Metrics module

The metrics module includes functions to compute various metrics related to spike sorting.

Currently, it contains the following submodules:

• template metrics: Computes commonly used waveform/template metrics.

• quality metrics: Computes a variety of quality metrics to assess the goodness of spike sorting outputs.

• spiketrain metrics: Computes metrics based on spike train statistics and correlogram shapes.

All metrics extensions inherit from the BaseMetricExtension base class, which provides a common interface for computing and retrieving metrics and has convenience method to access metric information. For example, you can get the list of available metrics using the and their descriptions with:

from spikeinterface.metrics import ComputeTemplateMetrics
# ComputeTemplateMetrics inherits from BaseMetricExtension

available_metric_columns = ComputeTemplateMetrics.get_metric_columns()
print(f"Available metric columns: ")
print(available_metric_columns)

Available metric columns:
['peak_to_valley', 'peak_trough_ratio', 'half_width', 'repolarization_slope',
 'recovery_slope', 'num_positive_peaks', 'num_negative_peaks', 'velocity_above',
 'velocity_below', 'exp_decay', 'spread']

metric_descriptions = ComputeTemplateMetrics.get_metric_descriptions()
print("Metric descriptions: ")
print(metric_descriptions)

Metric descriptions:
{
    'peak_to_valley': 'Duration in s between the trough (minimum) and the peak (maximum) of the spike waveform.',
    'peak_trough_ratio': 'Ratio of the amplitude of the peak (maximum) to the trough (minimum) of the spike waveform.',
    'half_width': 'Duration in s at half the amplitude of the trough (minimum) of the spike waveform.',
    'repolarization_slope': 'Slope of the repolarization phase of the spike waveform, between the trough (minimum) and return to baseline in uV/s.',
    'recovery_slope': 'Slope of the recovery phase of the spike waveform, after the peak (maximum) returning to baseline in uV/s.',
    'num_positive_peaks': 'Number of positive peaks in the template',
    'num_negative_peaks': 'Number of negative peaks in the template',
    'velocity_above': 'Velocity of the spike propagation above the max channel in um/ms',
    'velocity_below': 'Velocity of the spike propagation below the max channel in um/ms',
    'exp_decay': 'Exponential decay of the template amplitude over distance from the extremum channel (1/um).',
    'spread': 'Spread of the template amplitude in um, calculated as the distance between channels whose templates exceed the spread_threshold.'
}

Metrics submodules

• Template Metrics
• Quality Metrics module
• Spike Train Metrics