Frontiers in Neuroinformatics

Journal: Frontiers in Neuroinformatics

Abbreviation

Front. neuroinform.

Publisher

Frontiers Media

ISSN

1662-5196

Show all metadata

Search Results

Publications 1 - 10 of 18

Automatic spike sorting evaluation: A website based community approach
Franke, Felix; Meier, Philipp; Sobolev, Andrey; et al. (2012)
Frontiers in Neuroinformatics
Electroencephalogram approximate entropy influenced by both age and sleep
Lee, Gerick M.H.; Fattinger, Sara; Mouthon, Anne-Laure; et al. (2013)
Frontiers in Neuroinformatics
The use of information-based measures to assess changes in conscious state is an increasingly popular topic. Though recent results have seemed to justify the merits of such methods, little has been done to investigate the applicability of such measures to children. For our work, we used the approximate entropy (ApEn), a measure previously shown to correlate with changes in conscious state when applied to the electroencephalogram (EEG), and sought to confirm whether previously reported trends in adult ApEn values across wake and sleep were present in children. Besides validating the prior findings that ApEn decreases from wake to sleep (including wake, rapid eye movement (REM) sleep, and non-REM sleep) in adults, we found that previously reported ApEn decreases across vigilance states in adults were also present in children (ApEn trends for both age groups: wake > REM sleep > non-REM sleep). When comparing ApEn values between age groups, adults had significantly larger ApEn values than children during wakefulness. After the application of an 8 Hz high-pass filter to the EEG signal, ApEn values were recalculated. The number of electrodes with significant vigilance state effects dropped from all 109 electrodes with the original 1 Hz filter to 1 electrode with the 8 Hz filter. The number of electrodes with significant age effects dropped from 10 to 4. Our results support the notion that ApEn can reliably distinguish between vigilance states, with low-frequency sleep-related oscillations implicated as the driver of changes between vigilance states. We suggest that the observed differences between adult and child ApEn values during wake may reflect differences in connectivity between age groups, a factor which may be important in the use of EEG to measure consciousness.
Topological Filtering of Dynamic Functional Brain Networks Unfolds Informative Chronnectomics: A Novel Data-Driven Thresholding Scheme Based on Orthogonal Minimal Spanning Trees (OMSTs)
Dimitriadis, Stavros I.; Salis, Christos; Tarnanas, Ioannis; et al. (2017)
Frontiers in Neuroinformatics
The human brain is a large-scale system of functionally connected brain regions. This system can be modeled as a network, or graph, by dividing the brain into a set of regions, or “nodes,” and quantifying the strength of the connections between nodes, or “edges,” as the temporal correlation in their patterns of activity. Network analysis, a part of graph theory, provides a set of summary statistics that can be used to describe complex brain networks in a meaningful way. The large-scale organization of the brain has features of complex networks that can be quantified using network measures from graph theory. The adaptation of both bivariate (mutual information) and multivariate (Granger causality) connectivity estimators to quantify the synchronization between multichannel recordings yields a fully connected, weighted, (a)symmetric functional connectivity graph (FCG), representing the associations among all brain areas. The aforementioned procedure leads to an extremely dense network of tens up to a few hundreds of weights. Therefore, this FCG must be filtered out so that the “true” connectivity pattern can emerge. Here, we compared a large number of well-known topological thresholding techniques with the novel proposed data-driven scheme based on orthogonal minimal spanning trees (OMSTs). OMSTs filter brain connectivity networks based on the optimization between the global efficiency of the network and the cost preserving its wiring. We demonstrated the proposed method in a large EEG database (N = 101 subjects) with eyes-open (EO) and eyes-closed (EC) tasks by adopting a time-varying approach with the main goal to extract features that can totally distinguish each subject from the rest of the set. Additionally, the reliability of the proposed scheme was estimated in a second case study of fMRI resting-state activity with multiple scans. Our results demonstrated clearly that the proposed thresholding scheme outperformed a large list of thresholding schemes based on the recognition accuracy of each subject compared to the rest of the cohort (EEG). Additionally, the reliability of the network metrics based on the fMRI static networks was improved based on the proposed topological filtering scheme. Overall, the proposed algorithm could be used across neuroimaging and multimodal studies as a common computationally efficient standardized tool for a great number of neuroscientists and physicists working on numerous of projects.
Detecting Large-Scale Brain Networks Using EEG: Impact of Electrode Density, Head Modeling and Source Localization
Liu, Quanying; Ganzetti, Marco; Wenderoth, Nicole; et al. (2018)
Frontiers in Neuroinformatics
Predicting in vitro single-neuron firing rates upon pharmacological perturbation using Graph Neural Networks
Kim, Taehoon; Chen, Dexiong; Hornauer, Philipp; et al. (2023)
Frontiers in Neuroinformatics
Modern Graph Neural Networks (GNNs) provide opportunities to study the determinants underlying the complex activity patterns of biological neuronal networks. In this study, we applied GNNs to a large-scale electrophysiological dataset of rodent primary neuronal networks obtained by means of high-density microelectrode arrays (HD-MEAs). HD-MEAs allow for long-term recording of extracellular spiking activity of individual neurons and networks and enable the extraction of physiologically relevant features at the singleneuron and population level. We employed established GNNs to generate a combined representation of single-neuron and connectivity features obtained from HD-MEA data, with the ultimate goal of predicting changes in single-neuron firing rate induced by a pharmacological perturbation. The aim of the main prediction task was to assess whether single-neuron and functional connectivity features, inferred under baseline conditions, were informative for predicting changes in neuronal activity in response to a perturbation with Bicuculline, a GABAA receptor antagonist. Our results suggest that the joint representation of node features and functional connectivity, extracted from a baseline recording, was informative for predicting firing rate changes of individual neurons after the perturbation. Specifically, our implementation of a GNN model with inductive learning capability (GraphSAGE) outperformed other prediction models that relied only on single-neuron features. We tested the generalizability of the results on two additional datasets of HD-MEA recordings–a second dataset with cultures perturbed with Bicuculline and a dataset perturbed with the GABAA receptor antagonist Gabazine. GraphSAGE models showed improved prediction accuracy over other prediction models. Our results demonstrate the added value of taking into account the functional connectivity between neurons and the potential of GNNs to study complex interactions between neurons.
Tracking axon initial segment plasticity using high-density microelectrode arrays: A computational study
Kumar, Sreedhar S.; Gänswein, Tobias; Buccino, Alessio Paolo; et al. (2022)
Frontiers in Neuroinformatics
Despite being composed of highly plastic neurons with extensive positive feedback, the nervous system maintains stable overall function. To keep activity within bounds, it relies on a set of negative feedback mechanisms that can induce stabilizing adjustments and that are collectively termed “homeostatic plasticity.” Recently, a highly excitable microdomain, located at the proximal end of the axon – the axon initial segment (AIS) – was found to exhibit structural modifications in response to activity perturbations. Though AIS plasticity appears to serve a homeostatic purpose, many aspects governing its expression and its functional role in regulating neuronal excitability remain elusive. A central challenge in studying the phenomenon is the rich heterogeneity of its expression (distal/proximal relocation, shortening, lengthening) and the variability of its functional role. A potential solution is to track AISs of a large number of neurons over time and attempt to induce structural plasticity in them. To this end, a promising approach is to use extracellular electrophysiological readouts to track a large number of neurons at high spatiotemporal resolution by means of high-density microelectrode arrays (HD-MEAs). However, an analysis framework that reliably identifies specific activity signatures that uniquely map on to underlying microstructural changes is missing. In this study, we assessed the feasibility of such a task and used the distal relocation of the AIS as an exemplary problem. We used sophisticated computational models to systematically explore the relationship between incremental changes in AIS positions and the specific consequences observed in simulated extracellular field potentials. An ensemble of feature changes in the extracellular fields that reliably characterize AIS plasticity was identified. We trained models that could detect these signatures with remarkable accuracy. Based on these findings, we propose a hybrid analysis framework that could potentially enable high-throughput experimental studies of activity-dependent AIS plasticity using HD-MEAs.
Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN
Valevicius, Darius; Beck, Natacha; Kasper, Lars; et al. (2023)
Frontiers in Neuroinformatics
Neuroimaging research requires sophisticated tools for analyzing complex data, but efficiently leveraging these tools can be a major challenge, especially on large datasets. CBRAIN is a web-based platform designed to simplify the use and accessibility of neuroimaging research tools for large-scale, collaborative studies. In this paper, we describe how CBRAIN’s unique features and infrastructure were leveraged to integrate TAPAS PhysIO, an open-source MATLAB toolbox for physiological noise modeling in fMRI data. This case study highlights three key elements of CBRAIN’s infrastructure that enable streamlined, multimodal tool integration: a user-friendly GUI, a Brain Imaging Data Structure (BIDS) data-entry schema, and convenient in-browser visualization of results. By incorporating PhysIO into CBRAIN, we achieved significant improvements in the speed, ease of use, and scalability of physiological preprocessing. Researchers now have access to a uniform and intuitive interface for analyzing data, which facilitates remote and collaborative evaluation of results. With these improvements, CBRAIN aims to become an essential open-science tool for integrative neuroimaging research, supporting FAIR principles and enabling efficient workflows for complex analysis pipelines.
ProbeInterface: A Unified Framework for Probe Handling in Extracellular Electrophysiology
Garcia, Samuel; Sprenger, Julia; Holtzman, Tahl; et al. (2022)
Frontiers in Neuroinformatics
Recording neuronal activity with penetrating extracellular multi-channel electrode arrays, more commonly known as neural probes, is one of the most widespread approaches to probe neuronal activity. Despite a plethora of available extracellular probe designs, the time-consuming process of mapping of electrode channel order and relative geometries, as required by spike-sorting software is invariably left to the end-user. Consequently, this manual process is prone to mis-mapping mistakes, which in turn lead to undesirable spike-sorting errors and inefficiencies. Here, we introduce ProbeInterface, an open-source project that aims to unify neural probe metadata descriptions by removing the manual step of probe mapping prior to spike-sorting for the analysis of extracellular neural recordings. ProbeInterface is first of all a Python API, which enables users to create and visualize probes and probe groups at any required complexity level. Second, ProbeInterface facilitates the generation of comprehensive wiring description in a reproducible fashion for any specific data-acquisition setup, which usually involves the use of a recording probe, a headstage, adapters, and an acquisition system. Third, we collaborate with probe manufacturers to compile an open library of available probes, which can be downloaded at run time using our Python API. Finally, with ProbeInterface we define a file format for probe handling which includes all necessary information for a FAIR probe description and is compatible with and complementary to other open standards in neuroscience.
An Automated Open-Source Workflow for Standards-Compliant Integration of Small Animal Magnetic Resonance Imaging Data
Ioanas, Horea-Ioan; Marks, Markus; Garin, Clément M.; et al. (2020)
Frontiers in Neuroinformatics
Large-scale research integration is contingent on seamless access to data in standardized formats. Standards enable researchers to understand external experiment structures, pool results, and apply homogeneous preprocessing and analysis workflows. Particularly, they facilitate these features without the need for numerous potentially confounding compatibility add-ons. In small animal magnetic resonance imaging, an overwhelming proportion of data is acquired via the ParaVision software of the Bruker Corporation. The original data structure is predominantly transparent, but fundamentally incompatible with modern pipelines. Additionally, it sources metadata from free-field operator input, which diverges strongly between laboratories and researchers. In this article we present an open-source workflow which automatically converts and reposits data from the ParaVision structure into the widely supported and openly documented Brain Imaging Data Structure (BIDS). Complementing this workflow we also present operator guidelines for appropriate ParaVision data input, and a programmatic walk-through detailing how preexisting scans with uninterpretable metadata records can easily be made compliant after the acquisition.
Experimental Pipeline (Expipe): A Lightweight Data Management Platform to Simplify the Steps From Experiment to Data Analysis
Lepperød, Mikkel Elle; Dragly, Svenn-Arne; Buccino, Alessio Paolo; et al. (2020)
Frontiers in Neuroinformatics
As experimental neuroscience is moving toward more integrative approaches, with a variety of acquisition techniques covering multiple spatiotemporal scales, data management is becoming increasingly challenging for neuroscience laboratories. Often, datasets are too large to practically be stored on a laptop or a workstation. The ability to query metadata collections without retrieving complete datasets is therefore critical to efficiently perform new analyses and explore the data. At the same time, new experimental paradigms lead to constantly changing specifications for the metadata to be stored. Despite this, there is currently a serious lack of agile software tools for data management in neuroscience laboratories. To meet this need, we have developed Expipe, a lightweight data management framework that simplifies the steps from experiment to data analysis. Expipe provides the functionality to store and organize experimental data and metadata for easy retrieval in exploration and analysis throughout the experimental pipeline. It is flexible in terms of defining the metadata to store and aims to solve the storage and retrieval challenges of data/metadata due to ever changing experimental pipelines. Due to its simplicity and lightweight design, we envision Expipe as an easy-to-use data management solution for experimental laboratories, that can improve provenance, reproducibility, and sharing of scientific projects.

Publications 1 - 10 of 18

Journal: Frontiers in Neuroinformatics

Abbreviation

Publisher

Journal Volumes

ISSN

Description

Filters

Search Results