neat.NeuronSimTree.run

NeuronSimTree.run(t_max, downsample=1, record_from_syns=False, record_from_iclamps=False, record_from_vclamps=False, record_from_channels=False, record_v_deriv=False, record_concentrations=[], pprint=False)[source]

Run the NEURON simulation. Records at all locations stored under the name ‘rec locs’ on self (see MorphTree.storeLocs())

Parameters

  • t_max (float) – Duration of the simulation

  • downsample (int (> 0)) – Records the state of the model every downsample time-steps

  • record_from_syns (bool (default False)) – Record currents of synapstic point processes (in self.syns). Accessible as np.ndarray in the output dict under key ‘i_syn’

  • record_from_iclamps (bool (default False)) – Record currents of iclamps (in self.iclamps) Accessible as np.ndarray in the output dict under key ‘i_clamp’

  • record_from_vclamps (bool (default False)) – Record currents of vclamps (in self.vclamps) Accessible as np.ndarray in the output dict under key ‘i_vclamp’

  • record_from_channels (bool (default False)) – Record channel state variables from neat defined channels in self, at locations stored under ‘rec locs’ Accessible as np.ndarray in the output dict under key ‘chan’

  • record_v_deriv (bool (default False)) – Record voltage derivative at locations stored under ‘rec locs’ Accessible as np.ndarray in the output dict under key ‘dv_dt’

  • record_from_concentrations (bool (default False)) – Record ion concentration at locations stored under ‘rec locs’ Accessible as np.ndarray in the output dict with as key the ion’s name

Returns

Dictionary with the results of the simulation. Contains time and voltage as np.ndarray at locations stored under the name ‘ rec locs’, respectively with keys ‘t’ and ‘v_m’. Also contains traces of other recorded variables if the option to record them was set to True

Return type

dict