myelinated

class nrv.nmod.myelinated(y=0, z=0, d=10, L=10000, model='MRG', dt=0.001, node_shift=0, Nseg_per_sec=1, freq=100, freq_min=0, mesh_shape='plateau_sigmoid', alpha_max=0.3, d_lambda=0.1, rec='nodes', v_init=None, T=None, ID=0, threshold=-40, **kwargs)

Myelinated axon class. Automatic refinition of all neuron sections and properties. User-friendly object including model definition Inherit from axon class. see axon for further detail.

Parameters:

• y (float) – y coordinate for the axon, in um

• z (float) – z coordinate for the axon, in um

• d (float) – axon diameter, in um

• L (float) – axon length along the x axins, in um

• model (str) –

  choice of conductance double-cable based model, possibly:

  ”MRG” : see [1] for details “Gaines_motor” : Gaines motor model, see [2] “Gaines_sensory”: Gaines sensory model, see [2]

• dt (float) – computation step for simulations, in ms. By default equal to 1 us

• node_shift (float) – shift of the first node of Ranvier to zeros, as a fraction of internode length (0<= node_shift < 1)

• Nseg_per_sec (int) – Number of segment per section in the axon. If set to 0, the number of segment is automatically computed using d-lambda rule and following paramters. If set by user, please use odd numbers

• freq (float) – Frequency used for the d-lmbda rule, corresponding to the maximum membrane current frequency, by default set to 100 Hz

• freq_min (float) – Minimal frequency fot the d-lambda rule when using an irregular number of segment along the axon, if set to 0, all sections have the same frequency determined by the previous parameter

• mesh_shape (str) –

  Shape of the frequencial distribution for the dlmabda rule along the axon, pick between:

  ”pyramidal” -> min frequencies on both sides and linear increase up to the middle at the maximum frequency “sigmoid” -> same a befor with sigmoid increase instead of linear “plateau” -> sale as pyramidal except the max frequency is holded on a central plateau “plateau_sigmoid” -> same as previous with sigmoid increase

• alpha_max (float) – Proportion of the axon set to the maximum frequency for plateau shapes, by default set to 0.3

• d_lambda (float) – value of d-lambda for the dlambda rule

• rec (str) –

  recording zones for the membrane potential, eiter:

  ”nodes” -> record only at the nodes of Ranvier

  or

  ”all” -> all computation points in nodes of Ranvier and over myelin

• v_init (float) – Initial value of the membrane voltage in mV, set None to get an automatically model attributed value

• T (gloat) – temperature in C, set None to get an automatically model attributed value

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

• threshold (float) – voltage threshold in mV for further spike detection in post-processing, by defautl set to -40mV, see post-processing library for further help

Note

scientific sources for models: [1] McIntyre CC, Richardson AG, and Grill WM. Modeling the excitability of mammalian nerve fibers: influence of afterpotentials on the recovery cycle. Journal of Neurophysiology 87:995-1006, 2002. [2] Gaines, J. L., Finn, K. E., Slopsema, J. P., Heyboer, L. A., Polasek, K. H. (2018). A model of motor and sensory axon activation in the median nerve using surface electrical stimulation. Journal of computational neuroscience, 45(1), 29-43.

Methods

myelinated.__init__([y, z, d, L, model, dt, ...])	initialisation of a myelinted axon
myelinated.attach_extracellular_recorder(rec)	attach an extracellular recorder to the axon
myelinated.attach_extracellular_stimulation(stim)	attach a extracellular context of simulation for an axon
myelinated.change_stimulus_from_electrode(...)	Change the stimulus of the ID_elec electrods
myelinated.extracel_status()	Check if an extracellular context is attached to the instance
myelinated.get_Nav_values()	get the markov model at the end of simulation.
myelinated.get_electrodes_footprints_on_axon([...])	get electrodes footprints on each axon segment
myelinated.get_ionic_conductance()	get the ionic channels conductance at the end of simulation.
myelinated.get_ionic_current()	get the ionic channels currents at the end of simulation.
myelinated.get_membrane_capacitance()	get the membrane capacitance NB: [uF/cm^{2}] (see Neuron unit)
myelinated.get_membrane_conductance()	get the total membrane conductance at the end of simulation.
myelinated.get_membrane_current()	get the membrane current at the end of simulation.
myelinated.get_membrane_voltage()	get the membrane voltage at the end of simulation.
myelinated.get_myelin_capacitance()	get the membrane capacitance NB: [uF/cm^{2}] (see Neuron unit)
myelinated.get_myelin_conductance()	get the membrane capacitance NB: [S/cm^{2}] (see Neuron unit)
myelinated.get_parameters()	Generic method returning all the atributes of an NRV_class instance
myelinated.get_particles_values()	get the particules values at the end of simulation.
myelinated.get_particules_values()
myelinated.insert_I_Clamp(position, t_start, ...)	Insert a IC clamp stimulation at the midd point of the nearest node to the specified position
myelinated.insert_I_Clamp_node(index, ...)	Insert a IC clamp stimulation on a Ranvier node at its midd point position
myelinated.insert_V_Clamp(position, stimulus)	Insert a V clamp stimulation at the midd point of the nearest node to the specified position
myelinated.insert_V_Clamp_node(index, stimulus)	Insert a V clamp stimulation
myelinated.intracel_status()	Check if an intracellular context is attached to the instance
myelinated.load(data[, extracel_context, ...])	Load all axon properties from a dictionary or a json file
myelinated.load_axon(data[, ...])
myelinated.plot(axes[, color, node_color, ...])
myelinated.rec_status()	Check if a recording context is attached to the instance
myelinated.save([save, fname, ...])	Return axon as dictionary and eventually save it as json file
myelinated.save_axon([save, fname, ...])
myelinated.set_Markov_Nav([list_of_nodes])	Change typical particle-Na sodium in Hodgking-Huxley formalism to Markov-channel population model.
myelinated.set_Nav_recorders()	setup the markov model recording.
myelinated.set_conductance_recorders()	setup the ionic channels conductance recording.
myelinated.set_ionic_current_recorders()	setup the ionic channels current recording.
myelinated.set_membrane_current_recorders()	setup the membrane current recording.
myelinated.set_membrane_voltage_recorders()	setup the membrane voltage recording.
myelinated.set_parameters(**kawrgs)	Generic method to set any attribute of NRV_class instance
myelinated.set_particules_values_recorders()	setup the particules current recording.
myelinated.shut_recorder_down()	Shuts down the recorder locally
myelinated.simulate(**kwargs)	Simulates the axon using neuron framework
myelinated.topology()	call the neuron topology function to plot the current topology on prompt