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Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue.

Tomsett RJ, Ainsworth M, Thiele A, Sanayei M, Chen X, Gieselmann MA, Whittington MA, Cunningham MO, Kaiser M - Brain Struct Funct (2014)

Bottom Line: We first identified a reduced neuron model that retained the spatial and frequency filtering characteristics of extracellular potentials from neocortical neurons.A VERTEX-based simulation successfully reproduced features of the LFPs from an in vitro multi-electrode array recording of macaque neocortical tissue.We envisage that VERTEX will stimulate experimentalists, clinicians, and computational neuroscientists to use models to understand the mechanisms underlying measured brain dynamics in health and disease.

View Article: PubMed Central - PubMed

Affiliation: School of Computing Science, Newcastle University, Claremont Tower, Newcastle upon Tyne, NE1 7RU, UK, indigentmartian@gmail.com.

ABSTRACT
Local field potentials (LFPs) sampled with extracellular electrodes are frequently used as a measure of population neuronal activity. However, relating such measurements to underlying neuronal behaviour and connectivity is non-trivial. To help study this link, we developed the Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX). We first identified a reduced neuron model that retained the spatial and frequency filtering characteristics of extracellular potentials from neocortical neurons. We then developed VERTEX as an easy-to-use Matlab tool for simulating LFPs from large populations (>100,000 neurons). A VERTEX-based simulation successfully reproduced features of the LFPs from an in vitro multi-electrode array recording of macaque neocortical tissue. Our model, with virtual electrodes placed anywhere in 3D, allows direct comparisons with the in vitro recording setup. We envisage that VERTEX will stimulate experimentalists, clinicians, and computational neuroscientists to use models to understand the mechanisms underlying measured brain dynamics in health and disease.

No MeSH data available.


Overview of the VERTEX simulation software. a Simulation workflow. The user provides parameters as Matlab structures to setup the neuron populations, position them in layers, connect them together, and simulate their dynamics and the resultant LFPs. Functionality to export to NeuroML is currently under development. b Example program structure. The main simulation program only requires calls to the initNetwork() function and the runSimulation() function, with the information required to setup the simulation specified in separate script files
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Fig3: Overview of the VERTEX simulation software. a Simulation workflow. The user provides parameters as Matlab structures to setup the neuron populations, position them in layers, connect them together, and simulate their dynamics and the resultant LFPs. Functionality to export to NeuroML is currently under development. b Example program structure. The main simulation program only requires calls to the initNetwork() function and the runSimulation() function, with the information required to setup the simulation specified in separate script files

Mentions: To simulate large networks, we wrote custom Matlab software to setup neuron populations, position them, connect them together, and simulate their dynamics and the resultant LFPs. We designed this simulation tool to be easily adaptable to create models of any layered brain tissue containing populations of spiking neurons (Fig. 3). Model parameters are specified by the user in Matlab structures, defining:Fig. 3


Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue.

Tomsett RJ, Ainsworth M, Thiele A, Sanayei M, Chen X, Gieselmann MA, Whittington MA, Cunningham MO, Kaiser M - Brain Struct Funct (2014)

Overview of the VERTEX simulation software. a Simulation workflow. The user provides parameters as Matlab structures to setup the neuron populations, position them in layers, connect them together, and simulate their dynamics and the resultant LFPs. Functionality to export to NeuroML is currently under development. b Example program structure. The main simulation program only requires calls to the initNetwork() function and the runSimulation() function, with the information required to setup the simulation specified in separate script files
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4481302&req=5

Fig3: Overview of the VERTEX simulation software. a Simulation workflow. The user provides parameters as Matlab structures to setup the neuron populations, position them in layers, connect them together, and simulate their dynamics and the resultant LFPs. Functionality to export to NeuroML is currently under development. b Example program structure. The main simulation program only requires calls to the initNetwork() function and the runSimulation() function, with the information required to setup the simulation specified in separate script files
Mentions: To simulate large networks, we wrote custom Matlab software to setup neuron populations, position them, connect them together, and simulate their dynamics and the resultant LFPs. We designed this simulation tool to be easily adaptable to create models of any layered brain tissue containing populations of spiking neurons (Fig. 3). Model parameters are specified by the user in Matlab structures, defining:Fig. 3

Bottom Line: We first identified a reduced neuron model that retained the spatial and frequency filtering characteristics of extracellular potentials from neocortical neurons.A VERTEX-based simulation successfully reproduced features of the LFPs from an in vitro multi-electrode array recording of macaque neocortical tissue.We envisage that VERTEX will stimulate experimentalists, clinicians, and computational neuroscientists to use models to understand the mechanisms underlying measured brain dynamics in health and disease.

View Article: PubMed Central - PubMed

Affiliation: School of Computing Science, Newcastle University, Claremont Tower, Newcastle upon Tyne, NE1 7RU, UK, indigentmartian@gmail.com.

ABSTRACT
Local field potentials (LFPs) sampled with extracellular electrodes are frequently used as a measure of population neuronal activity. However, relating such measurements to underlying neuronal behaviour and connectivity is non-trivial. To help study this link, we developed the Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX). We first identified a reduced neuron model that retained the spatial and frequency filtering characteristics of extracellular potentials from neocortical neurons. We then developed VERTEX as an easy-to-use Matlab tool for simulating LFPs from large populations (>100,000 neurons). A VERTEX-based simulation successfully reproduced features of the LFPs from an in vitro multi-electrode array recording of macaque neocortical tissue. Our model, with virtual electrodes placed anywhere in 3D, allows direct comparisons with the in vitro recording setup. We envisage that VERTEX will stimulate experimentalists, clinicians, and computational neuroscientists to use models to understand the mechanisms underlying measured brain dynamics in health and disease.

No MeSH data available.