Presence ratio (presence_ratio
)¶
Calculation¶
Presence ratio is the proportion of discrete time bins in which at least one spike occurred.
\(B_s\) : number of bins in which spikes occurred.
\(B_n\) : number of bins in which no spikes occurred.
Expectation and use¶
Complete units are expected to have a presence ratio of 90% or more. Low presence ratio (close to 0) can indicate incompleteness (type II error) or highly selective firing pattern.
Example code¶
import spikeinterface.qualitymetrics as qm
# Make recording, sorting and wvf_extractor object for your data.
presence_ratio = qm.compute_presence_ratio(wvf_extractor)
# presence_ratio is a dict containing the units' ID as keys
# and their presence ratio (between 0 and 1) as values.
Links to source code¶
From SpikeInterface
From the AllenSDK
References¶
Various cluster quality metrics.
Some of then come from or the old implementation: * https://github.com/AllenInstitute/ecephys_spike_sorting/tree/master/ecephys_spike_sorting/modules/quality_metrics * https://github.com/SpikeInterface/spikemetrics
Implementations here have been refactored to support the multi-segment API of spikeinterface.
- spikeinterface.toolkit.qualitymetrics.misc_metrics.compute_presence_ratio(waveform_extractor, num_bin_edges=101, **kwargs)¶
Calculate the presence ratio, representing the fraction of time the unit is firing.
- Parameters
- waveform_extractorWaveformExtractor
The waveform extractor object.
- num_bin_edgesint, optional, default: 101
The number of bins edges to use to compute the presence ratio.
- Returns
- presence_ratiodict
The presence ratio for each unit ID.
Notes
The total duration, across all segments, is divide into “num_bins”. To do so, spiketrains across segments are concatenated to mimic a continuous segment.
Literature¶
Unknown origin.