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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 for highly correlated input at the soma compartment. Top (red) L2/3 pyramidal neurons, bottom (blue) L5 pyramidal neurons. a Range and magnitude of simulated LFPs. Bright red/blue lines show range and magnitude values for the Mainen cell populations, dark red/blue lines show range and magnitude values for the Bush cell populations. The faded red/blue dashed lines show these values for the additionally tested cell populations in L2/3 and in L5. Grey dashed lines show layer boundaries, black solid lines show the maximum and minimum soma depths. All y-axis values in μm. c Overlap of the 95 % confidence intervals for the estimated LFP power spectra produced by the L2/3 and L5 pyramidal neuron populations at each electrode location shaded dark (correlated input at soma). Non-overlapping sections of the 95 % confidence intervals are shaded light. Power is plotted in dimensionless, normalised units for ease of comparison. Comparisons for only 13 out of the 26 LFP measurement points for the L5 populations are shown for ease of visualisation
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Fig2: Comparison of simulated LFPs from the Bush and Mainen cell models for highly correlated input at the soma compartment. Top (red) L2/3 pyramidal neurons, bottom (blue) L5 pyramidal neurons. a Range and magnitude of simulated LFPs. Bright red/blue lines show range and magnitude values for the Mainen cell populations, dark red/blue lines show range and magnitude values for the Bush cell populations. The faded red/blue dashed lines show these values for the additionally tested cell populations in L2/3 and in L5. Grey dashed lines show layer boundaries, black solid lines show the maximum and minimum soma depths. All y-axis values in μm. c Overlap of the 95 % confidence intervals for the estimated LFP power spectra produced by the L2/3 and L5 pyramidal neuron populations at each electrode location shaded dark (correlated input at soma). Non-overlapping sections of the 95 % confidence intervals are shaded light. Power is plotted in dimensionless, normalised units for ease of comparison. Comparisons for only 13 out of the 26 LFP measurement points for the L5 populations are shown for ease of visualisation

Mentions: Figure 2 shows the spatial profiles of the LFP for the different populations. In these simulations, we measured the LFP at 50 intervals, to see how well the Bush models preserved the LFP at this level of detail. We used 11 electrode points in L1 and L2/3 for the L2/3 populations, and 26 electrode points spanning all layers for the L5 populations. Both the range and magnitude profiles show that the LFP from the Bush population matched the LFP from the Mainen population well, again within the bounds of the LFP profile of the extra comparison populations. The minimum range and magnitude in the L2/3 populations are just above the minimum soma depth, and a few 100 μm above the minimum soma depth in the L5 population. This depth is where the synaptic currents at the soma are approximately balanced by the opposite return currents in the dendrites; below and above this minimum point, the somatic or the apical dendritic currents dominate the LFP signal, respectively. These simulations also show substantial overlap of the 95 % confidence intervals for the power spectra at each electrode (Fig. 2b). The biggest discrepancy between the LFP power spectra for each model occurs around the level of the LFP range minimum. The LFP power up to 100 Hz is reliably reproduced at every measurement point, and up to 450 Hz at all but one point with the L2/3 populations. This point corresponds to the point at which the LFP range and magnitude are lowest. The reduced accuracy at higher frequencies in the L5 models should be taken into account if frequencies above 100 Hz are analysed in models containing L5 pyramidal cells.Fig. 2


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 for highly correlated input at the soma compartment. Top (red) L2/3 pyramidal neurons, bottom (blue) L5 pyramidal neurons. a Range and magnitude of simulated LFPs. Bright red/blue lines show range and magnitude values for the Mainen cell populations, dark red/blue lines show range and magnitude values for the Bush cell populations. The faded red/blue dashed lines show these values for the additionally tested cell populations in L2/3 and in L5. Grey dashed lines show layer boundaries, black solid lines show the maximum and minimum soma depths. All y-axis values in μm. c Overlap of the 95 % confidence intervals for the estimated LFP power spectra produced by the L2/3 and L5 pyramidal neuron populations at each electrode location shaded dark (correlated input at soma). Non-overlapping sections of the 95 % confidence intervals are shaded light. Power is plotted in dimensionless, normalised units for ease of comparison. Comparisons for only 13 out of the 26 LFP measurement points for the L5 populations are shown for ease of visualisation
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Related In: Results  -  Collection

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Fig2: Comparison of simulated LFPs from the Bush and Mainen cell models for highly correlated input at the soma compartment. Top (red) L2/3 pyramidal neurons, bottom (blue) L5 pyramidal neurons. a Range and magnitude of simulated LFPs. Bright red/blue lines show range and magnitude values for the Mainen cell populations, dark red/blue lines show range and magnitude values for the Bush cell populations. The faded red/blue dashed lines show these values for the additionally tested cell populations in L2/3 and in L5. Grey dashed lines show layer boundaries, black solid lines show the maximum and minimum soma depths. All y-axis values in μm. c Overlap of the 95 % confidence intervals for the estimated LFP power spectra produced by the L2/3 and L5 pyramidal neuron populations at each electrode location shaded dark (correlated input at soma). Non-overlapping sections of the 95 % confidence intervals are shaded light. Power is plotted in dimensionless, normalised units for ease of comparison. Comparisons for only 13 out of the 26 LFP measurement points for the L5 populations are shown for ease of visualisation
Mentions: Figure 2 shows the spatial profiles of the LFP for the different populations. In these simulations, we measured the LFP at 50 intervals, to see how well the Bush models preserved the LFP at this level of detail. We used 11 electrode points in L1 and L2/3 for the L2/3 populations, and 26 electrode points spanning all layers for the L5 populations. Both the range and magnitude profiles show that the LFP from the Bush population matched the LFP from the Mainen population well, again within the bounds of the LFP profile of the extra comparison populations. The minimum range and magnitude in the L2/3 populations are just above the minimum soma depth, and a few 100 μm above the minimum soma depth in the L5 population. This depth is where the synaptic currents at the soma are approximately balanced by the opposite return currents in the dendrites; below and above this minimum point, the somatic or the apical dendritic currents dominate the LFP signal, respectively. These simulations also show substantial overlap of the 95 % confidence intervals for the power spectra at each electrode (Fig. 2b). The biggest discrepancy between the LFP power spectra for each model occurs around the level of the LFP range minimum. The LFP power up to 100 Hz is reliably reproduced at every measurement point, and up to 450 Hz at all but one point with the L2/3 populations. This point corresponds to the point at which the LFP range and magnitude are lowest. The reduced accuracy at higher frequencies in the L5 models should be taken into account if frequencies above 100 Hz are analysed in models containing L5 pyramidal cells.Fig. 2

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.