Objective. In electrophysiology, microelectrodes are the primary source for recording neural data (single unit activity). These microelectrodes can be implanted individually or in the form of arrays containing dozens to hundreds of channels. Recordings of some channels contain neural activity, which are often contaminated with noise. Another fraction of channels does not record any neural data, but only noise. By noise, we mean physiological activities unrelated to spiking, including technical artifacts and neural activities of neurons that are too far away from the electrode to be usefully processed. For further analysis, an automatic identification and continuous tracking of channels containing neural data is of great significance for many applications, e.g. automated selection of neural channels during online and offline spike sorting. Automated spike detection and sorting is also critical for online decoding in brain–computer interface (BCI) applications, in which only simple threshold crossing events are often considered for feature extraction. To our knowledge, there is no method that can universally and automatically identify channels containing neural data. In this study, we aim to identify and track channels containing neural data from implanted electrodes, automatically and more importantly universally. By universally, we mean across different recording technologies, different subjects and different brain areas. Approach. We propose a novel algorithm based on a new way of feature vector extraction and a deep learning method, which we call SpikeDeeptector. SpikeDeeptector considers a batch of waveforms to construct a single feature vector and enables contextual learning. The feature vectors are then fed to a deep learning method, which learns contextualized, temporal and spatial patterns, and classifies them as channels containing neural spike data or only noise. Main results. We trained the model of SpikeDeeptector on data recorded from a single tetraplegic patient with two Utah arrays implanted in different areas of the brain. The trained model was then evaluated on data collected from six epileptic patients implanted with depth electrodes, unseen data from the tetraplegic patient and data from another tetraplegic patient implanted with two Utah arrays. The cumulative evaluation accuracy was 97.20% on 1.56 million hand labeled test inputs. Significance. The results demonstrate that SpikeDeeptector generalizes not only to the new data, but also to different brain areas, subjects, and electrode types not used for training. Clinical trial registration number. The clinical trial registration number for patients implanted with the Utah array is NCT 01849822. For the epilepsy patients, approval from the local ethics committee at the Ruhr-University Bochum, Germany, was obtained prior to implantation.
Objective. Advancements in electrode design have resulted in micro-electrode arrays with hundreds of channels for single cell recordings. In the resulting electrophysiological recordings, each implanted electrode can record spike activity (SA) of one or more neurons along with background activity (BA). The aim of this study is to isolate SA of each neural source. This process is called spike sorting or spike classification. Advanced spike sorting algorithms are time consuming because of the human intervention at various stages of the pipeline. Current approaches lack generalization because the values of hyperparameters are not fixed, even for multiple recording sessions of the same subject. In this study, a fully automatic spike sorting algorithm called "SpikeDeep-Classifier" is proposed. The values of hyperparameters remain fixed for all the evaluation data. Approach. The proposed approach is based on our previous study (SpikeDeeptector) and a novel background activity rejector (BAR), which are both supervised learning algorithms and an unsupervised learning algorithm (K-means). SpikeDeeptector and BAR are used to extract meaningful channels and remove BA from the extracted meaningful channels, respectively. The process of clustering becomes straightforward once the BA is completely removed from the data. Then, K-means with a predefined maximum number of clusters is applied on the remaining data originating from neural sources only. Lastly, a similarity-based criterion and a threshold are used to keep distinct clusters and merge similar looking clusters. The proposed approach is called cluster accept or merge (CAOM) and it has only two hyperparameters (maximum number of clusters and similarity threshold) which are kept fixed for all the evaluation data after tuning. Main Results. We compared the results of our algorithm with ground-truth labels. The algorithm is evaluated on data of human patients and publicly available labeled non-human primates (NHPs) datasets. The average accuracy of BAR on datasets of human patients is 92.3% which is further reduced to 88.03% after (Kmeans + CAOM). In addition, the average accuracy of BAR on a publicly available labeled dataset of NHPs is 95.40% which reduces to 86.95% after (K-mean + CAOM). Lastly, we compared the performance of the SpikeDeep-Classifier with two human experts, where SpikeDeep-Classifier has produced comparable results. Significance. The SpikeDeep-Classifier is evaluated on the datasets of multiple recording sessions of different species, different brain areas and different electrode types without further retraining. The results demonstrate that "SpikeDeep-Classifier" possesses the ability to generalize well on a versatile dataset and henceforth provides a generalized and fully automated solution to offline spike sorting.
Objective Accurate decoding of surface electromyography (sEMG) is pivotal for muscle-to-machine-interfaces (MMI) and their application e.g. rehabilitation therapy. sEMG signals have high inter-subject variability, due to various factors, including skin thickness, body fat percentage, and electrode placement. Deep learning algorithms require long training time and tend to overfit if only few samples are available. In this study, we aim to investigate methods to calibrate deep learning models to a new user when only a limited amount of training data is available. Approach Two methods are commonly used in the literature, subject-specific modeling and transfer learning. In this study, we investigate the effectiveness of transfer learning using weight initialization for recalibration of two different pretrained deep learning models on new subjects data and compare their performance to subject- specific models. We evaluate two models on three publicly available databases (NinaPro Database 2,3 and 4) and compare the performance of both calibration schemes in terms of accuracy, required training data, and calibration time. Main results On average over all settings, our transfer learning approach improves 5 %-points on the pretrained models without fine-tuning, and 12 %-points on the subject-specific models, while being trained for 22% fewer epochs on average. Our results indicate that transfer learning enables faster learning on fewer training samples than user-specific models. Significance To the best of our knowledge, this is the first comparison of subject- specific modeling and transfer learning. These approaches are ubiquitously used in the field of sEMG decoding. But the lack of comparative studies until now made it difficult for scientists to assess appropriate calibration schemes. Our results guide engineers evaluating similar use cases.
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