Quality metrics allows one to quantitatively assess the goodness of a spike sorting output. The :py:mod:`~spikeinterface.qualitymetrics` module includes functions to compute a large variety of available metrics. All of the metrics currently implemented in spikeInterface are per unit (pairwise metrics do appear in the literature).
Each metric aims to identify some quality of the unit. Contamination metrics (also sometimes called 'false positive' or 'type I' metrics) aim to identify the amount of noise present in the unit. Examples include: ISI violations, sliding refractory period violations, SNR, NN-hit rate. Completeness metrics (or 'false negative'/'type II' metrics) aim to identify whether any of the spiking activity is missing from a unit. Examples include: presence ratio, amplitude cutoff, NN-miss rate. Drift metrics aim to identify changes in waveforms which occur when spike sorters fail to successfully track neurons in the case of electrode drift.
Some metrics make use of principal component analysis (PCA) to reduce the dimensionality of computations. Various approaches to computing the principal components are possible, and choice should be carefully considered in relation to the recording equipment used. The following metrics make use of PCA: isolation distance, L-ratio, D-prime, Silhouette score and NN-metrics. By contrast, the following metrics are based on spike times only: firing rate, ISI violations, presence ratio. And amplitude cutoff and SNR are based on spike times as well as waveforms.
For more details about each metric and it's availability and use within SpikeInterface, see the individual pages for each metrics.
.. toctree:: :maxdepth: 1 :glob: qualitymetrics/amplitude_cutoff qualitymetrics/amplitude_cv qualitymetrics/amplitude_median qualitymetrics/d_prime qualitymetrics/drift qualitymetrics/firing_range qualitymetrics/firing_rate qualitymetrics/isi_violations qualitymetrics/isolation_distance qualitymetrics/l_ratio qualitymetrics/nearest_neighbor qualitymetrics/presence_ratio qualitymetrics/sliding_rp_violations qualitymetrics/snr qualitymetrics/noise_cutoff qualitymetrics/silhouette_score qualitymetrics/synchrony
This code snippet shows how to compute quality metrics (with or without principal components) in SpikeInterface:
we = si.load_waveforms(folder='waveforms') # start from a waveform extractor
# without PC
metrics = compute_quality_metrics(waveform_extractor=we, metric_names=['snr'])
assert 'snr' in metrics.columns
# with PCs
from spikeinterface.postprocessing import compute_principal_components
pca = compute_principal_components(waveform_extractor=we, n_components=5, mode='by_channel_local')
metrics = compute_quality_metrics(waveform_extractor=we)
assert 'isolation_distance' in metrics.columnsFor more information about quality metrics, check out this excellent documentation from the Allen Institute.
.. toctree:: :maxdepth: 1 qualitymetrics/references