bluepyefe.rheobase

Functions related to the computation of the rheobase

Functions

compute_rheobase_absolute(cell, ...[, ...])

Compute the rheobase by finding the smallest current amplitude triggering at least one spike.

compute_rheobase_flush(cell, protocols_rheobase)

Compute the rheobase by finding the smallest current amplitude that.

compute_rheobase_interpolation(cell, ...)

Compute the rheobase by fitting the reverse IF curve and finding the intersection with the line x = 1.

compute_rheobase_majority_bin(cell, ...[, ...])

Compute the rheobase by finding the smallest current amplitude triggering at least 1 spikes in the majority (default 50%) of the recordings.
compute_rheobase_absolute(cell, protocols_rheobase, spike_threshold=1)[source]

Compute the rheobase by finding the smallest current amplitude triggering at least one spike.

Parameters:

  • cell (Cell) – cell for which to compute the rheobase

  • protocols_rheobase (list) – names of the protocols that will be used to compute the rheobase of the cells. E.g: [‘IDthresh’].

  • spike_threshold (int) – number of spikes above which a recording is considered to compute the rheobase.

compute_rheobase_flush(cell, protocols_rheobase, flush_length=1, upper_bound_spikecount=None)[source]

Compute the rheobase by finding the smallest current amplitude that:

1. Triggered at least one spike
2. Is followed by flush_length other traces that also trigger spikes.

The advantage of this strategy is that it ignores traces showing spurious spikes at low amplitudes.

Parameters:

  • cell (Cell) – cell for which to compute the rheobase

  • protocols_rheobase (list) – names of the protocols that will be used to compute the rheobase of the cells. E.g: [‘IDthresh’].

  • flush_length (int) – number of traces that needs to show spikes for the candidate trace to be considered the rheobase.

  • upper_bound_spikecount (int) – if the spikecount of a recording is higher than this number, the recording will not trigger the start of a flush

compute_rheobase_interpolation(cell, protocols_rheobase)[source]

Compute the rheobase by fitting the reverse IF curve and finding the intersection with the line x = 1.

Parameters:

  • cell (Cell) – cell for which to compute the rheobase

  • protocols_rheobase (list) – names of the protocols that will be used to compute the rheobase of the cells. E.g: [‘IDthresh’].

compute_rheobase_majority_bin(cell, protocols_rheobase, min_step=0.01, majority=0.5)[source]

Compute the rheobase by finding the smallest current amplitude triggering at least 1 spikes in the majority (default 50%) of the recordings.

Parameters:

  • cell (Cell) – cell for which to compute the rheobase

  • protocols_rheobase (list) – names of the protocols that will be used to compute the rheobase of the cells. E.g: [‘IDthresh’].

  • min_step (float) – minimum step above which amplitudes can be considered as separate steps

  • majority (float) – the proportion of sweeps with spike_threshold spikes to consider the target amplitude as rheobase