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Optical imaging of genetically encoded calcium indicators is a powerful tool to record the activity of a large number of neurons simultaneously over a long period of time from freely behaving animals. However, determining the exact time at which a neuron spikes and estimating the underlying firing rate from calcium fluorescence data remains challenging, especially for calcium imaging data obtained from a longitudinal study. We propose a multi-trial time-varying ℓ0 penalized method to jointly detect spikes and estimate firing rates by robustly integrating evolving neural dynamics across trials. Our simulation study shows that the proposed method performs well in both spike detection and firing rate estimation. We demonstrate the usefulness of our method on calcium fluorescence trace data from two studies, with the first study showing differential firing rate functions between two behaviors and the second study showing evolving firing rate functions across trials due to learning.

BackgroundWith 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.MethodsIn 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.ResultsWe 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 methodsOur 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.ConclusionWe 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.

In the last decades, deep learning neural decoding algorithms have gained momentum in the field of neural interfaces and neural processing systems. However, to be deployed on low-budget portable devices while maintaining real-time operability, these models must withstand strict computational and power limitations. This work presents a spike decoding system implemented on a low-end Zynq-7010 FPGA, which includes a multiplier-less spike detection pipeline and a spiking-neural-network-based decoder mapped in the programmable logic. We tested the system on two publicly available datasets and achieved comparable results with state-of-the-art neural decoders that use more complex deep learning models. The system required 7.36 times fewer parameters than the smallest architecture tested on the same dataset. Moreover, by exploiting the spike sparsity property of the neural signal, the total amount of computations is reduced by about 90% during a test carried out on real recorded data. The low computational complexity of the chosen spike detection setup, combined with the power efficiency of spiking neural networks, makes this prototype a well-suited choice for low-power real-time neural decoding at the edge.

In recent years, the development of microelectrode arrays and multichannel recordings has provided opportunities for high‐precision detection in signal processing. The study of neuronal frontal potentials has been rapidly emerging as an important component in brain‐computer interface and neuroscience research. Neuronal spike detection provides a basis for neuronal discharge analysis and nucleus cluster identification; its accuracy depends on feature extraction and classification, which affect neuronal decoding analysis. However, improving the detection accuracy of spike potentials in highly noisy signals remains a problem. IThe authors propose a heuristic adaptive threshold spike‐detection algorithm that removes noise and reduces the phase shift using a zero‐phase Butterworth infinite impulse response filter. Next, heuristic thresholding is applied to obtain spike points, remove repetitions, and achieve robust spike detection. The proposed algorithm achieved an average accuracy of 95.40% using extracellular spiked datasets and effectively detected spikes. [ABSTRACT FROM AUTHOR]

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 templatematchingmethod 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%. [ABSTRACT FROM AUTHOR]

Neuroscientists seek efficient solutions for deciphering the sophisticated unknowns of the brain. Effective development of complicated brain-related tools is the focal point of research in neuroscience and neurotechnology. Thanks to today’s technological advancements, the physical development of high-density and high-resolution neural interfaces has been made possible. This is where the critical bottleneck in receiving the expected functionality from such devices shifts to transferring, processing, and subsequently analyzing the massive neurophysiological extra-cellular data recorded. To respond to this inevitable concern, a spectrum of neuronal signal processing techniques have been proposed to extract task-related informative content of the signals conveying neuronal activities, and eliminate the irrelevant contents. Such techniques provide powerful tools for a wide range of neuroscience research, from low-level perception to high-level cognition. Data transformations are among the most efficient processing techniques that serve this purpose by properly changing the data representation. Mapping the data from its original domain (i.e., the time-space domain) to a new representational domain, data transformations change the viewing angle of observing the informative content of the data. This paper reviews the employment of data transformations in order to process neuronal signals and their three key applications, including spike detection, spike sorting, and data compression. [ABSTRACT FROM AUTHOR]

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., (Creative Commons Attribution license.)

Correct detection of peaks in electroencephalogram (EEG) signals is of essence due to the significant correlation of those potentials with cognitive performance and disorders. This paper proposes a novel and non-parametric approach to detect prediction error negativity (PEN) in cognitive conflict processing. The PEN candidates are first located from the input signal via an adaptation of a recent effective method for local maxima extraction, processed in a multi-scale manner. The found candidates are then fused and ranked based on their shape and location-based features. False positives caused by candidates’ magnitude are eliminated by rotating the sorted candidate list where the one with the second-best ranking score will be identified as PEN. The EEG data collected from a 3D object selection task have been used to verify the efficacy of the proposed approach. Compared with the state-of-the-art peak detection techniques, the proposed method shows an improvement of at least 2.67% in accuracy and 6.27% in sensitivity while requires only about 4 ms to process an epoch. The accuracy and computational efficiency of the proposed technique in the detection of PEN in cognitive conflict processing would lead to promising applications in performance improvement of brain-computer interfaces (BCIs).

Interictal epileptiform spike (referred to as spike) detected from electroencephalograms lasting only 20- to 200-ms can provide a reliable evidence-based indicator for clinical seizure type diagnosis. Recent feature representation approaches focus either on the concrete-level or abstract-level information mining of the spike, thus demonstrating suboptimal detection performance. Additionally, existing abstract-level information mining methods of the spike based deep learning networks have not realized the effective feature representation of long-term dependent distinguished information within similar waveform cycles caused by morphological heterogeneity, which affects detection performance. Thus, a multilevel feature learning method for accurate spike detection was proposed in this study. Specifically, the spatio-temporal-frequency multidomain information in concrete-level first are inferred the common mimetic properties of the spike using the multidomain feature extractors. Then, the effective feature representation of long-term dependent distinguished information within similar waveform cycles caused by morphological heterogeneity is suitably captured using the temporal convolutional network. Finally, the spatio-temporal-frequency multidomain long-term dependent feature representation of spike is calculated using the element-wise manner to fuse the feature representation in concrete- and abstract-levels. The experimental results indicate that the proposed method can achieve an accuracy of 90.62±1.38%, sensitivity of 90.38±1.52%, specificity of 91.00±1.60%, precision of 90.33±4.71%, and the false detection rate per minute is $0.148\pm 0.020\text{m}^{-1}$ , which are higher than when using the feature representation in the concrete-or abstract-level alone. Additionally, the detection results indicate that the proposed method avoids the subjectivity and inefficiency of visual inspection, and it enables a highly accurate detection of the spike.

Centrotemporal spike-waves (CTSWs) are typical interictal epileptiform discharges (IEDs) observed in centrotemporal regions in self-limited epilepsy with centrotemporal spikes (SLECTS). This study aims to develop a deep learning-based approach for automated detection of CTSWs in scalp electroencephalography (EEG) recordings of patients with SLECTS. To lower the substantial burden of IED annotation on clinicians, we simplified it by limiting IEDs to CTSWs because electroencephalographic patterns of CTSWs are known to be highly consistent. Two neurologists annotated 1672 CTSWs of 20 patients with SLECTS. Thereafter, we performed a two-level CTSW detection procedure: epoch-level and EEG-level. In the epoch-level detection, we constructed convolutional neural network-based classification models for CTSW and non-CTSW binary classification using the recordings of 20 patients and 20 controls. We then set the thresholds of the classification models for 100% specificity. In the EEG-level detection, we applied the threshold-adjusted classification models to the recordings of 50 patients and 50 controls that were not used in the epoch-level detection to distinguish between CTSW-positive (with one or more CTSWs) and CTSW-negative (with no CTSW) recordings based on the detection of CTSW presence. We obtained an average sensitivity, specificity, and accuracy of 99.8%, 98.4%, and 99.1%, respectively, with an average false detection rate of 0.19/hr for the controls. Our approach showed high detectability for CTSWs despite the simplified annotation process. We expect that the proposed CTSW detectors have potential clinical usefulness for efficiently reading EEGs and diagnosing SLECTS, and can significantly reduce the burden of IED annotation on clinicians.

Magnetoencephalography (MEG) is a useful tool for clinically evaluating the localization of interictal spikes. Neurophysiologists visually identify spikes from the MEG waveforms and estimate the equivalent current dipoles (ECD). However, presently, these analyses are manually performed by neurophysiologists and are time-consuming. Another problem is that spike identification from MEG waveforms largely depends on neurophysiologists’ skills and experiences. These problems cause poor cost-effectiveness in clinical MEG examination. To overcome these problems, we fully automated spike identification and ECD estimation using a deep learning approach fully automated AI-based MEG interictal epileptiform discharge identification and ECD estimation (FAMED). We applied a semantic segmentation method, which is an image processing technique, to identify the appropriate times between spike onset and peak and to select appropriate sensors for ECD estimation. FAMED was trained and evaluated using clinical MEG data acquired from 375 patients. FAMED training was performed in two stages: in the first stage, a classification network was learned, and in the second stage, a segmentation network that extended the classification network was learned. The classification network had a mean AUC of 0.9868 (10-fold patient-wise cross-validation); the sensitivity and specificity were 0.7952 and 0.9971, respectively. The median distance between the ECDs estimated by the neurophysiologists and those using FAMED was 0.63 cm. Thus, the performance of FAMED is comparable to that of neurophysiologists, and it can contribute to the efficiency and consistency of MEG ECD analysis. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

• A novel automatic detection procedure of epileptic discharges is developed for SeLECTS; • The procedure demonstrated the highest spatio-temporal resolution, distinguishing the timing and location of single IEDs; • The procedure provides a quantitative way to study interictal epileptiform discharges. Scalp-visible interictal epileptiform discharges (IEDs) are known to be crucial for the diagnosis of self-limited epilepsy with centrotemporal spikes (SeLECTS). However, labeling and mapping these discharges over electroencephalography (EEG) recordings are repetitive and time-consuming, requiring much tedious and careful efforts. Fully automated IEDs detection algorithm with high accuracy and generalization ability is much desired. We designed an efficient data preprocessing-feature extraction-classification workflow, which is composed by the independent component analysis, clinical knowledge-based waveform dictionary and transformer based deep neural network classifier, to identify the timing and recording electrode associated with each individual IEDs and the dipole patterns. A total of 44,908 IEDs labeled within video EEG recordings were collected from 25 SeLECTS patients. The proposed procedure achieved an averaged accuracy of 99.8% and sensitivity of 97.8% in the test dataset consisting of 8 patients, with the false alarm rate been 1.8 per hour for nonepileptic EEG recordings. All the eight SeLECTS patients in the test set have been detected dipole pattern and five of them is found to have IEDs frequencies 10 times higher in sleep stage compared with the awake period. The generalization ability of the procedure is further confirmed through a cross-dataset evaluation in the publicly available TUEV dataset. The proposed fully automated IEDs detection procedure shows high accuracy and good generalization ability. The proposed procedure can significantly lower the work burden of neurologists and provide a quantitative tool for IEDs analysis in further epilepsy research. [ABSTRACT FROM AUTHOR]

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.

Centrotemporal spike-waves (CTSWs) are typical interictal epileptiform discharges (IEDs) observed in centrotemporal regions in self-limited epilepsy with centrotemporal spikes (SLECTS). This study aims to develop a deep learning-based approach for automated detection of CTSWs in scalp electroencephalography (EEG) recordings of patients with SLECTS. To lower the substantial burden of IED annotation on clinicians, we simplified it by limiting IEDs to CTSWs because electroencephalographic patterns of CTSWs are known to be highly consistent. Two neurologists annotated 1672 CTSWs of 20 patients with SLECTS. Thereafter, we performed a two-level CTSW detection procedure: epoch-level and EEG-level. In the epoch-level detection, we constructed convolutional neural network-based classification models for CTSW and non-CTSW binary classification using the recordings of 20 patients and 20 controls. We then set the thresholds of the classification models for 100% specificity. In the EEG-level detection, we applied the threshold-adjusted classification models to the recordings of 50 patients and 50 controls that were not used in the epoch-level detection to distinguish between CTSW-positive (with one or more CTSWs) and CTSW-negative (with no CTSW) recordings based on the detection of CTSW presence. We obtained an average sensitivity, specificity, and accuracy of 99.8%, 98.4%, and 99.1%, respectively, with an average false detection rate of 0.19/hr for the controls. Our approach showed high detectability for CTSWs despite the simplified annotation process. We expect that the proposed CTSW detectors have potential clinical usefulness for efficiently reading EEGs and diagnosing SLECTS, and can significantly reduce the burden of IED annotation on clinicians. [ABSTRACT FROM AUTHOR]

Interictal epileptiform spike (referred to as spike) detected from electroencephalograms lasting only 20- to 200-ms can provide a reliable evidence-based indicator for clinical seizure type diagnosis. Recent feature representation approaches focus either on the concrete-level or abstract-level information mining of the spike, thus demonstrating suboptimal detection performance. Additionally, existing abstract-level information mining methods of the spike based deep learning networks have not realized the effective feature representation of long-term dependent distinguished information within similar waveform cycles caused by morphological heterogeneity, which affects detection performance. Thus, a multilevel feature learning method for accurate spike detection was proposed in this study. Specifically, the spatio-temporal-frequency multidomain information in concrete-level first are inferred the common mimetic properties of the spike using the multidomain feature extractors. Then, the effective feature representation of long-term dependent distinguished information within similar waveform cycles caused by morphological heterogeneity is suitably captured using the temporal convolutional network. Finally, the spatio-temporal-frequency multidomain long-term dependent feature representation of spike is calculated using the element-wise manner to fuse the feature representation in concrete- and abstract-levels. The experimental results indicate that the proposed method can achieve an accuracy of 90.62±1.38%, sensitivity of 90.38±1.52%, specificity of 91.00±1.60%, precision of 90.33±4.71%, and the false detection rate per minute is $0.148\pm 0.020\text{m}^{-1}$ , which are higher than when using the feature representation in the concrete-or abstract-level alone. Additionally, the detection results indicate that the proposed method avoids the subjectivity and inefficiency of visual inspection, and it enables a highly accurate detection of the spike. [ABSTRACT FROM AUTHOR]

Correct detection of peaks in electroencephalogram (EEG) signals is of essence due to the significant correlation of those potentials with cognitive performance and disorders. This paper proposes a novel and non-parametric approach to detect prediction error negativity (PEN) in cognitive conflict processing. The PEN candidates are first located from the input signal via an adaptation of a recent effective method for local maxima extraction, processed in a multi-scale manner. The found candidates are then fused and ranked based on their shape and location-based features. False positives caused by candidates’ magnitude are eliminated by rotating the sorted candidate list where the one with the second-best ranking score will be identified as PEN. The EEG data collected from a 3D object selection task have been used to verify the efficacy of the proposed approach. Compared with the state-of-the-art peak detection techniques, the proposed method shows an improvement of at least 2.67% in accuracy and 6.27% in sensitivity while requires only about 4 ms to process an epoch. The accuracy and computational efficiency of the proposed technique in the detection of PEN in cognitive conflict processing would lead to promising applications in performance improvement of brain-computer interfaces (BCIs). [ABSTRACT FROM AUTHOR]

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To cope with the lack of highly skilled professionals, machine learning with proper signal processing is key for establishing automated diagnostic-aid technologies with which to conduct epileptic electroencephalogram (EEG) testing. In particular, frequency filtering with the appropriate passbands is essential for enhancing the biomarkers—such as epileptic spike waves—that are noted in the EEG. This paper introduces a novel class of neural networks (NNs) that have a bank of linear-phase finite impulse response filters at the first layer as a preprocessor that can behave as bandpass filters that extract biomarkers without destroying waveforms because of a linear-phase condition. Besides, the parameters of the filters are also data-driven. The proposed NNs were trained with a large amount of clinical EEG data, including 15 833 epileptic spike waveforms recorded from 50 patients, and their labels were annotated by specialists. In the experiments, we compared three scenarios for the first layer: no preprocessing, discrete wavelet transform, and the proposed data-driven filters. The experimental results show that the trained data-driven filter bank with supervised learning behaves like multiple bandpass filters. In particular, the trained filter passed a frequency band of approximately 10–30 Hz. Moreover, the proposed method detected epileptic spikes, with the area under the receiver operating characteristic curve of 0.967 in the mean of 50 intersubject validations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract The electroencephalogram (EEG) is a tool for diagnosing epilepsy; by analyzing it, neurologists can identify alterations in brain activity associated with epilepsy. However, this task is not always easy to perform because of the duration of the EEG or the subjectivity of the specialist in detecting alterations. Aim To propose the use of an epileptic spike detector based on a matched filter and a neural network for supporting the diagnosis of epilepsy through a tool capable of automatically detecting spikes in pediatric EEGs. Results Automatic detection of spikes from an EEG waveform involved the creation of an epileptic spike template. The template was used in order to detect spikes by using a matched filter, and each spike detected was confirmed by a Neural Network to improve sensitivity and specificity. Thus, the detector developed achieved a sensitivity of 99.96% which is better than the range of what has been reported in the literature (82.68% and 94.4%), and a specificity of 99.26%, improving the specificity found in the best-reviewed studies. Conclusions Considering the results obtained in the evaluation, the solution becomes a promising alternative to support the automatic identification of epileptic spikes by neurologists.

Effective risk control strategies require reliable risk assessment models to provide support. In recent years, the risk of extreme weather events has increased due to climate change. However, existing assessment models are not essentially used to explore short-term drastic changes in the environment, such as extreme heat or cold. Therefore, we proposed a climate-food risk assessment system that could detect drastic changes, such as extreme weather events and price fluctuations, in a timely and thorough manner. On the one hand, spikes were detected in the climate system. On the other hand, change points were detected in the food system. Finally, an innovative integrated analysis algorithm is carried out to obtain the ranking of highly impacted foods. Across all food supply chains, we found that sugar, bread and grains, and wine in grapes are most closely related to extreme weather events. This discovery needs to be treated with caution. To initiate a feasible control strategy for climate risk, a concrete policy implication was discussed in detail. If properly organized and supervised, the extreme weather agricultural insurance can become a transformative mechanism toward climate resilience. [Display omitted] • We study how extreme weather events may affect the price of food supply chains. • The top three food supply chains affected by extreme temperature are sugar, bread and cereals, and wine from grapes. • An innovative algorithm is provided to perform this integrated impact assessment. • A concrete policy application of extreme weather agricultural insurance is thoroughly discussed. [ABSTRACT FROM AUTHOR]

Spike detection is of great significance in the detection of epileptic seizures. Many spike detection algorithms have been proposed, but available algorithms often miss spikes during high firing rate epochs or with artifacts. Also, there exists methodological limitations when there are great variations in spike morphology between different patients or the same patient in different EEG epoch. Thus a data-driven spike detection method using multi-template matching, feature extraction and threshold method is proposed in this work to improve the detection performance under different circumstances. First, universal template matching and feature extraction are used to get putative spikes. Then clustering algorithm and adaptive template matching algorithm are applied to maximize the number of detected spikes for these specific candidate single units obtained from the clustering method. In addition, a data-driven approach based on receiver operating characteristic (ROC) is used for low false identification rate detection. The performance is evaluated on real EEG samples and the evaluating results shows that this algorithm has achieved 97.12% average sensitivity and 0.55 average false negative rate per minute. The least sensitivity is 94.32% and the most false negative rate per minute is 1.23. [ABSTRACT FROM AUTHOR]

A non-implantable Micro system typically is used to monitor activity of the brain. It requires on-chip real time processor which is processing of multi-channel neural signal with less power consumption and less area utilization. However, it is a challenge to get the less area and minimum consumption of power when the processing of multi-channel neural signal in real-time hardware with spike sorting algorithms. Hence, proposing an efficient neural signal processor (NSP) with optimal design constraints for multi-channel. The Haar discrete wavelet transform (HDWT) algorithm is designed for the NSP to process the spike data detection and sorting of the spikes. The NSP is simulated in Model Simulator 6.4a software and implemented on FPGA target device. The proposed NSP got 3.44?s of delay and 79.98mw% of power consumption when it is implemented on Cyclone FPGA device. [ABSTRACT FROM AUTHOR]

• Transmitting full-BW neural data imposes a significant power demand on wireless systems. • Spike rates often provide adequate information for the analysis of brain activities. • Operator-based spike detection outperforms simple thresholding in terms of error rate. • High fidelity low power microsystem can be achieved with operator-based spike detection. We introduce an innovative approach that incorporates operator-based spike detection in wireless microsystems for neural signal processing. Through comparative analyses between simple thresholding and operator-based detection conducted on pre-recorded spike detection experiments, our research emphasizes the superiority of the operator-based spike detection approach. The operator-based spike detection emerges as a promising technique for miniaturized wireless neural signal devices, primarily due to its proficient noise-handling capabilities paired with reduced power consumption. Furthermore, its adaptability across various experimental conditions amplifies its versatility. Empirical tests underscored its low power requisites and compactness, emphasizing practical utility of the detection scheme in the neural microsystems. Collectively, our results mark a significant progression in wireless cerebral signal recording methodologies, paving the way for optimized wireless brain-machine interface (BMI) systems. [ABSTRACT FROM AUTHOR]

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.

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. [ABSTRACT FROM AUTHOR]

The diagnosis of epilepsy often relies on a reading of routine scalp electroencephalograms (EEGs). Since seizures are highly unlikely to be detected in a routine scalp EEG, the primary diagnosis depends heavily on the visual evaluation of Interictal Epileptiform Discharges (IEDs). This process is tedious, expert-centered, and delays the treatment plan. Consequently, the development of an automated, fast, and reliable epileptic EEG diagnostic system is essential. In this study, we propose a system to classify EEG as epileptic or normal based on multiple modalities extracted from the interictal EEG. The ensemble system consists of three components: a Convolutional Neural Network (CNN)-based IED detector, a Template Matching (TM)-based IED detector, and a spectral feature-based classifier. We evaluate the system on datasets from six centers from the USA, Singapore, and India. The system yields a mean Leave-One-Institution-Out (LOIO) cross-validation (CV) area under curve (AUC) of 0.826 (balanced accuracy (BAC) of 76.1%) and Leave-One-Subject-Out (LOSO) CV AUC of 0.812 (BAC of 74.8%). The LOIO results are found to be similar to the interrater agreement (IRA) reported in the literature for epileptic EEG classification. Moreover, as the proposed system can process routine EEGs in a few seconds, it may aid the clinicians in diagnosing epilepsy efficiently. [ABSTRACT FROM AUTHOR]

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., Competing Interests: Declaration of interests The authors declare no competing financial interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Spike is one of the crop yield organs in wheat plants. Determination of the phenological stages, including heading time point (HTP), and area of spike from non-invasive phenotyping images provides the necessary information for the inference of growth-related traits. The algorithm previously developed by Qiongyan et al. for spike detection in 2-D images turns out to be less accurate when applied to the European cultivars that produce many more leaves. Therefore, we here present an improved and extended method where (i) wavelet amplitude is used as an input to the Laws texture energy-based neural network instead of original grayscale images and (ii) non-spike structures (e.g., leaves) are subsequently suppressed by combining the result of the neural network prediction with a Frangi-filtered image. Using this two-step approach, a 98.6% overall accuracy of neural network segmentation based on direct comparison with ground-truth data could be achieved. Moreover, the comparative error rate in spike HTP detection and growth correlation among the ground truth, the algorithm developed by Qiongyan et al., and the proposed algorithm are discussed in this paper. The proposed algorithm was also capable of significantly reducing the error rate of the HTP detection by 75% and improving the accuracy of spike area estimation by 50% in comparison with the Qionagyan et al. method. With these algorithmic improvements, HTP detection on a diverse set of 369 plants was performed in a high-throughput manner. This analysis demonstrated that the HTP of 104 plants (comprises of 57 genotypes) with lower biomass and tillering range (e.g., earlier-heading types) were correctly determined. However, fine-tuning or extension of the developed method is required for high biomass plants where spike emerges within green bushes. In conclusion, our proposed method allows significantly more reliable results for HTP detection and spike growth analysis to be achieved in application to European cultivars with earlier-heading types.

An ultralow power 0.6 V neural amplifier with on-chip analog spike detection is presented. A capacitively-coupled instrumentation amplifier (CCIA) with the current-reused and self-biased scheme is proposed to reduce the overall power consumption and to enhance the noise efficiency. The transistors in the amplifier are operated in the subthreshold region to enhance noise performance. The analog-domain spike detection based on a low power peak detector can reduce the overall power consumption. The circuit is fabricated using the standard 0.18 μm CMOS process. The passband of the circuit is from 6.4 Hz to 4.46 kHz. Input-referred noise is 10.68 μVrms. The supply voltage is 0.6 V, and the power consumption of the singlestage CCIA is 50.6 nW. The CCIA achieves a good noise efficiency factor and power efficiency factor of 1.79 and 1.93, respectively. The overall power consumption including two CCIAs, the programmable gain amplifier, and the analog spike detector is 269.8 nW. Input spikes with an amplitude of 50 μV at 100-Hz intervals are accurately detected.

Epilepsy is a disease in which patients undergo seizures caused by brain functionality disorder. Clinically, it is usually diagnosed by experienced clinicians according to continuous electroencephalography (cEEG), which is time consuming even for experienced doctors. Meanwhile, amplitude integrated electroencephalography (aEEG) has shown potential to detect epileptic seizures. Therefore, the paper proposes a hybrid seizure detection algorithm by combining cEEG-based seizure detection algorithm and aEEG-based seizure detection algorithm to detect seizures. In cEEG-based seizure detection algorithm, cEEG signals are divided into 5 s epoch with 4 s overlap and multi-domain features are extracted from each epoch. Then random forest classification is applied to do seizure detection. In aEEG-based seizure detection algorithm, morphological filter is applied to do spike detection and determine whether there are seizures after transforming the cEEG signals into aEEG signals. In order to evaluate the generality of the proposed method, experiments are performed on two independent datasets, including a publicly available EEG dataset (CHB-MIT) and an epileptic dataset collected by using the EEG device developed by the Hangzhou Neuro Science and Technology Co., Ltd. In the CHB-MIT dataset, the accuracy (AC), specificity (SP), sensitivity based on the event (SE), and false positive ratio based on the event (FPRE) obtained by the hybrid method are 99.36%, 82.98%, 99.41%, and 0.57 times/h, respectively. In the dataset we collected, the AC, SP, SE, and FPRE obtained by the hybrid method are 99.23%, 89.47%, 99.23%, and 0.71 times/h, respectively. The experimental results show that the performance of the proposed method is competitive with state-of-the-art methods and results. Furthermore, basing on the hybrid method, this paper has developed a portable automatic seizure detection system, which can reduce the burden of clinicians in processing the large amounts of cEEG signals by detecting seizure automatically.

Abstract Background Field phenotyping by remote sensing has received increased interest in recent years with the possibility of achieving high-throughput analysis of crop fields. Along with the various technological developments, the application of machine learning methods for image analysis has enhanced the potential for quantitative assessment of a multitude of crop traits. For wheat breeding purposes, assessing the production of wheat spikes, as the grain-bearing organ, is a useful proxy measure of grain production. Thus, being able to detect and characterize spikes from images of wheat fields is an essential component in a wheat breeding pipeline for the selection of high yielding varieties. Results We have applied a deep learning approach to accurately detect, count and analyze wheat spikes for yield estimation. We have tested the approach on a set of images of wheat field trial comprising 10 varieties subjected to three fertilizer treatments. The images have been captured over one season, using high definition RGB cameras mounted on a land-based imaging platform, and viewing the wheat plots from an oblique angle. A subset of in-field images has been accurately labeled by manually annotating all the spike regions. This annotated dataset, called SPIKE, is then used to train four region-based Convolutional Neural Networks (R-CNN) which take, as input, images of wheat plots, and accurately detect and count spike regions in each plot. The CNNs also output the spike density and a classification probability for each plot. Using the same R-CNN architecture, four different models were generated based on four different datasets of training and testing images captured at various growth stages. Despite the challenging field imaging conditions, e.g., variable illumination conditions, high spike occlusion, and complex background, the four R-CNN models achieve an average detection accuracy ranging from 88 to $$94\%$$ 94% across different sets of test images. The most robust R-CNN model, which achieved the highest accuracy, is then selected to study the variation in spike production over 10 wheat varieties and three treatments. The SPIKE dataset and the trained CNN are the main contributions of this paper. Conclusion With the availability of good training datasets such us the SPIKE dataset proposed in this article, deep learning techniques can achieve high accuracy in detecting and counting spikes from complex wheat field images. The proposed robust R-CNN model, which has been trained on spike images captured during different growth stages, is optimized for application to a wider variety of field scenarios. It accurately quantifies the differences in yield produced by the 10 varieties we have studied, and their respective responses to fertilizer treatment. We have also observed that the other R-CNN models exhibit more specialized performances. The data set and the R-CNN model, which we make publicly available, have the potential to greatly benefit plant breeders by facilitating the high throughput selection of high yielding varieties.

Visual evaluation of electroencephalogram (EEG) for Interictal Epileptiform Discharges (IEDs) as distinctive biomarkers of epilepsy has various limitations, including time-consuming reviews, steep learning curves, interobserver variability, and the need for specialized experts. The development of an automated IED detector is necessary to provide a faster and reliable diagnosis of epilepsy. In this paper, we propose an automated IED detector based on Convolutional Neural Networks (CNNs). We have evaluated the proposed IED detector on a sizable database of 554 scalp EEG recordings (84 epileptic patients and 461 nonepileptic subjects) recorded at Massachusetts General Hospital (MGH), Boston. The proposed CNN IED detector has achieved superior performance in comparison with conventional methods with a mean cross-validation area under the precision–recall curve (AUPRC) of 0.838 ± 0.040 and false detection rate of 0.2 ± 0.11 per minute for a sensitivity of 80%. We demonstrated the proposed system to be noninferior to 30 neurologists on a dataset from the Medical University of South Carolina (MUSC). Further, we clinically validated the system at National University Hospital (NUH), Singapore, with an agreement accuracy of 81.41% with a clinical expert. Moreover, the proposed system can be applied to EEG recordings with any arbitrary number of channels. [ABSTRACT FROM AUTHOR]

This paper presents a novel spike detection algorithm in nonstationary signals using a time–frequency (t–f) approach. The proposed algorithm exploits the direction of signal energy in the t–f domain to detect spikes in the presence of high-frequency nonstationary signals even at low signal-to-noise ratio. The performance of the proposed approach is evaluated using synthetic nonstationary signals, synthesized signals mimicking electroencephalogram (EEG) signals, manually selected segments of speech signals, and manually selected segments of real EEG signals. The statistical measures, such as hit rate and precision, are used to demonstrate that the proposed algorithm performs better than other widely used algorithms, such as the smoothed nonlinear energy detector. [ABSTRACT FROM AUTHOR]

Purpose: Complete visual review of prolonged video-EEG recordings at an EMU (Epilepsy Monitoring Unit) is time consuming and can cause problems in times of paucity of educated personnel. In this study we aimed to show non inferiority for electroclinical diagnosis using sampled review in combination with EEG analysis softreferware (P13 software, Persyst Corporation), in comparison to complete visual review.Method: Fifty prolonged video-EEG recordings in adults were prospectively evaluated using sampled visual EEG review in combination with automated detection software of the complete EEG record. Visually assessed samples consisted of one hour during wakefulness, one hour during sleep, half an hour of wakefulness after wake-up and all clinical events marked by the individual and/or nurses. The final electro-clinical diagnosis of this new review approach was compared with the electro-clinical diagnosis after complete visual review as presently used.Results: The electro-clinical diagnosis based on sampled visual review combined with automated detection software did not differ from the diagnosis based on complete visual review. Furthermore, the detection software was able to detect all records containing epileptiform abnormalities and epileptic seizures.Conclusion: Sampled visual review in combination with automated detection using Persyst 13 is non-inferior to complete visual review for electroclinical diagnosis of prolonged video-EEG at an EMU setting, which makes this approach promising. [ABSTRACT FROM AUTHOR]

Spike is one of the crop yield organs in wheat plants. Determination of the phenological stages, including heading time point (HTP), and area of spike from non-invasive phenotyping images provides the necessary information for the inference of growth-related traits. The algorithm previously developed by Qiongyan et al. for spike detection in 2-D images turns out to be less accurate when applied to the European cultivars that produce many more leaves. Therefore, we here present an improved and extended method where (i) wavelet amplitude is used as an input to the Laws texture energy-based neural network instead of original grayscale images and (ii) non-spike structures (e.g., leaves) are subsequently suppressed by combining the result of the neural network prediction with a Frangi-filtered image. Using this two-step approach, a 98.6% overall accuracy of neural network segmentation based on direct comparison with ground-truth data could be achieved. Moreover, the comparative error rate in spike HTP detection and growth correlation among the ground truth, the algorithm developed by Qiongyan et al., and the proposed algorithm are discussed in this paper. The proposed algorithm was also capable of significantly reducing the error rate of the HTP detection by 75% and improving the accuracy of spike area estimation by 50% in comparison with the Qionagyan et al. method. With these algorithmic improvements, HTP detection on a diverse set of 369 plants was performed in a high-throughput manner. This analysis demonstrated that the HTP of 104 plants (comprises of 57 genotypes) with lower biomass and tillering range (e.g., earlier-heading types) were correctly determined. However, fine-tuning or extension of the developed method is required for high biomass plants where spike emerges within green bushes. In conclusion, our proposed method allows significantly more reliable results for HTP detection and spike growth analysis to be achieved in application to European cultivars with earlier-heading types. [ABSTRACT FROM AUTHOR]

Epilepsy is a neurological disorder characterized by sudden and unpredictable epileptic seizures, which incurs significant negative impacts on patients’ physical, psychological and social health. A practical approach to assist with the clinical assessment and treatment planning for patients is to process magnetoencephalography (MEG) data to identify epileptogenic zones. As a widely accepted biomarker of epileptic foci, epileptic MEG spikes need to be precisely detected. Given that the visual inspection of spikes is time consuming, an automatic and efficient system with adequate accuracy for spike detection is valuable in clinical practice. However, current approaches for MEG spike autodetection are dependent on hand-engineered features. Here, we propose a novel multiview Epileptic MEG Spikes detection algorithm based on a deep learning Network (EMS-Net) to accurately and efficiently recognize the spike events from MEG raw data. The results of the leave-k-subject-out validation tests for multiple datasets (i.e., balanced and realistic datasets) showed that EMS-Net achieved state-of-the-art classification performance (i.e., accuracy: 91.82% – 99.89%; precision: 91.90% – 99.45%; sensitivity: 91.61% – 99.53%; specificity: 91.60% – 99.96%; f1 score: 91.70% – 99.48%; and area under the curve: 0.9688 – 0.9998). [ABSTRACT FROM AUTHOR]