emodelrunner.protocols.thalamus_protocols¶
Ephys protocols for the Thalamus packages.
Classes
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Main protocol to fit RatSSCx neuron ephys parameters. |
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IDRest protocol to fit RatSSCx neuron ephys parameters. |
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IDRest protocol to fit RatSSCx neuron ephys parameters. |
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Step protocol with custom options to turn stochkv_det on or off. |
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Step protocol based on threshold. |
- class emodelrunner.protocols.thalamus_protocols.RatSSCxMainProtocol(name, rmp_protocol=None, rmp_efeature=None, rinhold_protocol_dep=None, rinhold_protocol_hyp=None, rin_efeature_dep=None, rin_efeature_hyp=None, thdetect_protocol_dep=None, thdetect_protocol_hyp=None, other_protocols=None, pre_protocols=None)[source]¶
Bases:
Protocol
Main protocol to fit RatSSCx neuron ephys parameters.
- Pseudo code:
Find resting membrane potential Find input resistance If both of these scores are within bounds, run other protocols: - Find holding current - Find rheobase - Run IDRest - Possibly run other protocols (based on constructor arguments) - Return all the responses Otherwise return Rin and RMP protocol responses
- generate_current(thres_i_hyp, thres_i_dep, holding_i_hyp, holding_i_dep, dt)[source]¶
Generate current for all protocols except rin and threshold detection.
- Parameters:
thres_i_hyp (float) – hyperpolarization threshold current (nA)
thres_i_dep (float) – depolarization threshold current (nA)
holding_i_hyp (float) – hyperpolarization holding current (nA)
holding_i_dep (float) – depolarization holding current (nA)
dt (float) – timestep of the generated currents (ms)
- Returns:
dict containing the generated currents
- property rin_efeature_dep¶
Get in_efeature.
- property rin_efeature_hyp¶
Get in_efeature.
- class emodelrunner.protocols.thalamus_protocols.RatSSCxRinHoldcurrentProtocol(name, rin_protocol_template=None, voltagebase_efeature=None, holdi_estimate_multiplier=2, holdi_precision=0.1, holdi_max_depth=5, prefix=None)[source]¶
Bases:
Protocol
IDRest protocol to fit RatSSCx neuron ephys parameters.
- binsearch_holdi(holding_voltage, cell_model, param_values, sim=None, lower_bound=None, upper_bound=None, precision=None, max_depth=None, depth=1)[source]¶
Do binary search to find holding current.
- generate_current(threshold_current=None, holding_current=None, dt=0.1)[source]¶
Return current time series.
- Parameters:
threshold_current (float) – the threshold current (nA)
holding_current (float) – the holding current (nA)
dt (float) – timestep of the generated currents (ms)
- Returns:
dict containing the generated current
- class emodelrunner.protocols.thalamus_protocols.RatSSCxThresholdDetectionProtocol(name, step_protocol_template=None, max_threshold_voltage=None, holding_voltage=None, prefix=None)[source]¶
Bases:
Protocol
IDRest protocol to fit RatSSCx neuron ephys parameters.
- binsearch_spike_threshold(cell_model, param_values, sim=None, holdi=None, lower_bound=None, upper_bound=None, precision=0.01, max_depth=5, depth=1)[source]¶
Do binary search to find spike threshold.
Assumption is that lower_bound has no spike, upper_bound has.
- create_short_threshold_protocol(holdi=None, step_current=None)[source]¶
Create short threshold protocol.
- detect_spike(cell_model, param_values, sim=None, step_current=None, holdi=None, short=False)[source]¶
Detect if spike is present at current level.
- search_max_threshold_current(rin=None)[source]¶
Find the current necessary to get to max_threshold_voltage.
- class emodelrunner.protocols.thalamus_protocols.StepProtocolCustom(name=None, step_stimulus=None, holding_stimulus=None, recordings=None, cvode_active=None, stochkv_det=None)[source]¶
Bases:
StepProtocol
,CurrentOutputKeyMixin
Step protocol with custom options to turn stochkv_det on or off.
- generate_current(threshold_current=None, holding_current=None, dt=0.1)[source]¶
Return current time series.
- Parameters:
threshold_current (float) – the threshold current (nA)
holding_current (float) – the holding current (nA)
dt (float) – timestep of the generated currents (ms)
- Returns:
dict containing the generated current
- property step_amplitude¶
Stimuli amplitude.
- Returns:
the amplitude of the step stimuli (nA)
- property stim_end¶
Time stimulus ends.
- Returns:
the time at which the stimulus ends (ms)
- property stim_start¶
Time stimulus starts.
- Returns:
the time at which the stimulus starts (ms)
- class emodelrunner.protocols.thalamus_protocols.StepThresholdProtocol(name, thresh_perc=None, step_stimulus=None, holding_stimulus=None, recordings=None, cvode_active=None, stochkv_det=None)[source]¶
Bases:
StepProtocolCustom
Step protocol based on threshold.
- generate_current(threshold_current, holding_current, dt=0.1)[source]¶
Return current time series.
- Parameters:
threshold_current (float) – the threshold current (nA)
holding_current (float) – the holding current (nA)
dt (float) – timestep of the generated currents (ms)
- Returns:
dict containing the generated current