biophysics_fitting ❭ hay ❭ evaluation ❭ bAP

bAP¶

class biophysics_fitting.hay.evaluation.bAP(soma_thresh=-30, stim_onset=295, stim_duration=5, bAP_thresh='+2mV', punish=250.0, punish_last_spike_after_deadline=True, punish_minspikenum=1, punish_returning_to_rest_tolerance=2.0, definitions=HAY_BAP_DEFINITIONS)¶

Evaluate the \(bAP\) 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_bAP() 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 \(295\ ms\).

• stim_duration (float) – The duration of the stimulus (\(ms\)). Defaults to \(5\ ms\).

• bAP_thresh (float) – The threshold for the backpropagating action potential. Defaults to \(+2\ mV\).

• 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 \(250 \sigma\).

• 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 \(1\).

• 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.

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 \(295\) ms.

Type:¶

float

stim_duration¶

The duration of the stimulus (ms). Defaults to \(5\) ms.

Type:¶

float

bAP_thresh¶

The threshold for the backpropagating action potential. Defaults to \(+2\) 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 \(250 \sigma\).

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

definitions¶

The empirical means and standard deviations for the evaluation metrics. Defaults to:

{
    'bAP_APheight': ('AP_height', 25.0, 5.0),
    'bAP_APwidth': ('AP_width', 2.0, 0.5),
    'bAP_att2': ('BPAPatt2', 45.0, 10.0),
    'bAP_att3': ('BPAPatt3', 36.0, 9.33),
    'bAP_spikecount': ('Spikecount', 1.0, 0.01)
}

Type:¶

dict

Methods:¶

get(**voltage_traces)	Get the full evaluation of the voltage traces for bAP firing.
check(out, voltage_traces)	Check for problems in the voltage trace.
bAP_APheight(voltage_traces)	Get the height of the first action potential in the somatic voltage trace.
bAP_APwidth(voltage_traces)	Get the width of the first action potential in the somatic voltage trace.
bAP_spikecount(voltage_traces)	Get the number of spikes in the somatic voltage trace.
_bAP_att(voltage_traces, _n)	Get the backpropagating action potential attenuation.
bAP_att2(voltage_traces)	Get the backpropagating action potential attenuation between the soma and first dendritic pipette location.
bAP_att3(voltage_traces)	Get the backpropagating action potential attenuation between the soma and second dendritic pipette location.