biophysics_fitting ❭ hay ❭ evaluation ❭ _Step

_Step

class biophysics_fitting.hay.evaluation._Step(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=None, name='StepTemplate', step_index=0)

Template class for evaluating step current injections.

These metrics were introduced by Hay et al. [2], and illustrated in Bast et al. [3].

See also

biophysics_fitting.setup_stim() for more information on the stimulus protocols.

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].

Attributes:

soma_thresh

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

Type:

float

stim_onset

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

Type:

float

stim_duration

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

Type:

float

punish

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 \(250\).

Type:

float

punish_last_spike_after_deadline

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

Type:

bool

punish_minspikenum

The minimum number of spikes required for this stimulus protocol.

Type:

int

punish_returning_to_rest_tolerance

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

Type:

float

prefix

The prefix for the evaluation metric checks. Defaults to an empty string.

Type:

str

definitions

The empirical means and standard deviations for the evaluation metrics. These are overridden by each child class.

Type:

dict

name

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

Type:

str

step_index

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

Type:

int

Methods:

get(**voltage_traces)

Get the full evaluation of the voltage traces for the step current injection.

check(out, voltage_traces)

Check for problems in the voltage trace.

mf(voltage_traces)

Get the mean frequency of the somatic voltage trace.

AI(voltage_traces)

Get the adaptation index of the somatic voltage trace.

ISIcv(voltage_traces)

Get the coefficient of variation of the interspike interval in the somatic voltage trace.

DI(voltage_traces)

Get the ISI of the first two spikes in the somatic voltage trace.

TTFS(voltage_traces)

Get the time to first spike in the somatic voltage trace.

AHP_depth_abs(voltage_traces)

Get the afterhyperpolarization depth in the somatic voltage trace.

APh(voltage_traces)

Get the AP heights fo all APs in the somatic voltage trace.

fAHPd(voltage_traces)

Get the fast afterhyperpolarization depth in the somatic voltage trace.

sAHPd(voltage_traces)

Get the slow afterhyperpolarization depth in the somatic voltage trace.

sAHPt(voltage_traces)

Get the slow afterhyperpolarization time in the somatic voltage trace.

APw(voltage_traces)

Get the AP widths of all APs in the somatic voltage trace.