Simulators

class dendrotweaks.simulators.NeuronSimulator(temperature=37, v_init=-70, dt=0.025, cvode=False)[source]

Bases: Simulator

A class to represent the NEURON simulator.

Parameters:

  • temperature (float) – The temperature of the simulation in Celsius.

  • v_init (float) – The initial membrane potential of the neuron in mV.

  • dt (float) – The time step of the simulation in ms.

  • cvode (bool) – Whether to use the CVode variable time step integrator.

temperature

The temperature of the simulation in Celsius.

Type:

float

v_init

The initial membrane potential of the neuron in mV.

Type:

float

dt

The time step of the simulation in ms.

Type:

float

property recordings
property t
add_recording(sec, loc, var='v')[source]

Add a recording to the simulator.

Parameters:

  • sec (Section) – The section to record from.

  • loc (float) – The location along the normalized section length to record from.

  • var (str) – The variable to record. Default is ‘v’ (voltage).

remove_recording(sec, loc, var='v')[source]

Remove a recording from the simulator.

Parameters:

  • sec (Section) – The section to remove the recording from.

  • loc (float) – The location along the normalized section length to remove the recording from.

remove_all_recordings(var=None)[source]

Remove all recordings from the simulator.

run(duration=300)[source]

Run a simulation.

Parameters:

duration (float) – The duration of the simulation in milliseconds.

to_dict()[source]

Convert the simulator to a dictionary.

Returns:

A dictionary representation of the simulator.

Return type:

dict

from_dict(data)[source]

Create a simulator from a dictionary.

Parameters:

data (dict) – The dictionary representation of the simulator.

plot_currents(**kwargs)

Plot the recorded currents.

plot_var(var='v', ax=None, segments=None, **kwargs)
plot_voltage(**kwargs)

Plot the recorded voltages.