Stimulator

class managers.operatorsSimaudit.stimulator.Stimulator

Available methods:

Method name Method type
inject_IClamp() static method
inject_IRamp() static method
inject_GrC_Sine() static method
inject_current_NEURON() class method
inject_SEClamp() static method
inject_VClamp() static method
inject_voltage_NEURON() class method

NOTE:

  • inject_IClamp returns list_of_currents where each element is hoc object h.IClamp
  • inject_IRamp returns list_of_currents where each element is hoc object h.IRamp
  • inject_current_NEURON returns stimuli_list where each element is hoc object h.IClamp or ``h.IRamp` depending on current type.

Notice that h.IClamp is a default object in NEURON but h.IRamp and h.GrC_Sine are custom built objects. The former is built here in DummyModel of a cell which will get compiled. The later is build in the GrC2001Egidio model, a sinusoidal current injection for the Granule cell. However, h.IRamp is for injecting ramping current of the form “/” (up ramp), “” (down ramp) or a combination (“/”).

static inject_GrC_Sine(parameters, injecsite)

Injects GrC_Sine for NEURON

Keyword Arguments:

Keys Value type
parameters

  • list such that each element is a dictionary [ {}, {}, {} ]

  • Eg: [ {“amp”: 0.006, “dur”: 800.0, “delay”: 100.0,

    “freq”: 4.0, “phase”: 0.0},

    {“amp”: 0.006, “dur”: 400.0, “delay”: 100.0+800.0,

    “freq”: 8.0, “phase”: 0.0} ]
injectsite neuron section, for e.g., cell.soma

Returned values: list of currents where each element is a hoc object h.GrC_Sine.

NOTE: This function is available in ~/cerebmodels/models/cells/GrC2001Dangelo/mod_files/Grc_sine.mod.

static inject_IClamp(parameters, injectsite)

Injects IClamp for NEURON

Keyword Arguments:

Keys Value type
parameters
  • list such that each element is a dictionary [ {}, {}, {} ]
  • Eg: [ {“amp”: 0.5, “dur”: 100.0, “delay”: 10.0},
    {“amp”: 1.0, “dur”: 50.0, “delay”: 10.0+100.0} ]
injectsite neuron section, for e.g., cell.soma

Returned values: list of currents where each element is a hoc object h.IClamp.

NOTE: The h.IClamp function is available in NEURON by default.

static inject_IRamp(parameters, injectsite)

Injects IRamp for NEURON

Keyword Arguments:

Keys Value type
parameters

  • list such that each element is a dictionary [ {}, {}, {} ]

  • Eg: [ {“amp_initial”: 0.0, “amp_final”: 1.0, “dur”: 100.0,

    “delay”: 10.0},

    {“amp_initial””: 1.0, “amp_final”: 0.0, “dur”: 100.0,

    “delay”: 10.0+100.0} ]
injectsite neuron section, for e.g., cell.soma

Returned values: list of currents where each element is a hoc object h.IRamp.

NOTE: The h.IRamp function is available in ~/cerebmodels/models/cells/DummyModel/mod_files/CurrentRamp.mod.

static inject_SEClamp(parameters, injectsite)

Injects SEClamp for NEURON

Keyword Arguments:

Keys Value type
parameters
  • list such that each element is a dictionary [ {}, {}, {} ]
  • Eg: [ {“amp1”: 0.0, “dur1”: 50.0, “rs”: 1E-6},
    {“amp2”: 10.0, “dur2”: 100.0}, {“amp3”: 20.0, “dur3”: 150.0} ]
NOTE There is no “amp>3” (therefore no “dur>3”)
  • To add the electrode/pipette resistance do it just once

with key “rs”. This should be the same for all because its the same setup, just the amplitudes differ. - Since “Clamp is on at time 0, off at time dur1+dur2+dur3”

if you don’t want to start the simulation with it just set “amp1”: 0.0
injectsite neuron section, for e.g., cell.soma

Returned values: list of currents where each element is a hoc object h.SEClamp.

NOTE:

  • The h.SEClamp function is available in NEURON as SEClamp by default.
  • By default the electrode resistance (Re but SEClamp attribute is rs) is made very small 1E-6. This is because the input resistance (Rin) for the voltmeter (i.e, the measuring circuit) must be very large (i.e, infinite resistance) so that the voltage drop across the voltmeter (given by the voltage divider equation, the resistance is Rin/(Rin+Re)) is as close as possible to the membrane voltage it is supposed to be clamping. By making the electrode resistance very small it is the same as infinite Rin.
static inject_VClamp(parameters, injectsite)

Injects SEClamp for NEURON

Keyword Arguments:

} |"tau1" and "tau2", do it just once. They should be the same | | |for all because its the same setup, just the amplitude changes| | | - Since “Clamp is on at 0, off at time dur[0]+dur[1]+dur[2]” | | |if you don't want to start the simulation with it just set the| | | first “amp”: 0.0 | +—————-+————————————————————–+ | injectsite | neuron section, for e.g., cell.soma | +—————-+————————————————————–+

Returned values: a hoc object h.VClamp.

NOTE:

  • The h.VClamp function is available in NEURON as VClamp by default.
  • By default the electrode resistance (Re but VClamp attribute is rstim) is made very small 1E-6. This is because the input resistance (Rin) for the voltmeter (i.e, the measuring circuit) must be very large (i.e, infinite resistance) so that the voltage drop across the voltmeter (given by the voltage divider equation, the resistance is Rin/(Rin+Re)) is as close as possible to the membrane voltage it is supposed to be clamping. By making the electrode resistance very small it is the same as infinite Rin.
inject_current_NEURON(currenttype=None, injparameters=None, neuronsection=None)

Sets current injection parameters to either h.IClamp, h.IRamp, GrC_Sine

Keyword Arguments:

Keys Value type
currenttype string; "IClamp", "IRamp", or "GrC_Sine".
injparameters
neuronsection neuron section, for e.g., cell.soma

**Returned values:**Stimuli list where each element is hoc object h.IClamp, h.IRamp or h.GrC_Sine, depending on the given currenttype parameter.

NOTE:

  • depending on the currenttype choice inject_IClamp(), inject_IRamp() or inject_GrC_Sine() is called
  • h.IClamp is available in NEURON by default
  • h.IRamp is custom available in ~/cerebmodels/models/cells/DummyModel/mod_files/CurrentRamp.mod
  • h.GrC_Sine is custom available in ~/cerebmodels/models/cells/GrC2001DAngela/mod_files/Grc_sine.mod
inject_voltage_NEURON(voltagetype=None, injparameters=None, neuronsection=None)

Sets voltage injection parameters to either h.SEClamp, h.VClamp,

Keyword Arguments:

Keys Value type
voltagetype string; "SEClamp" or "VClamp".
injparameters
neuronsection neuron section, for e.g., cell.soma

**Returned values:**Stimuli list where each element is hoc object h.SEClamp or h.VClamp, depending on the given voltagetype parameter.

NOTE: