fascicle

class nrv.nmod.fascicle(diameter=None, ID=0, **kwargs)

Class for Fascicle, defined as a group of axons near one to the other in the same Perineurium Sheath. All axons are independant of each other, no ephaptic coupling.

See also

Simulables users guide, Nerve-class, Axon-class

Customizable Attributes:

Attributes	Type	Default	Description
ID	int	0	Identification number of the fascicle.
L	float	None	Length of the fascicle.
D	float	None	Diameter of the fascicle.
y_grav_center	float	0	y-position of the fascicle center.
z_grav_center	float	0	z-position of the fascicle center.
postproc_label	str	None	Label of the axon postprocessing funtion, used for the buildin postproc functions.
postproc_function	function	None	Axon postprocessing funtion, used for the custom postproc functions.
postproc_script	str | function	None	Either postprocessing funtion or postprocessing funtion label, automatically set depending on the type
postproc_kwargs	dict	None	key arguments of the postporcessing function
save_results	bool	False	If True, fascicle configuration and all axon simulations results are saved in save_path directory.
save_path	str	“”	Path of the directory where simulation results should be saved.
return_parameters_only	bool	False	If True (and save_results also True), only the parameters should be returned from the simulation.
loaded_footprints	bool	False	If False, the footprints already computed are favored over new footprint computation.
verbose	bool	False	Plot or not.

Note

Customizable attributes can either be set using fascicle.set_parameters() or simply by reafecting the value of the attribute.

Tip

Additional simulation parameters can be changed using (fascicle.set_axons_parameters(), fascicle.change_stimulus_from_electrode(), …).

Attributes

fascicle.A	Area of the fascicle
fascicle.N
fascicle.n_ax	Number of axons in the fascicle

Methods

fascicle.__init__([diameter, ID])	Instantation of a Fascicle
fascicle.attach_extracellular_recorder(rec)	attach an extracellular recorder to the axon
fascicle.attach_extracellular_stimulation(...)	attach a extracellular context of simulation for an axon.
fascicle.change_stimulus_from_electrode(...)	Change the stimulus of the ID_elec electrods
fascicle.clear_context([extracel_context, ...])	Clear all stimulation and recording mecanism
fascicle.compute_electrodes_footprints([...])	get electrodes footprints on each segment of each axon
fascicle.define_circular_contour(D[, y_c, z_c])	Define a circular countour to the fascicle
fascicle.define_ellipsoid_contour(a, b[, ...])	Define ellipsoidal contour
fascicle.define_length(L)	set the length over the x axis of the fascicle
fascicle.extracel_status()	Check if an extracellular context is attached to the instance
fascicle.fill([parallel, percent_unmyel, ...])	Fill a geometricaly defined contour with axons
fascicle.fill_with_population(...[, delta, ...])	Fill the fascicle with an axon population
fascicle.fit_circular_contour([y_c, z_c, Delta])	Define a circular countour to the fascicle
fascicle.fit_population_to_size([delta])	Fit the axon positions to the size of the fascicle
fascicle.generate_ligned_NoR_position([x])	Generates Node of Ranvier shifts to aligned a node of each axon to x postition.
fascicle.generate_random_NoR_position()	Generates radom Node of Ranvier shifts to prevent from axons with the same diamters to be aligned.
fascicle.get_axons_parameters([...])	get parameters of axons in the fascicle
fascicle.get_circular_contour()	Returns the properties of the fascicle contour considered as a circle (y and z center and diameter)
fascicle.get_electrodes_footprints_on_axons([...])
fascicle.get_parameters()	Generic method returning all the atributes of an NRV_class instance
fascicle.import_contour(smthing_else)	Define contour from a file
fascicle.insert_I_Clamp(position, t_start, ...)	Insert a IC clamp stimulation
fascicle.intracel_status()	Check if an intracellular context is attached to the instance
fascicle.load(data[, extracel_context, ...])	Load a fascicle configuration from a json file
fascicle.load_fascicle_configuration(fname)
fascicle.plot(axes[, contour_color, ...])	plot the fascicle in the Y-Z plane (transverse section)
fascicle.plot_x(axes[, myel_color, ...])	plot the fascicle's axons along Xline (longitudinal)
fascicle.rec_status()	Check if a recording context is attached to the instance
fascicle.remove_axons_electrode_overlap(...)	Remove the axons that could overlap an electrode
fascicle.remove_axons_size_threshold(d[, min])	Remove fibers with diameters below/above a threshold
fascicle.remove_myelinated_axons()	Remove all myelinated fibers from the
fascicle.remove_unmyelinated_axons()	Remove all unmyelinated fibers from the fascicle
fascicle.rotate_axons(theta[, y_c, z_c])	Move axons only in a fascicle by group rotation
fascicle.rotate_fascicle(theta[, y_c, z_c])	Rotate a complete fascicle
fascicle.save([fname, extracel_context, ...])	Save a fascicle in a json file
fascicle.save_fascicle_configuration(fname)
fascicle.set_ID(ID)	set the ID of the fascicle
fascicle.set_axons_parameters([...])	set parameters of axons in the fascicle
fascicle.set_parameters(**kawrgs)	Generic method to set any attribute of NRV_class instance
fascicle.shut_recorder_down()	Shuts down the recorder locally
fascicle.simulate([save_V_mem])	Simulates the fascicle using neuron framework.
fascicle.translate_axons(y, z)	Move axons only in a fascicle by group translation
fascicle.translate_fascicle(y, z)	Translate a complete fascicle