StepOne¶

class biophysics_fitting.hay.evaluation.StepOne(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_STEP1_DEFINITIONS, name='StepOne', step_index=1)¶

Bases: _Step

Evaluate Step current one.

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

{
    "mf1": ["Mean frequency", 9.0, 0.88],
    "AI1": ["Adaptation Index", 0.0036, 0.0091],
    "ISIcv1": ["Interspike interval coefficient of variation", 0.1204, 0.0321],
    "DI1": ["Doublet Interspike Interval", 57.75, 33.48],
    "TTFS1": ["Time to first spike", 43.25, 7.32],
    "APh1": ["AP height", 26.2274, 4.9703],
    "fAHPd1": ["Fast after-hyperpolarization depth", -51.9511, 5.8213],
    "sAHPd1": ["Slow after-hyperpolarization depth", -58.0443, 4.5814],
    "sAHPt1": ["Slow after-hyperpolarization time", 0.2376, 0.0299],
    "APw1": ["AP width", 1.3077, 0.1665]
}

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_StepOne() 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].