StepThree¶

class biophysics_fitting.hay.evaluation.StepThree(soma_thresh=-30, stim_onset=700, stim_duration=2000, punish=250.0, punish_last_spike_after_deadline=True, punish_minspikenum=5, punish_returning_to_rest_tolerance=2.0, definitions=HAY_STEP3_DEFINITIONS, name='StepThree', step_index=3)¶

Bases: _Step

Evaluate Step current three.

This class initializes all the evaluation metrics for the StepThree stimulus protocol. The empirically observed objectives are in this case:

{
    "mf3": ["Mean frequency", 22.5, 2.2222],
    "AI3": ["Adaptation index", 0.0046, 0.0026],
    "ISIcv3": ["Interspike interval coefficient of variation", 0.0954, 0.014],
    "DI3": ["Doublet interspike interval", 5.38, 0.83],
    "TTFS3": ["Time to first spike", 7.25, 1.0],
    "APh3": ["AP height", 16.4368, 6.9322],
    "fAHPd3": ["Fast after-hyperpolarization depth", -56.5579, 3.5834],
    "sAHPd3": ["Slow after-hyperpolarization depth", -59.9923, 3.9247],
    "sAHPt3": ["Slow after-hyperpolarization time", 0.2131, 0.0368],
    "APw3": ["AP width", 1.8647, 0.4119]
}

Here, the format of each line is: acronym: [full name, mean, std]

See also

_Step for the template class, and biophysics_fitting.setup_stim.setup_StepThree() for more information on the stimulus protocol.

Parameters:¶

soma_thresh : float¶

The threshold for APs in the somatic voltage trace. Defaults to \(-30\ mV\).

stim_onset : float¶

The onset of the stimulus (\(ms\)). Defaults to \(700\ ms\).

stim_duration : float¶

The duration of the stimulus (\(ms\)). Defaults to \(2000\ ms\).

punish : float¶

The punishment value in units of \(\sigma\). Used as a baseline if the voltage trace cannot be evaluated on a metric (e.g. if it does not contain an AP). Defaults to \(250 \sigma\).

punish_last_spike_after_deadline : bool¶

Whether to punish if the last spike is after the deadline. Defaults to True

punish_minspikenum : int¶

The minimum number of spikes required for this stimulus protocol. Defaults to \(5\).

punish_returning_to_rest_tolerance : float¶

The tolerance for returning to rest (\(mV\)). Defaults to \(2 mV\).

definitions : dict¶

The definitions for the evaluation metrics. See also: definitions.

name : str¶

The name of the stimulus protocol. Defaults to 'StepTemplate'.

step_index : int¶

The index of the step stimulus protocol. Defaults to \(0\). Options are: [1, 2, 3].