axons.mat

Axon population data file

axons~/axons (name).mat contains the data for an axon population and nerve fascicle outline. Generated by models.axon_population. Used by models.membrane_currents, models.axon_thresholds, and models.nerve_stimulation.

The variables saved in an axons.mat file are:

Variable	Type	Description
nerve	struct	cross-sectional anatomy of the nerve, as returned by mesh.insert_gmsh_fascicles at the time of axon population generation.
nerve.filename	char	source filename (typically a MBF .xml) for nerve cross-section.
nerve.coeffs	double 2 x nPoints x nFascicles	spline coefficients for anatomy as meshed in GMSH. nerve.coeffs(1,:,1) returns the x-coordinate of the outline of fascicle 1, nerve.coeffs(2,:,1) returns the y-coordinate of the outline of fascicle 1.
nerve.outline	double nPoints x 2 x nFascicles	higher-resolution outline of the fascicle for visualisation purposes.
nerve.type	char `{'Fascicle'}	what type of object is described by this set of outlines?
nerve.info	char	information about fascicle generation process
opts	cell	input arguments passed into models.axon_population at time of axon population generation
pop	struct array (1 x n_types)	data about each axon population (typically in the order: Myelinated Afferents, Myelinated Efferents, Unmyelinated Afferents, Unmyelinated Efferents)

the pop structure:

Variable	Type	Description
pop.axon_type	char	Axon type e.g. 'Myelinated Afferent'
pop.axon_model	char	Corresponding axon model e.g. 'Gaines'. See models.axon_model for more information.
pop.afferent	logical scalar	Is this axon class an afferent class? (affects models.nerve_recording
pop.myelinated	logical scalar	Is this axon class myelinated?
pop.fibre_diam	double (nAxons x 1)	Fibre diameter for each axon in µm (axon + myelin for myelinated axons, axon diameter for unmyelinated axons)
pop.axon_diam	double (nAxons x 1)	Inner (axon) diameter for each axon in µm (myelinated axons only; [] for unmyelinated axons)
pop.g_ratio	double (nAxons x 1)	Ratio of inner (axon) to outer (fibre) diameter for each axon in µm (myelinated axons only; [] for unmyelinated axons)
pop.axon_xy	double (nAxons x 2)	Location of each axon in the same coordinate system as nerve.outline, in µm
pop.fascicle	integer (nAxons x 1)	To which fascicle does each axon belong?
pop.size_sample	integer (nAxons x 1)	Based on clustering of axon properties, which subgroup is this axon a member of?
pop.color	color (1 x 3), range 0-1	When displaying this axon class in graphics (e.g. plots.preview_axons, what color marker or trace should this axon class use for display?