro-temporal spikes (BECT) have spikes, sharps, and composite waves on their electroencephalogram (EEG). It is necessary to detect spikes to diagnose BECT clinically. The template matching method can identify spikes effectively. However, due to the individual specificity, finding representative templates to detect spikes in actual applications is often challenging. Purpose: This paper proposes a spike detection method using functional brain networks based on phase locking value (FBN-PLV) and deep learning. Methods: To obtain high detection effect, this method uses a specific template matching method and the 'peak-to-peak' phenomenon of montages to obtain a set of candidate spikes. With the set of candidate spikes, functional brain networks (FBN) are constructed based on phase locking value (PLV) to extract the features of the network structure during spike discharge with phase synchronization. Finally, the time domain features of the candidate spikes and the structural features of the FBN-PLV are input into the artificial neural network (ANN) to identify the spikes. Results: Based on FBN-PLV and ANN, the EEG data sets of four BECT cases from the Children's Hospital, Zhejiang University School of Medicine are tested with the AC of 97.6%, SE of 98.3%, and SP 96.8%.

A wheat spike detection method based on Transformer.

Wheat spike detection has important research significance for production estimation and crop field management. With the development of deep learning-based algorithms, researchers tend to solve the detection task by convolutional neural networks (CNNs). However, traditional CNNs equip with the inductive bias of locality and scale-invariance, which makes it hard to extract global and long-range dependency. In this paper, we propose a Transformer-based network named Multi-Window Swin Transformer (MW-Swin Transformer). Technically, MW-Swin Transformer introduces the ability of feature pyramid network to extract multi-scale features and inherits the characteristic of Swin Transformer that performs self-attention mechanism by window strategy. Moreover, bounding box regression is a crucial step in detection. We propose a Wheat Intersection over Union loss by incorporating the Euclidean distance, area overlapping, and aspect ratio, thereby leading to better detection accuracy. We merge the proposed network and regression loss into a popular detection architecture, fully convolutional one-stage object detection, and name the unified model WheatFormer. Finally, we construct a wheat spike detection dataset (WSD-2022) to evaluate the performance of the proposed methods. The experimental results show that the proposed network outperforms those state-of-the-art algorithms with 0.459 mAP (mean average precision) and 0.918 AP50. It has been proved that our Transformer-based method is effective to handle wheat spike detection under complex field conditions.

Satelight: self-attention-based model for epileptic spike detection from multi-electrode EEG.

Objective.Because of the lack of highly skilled experts, automated technologies that support electroencephalogram (EEG)-based in epilepsy diagnosis are advancing. Deep convolutional neural network-based models have been used successfully for detecting epileptic spikes, one of the biomarkers, from EEG. However, a sizeable number of supervised EEG records are required for training.Approach.This study introduces the Satelight model, which uses the self-attention (SA) mechanism. The model was trained using a clinical EEG dataset labeled by five specialists, including 16 008 epileptic spikes and 15 478 artifacts from 50 children. The SA mechanism is expected to reduce the number of parameters and efficiently extract features from a small amount of EEG data. To validate the effectiveness, we compared various spike detection approaches with the clinical EEG data.Main results.The experimental results showed that the proposed method detected epileptic spikes more effectively than other models (accuracy = 0.876 and false positive rate = 0.133).Significance.The proposed model had only one-tenth the number of parameters as the other effective model, despite having such a high detection performance. Further exploration of the hidden parameters revealed that the model automatically attended to the EEG's characteristic waveform locations of interest.

SlypNet: Spikelet-based yield prediction of wheat using advanced plant phenotyping and computer vision techniques.

The application of computer vision in agriculture has already contributed immensely to restructuring the existing field practices starting from the sowing to the harvesting. Among the different plant parts, the economic part, the yield, has the highest importance and becomes the ultimate goal for the farming community. It depends on many genetic and environmental factors, so this curiosity about knowing the yield brought several precise pre-harvest prediction methods using different ways. Out of those techniques, non-invasive yield prediction techniques using computer vision have been proved to be the most efficient and trusted platform. This study developed a novel methodology, called SlypNet, using advanced deep learning networks, i.e., Mask R-CNN and U-Net, which can extract various plant morphological features like spike and spikelet from the visual image of the wheat plant and provide a high-throughput yield estimate with great precision. Mask R-CNN outperformed previous networks in spike detection by its precise detection performance with a mean average precision (mAP) of 97.57%, a F1 score of 0.67, and an MCC of 0.91 by overcoming several natural field constraints like overlapping and background interference, variable resolution, and high bushiness of plants. The spikelet detection module's accuracy and consistency were tested with about 99% validation accuracy of the model and the least error, i.e., a mean square error of 1.3 from a set of typical and complex views of wheat spikes. Spikelet yield cumulatively showed the probable production capability of each plant. Our method presents an integrated deep learning platform of spikelet-based yield prediction comprising spike and spikelet detection, leading to higher precision over the existing methods.

Algorithm and hardware considerations for real-time neural signal on-implant processing.

Objective.Various on-workstation neural-spike-based brain machine interface (BMI) systems have reached the point of in-human trials, but on-node and on-implant BMI systems are still under exploration. Such systems are constrained by the area and battery. Researchers should consider the algorithm complexity, available resources, power budgets, CMOS technologies, and the choice of platforms when designing BMI systems. However, the effect of these factors is currently still unclear.Approaches.Here we have proposed a novel real-time 128 channel spike detection algorithm and optimised it on microcontroller (MCU) and field programmable gate array (FPGA) platforms towards consuming minimal power and memory/resources. It is presented as a use case to explore the different considerations in system design.Main results.The proposed spike detection algorithm achieved over 97% sensitivity and a smaller than 3% false detection rate. The MCU implementation occupies less than 3 KB RAM and consumes 31.5 µW ch-1. The FPGA platform only occupies 299 logic cells and 3 KB RAM for 128 channels and consumes 0.04 µW ch-1.Significance.On the spike detection algorithm front, we have eliminated the processing bottleneck by reducing the dynamic power consumption to lower than the hardware static power, without sacrificing detection performance. More importantly, we have explored the considerations in algorithm and hardware design with respect to scalability, portability, and costs. These findings can facilitate and guide the future development of real-time on-implant neural signal processing platforms.

Automated spike detection: Which software package?

PURPOSE: We assessed three commercial automated spike detection software packages (Persyst, Encevis and BESA) to see which had the best performance. METHODS: Thirty prolonged EEG records from people aged at least 16 years were collected and 30-minute representative epochs were selected. Interictal epileptiform discharges (IEDs) were marked by three human experts and by all three software packages. For each 30-minutes selection and for each 10-second epoch we measured whether or not IEDs had occurred. We defined the gold standard as the combined detections of the experts. Kappa scores, sensitivity and specificity were estimated for each software package. RESULTS: Sensitivity for Persyst in the default setting was 95% for 30-minute selections and 82% for 10-second epochs. Sensitivity for Encevis was 86% (30-minute selections) and 61% (10-second epochs). The specificity for both packages was 88% for 30-minute selections and 96%-99% for the 10-second epochs. Interrater agreement between Persyst and Encevis and the experts was similar than between experts (0.67-0.83 versus 0.63-0.67). Sensitivity for BESA was 40% and specificity 100%. Interrater agreement (0.25) was low. CONCLUSIONS: IED detection by the Persyst automated software is better than the Encevis and BESA packages, and similar to human review, when reviewing 30-minute selections and 10-second epochs. This findings may help prospective users choose a software package.

To deconvolve, or not to deconvolve: Inferences of neuronal activities using calcium imaging data.

BACKGROUND: With the increasing popularity of calcium imaging in neuroscience research, choosing the right methods to analyze calcium imaging data is critical to address various scientific questions. Unlike spike trains measured using electrodes, fluorescence intensity traces provide an indirect and noisy measurement of the underlying neuronal activities. The observed calcium traces are either analyzed directly or deconvolved to spike trains to infer neuronal activities. When both approaches are applicable, it is unclear whether deconvolving calcium traces is a necessary step. METHODS: In this article, we compare the performance of using calcium traces or their deconvolved spike trains for three common analyses: clustering, principal component analysis (PCA), and population decoding. RESULTS: We found that (1) the two approaches lead to diverging results; (2) estimated spike trains, when smoothed or binned appropriately, usually lead to satisfactory performances, such as more accurate estimation of cluster membership; (3) although estimate spike train produce results more similar to true spike data than trace data, we found that the PCA results from trace data might better reflect the underlying neuronal ensembles (clusters); and (4) for both approaches, decobability can be improved by using denoising or smoothing methods. COMPARISON WITH EXISTING METHODS: Our simulations and applications to real data suggest that estimated spike data outperform trace data in cluster analysis and give comparable results for population decoding. In addition, the decobability of estimated spike data can be slightly better than that of calcium trace data with appropriate filtering / smoothing methods. CONCLUSION: We conclude that spike detection might be a useful pre-processing step for certain problems such as clustering; however, the continuous nature of calcium imaging data provides a natural smoothness that might be helpful for problems such as dimensional reduction.

Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods.

Automated analysis of small and optically variable plant organs, such as grain spikes, is highly demanded in quantitative plant science and breeding. Previous works primarily focused on the detection of prominently visible spikes emerging on the top of the grain plants growing in field conditions. However, accurate and automated analysis of all fully and partially visible spikes in greenhouse images renders a more challenging task, which was rarely addressed in the past. A particular difficulty for image analysis is represented by leaf-covered, occluded but also matured spikes of bushy crop cultivars that can hardly be differentiated from the remaining plant biomass. To address the challenge of automated analysis of arbitrary spike phenotypes in different grain crops and optical setups, here, we performed a comparative investigation of six neural network methods for pattern detection and segmentation in RGB images, including five deep and one shallow neural network. Our experimental results demonstrate that advanced deep learning methods show superior performance, achieving over 90% accuracy by detection and segmentation of spikes in wheat, barley and rye images. However, spike detection in new crop phenotypes can be performed more accurately than segmentation. Furthermore, the detection and segmentation of matured, partially visible and occluded spikes, for which phenotypes substantially deviate from the training set of regular spikes, still represent a challenge to neural network models trained on a limited set of a few hundreds of manually labeled ground truth images. Limitations and further potential improvements of the presented algorithmic frameworks for spike image analysis are discussed. Besides theoretical and experimental investigations, we provide a GUI-based tool (SpikeApp), which shows the application of pre-trained neural networks to fully automate spike detection, segmentation and phenotyping in images of greenhouse-grown plants.

Rapid and Accurate Data Processing for Silver Nanoparticle Oxidation in Nano-Impact Electrochemistry.

In recent years, nano-impact electrochemistry (NIE) has attracted widespread attention as a new electroanalytical approach for the analysis and characterization of single nanoparticles in solution. The accurate analysis of the large volume of the experimental data is of great significance in improving the reliability of this method. Unfortunately, the commonly used data analysis approaches, mainly based on manual processing, are often time-consuming and subjective. Herein, we propose a spike detection algorithm for automatically processing the data from the direct oxidation of sliver nanoparticles (AgNPs) in NIE experiments, including baseline extraction, spike identification and spike area integration. The resulting size distribution of AgNPs is found to agree very well with that from transmission electron microscopy (TEM), showing that the current algorithm is promising for automated analysis of NIE data with high efficiency and accuracy.

Automatic detection of generalized paroxysmal fast activity in interictal EEG using time-frequency analysis.

OBJECTIVE: Markup of generalized interictal epileptiform discharges (IEDs) on EEG is an important step in the diagnosis and characterization of epilepsy. However, manual EEG markup is a time-consuming, subjective, and the specialized task where the human reviewer needs to visually inspect a large amount of data to facilitate accurate clinical decisions. In this study, we aimed to develop a framework for automated detection of generalized paroxysmal fast activity (GPFA), a generalized IED seen in scalp EEG recordings of patients with the severe epilepsy of Lennox-Gastaut syndrome (LGS). METHODS: We studied 13 children with LGS who had GPFA events in their interictal EEG recordings. Time-frequency information derived from manually marked IEDs across multiple EEG channels was used to automatically detect similar events in each patient's interictal EEG. We validated true positives and false positives of the proposed spike detection approach using both standalone scalp EEG and simultaneous EEG-functional MRI (EEG-fMRI) recordings. RESULTS: GPFA events displayed a consistent low-high frequency arrangement in the time-frequency domain. This 'bimodal' spectral feature was most prominent over frontal EEG channels. Our automatic detection approach using this feature identified EEG events with similar time-frequency properties to the manually marked GPFAs. Brain maps of EEG-fMRI signal change during these automatically detected IEDs were comparable to the EEG-fMRI brain maps derived from manual IED markup. CONCLUSION: GPFA events have a characteristic bimodal time-frequency feature that can be automatically detected from scalp EEG recordings in patients with LGS. The validity of this time-frequency feature is demonstrated by EEG-fMRI analysis of automatically detected events, which recapitulates the brain maps we have previously shown to underlie generalized IEDs in LGS. SIGNIFICANCE: This study provides a novel methodology that enables a fast, automated, and objective inspection of generalized IEDs in LGS. The proposed framework may be extendable to a wider range of epilepsy syndromes in which monitoring the burden of epileptic activity can aid clinical decision-making and faster assessment of treatment response and estimation of future seizure risk.

Investigating well potential parameters on neural spike enhancement in a stochastic-resonance pre-emphasis algorithm.

Objective.Background noise experienced during extracellular neural recording limits the number of spikes that can be reliably detected, which ultimately limits the performance of next-generation neuroscientific work. In this study, we aim to utilize stochastic resonance (SR), a technique that can help identify weak signals in noisy environments, to enhance spike detectability.Approach.Previously, an SR-based pre-emphasis algorithm was proposed, where a particle inside a 1D potential well is exerted by a force defined by the extracellular recording, and the output is obtained as the displacement of the particle. In this study, we investigate how the well shape and damping status impact the output signal-to-noise ratio (SNR). We compare the overdamped and underdamped solutions of shallow- and steep-wall monostable wells and bistable wells in terms of SNR improvement using two synthetic datasets. Then, we assess the spike detection performance when thresholding is applied on the output of the well shape-damping status configuration giving the best SNR enhancement.Main results.The SNR depends on the well-shape and damping-status type as well as the input noise level. The underdamped solution of the shallow-wall monostable well can yield to more than four orders of magnitude greater SNR improvement compared to other configurations for low noise intensities. Using this configuration also results in better spike detection sensitivity and positive predictivity than the state-of-the-art spike detection algorithms for a public synthetic dataset. For larger noise intensities, the overdamped solution of the steep-wall monostable well provides better spike enhancement than the others.Significance.The dependence of SNR improvement on the input signal noise level can be used to design a detector with multiple outputs, each more sensitive to a certain distance from the electrode. Such a detector can potentially enhance the performance of a successive spike sorting stage.

Empirical Mode Decomposition-Based Method for Artefact Removal in Raw Intracranial Pressure Signals.

Intracranial pressure (ICP) signals are often contaminated by artefacts and segments of missing values. Some of these artefacts can be observed as very high and short spikes with a physiologically impossible high slope. The presence of these spikes reduces the accuracy of pattern recognition techniques. Thus, we propose a modified empirical mode decomposition (EMD) method for spike removal in raw ICP signals. The EMD breaks down the signal into 16 intrinsic mode functions (IMFs), combines the first 4 to localize spikes using adaptive thresholding, and then either removes or imputes the identified ICP spikes.

Adaptive spike detection and hardware optimization towards autonomous, high-channel-count BMIs.

BACKGROUND: The progress in microtechnology has enabled an exponential trend in the number of neurons that can be simultaneously recorded. The data bandwidth requirement is however increasing with channel count. The vast majority of experimental work involving electrophysiology stores the raw data and then processes this offline; to detect the underlying spike events. Emerging applications however require new methods for local, real-time processing. NEW METHODS: We have developed an adaptive, low complexity spike detection algorithm that combines three novel components for: (1) removing the local field potentials; (2) enhancing the signal-to-noise ratio; and (3) computing an adaptive threshold. The proposed algorithm has been optimised for hardware implementation (i.e. minimising computations, translating to a fixed-point implementation), and demonstrated on low-power embedded targets. MAIN RESULTS: The algorithm has been validated on both synthetic datasets and real recordings yielding a detection sensitivity of up to 90%. The initial hardware implementation using an off-the-shelf embedded platform demonstrated a memory requirement of less than 0.1 kb ROM and 3 kb program flash, consuming an average power of 130 µW. COMPARISON WITH EXISTING METHODS: The method presented has the advantages over other approaches, that it allows spike events to be robustly detected in real-time from neural activity in a completely autonomous way, without the need for any calibration, and can be implemented with low hardware resources. CONCLUSION: The proposed method can detect spikes effectively and adaptively. It alleviates the need for re-calibration, which is critical towards achieving a viable BMI, and more so with future 'high bandwidth' systems' targeting 1000s of channels.