axon

class nrv.nmod.axon(y=0, z=0, d=1, L=100, dt=0.001, Nseg_per_sec=0, freq=100, freq_min=0, mesh_shape='plateau_sigmoid', alpha_max=0.3, d_lambda=0.1, v_init=None, T=None, ID=0, threshold=-40, **kwargs)

A generic object to describe an axonal fiber (soma and interconnection are not taken into account, all axons are independant from others).

Note

• axon is an abstract class so it cannot be used directly. From the user’s point of view, only the child classes myelinated and unmyelinated should be used.

• All axons are assumed to be along the x-axis, as Neuron would do when creatnig a basic longitudinal geometry.

Parameters:

• y (float) – y-axis coordinate of the axon (um)

• z (float) – z-axis coordinate of the axon (um)

• d (float) – axon diameter (um)

• L (float) – axon length (um)

• dt (float) – simulation time stem for Neuron (ms), by default 1us

• Nseg_per_sec (float) – number of segment per section in Neuron. If set to 0, the number of segment per section is calculated with the d-lambda rule

• freq (float) – frequency of the d-lambda rule (Hz), by default 100Hz

• freq_min (float) – minimum frequency for the d-lambda rule when meshing is irregular, 0 for regular meshing

• v_init (float) – initial value for the membrane voltage (mV), specify None for automatic model choice of v_init

• T (float) – temperature (C), specify None for automatic model choice of temperature

• ID (int) – axon ID, by default set to 0

• threshold (int) – membrane voltage threshold for spike detection (mV), by default -40mV

Warning

do not create more than one axon at a time for one process, to prevent from parameters overlaps in Neuron

Methods

axon.__init__([y, z, d, L, dt, ...])	initialisation of the axon,
axon.attach_extracellular_recorder(rec)	attach an extracellular recorder to the axon
axon.attach_extracellular_stimulation(stim)	attach a extracellular context of simulation for an axon
axon.change_stimulus_from_electrode(ID_elec, ...)	Change the stimulus of the ID_elec electrods
axon.extracel_status()	Check if an extracellular context is attached to the instance
axon.get_electrodes_footprints_on_axon([...])	get electrodes footprints on each axon segment
axon.get_ionic_current()
axon.get_membrane_capacitance()
axon.get_membrane_conductance()
axon.get_membrane_current()
axon.get_membrane_voltage()
axon.get_parameters()	Generic method returning all the atributes of an NRV_class instance
axon.get_particules_values()
axon.insert_I_Clamp()
axon.insert_V_Clamp()
axon.intracel_status()	Check if an intracellular context is attached to the instance
axon.load(data[, extracel_context, ...])	Load all axon properties from a dictionary or a json file
axon.load_axon(data[, extracel_context, ...])
axon.plot(axes[, color, elec_color])
axon.rec_status()	Check if a recording context is attached to the instance
axon.save([save, fname, extracel_context, ...])	Return axon as dictionary and eventually save it as json file WARNING to use BEFORE stimulation, (for post simulation savings use save_axon_results_as_json on results dictionary
axon.save_axon([save, fname, ...])
axon.set_conductance_recorders()
axon.set_ionic_current_recorders()
axon.set_membrane_current_recorders()
axon.set_membrane_voltage_recorders()
axon.set_parameters(**kawrgs)	Generic method to set any attribute of NRV_class instance
axon.set_particules_values_recorders()
axon.shut_recorder_down()	Shuts down the recorder locally
axon.simulate(**kwargs)	Simulates the axon using neuron framework
axon.topology()	call the neuron topology function to plot the current topology on prompt