biophysics_fitting ❭ hay ❭ evaluation ❭ StepThree

StepThree

class biophysics_fitting.hay.evaluation.StepThree

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]
}

See also

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