biophysics_fitting ❭ hay ❭ evaluation ❭ StepTwo

StepTwo

class biophysics_fitting.hay.evaluation.StepTwo

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]
}

See also

_Step for the template class, and biophysics_fitting.setup_stim.setp_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].