simrun ❭ PSP_with_cell_modification ❭ PSP_with_current_injection

PSP_with_current_injection¶

class simrun.PSP_with_cell_modification.PSP_with_current_injection(neuron_param, confile, target_vm=-70, delay=100, duration=200, optimize_for_timepoint=150, tEnd=300, cell_modify_functions={}, bounds=(0, 0.7))¶

Simulate EPSPs and IPSPs while the soma is voltage-clamped to a fixed membrane potential.

The membrane potential is clamped by injecting a current into the soma.

See also

single_cell_parser.cell_modify_functions for available cell modification functions.

Parameters:¶

neuron_param (NTParameterSet) – Parameters of the neuron model.
confile (str) – Path to the network connectivity (.con) file.
target_vm (float) – Membrane potential to clamp the soma to (in \(mV\)).
delay (float) – Delay before the current injection starts (in \(ms\)).
duration (float) – Duration of the current injection (in \(ms\)).
optimize_for_timepoint (float) – Timepoint for membrane voltage optimization (in \(ms\)). This usually coincides with the timepoint of a single synapse activation, after the membrane voltage has stabilized.
tEnd (float) – End time of the simulation (in \(ms\)).
cell_modify_functions (dict) – Dictionary of cell modification functions (see cell_modify_functions). The keys are the names of the functions, the values are the parameters of the functions.
bounds (tuple) – Limits for the current injection optimization to clamp the membrane potential (in \(nA\)).

Attributes:¶

neuron_param¶

Parameters of the neuron model.

Type:¶: NTParameterSet

confile¶

Path to the network connectivity (.con) file.

Type:¶: str

target_vm¶

Membrane potential to clamp the soma to (in \(mV\)).

Type:¶: float

delay¶

Delay before the current injection starts (in \(ms\)).

Type:¶: float

duration¶

Duration of the current injection (in \(ms\)).

Type:¶: float

optimize_for_timepoint¶

Timepoint for membrane voltage optimization (in \(ms\)). This usually coincides with the timepoint of a single synapse activation, after the membrane voltage has stabilized.

Type:¶: float

tEnd¶

End time of the simulation (in \(ms\)).

Type:¶: float

cell_modify_functions¶

Dictionary of cell modification functions (see cell_modify_functions). The keys are the names of the functions, the values are the parameters of the functions.

Type:¶: dict

bounds¶

Limits for the current injection optimization to clamp the membrane potential (in \(nA\)).

Type:¶: tuple

holding_current¶

Current that needs to be injected to hold the somatic potential at target_vm.

Type:¶: float

Methods:¶

`optimize_holding_current`()	Calculate the current that needs to be injected to hold the somatic potential at `target_vm`.
`_objective_fun`(current)	Callable to optimize.
`_get_current_dependent_vt`(current)	Run the current injection simulation
`plot_current_injection_voltage_trace`()	Visualize the voltage trace during the current injection
`get_neuron_param_with_current_injection`()	Get a Cell parameters file with a current injection.
`get_psp_simulator`(gExRange, exc_inh, mode)	Set up a `PSPs` object to simulate individual synapse PSPs.
`get_psp_simulator_exc_and_inh_combined`(gExRange, mode)	Set up and combine excitatory and inhibitory PSP simulators.
`get`()	Get the final `PSPs` object.