biophysics_fitting ❭ hay ❭ evaluation ❭ BAC

BAC

class biophysics_fitting.hay.evaluation.BAC(hot_zone_thresh=-55, soma_thresh=-30, ca_max_after_nth_somatic_spike=2, stim_onset=295, stim_duration=45, repolarization=-55, punish=250, punish_last_spike_after_deadline=True, punish_minspikenum=2, punish_returning_to_rest_tolerance=2.0, punish_max_prestim_dendrite_depo=-50, prefix='', definitions=HAY_BAC_DEFINITIONS)

Evaluate the \(BAC\) stimulus protocol.

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

See also

biophysics_fitting.setup_stim.setup_BAC() for more information on the stimulus protocol.

Parameters:

  • hot_zone_thresh (float) – The threshold for APs in the dendritic voltage trace. Defaults to \(-55\) mV.

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

  • ca_max_after_nth_somatic_spike (int) – The number of somatic spikes after which the calcium spike maximum should occur. Defaults to \(2\).

  • stim_onset (float) – The onset of the stimulus (ms). Defaults to \(295\) ms.

  • stim_duration (float) – The duration of the stimulus (ms). Defaults to \(45\) ms.

  • repolarization (float) – The target repolarization voltage after the stimulus. See BAC_ISI_check_repolarization(). Defaults to \(-55\) mV.

  • 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 \(250\).

  • 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.

  • punish_returning_to_rest_tolerance (float) – The tolerance for returning to rest (\(mV\)). Defaults to \(2 mV\).

  • prefix (str) – The prefix for the evaluation metric checks. Defaults to an empty string.

  • definitions (dict) – The definitions for the evaluation metrics. See also: definitions.

Attributes:

hot_zone_thresh

The threshold for APs in the dendritic voltage trace. Defaults to \(-55\) mV.

Type:

float

soma_thresh

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

Type:

float

ca_max_after_nth_somatic_spike

The number of somatic spikes after which the calcium spike maximum should occur. Defaults to \(2\).

Type:

int

stim_onset

The onset of the stimulus (ms). Defaults to \(295\) ms.

Type:

float

stim_duration

The duration of the stimulus (ms). Defaults to \(45\) ms.

Type:

float

repolarization

The target repolarization voltage after the stimulus. See BAC_ISI_check_repolarization(). Defaults to \(-55\) mV.

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. Defaults to:

{
    'BAC_APheight': ('AP_height', 25.0, 5.0),
    'BAC_ISI': ('BAC_ISI', 9.901, 0.8517),
    'BAC_ahpdepth': ('AHP_depth_abs', -65.0, 4.0),
    'BAC_caSpike_height': ('BAC_caSpike_height', 6.73, 2.54),
    'BAC_caSpike_width': ('BAC_caSpike_width', 37.43, 1.27),
    'BAC_spikecount': ('Spikecount', 3.0, 0.01)
}
Type:

dict

Methods:

get(**voltage_traces)

Get the full evaluation of the voltage traces for BAC firing.

check(out, voltage_traces)

Check for problems in the voltage trace.

BAC_spikecount(voltage_traces)

Get the number of spikes in the somatic voltage trace.

BAC_APheight(voltage_traces)

Get the height of the first action potential in the somatic voltage trace.

BAC_ISI(voltage_traces)

Get the interspike interval in the somatic voltage trace.

BAC_ahpdepth(voltage_traces)

Get the afterhyperpolarization depth in the somatic voltage trace.

BAC_caSpike_height(voltage_traces)

Get the height of the calcium spike in the dendritic voltage trace.

BAC_caSpike_width(voltage_traces)

Get the width of the calcium spike in the dendritic voltage trace.