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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.


Comparison of simulated LFPs from the Bush and Mainen cell models. Top (red) L2/3 pyramidal neuron, middle (green) spiny stellate cell (morphology also used for interneurons), bottom (blue) L5 pyramidal neuron. a Comparison of original and reduced multi-compartment models of each neuron type. b Range and magnitude of simulated LFPs. Circles show values for the original cell reconstruction populations, triangles for the reduced neuron model populations. Light red dashed lines in the top panel and light blue circles in bottom panel show values for the extra cat pyramidal neurons tested, as described in the main text. All y-axis values in μm. c Overlap of the 95 % confidence intervals for the estimated LFP power spectra produced by each population in each layer shadeddark. Non-overlapping sections of the 95 % confidence intervals are shaded light. Power is plotted in dimensionless, normalised units for ease of comparison
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Fig1: Comparison of simulated LFPs from the Bush and Mainen cell models. Top (red) L2/3 pyramidal neuron, middle (green) spiny stellate cell (morphology also used for interneurons), bottom (blue) L5 pyramidal neuron. a Comparison of original and reduced multi-compartment models of each neuron type. b Range and magnitude of simulated LFPs. Circles show values for the original cell reconstruction populations, triangles for the reduced neuron model populations. Light red dashed lines in the top panel and light blue circles in bottom panel show values for the extra cat pyramidal neurons tested, as described in the main text. All y-axis values in μm. c Overlap of the 95 % confidence intervals for the estimated LFP power spectra produced by each population in each layer shadeddark. Non-overlapping sections of the 95 % confidence intervals are shaded light. Power is plotted in dimensionless, normalised units for ease of comparison

Mentions: The results of these experiments are shown in Fig. 1. For each neuron type, the LFP range and magnitude in each layer for the population of Bush cells are close to those for the population of Mainen cells. The LFP range is smallest in the soma layer (<250 μm) with the range increasing in the layers above and below the soma, while the LFP magnitude is largest in the soma layer and decreases in the layers above and below the soma. The differences between the results for the L4 spiny stellate models are small, so we concentrate on the pyramidal neuron population results. For the L2/3 pyramidal neurons, the LFP spatial range in the soma layer is very similar between the Bush and Mainen populations, but above and below this layer the discrepancy increases, with the largest difference of 200 μm in L1. The range differences in all other layers are ≤110 μm. For the L5 pyramidal neurons, the LFP spatial range difference is again smallest in the soma layer, and <100 μm in layers 4 and 1. The largest difference is 320 μm in L2/3.Fig. 1


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)

Comparison of simulated LFPs from the Bush and Mainen cell models. Top (red) L2/3 pyramidal neuron, middle (green) spiny stellate cell (morphology also used for interneurons), bottom (blue) L5 pyramidal neuron. a Comparison of original and reduced multi-compartment models of each neuron type. b Range and magnitude of simulated LFPs. Circles show values for the original cell reconstruction populations, triangles for the reduced neuron model populations. Light red dashed lines in the top panel and light blue circles in bottom panel show values for the extra cat pyramidal neurons tested, as described in the main text. All y-axis values in μm. c Overlap of the 95 % confidence intervals for the estimated LFP power spectra produced by each population in each layer shadeddark. Non-overlapping sections of the 95 % confidence intervals are shaded light. Power is plotted in dimensionless, normalised units for ease of comparison
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4481302&req=5

Fig1: Comparison of simulated LFPs from the Bush and Mainen cell models. Top (red) L2/3 pyramidal neuron, middle (green) spiny stellate cell (morphology also used for interneurons), bottom (blue) L5 pyramidal neuron. a Comparison of original and reduced multi-compartment models of each neuron type. b Range and magnitude of simulated LFPs. Circles show values for the original cell reconstruction populations, triangles for the reduced neuron model populations. Light red dashed lines in the top panel and light blue circles in bottom panel show values for the extra cat pyramidal neurons tested, as described in the main text. All y-axis values in μm. c Overlap of the 95 % confidence intervals for the estimated LFP power spectra produced by each population in each layer shadeddark. Non-overlapping sections of the 95 % confidence intervals are shaded light. Power is plotted in dimensionless, normalised units for ease of comparison
Mentions: The results of these experiments are shown in Fig. 1. For each neuron type, the LFP range and magnitude in each layer for the population of Bush cells are close to those for the population of Mainen cells. The LFP range is smallest in the soma layer (<250 μm) with the range increasing in the layers above and below the soma, while the LFP magnitude is largest in the soma layer and decreases in the layers above and below the soma. The differences between the results for the L4 spiny stellate models are small, so we concentrate on the pyramidal neuron population results. For the L2/3 pyramidal neurons, the LFP spatial range in the soma layer is very similar between the Bush and Mainen populations, but above and below this layer the discrepancy increases, with the largest difference of 200 μm in L1. The range differences in all other layers are ≤110 μm. For the L5 pyramidal neurons, the LFP spatial range difference is again smallest in the soma layer, and <100 μm in layers 4 and 1. The largest difference is 320 μm in L2/3.Fig. 1

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.