nrv.nmod

Description

NEURON Models - nmod: handles neural fiber models using the NEURON software.

nmod contains all the code to describe the axonal fibers using .mod mechanisms with NEURON. This subpackage contains all primitives to describe:

• unmyelinated axons with different models of nonlinear conductances,

• myelinated axons with different models of nonlinear conductances,

• fascicles consisting in bundles of (potentiallymixed ) axons,

• nerves containing one or more fascicles.

nmod also contains tools to automatically generate fascicles and nerves, with fiber repartition mimicking realistic anatomical observations.

Classes describing fibers, fascicles and nerves are simulable, meaning they all have a simulate method that triggers the simulation. Only the top level structure of the simulated scenario has to be simulated by the user, nrv takes care of handling the simulation, potential combination with subpackages (such as nmod or eit for instance). Parallel computing is also handled internally.

Note

for scientific details of how nmod works and an overview of the general implementation, refer to the ‘Scientific foundations’ section of the documentation.

Subpackages

results

nmod Results: standardized result gathering for nmod simulations.

Classes

axon([y, z, d, L, dt, Nseg_per_sec, freq, ...])	A generic object to describe an axonal fiber (soma and interconnection are not taken into account, all axons are independant from others).
unmyelinated([y, z, d, L, model, dt, Nrec, ...])	Unmyelinated axon class.
myelinated([y, z, d, L, model, dt, ...])	Myelinated axon class.
fascicle([diameter, ID])	Class for Fascicle, defined as a group of axons near one to the other in the same Perineurium Sheath.
nerve([length, diameter, Outer_D, ID])	A nerve in NRV is defined as:

Functions

create_axon_population(N[, percent_unmyel, ...])	Create a virtual population of axons (no Neuron implementation, axon class not called) of a controled number, with controlled statistics.
plot_population(diameters, y_axons, z_axons, ...)	Display a population of axons.
save_axon_population(f_name, ...[, y_axons, ...])	Save a placed axonal population to a file
load_axon_population(f_name)	Load a placed population from a file
fill_area_with_axons(A[, percent_unmyel, ...])	Create a virtual population of axons (no Neuron implementation, axon class not called) to fill a specified area, with controlled statistics.
axon_packer(diameters[, y_gc, z_gc, delta, ...])	Axon Packing algorithm: this operation takes a vector of diameter (random population) and places it at best.
expand_pop(y_axons, z_axons, factor)	Expand population of placed axons by a specified number
remove_collision(axons_diameters, y_axons, ...)	Remove collinding axons in a population
remove_outlier_axons(axons_diameters, ...[, ...])	Remove axons in a population located outside a circular border, defined by its diameter
get_circular_contour(axons_diameters, ...[, ...])	Get a circular contour diameter of the axon population
load_stat(stat_name)	Load a statistic stored in the included librairy or specified by the user in a csv file (first corlumn: axon diameter bin start - second corlumn: proportion)