Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0

Abstract

Recordings of extracellular electrical, and later also magnetic, brain signals have been the dominant technique for measuring brain activity for decades. The interpretation of such signals is however nontrivial, as the measured signals result from both local and distant neuronal activity. In volume-conductor theory the extracellular potentials can be calculated from a distance-weighted sum of contributions from transmembrane currents of neurons. Given the same transmembrane currents, the contributions to the magnetic field recorded both inside and outside the brain can also be computed. This allows for the development of computational tools implementing forward models grounded in the biophysics underlying electrical and magnetic measurement modalities. LFPy (LFPy.readthedocs.io) incorporated a well-established scheme for predicting extracellular potentials of individual neurons with arbitrary levels of biological detail. It relies on NEURON (neuron.yale.edu) to compute transmembrane currents of multicompartment neurons which is then used in combination with an electrostatic forward model. Its functionality is now extended to allow for modeling of networks of multicompartment neurons with concurrent calculations of extracellular potentials and current dipole moments. The current dipole moments are then, in combination with suitable volume-conductor head models, used to compute non-invasive measures of neuronal activity, like scalp potentials (electroencephalographic recordings; EEG) and magnetic fields outside the head (magnetoencephalographic recordings; MEG). One such built-in head model is the four-sphere head model incorporating the different electric conductivities of brain, cerebrospinal fluid, skull and scalp. We demonstrate the new functionality of the software by constructing a network of biophysically detailed multicompartment neuron models from the Neocortical Microcircuit Collaboration (NMC) Portal (bbp.epfl.ch/nmc-portal) with corresponding statistics of connections and synapses, and compute in vivo-like extracellular potentials (local field potentials, LFP; electrocorticographical signals, ECoG) and corresponding current dipole moments. From the current dipole moments we estimate corresponding EEG and MEG signals using the four-sphere head model. We also show strong scaling performance of LFPy with different numbers of message-passing interface (MPI) processes, and for different network sizes with different density of connections. The open-source software LFPy is equally suitable for execution on laptops and in parallel on high-performance computing (HPC) facilities and is publicly available on GitHub.com.

LFPy – multimodal modeling of extracellular neuronal recordings in Python

“…Since LFPy 2.0 (Hagen et al, 2018), the tool has been extended to also support forward-model predictions accounting for anisotropic media, that is, with different conductivity in different directions (Goto et al, 2010), and discontinuous media where the conductivity is piecewise constant in a single direction. The latter can for example be used to mimic in vitro experimental setups using microelectrode arrays (MEAs) , or to mimic in vivo conditions where a jump in conductivity can be expected such as at the boundary between the brain and CSF.…”

“…Finally, in contrast to its first release where the tool only supported simulations with a single cell instantiation at the time, LFPy also supports networks of synaptically interconnected neurons. Such network simulations can be executed on a single physical machine, but larger network simulations is better executed in parallel on highperformance computing (HPC) facilities (Hagen et al, 2018).…”

“…LFPy is a Python package that presently (Hagen et al, 2018) provides different highlevel class definitions which represent cells, populations and networks of cells, synapses, intracellular stimulation devices (current and voltage clamps) and extracellular recording devices (representing both invasive and noninvasive equipment). LFPy's class definitions rely internally on NEURON's Python interface (Hines et al, 2009).…”

“…As the different electrostatic and magnetostatic forward models in LFPy are described in detail in Hagen et al (2018), we here briefly summarize their main assumptions.…”

MEArec: a fast and customizable testbench simulator for ground-truth extracellular spiking activity

“…Hagen et al developed ViSAPy [19], a Python-based simulator that uses multi-compartment simulation of single neurons to generate spikes, network modeling of point-neurons in NEST [10] to generate synaptic inputs onto the spiking neurons, and experimentally fitted noise. ViSAPy runs a full network simulation in NEURON [8] and computes the extracellular potentials using LFPy [30,18]. ViSAPy implements a Python application programming interface (API) which allows the user to set multiple parameters for the network simulation providing the synaptic input, the probe design, and the noise model generator.…”