scholarly journals The EBRAINS NeuroFeatureExtract: An Online Resource for the Extraction of Neural Activity Features From Electrophysiological Data

2021 ◽  
Vol 15 ◽  
Author(s):  
Luca L. Bologna ◽  
Roberto Smiriglia ◽  
Dario Curreri ◽  
Michele Migliore

The description of neural dynamics, in terms of precise characterizations of action potential timings and shape and voltage related measures, is fundamental for a deeper understanding of the neural code and its information content. Not only such measures serve the scientific questions posed by experimentalists but are increasingly being used by computational neuroscientists for the construction of biophysically detailed data-driven models. Nonetheless, online resources enabling users to perform such feature extraction operation are lacking. To address this problem, in the framework of the Human Brain Project and the EBRAINS research infrastructure, we have developed and made available to the scientific community the NeuroFeatureExtract, an open-access online resource for the extraction of electrophysiological features from neural activity data. This tool allows to select electrophysiological traces of interest, fetched from public repositories or from users’ own data, and provides ad hoc functionalities to extract relevant features. The output files are properly formatted for further analysis, including data-driven neural model optimization.

2014 ◽  
Vol 369 (1641) ◽  
pp. 20130211 ◽  
Author(s):  
Randolph Blake ◽  
Jan Brascamp ◽  
David J. Heeger

This essay critically examines the extent to which binocular rivalry can provide important clues about the neural correlates of conscious visual perception. Our ideas are presented within the framework of four questions about the use of rivalry for this purpose: (i) what constitutes an adequate comparison condition for gauging rivalry's impact on awareness, (ii) how can one distinguish abolished awareness from inattention, (iii) when one obtains unequivocal evidence for a causal link between a fluctuating measure of neural activity and fluctuating perceptual states during rivalry, will it generalize to other stimulus conditions and perceptual phenomena and (iv) does such evidence necessarily indicate that this neural activity constitutes a neural correlate of consciousness? While arriving at sceptical answers to these four questions, the essay nonetheless offers some ideas about how a more nuanced utilization of binocular rivalry may still provide fundamental insights about neural dynamics, and glimpses of at least some of the ingredients comprising neural correlates of consciousness, including those involved in perceptual decision-making.


2021 ◽  
Author(s):  
Sydney C. Weiser ◽  
Brian R. Mullen ◽  
Desiderio Ascencio ◽  
James B. Ackman

Recording neuronal group activity across the cortical hemispheres from awake, behaving mice is essential for understanding information flow across cerebral networks. Video recordings of cerebral function comes with challenges, including optical and movement-associated vessel artifacts, and limited references for time series extraction. Here we present a data-driven workflow that isolates artifacts from calcium activity patterns, and segments independent functional units across the cortical surface. Independent Component Analysis utilizes the statistical interdependence of pixel activation to completely unmix signals from background noise, given sufficient spatial and temporal samples. We also utilize isolated signal components to produce segmentations of the cortical surface, unique to each individual’s functional patterning. Time series extraction from these maps maximally represent the underlying signal in a highly compressed format. These improved techniques for data pre-processing, spatial segmentation, and time series extraction result in optimal signals for further analysis.


2021 ◽  
Author(s):  
Carlo Cristiano ◽  
◽  
Marco Pirrone ◽  

Risk-mitigation strategies are most effective when the major sources of uncertainty are determined through dedicated and in-depth studies. In the context of reservoir characterization and modeling, petrophysical uncertainty plays a significant role in the risk assessment phase, for instance in the computation of volumetrics. The conventional workflow for the propagation of the petrophysical uncertainty consists of physics-based model embedded into a Monte Carlo (MC) template. In detail, open-hole logs and their inherent uncertainties are used to estimate the important petrophysical properties (e.g. shale volume, porosity, water saturation) with uncertainty through the mechanistic model and MC simulations. In turn, model parameter uncertainties can be also considered. This standard approach can be highly time-consuming in case the physics-based model is complex, unknown, difficult to reproduce (e.g. old/legacy wells) and/or the number of wells to be processed is very high. In this respect, the aim of this paper is to show how a data-driven methodology can be used to propagate the petrophysical uncertainty in a fast and efficient way, speeding-up the complete process but still remaining consistent with the main outcomes. In detail, a fit-for-purpose Random Forest (RF) algorithm learns through experience how log measurements are related to the important petrophysical parameters. Then, a MC framework is used to infer the petrophysical uncertainty starting from the uncertainty of the input logs, still with the RF model as a driver. The complete methodology, first validated with ad-hoc synthetic case studies, has been then applied to two real cases, where the petrophysical uncertainty has been required for reservoir modeling purposes. The first one includes legacy wells intercepting a very complex lithological environment. The second case comprises a sandstone reservoir with a very high number of wells, instead. For both scenarios, the standard approach would have taken too long (several months) to be completed, with no possibility to integrate the results into the reservoir models in time. Hence, for each well the RF regressor has been trained and tested on the whole dataset available, obtaining a valid data-driven analytics model for formation evaluation. Next, 1000 scenarios of input logs have been generated via MC simulations using multivariate normal distributions. Finally, the RF regressor predicts the associated 1000 petrophysical characterization scenarios. As final outcomes of the workflow, ad-hoc statistics (e.g. P10, P50, P90 quantiles) have been used to wrap up the main findings. The complete data-driven approach took few days for both scenarios with a critical impact on the subsequent reservoir modeling activities. This study opens the possibility to quickly process a high number of wells and, in particular, it can be also used to effectively propagate the petrophysical uncertainty to legacy well data for which conventional approaches are not an option, in terms of time-efficiency.


Author(s):  
Shalin Hai-Jew

People often refer to the World Wide Web (WWW) and the Internet to conduct ad hoc and informal problem-solving. Their success in their endeavors has depended on a wide range of information access and crowd-sourcing; deeper analysis of problems; and growing self-efficacy through acclimating into certain problem-solving groups (with attendant new identities) and the “takeaway” learning by abstracting the problem-solving process. This chapter suggests that a greater awareness of site and online resource designers about the steps of problem-solving may enhance the building of self-discovery learning affordances for every phase of the informal problem-solving process.


2020 ◽  
Vol 16 (1) ◽  
pp. e1007571
Author(s):  
Christopher A. Lavender ◽  
Andrew J. Shapiro ◽  
Frank S. Day ◽  
David C. Fargo

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