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Jafarzadeh Esfahani M, Sikder N, Ter Horst R, Daraie AH, Appel K, Weber FD, Bevelander KE, Dresler M. Citizen neuroscience: Wearable technology and open software to study the human brain in its natural habitat. Eur J Neurosci 2024; 59:948-965. [PMID: 38328991 DOI: 10.1111/ejn.16227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 11/09/2023] [Accepted: 11/30/2023] [Indexed: 02/09/2024]
Abstract
Citizen science allows the public to participate in various stages of scientific research, including study design, data acquisition, and data analysis. Citizen science has a long history in several fields of the natural sciences, and with recent developments in wearable technology, neuroscience has also become more accessible to citizen scientists. This development was largely driven by the influx of minimal sensing systems in the consumer market, allowing more do-it-yourself (DIY) and quantified-self (QS) investigations of the human brain. While most subfields of neuroscience require sophisticated monitoring devices and laboratories, the study of sleep characteristics can be performed at home with relevant noninvasive consumer devices. The strong influence of sleep quality on waking life and the accessibility of devices to measure sleep are two primary reasons citizen scientists have widely embraced sleep research. Their involvement has evolved from solely contributing to data collection to engaging in more collaborative or autonomous approaches, such as instigating ideas, formulating research inquiries, designing research protocols and methodology, acting upon their findings, and disseminating results. In this article, we introduce the emerging field of citizen neuroscience, illustrating examples of such projects in sleep research. We then provide overviews of the wearable technologies for tracking human neurophysiology and various open-source software used to analyse them. Finally, we discuss the opportunities and challenges in citizen neuroscience projects and suggest how to improve the study of the human brain outside the laboratory.
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Affiliation(s)
| | - Niloy Sikder
- Donders Institute for Brain, Behaviour, and Cognition, Radboudumc, Nijmegen, The Netherlands
- Faculty of Technology and Bionics, Rhine-Waal University of Applied Sciences, Kleve, Germany
| | - Rob Ter Horst
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Amir Hossein Daraie
- Donders Institute for Brain, Behaviour, and Cognition, Radboudumc, Nijmegen, The Netherlands
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Frederik D Weber
- Donders Institute for Brain, Behaviour, and Cognition, Radboudumc, Nijmegen, The Netherlands
- Department of Sleep and Cognition, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Kirsten E Bevelander
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
- Primary and Community Care, Radboud University and Medical Center, Nijmegen, The Netherlands
| | - Martin Dresler
- Donders Institute for Brain, Behaviour, and Cognition, Radboudumc, Nijmegen, The Netherlands
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Tapia-Rivas NI, Estévez PA, Cortes-Briones JA. A robust deep learning detector for sleep spindles and K-complexes: towards population norms. Sci Rep 2024; 14:263. [PMID: 38167626 PMCID: PMC10762090 DOI: 10.1038/s41598-023-50736-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/24/2023] [Indexed: 01/05/2024] Open
Abstract
Sleep spindles (SSs) and K-complexes (KCs) are brain patterns involved in cognitive functions that appear during sleep. Large-scale sleep studies would benefit from precise and robust automatic sleep event detectors, capable of adapting the variability in both electroencephalography (EEG) signals and expert annotation rules. We introduce the Sleep EEG Event Detector (SEED), a deep learning system that outperforms existing approaches in SS and KC detection, reaching an F1-score of 80.5% and 83.7%, respectively, on the MASS2 dataset. SEED transfers well and requires minimal fine-tuning for new datasets and annotation styles. Remarkably, SEED substantially reduces the required amount of annotated data by using a novel pretraining approach that leverages the rule-based detector A7. An analysis of 11,224 subjects revealed that SEED's detections provide better estimates of SS population statistics than existing approaches. SEED is a powerful resource for obtaining sleep-event statistics that could be useful for establishing population norms.
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Affiliation(s)
| | - Pablo A Estévez
- Department of Electrical Engineering, University of Chile, Santiago, Chile.
- Millennium Institute of Intelligent Healthcare Engineering, Santiago, Chile.
- IMPACT, Center of Interventional Medicine for Precision and Advanced Cellular Therapy, Santiago, Chile.
| | - José A Cortes-Briones
- Schizophrenia and Neuropharmacology Research Group at Yale (SNRGY), Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Abraham Ribicoff Research Facilities, Connecticut Mental Health Center, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
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Khasawneh N, Fraiwan M, Fraiwan L. Detection of K-complexes in EEG waveform images using faster R-CNN and deep transfer learning. BMC Med Inform Decis Mak 2022; 22:297. [PMID: 36397034 PMCID: PMC9673349 DOI: 10.1186/s12911-022-02042-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Background The electroencephalography (EEG) signal carries important information about the electrical activity of the brain, which may reveal many pathologies. This information is carried in certain waveforms and events, one of which is the K-complex. It is used by neurologists to diagnose neurophysiologic and cognitive disorders as well as sleep studies.
Existing detection methods largely depend on tedious, time-consuming, and error-prone manual inspection of the EEG waveform. Methods In this paper, a highly accurate K-complex detection system is developed. Based on multiple convolutional neural network (CNN) feature extraction backbones and EEG waveform images, a regions with faster regions with convolutional neural networks (Faster R-CNN) detector was designed, trained, and tested. Extensive performance evaluation was performed using four deep transfer learning feature extraction models (AlexNet, ResNet-101, VGG19 and Inceptionv3). The dataset was comprised of 10948 images of EEG waveforms, with the location of the K-complexes included as separate text files containing the bounding boxes information. Results The Inceptionv3 and VGG19-based detectors performed consistently high (i.e., up to 99.8% precision and 0.2% miss rate) over different testing scenarios, in which the number of training images was varied from 60% to 80% and the positive overlap threshold was increased from 60% to 90%. Conclusions Our automated method appears to be a highly accurate automatic K-complex detection in real-time that can aid practitioners in speedy EEG inspection. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12911-022-02042-x.
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You J, Jiang D, Ma Y, Wang Y. SpindleU-Net: An Adaptive U-Net Framework for Sleep Spindle Detection in Single-Channel EEG. IEEE Trans Neural Syst Rehabil Eng 2021; 29:1614-1623. [PMID: 34398759 DOI: 10.1109/tnsre.2021.3105443] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The sleep spindles in EEG have become one type of biomarker used to assess cognitive abilities and related disorders, and thus their detection is crucial for clinical research. This task, traditionally performed by sleep experts, is time-consuming. Many methods have been proposed to automate this process, yet an increase in performance is still expected. Inspired by the application in image segmentation, we propose a point-wise spindle detection method based on the U-Net framework with an attention module (SpindleU-Net). It maps the sequences of arbitrary-length EEG inputs to those of dense labels of spindle or non-spindle on freely chosen intervals. The attention module that focuses on the salient spindle region allows better performance, and a task-specific loss function is defined to alleviate the problem of imbalanced classification. As a deep learning method, SpindleU-Net outperforms state-of-the-art methods on the widely used benchmark dataset of MASS as well as the DREAMS dataset with a small number of samples. On MASS dataset it achieves average F1 scores of 0.854 and 0.803 according to its consistency with the annotations by two sleep experts respectively. On DREAMS dataset, it shows the average F1 score of 0.739. Its cross-dataset performance is also better compared to other methods, showing the good generalization ability for cross-dataset applications.
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Kulkarni PM, Xiao Z, Robinson EJ, Jami AS, Zhang J, Zhou H, Henin SE, Liu AA, Osorio RS, Wang J, Chen Z. A deep learning approach for real-time detection of sleep spindles. J Neural Eng 2019; 16:036004. [PMID: 30790769 PMCID: PMC6527330 DOI: 10.1088/1741-2552/ab0933] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Sleep spindles have been implicated in memory consolidation and synaptic plasticity during NREM sleep. Detection accuracy and latency in automatic spindle detection are critical for real-time applications. APPROACH Here we propose a novel deep learning strategy (SpindleNet) to detect sleep spindles based on a single EEG channel. While the majority of spindle detection methods are used for off-line applications, our method is well suited for online applications. MAIN RESULTS Compared with other spindle detection methods, SpindleNet achieves superior detection accuracy and speed, as demonstrated in two publicly available expert-validated EEG sleep spindle datasets. Our real-time detection of spindle onset achieves detection latencies of 150-350 ms (~two-three spindle cycles) and retains excellent performance under low EEG sampling frequencies and low signal-to-noise ratios. SpindleNet has good generalization across different sleep datasets from various subject groups of different ages and species. SIGNIFICANCE SpindleNet is ultra-fast and scalable to multichannel EEG recordings, with an accuracy level comparable to human experts, making it appealing for long-term sleep monitoring and closed-loop neuroscience experiments.
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Affiliation(s)
- Prathamesh M Kulkarni
- Department of Psychiatry, School of Medicine, New York University, New York, NY 10016, United States of America
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LaRocco J, Franaszczuk PJ, Kerick S, Robbins K. Spindler: a framework for parametric analysis and detection of spindles in EEG with application to sleep spindles. J Neural Eng 2018; 15:066015. [PMID: 30132445 DOI: 10.1088/1741-2552/aadc1c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE EEG spindles, narrow-band oscillatory signal bursts, are widely-studied biomarkers of subject state and neurological function. Most existing methods for spindle detection select algorithm parameters by optimizing agreement with expert labels. We propose a new framework for selecting algorithm parameters based on stability of spindle properties and elucidate the dependence of these properties on parameter selection for several algorithms. APPROACH To demonstrate this approach we developed a new algorithm (Spindler) that decomposes the signal using matching pursuit with Gabor atoms and computes the spindles for each point in a fine grid of parameter values. After computing characteristic surfaces as a function of parameters, Spindler selects algorithm parameters based on the stability of characteristic surface geometry. MAIN RESULTS Spindler performs well relative to several common supervised and unsupervised EEG sleep spindle detection methods. Spindler is available as an open-source MATLAB toolbox (https://github.com/VisLab/EEG-Spindles). In addition to Spindler, the toolbox provides implementations of several other spindle detection algorithms as well as standardized methods for matching ground truth to predictions and a framework for understanding algorithm parameter surfaces. SIGNIFICANCE This work demonstrates that parameter selection based on physical constraints rather than labelled data can provide effective, fully-automated, unsupervised spindle detection. This work also exposes the dangers of applying cross-validation without considering the dependence of spindle properties on parameters. Parameters selected to optimize one performance metric or matching method are not optimized for others. Furthermore, elucidation of the stability of predicted indicators with respect to algorithm parameter selection is critical to practical application of these algorithms.
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Affiliation(s)
- J LaRocco
- University of Texas, Department of Computer Science, San Antonio, Texas 78249, United States of America. US Army Research Laboratory, Human Research and Engineering Directorate, Aberdeen Proving Ground, Maryland 21287, United States of America
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Combrisson E, Vallat R, Eichenlaub JB, O'Reilly C, Lajnef T, Guillot A, Ruby PM, Jerbi K. Sleep: An Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data. Front Neuroinform 2017; 11:60. [PMID: 28983246 PMCID: PMC5613192 DOI: 10.3389/fninf.2017.00060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/06/2017] [Indexed: 11/13/2022] Open
Abstract
We introduce Sleep, a new Python open-source graphical user interface (GUI) dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1) Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2) Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM), (3) Implementation of practical signal processing tools such as re-referencing or filtering, and (4) Display of main descriptive statistics including publication-ready tables and figures. The software package supports loading and reading raw EEG data from standard file formats such as European Data Format, in addition to a range of commercial data formats. Most importantly, Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. As a result, it is capable of efficiently handling and displaying large sleep datasets. Sleep is freely available (http://visbrain.org/sleep) and comes with sample datasets and an extensive documentation. Novel functionalities will continue to be added and open-science community efforts are expected to enhance the capacities of this module.
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Affiliation(s)
- Etienne Combrisson
- Département de Psychologie, Université de MontréalMontreal, QC, Canada
- Inter-University Laboratory of Human Movement Biology, Université Claude Bernard Lyon 1, Université de LyonLyon, France
| | - Raphael Vallat
- Lyon Neuroscience Research Center, Brain Dynamics and Cognition team, INSERM UMRS 1028, CNRS UMR 5292, Université Claude Bernard Lyon 1, Université de LyonLyon, France
| | - Jean-Baptiste Eichenlaub
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, United States
| | - Christian O'Reilly
- Blue Brain Project, École Polytechnique Fédérale de LausanneGeneva, Switzerland
| | - Tarek Lajnef
- Département de Psychologie, Université de MontréalMontreal, QC, Canada
- Center for Advanced Research in Sleep Medicine, Hôpital du Sacré-Coeur de MontréalMontreal, QC, Canada
| | - Aymeric Guillot
- Inter-University Laboratory of Human Movement Biology, Université Claude Bernard Lyon 1, Université de LyonLyon, France
| | - Perrine M. Ruby
- Lyon Neuroscience Research Center, Brain Dynamics and Cognition team, INSERM UMRS 1028, CNRS UMR 5292, Université Claude Bernard Lyon 1, Université de LyonLyon, France
| | - Karim Jerbi
- Département de Psychologie, Université de MontréalMontreal, QC, Canada
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Vallat R, Lajnef T, Eichenlaub JB, Berthomier C, Jerbi K, Morlet D, Ruby PM. Increased Evoked Potentials to Arousing Auditory Stimuli during Sleep: Implication for the Understanding of Dream Recall. Front Hum Neurosci 2017; 11:132. [PMID: 28377708 PMCID: PMC5360011 DOI: 10.3389/fnhum.2017.00132] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/07/2017] [Indexed: 11/13/2022] Open
Abstract
High dream recallers (HR) show a larger brain reactivity to auditory stimuli during wakefulness and sleep as compared to low dream recallers (LR) and also more intra-sleep wakefulness (ISW), but no other modification of the sleep macrostructure. To further understand the possible causal link between brain responses, ISW and dream recall, we investigated the sleep microstructure of HR and LR, and tested whether the amplitude of auditory evoked potentials (AEPs) was predictive of arousing reactions during sleep. Participants (18 HR, 18 LR) were presented with sounds during a whole night of sleep in the lab and polysomnographic data were recorded. Sleep microstructure (arousals, rapid eye movements (REMs), muscle twitches (MTs), spindles, KCs) was assessed using visual, semi-automatic and automatic validated methods. AEPs to arousing (awakenings or arousals) and non-arousing stimuli were subsequently computed. No between-group difference in the microstructure of sleep was found. In N2 sleep, auditory arousing stimuli elicited a larger parieto-occipital positivity and an increased late frontal negativity as compared to non-arousing stimuli. As compared to LR, HR showed more arousing stimuli and more long awakenings, regardless of the sleep stage but did not show more numerous or longer arousals. These results suggest that the amplitude of the brain response to stimuli during sleep determine subsequent awakening and that awakening duration (and not arousal) is the critical parameter for dream recall. Notably, our results led us to propose that the minimum necessary duration of an awakening during sleep for a successful encoding of dreams into long-term memory is approximately 2 min.
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Affiliation(s)
- Raphael Vallat
- Brain Dynamics and Cognition Team-Lyon Neuroscience Research Center (CRNL), INSERM U1028, CNRS UMR 5292, Centre Hospitalier Le Vinatier (Bat. 452)Bron, France; Lyon 1 UniversityLyon, France
| | - Tarek Lajnef
- LETI Lab, Sfax National Engineering School, University of SfaxSfax, Tunisia; Department of Psychology, Université de MontréalMontréal, QC, Canada
| | | | | | - Karim Jerbi
- Brain Dynamics and Cognition Team-Lyon Neuroscience Research Center (CRNL), INSERM U1028, CNRS UMR 5292, Centre Hospitalier Le Vinatier (Bat. 452)Bron, France; Department of Psychology, Université de MontréalMontréal, QC, Canada
| | - Dominique Morlet
- Brain Dynamics and Cognition Team-Lyon Neuroscience Research Center (CRNL), INSERM U1028, CNRS UMR 5292, Centre Hospitalier Le Vinatier (Bat. 452)Bron, France; Lyon 1 UniversityLyon, France
| | - Perrine M Ruby
- Brain Dynamics and Cognition Team-Lyon Neuroscience Research Center (CRNL), INSERM U1028, CNRS UMR 5292, Centre Hospitalier Le Vinatier (Bat. 452)Bron, France; Lyon 1 UniversityLyon, France
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