StepTwo¶

class biophysics_fitting.hay.evaluation.StepTwo(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_STEP2_DEFINITIONS, name='StepTwo', step_index=2)¶

Bases: _Step

Evaluate Step current two.

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

{
    "mf2": ["Mean frequency", 14.5, 0.56],
    "AI2": ["Adaptation Index", 0.0023, 0.0056],
    "ISIcv2": ["Interspike Interval coefficient of variation", 0.1083, 0.0368],
    "DI2": ["Doublet interspike interval", 6.625, 8.65],
    "TTFS2": ["Time to first spike", 19.125, 7.31],
    "APh2": ["AP height", 16.5209, 6.1127],
    "fAHPd2": ["Fast after-hyperpolarization depth", -54.1949, 5.5706],
    "sAHPd2": ["Slow after-hyperpolarization depth", -60.5129, 4.6717],
    "sAHPt2": ["Slow after-hyperpolarization time", 0.2787, 0.0266],
    "APw2": ["AP width", 1.3833, 0.2843]
}

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_StepTwo() 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].