SigMate: a MATLAB-based automated tool for extracellular neuronal signal processing and analysis

Rapid advances in neuronal probe technology for multisite recording of brain activity have posed a significant challenge to neuroscientists for processing and analyzing the recorded signals. To be able to infer meaningful conclusions quickly and accurately from large datasets, automated and sophisticated signal processing and analysis tools are required. This paper presents a Matlab-based novel tool, “SigMate”, incorporating standard methods to analyze spikes and EEG signals, and in-house solutions for local field potentials (LFPs) analysis. Available modules at present are – 1. In-house developed algorithms for: data display (2D and 3D), file operations (file splitting, file concatenation, and file column rearranging), baseline correction, slow stimulus artifact removal, noise characterization and signal quality assessment, current source density (CSD) analysis, latency estimation from LFPs and CSDs, determination of cortical layer activation order using LFPs and CSDs, and single LFP clustering; 2. Existing modules: spike detection, sorting and spike train analysis, and EEG signal analysis. SigMate has the flexibility of analyzing multichannel signals as well as signals from multiple recording sources. The in-house developed tools for LFP analysis have been extensively tested with signals recorded using standard extracellular recording electrode, and planar and implantable multi transistor array (MTA) based neural probes. SigMate will be disseminated shortly to the neuroscience community under the open-source GNU-General Public License

Ongoing EEG artifact correction using blind source separation

Objective: Analysis of the electroencephalogram (EEG) for epileptic spike and seizure detection or brain-computer interfaces can be severely hampered by the presence of artifacts. The aim of this study is to describe and evaluate a fast automatic algorithm for ongoing correction of artifacts in continuous EEG recordings, which can be applied offline and online. Methods: The automatic algorithm for ongoing correction of artifacts is based on fast blind source separation. It uses a sliding window technique with overlapping epochs and features in the spatial, temporal and frequency domain to detect and correct ocular, cardiac, muscle and powerline artifacts. Results: The approach was validated in an independent evaluation study on publicly available continuous EEG data with 2035 marked artifacts. Validation confirmed that 88% of the artifacts could be removed successfully (ocular: 81%, cardiac: 84%, muscle: 98%, powerline: 100%). It outperformed state-of-the-art algorithms both in terms of artifact reduction rates and computation time. Conclusions: Fast ongoing artifact correction successfully removed a good proportion of artifacts, while preserving most of the EEG signals. Significance: The presented algorithm may be useful for ongoing correction of artifacts, e.g., in online systems for epileptic spike and seizure detection or brain-computer interfaces.Comment: 16 pages, 4 figures, 3 table

Automated labeling and online evaluation for self-paced movement detection BCI

Electroencephalogram (EEG)-based brain–computer interfaces (BCIs) allow users to use brain signals to control external instruments, and movement intention detecting BCIs can aid in the rehabilitation of patients who have lost motor function. Existing studies in this area mostly rely on cue-based data collection that facilitates sample labeling but introduces noise from cue stimuli; moreover, it requires extensive user training, and cannot reflect real usage scenarios. In contrast, self-paced BCIs can overcome the limitations of the cue-based approach by supporting users to perform movements at their own initiative and pace, but they fall short in labeling. Therefore, in this study, we proposed an automated labeling approach that can cross-reference electromyography (EMG) signals for EEG labeling with zero human effort. Furthermore, considering that only a few studies have focused on evaluating BCI systems for online use and most of them do not report details of the online systems, we developed and present in detail a pseudo-online evaluation suite to facilitate online BCI research. We collected self-paced movement EEG data from 10 participants performing opening and closing hand movements for training and evaluation. The results show that the automated labeling method can contend well with noisy data compared with the baseline labeling method. We also explored popular machine learning models for online self-paced movement detection. The results demonstrate the capability of our online pipeline, and that a well-performing offline model does not necessarily translate to a well-performing online model owing to the specific settings of an online BCI system. Our proposed automated labeling method, online evaluation suite, and dataset take a concrete step towards real-world self-paced BCI systems.</p

Standardization of electroencephalography for multi-site, multi-platform and multi-investigator studies: Insights from the canadian biomarker integration network in depression

Subsequent to global initiatives in mapping the human brain and investigations of neurobiological markers for brain disorders, the number of multi-site studies involving the collection and sharing of large volumes of brain data, including electroencephalography (EEG), has been increasing. Among the complexities of conducting multi-site studies and increasing the shelf life of biological data beyond the original study are timely standardization and documentation of relevant study parameters. We presentthe insights gained and guidelines established within the EEG working group of the Canadian Biomarker Integration Network in Depression (CAN-BIND). CAN-BIND is a multi-site, multi-investigator, and multiproject network supported by the Ontario Brain Institute with access to Brain-CODE, an informatics platform that hosts a multitude of biological data across a growing list of brain pathologies. We describe our approaches and insights on documenting and standardizing parameters across the study design, data collection, monitoring, analysis, integration, knowledge-translation, and data archiving phases of CAN-BIND projects. We introduce a custom-built EEG toolbox to track data preprocessing with open-access for the scientific community. We also evaluate the impact of variation in equipment setup on the accuracy of acquired data. Collectively, this work is intended to inspire establishing comprehensive and standardized guidelines for multi-site studies

Artifact Removal Methods in EEG Recordings: A Review

To obtain the correct analysis of electroencephalogram (EEG) signals, non-physiological and physiological artifacts should be removed from EEG signals. This study aims to give an overview on the existing methodology for removing physiological artifacts, e.g., ocular, cardiac, and muscle artifacts. The datasets, simulation platforms, and performance measures of artifact removal methods in previous related research are summarized. The advantages and disadvantages of each technique are discussed, including regression method, filtering method, blind source separation (BSS), wavelet transform (WT), empirical mode decomposition (EMD), singular spectrum analysis (SSA), and independent vector analysis (IVA). Also, the applications of hybrid approaches are presented, including discrete wavelet transform - adaptive filtering method (DWT-AFM), DWT-BSS, EMD-BSS, singular spectrum analysis - adaptive noise canceler (SSA-ANC), SSA-BSS, and EMD-IVA. Finally, a comparative analysis for these existing methods is provided based on their performance and merits. The result shows that hybrid methods can remove the artifacts more effectively than individual methods

A Review on Machine Learning Techniques for Neurological Disorders Estimation by Analyzing EEG Waves

With the fast improvement of neuroimaging data acquisition strategies, there has been a significant growth in learning neurological disorders among data mining and machine learning communities. Neurological disorders are the ones that impact the central nervous system (including the human brain) and also include over 600 disorders ranging from brain aneurysm to epilepsy. Every year, based on World Health Organization (WHO), neurological disorders affect much more than one billion people worldwide and count for up to seven million deaths. Hence, useful investigation of neurological disorders is actually of great value. The vast majority of datasets useful for diagnosis of neurological disorders like electroencephalogram (EEG) are actually complicated and poses challenges that are many for data mining and machine learning algorithms due to their increased dimensionality, non stationarity, and non linearity. Hence, an better feature representation is actually key to an effective suite of data mining and machine learning algorithms in the examination of neurological disorders. With this exploration, we use a well defined EEG dataset to train as well as test out models. A preprocessing stage is actually used to extend, arrange and manipulate the framework of free data sets to the needs of ours for better training and tests results. Several techniques are used by us to enhance system accuracy. This particular paper concentrates on dealing with above pointed out difficulties and appropriately analyzes different EEG signals that would in turn help us to boost the procedure of feature extraction and enhance the accuracy in classification. Along with acknowledging above issues, this particular paper proposes a framework that would be useful in determining man stress level and also as a result, differentiate a stressed or normal person/subject

Processing and analysis of multichannel extracellular neuronal signals: state-of-the-art and challenges

In recent years multichannel neuronal signal acquisition systems have allowed scientists to focus on research questions which were otherwise impossible. They act as a powerful means to study brain (dys)functions in in-vivo and in in-vitro animal models. Typically, each session of electrophysiological experiments with multichannel data acquisition systems generate large amount of raw data. For example, a 128 channel signal acquisition system with 16 bits A/D conversion and 20 kHz sampling rate will generate approximately 17 GB data per hour (uncompressed). This poses an important and challenging problem of inferring conclusions from the large amounts of acquired data. Thus, automated signal processing and analysis tools are becoming a key component in neuroscience research, facilitating extraction of relevant information from neuronal recordings in a reasonable time. The purpose of this review is to introduce the reader to the current state-of-the-art of open-source packages for (semi)automated processing and analysis of multichannel extracellular neuronal signals (i.e., neuronal spikes, local field potentials, electroencephalogram, etc.), and the existing Neuroinformatics infrastructure for tool and data sharing. The review is concluded by pinpointing some major challenges that are being faced, which include the development of novel benchmarking techniques, cloud-based distributed processing and analysis tools, as well as defining novel means to share and standardize data

Recent Applications in Graph Theory

Graph theory, being a rigorously investigated field of combinatorial mathematics, is adopted by a wide variety of disciplines addressing a plethora of real-world applications. Advances in graph algorithms and software implementations have made graph theory accessible to a larger community of interest. Ever-increasing interest in machine learning and model deployments for network data demands a coherent selection of topics rewarding a fresh, up-to-date summary of the theory and fruitful applications to probe further. This volume is a small yet unique contribution to graph theory applications and modeling with graphs. The subjects discussed include information hiding using graphs, dynamic graph-based systems to model and control cyber-physical systems, graph reconstruction, average distance neighborhood graphs, and pure and mixed-integer linear programming formulations to cluster networks