11 research outputs found
ICLabel: An automated electroencephalographic independent component classifier, dataset, and website
The electroencephalogram (EEG) provides a non-invasive, minimally
restrictive, and relatively low cost measure of mesoscale brain dynamics with
high temporal resolution. Although signals recorded in parallel by multiple,
near-adjacent EEG scalp electrode channels are highly-correlated and combine
signals from many different sources, biological and non-biological, independent
component analysis (ICA) has been shown to isolate the various source generator
processes underlying those recordings. Independent components (IC) found by ICA
decomposition can be manually inspected, selected, and interpreted, but doing
so requires both time and practice as ICs have no particular order or intrinsic
interpretations and therefore require further study of their properties.
Alternatively, sufficiently-accurate automated IC classifiers can be used to
classify ICs into broad source categories, speeding the analysis of EEG studies
with many subjects and enabling the use of ICA decomposition in near-real-time
applications. While many such classifiers have been proposed recently, this
work presents the ICLabel project comprised of (1) an IC dataset containing
spatiotemporal measures for over 200,000 ICs from more than 6,000 EEG
recordings, (2) a website for collecting crowdsourced IC labels and educating
EEG researchers and practitioners about IC interpretation, and (3) the
automated ICLabel classifier. The classifier improves upon existing methods in
two ways: by improving the accuracy of the computed label estimates and by
enhancing its computational efficiency. The ICLabel classifier outperforms or
performs comparably to the previous best publicly available method for all
measured IC categories while computing those labels ten times faster than that
classifier as shown in a rigorous comparison against all other publicly
available EEG IC classifiers.Comment: Intended for NeuroImage. Updated from version one with minor
editorial and figure change
Furthering the Automation of Electroencephalographic Source Analysis
The electroencephalogram (EEG) provides a non-invasive, minimally restrictive, and relatively low-cost measure of mesoscale brain dynamics with high temporal resolution. Although signals recorded in parallel by multiple, near-adjacent EEG scalp electrode channels are highly correlated and combine signals from many different sources, biological and non-biological, independent component analysis (ICA) has been shown to isolate the various source generator processes underlying those recordings. While ICA-based methods have been seeing more and more use, EEG researchers are hampered by the additional manual intervention necessary for source-resolved analyses. These issues can be largely mitigated through the automation of several stages of EEG source analysis. To this end, we developed and evaluated the ICLabel classifier, an automated independent component classifier trained on a large dataset with crowdsourced labels. The crowdsourced labels were estimated using the novel crowd labeling (CL) algorithm, crowd labeling latent Dirichlet allocation (CL-LDA), developed here. The ICLabel dataset that was used to train the ICLabel classifier was also made public to aid in future development of IC classifiers. We also evaluated artifact subspace reconstruction (ASR), an algorithm for artifact removal which is applicable both offline and in real-time, and aids both channel-level and source-level analyses. These tools are combined in the Real-time EEG Source-mapping toolbox (REST) to showcase the utility and ease of real-time, source-level analyses once the individual components of an EEG analysis pipeline are automated. Finally we evaluate adaptive mixture ICA (AMICA) and explore its utility for automatic EEG segmentation and nonstationary analysis. All of these tools and methods are open-source and freely available online
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The ICLabel dataset of electroencephalographic (EEG) independent component (IC) features.
The ICLabel dataset is comprised of training and test sets of a set of spatiotemporal features of electroencephalographic (EEG) independent components (IC). The ICLabel training set feature sets were computed for over 200,000 EEG ICs from more than 6,000 existing EEG recordings. More than 8,000 of these ICs have accompanying crowdsourced IC labels across seven IC categories: Brain, Muscle, Eye, Heart, Line Nosie, Channel Noise, and Other. The feature-sets included in the ICLabel dataset are scalp topography images, channel-based scalp topography measures, power spectral densities (PSD) measures (median, variance and kurtosis) and autocorrelation functions, equivalent current dipole (ECD) model fits for single and bilaterally symmetric dipole models, plus features used in several published IC classifier approaches. The ICLabel test set is comprised of 130 ICs from 10 datasets not included in the training set. Each of the test set ICs has an associated IC label estimated based on labels provided by six ICA-EEG experts. Files necessary for adding to and amending the dataset are also included, plus a python class containing useful methods for interacting with the dataset, and IC classifications produced by several existing IC classifiers. These data are linked to the article, "ICLabel: An automated electroencephalographic independent component classifier, dataset, and website" [1]. An active tutorial and crowdsourcing website is available: iclabel.ucsd.edu/tutorial/overview
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The ICLabel dataset of electroencephalographic (EEG) independent component (IC) features.
The ICLabel dataset is comprised of training and test sets of a set of spatiotemporal features of electroencephalographic (EEG) independent components (IC). The ICLabel training set feature sets were computed for over 200,000 EEG ICs from more than 6,000 existing EEG recordings. More than 8,000 of these ICs have accompanying crowdsourced IC labels across seven IC categories: Brain, Muscle, Eye, Heart, Line Nosie, Channel Noise, and Other. The feature-sets included in the ICLabel dataset are scalp topography images, channel-based scalp topography measures, power spectral densities (PSD) measures (median, variance and kurtosis) and autocorrelation functions, equivalent current dipole (ECD) model fits for single and bilaterally symmetric dipole models, plus features used in several published IC classifier approaches. The ICLabel test set is comprised of 130 ICs from 10 datasets not included in the training set. Each of the test set ICs has an associated IC label estimated based on labels provided by six ICA-EEG experts. Files necessary for adding to and amending the dataset are also included, plus a python class containing useful methods for interacting with the dataset, and IC classifications produced by several existing IC classifiers. These data are linked to the article, "ICLabel: An automated electroencephalographic independent component classifier, dataset, and website" [1]. An active tutorial and crowdsourcing website is available: iclabel.ucsd.edu/tutorial/overview
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Modeling brain dynamic state changes with adaptive mixture independent component analysis
There is a growing interest in neuroscience in assessing the continuous, endogenous, and nonstationary dynamics of brain network activity supporting the fluidity of human cognition and behavior. This non-stationarity may involve ever-changing formation and dissolution of active cortical sources and brain networks. However, unsupervised approaches to identify and model these changes in brain dynamics as continuous transitions between quasi-stable brain states using unlabeled, noninvasive recordings of brain activity have been limited. This study explores the use of adaptive mixture independent component analysis (AMICA) to model multichannel electroencephalographic (EEG) data with a set of ICA models, each of which decomposes an adaptively learned portion of the data into statistically independent sources. We first show that AMICA can segment simulated quasi-stationary EEG data and accurately identify ground-truth sources and source model transitions. Next, we demonstrate that AMICA decomposition, applied to 6-13 channel scalp recordings from the CAP Sleep Database, can characterize sleep stage dynamics, allowing 75% accuracy in identifying transitions between six sleep stages without use of EEG power spectra. Finally, applied to 30-channel data from subjects in a driving simulator, AMICA identifies models that account for EEG during faster and slower response to driving challenges, respectively. We show changes in relative probabilities of these models allow effective prediction of subject response speed and moment-by-moment characterization of state changes within single trials. AMICA thus provides a generic unsupervised approach to identifying and modeling changes in EEG dynamics. Applied to continuous, unlabeled multichannel data, AMICA may likely be used to detect and study any changes in cognitive states
An optical-coding method to measure particle distribution in microfluidic devices
We demonstrated an optical coding method to measure the position of each particle in a microfluidic channel. The technique utilizes a specially designed pattern as a spatial mask to encode the forward scattering signal of each particle. From the waveform of the forward scattering signal, one can obtain the information about the particle position and velocity. The technique enables us to experimentally investigate the complex relations between particle positions within the microfluidic channel and flow conditions and particle sizes. The method also produces insight for important phenomenon in microfluidic and lab-on-a-chip devices such as inertial focusing, Dean flow, flow confinement, etc