SpikeInterface

SpikeInterface provides a unified interface for spike sorting — the process of detecting and classifying action potentials from extracellular recordings.

Input formats

.nwb, .bin, .dat, .raw, .mda, .h5, .zarr

Sorter backends

Sorter	GPU	Description
Kilosort4	Yes	Recommended. State-of-the-art GPU spike sorter
Kilosort3	Yes	Previous generation Kilosort
Kilosort2.5	Yes	Stable, widely-used version
IronClust	Yes	GPU-accelerated spike sorter
MountainSort5	No	CPU-based, fast for small recordings
SpyKING CIRCUS 2	No	Template-matching based sorter
Tridesclous2	No	CPU-based spike sorter

Parameters

Parameter	Range	Default	Description
Sampling rate	1k–100kHz	Auto-detected	Recording sampling rate
Channels	1–4096	Auto-detected	Number of recording channels
Data type	int16/float32/etc.	int16	Data type of recording
Bandpass filter	freq_min/freq_max	300–6000 Hz	Frequency range for filtering
Common median ref.	Toggle	On	Remove common noise via median subtraction
Detection threshold	2–20 std dev	6	Spike detection sensitivity
Drift correction	Toggle	On	Correct for electrode drift
ISI violation threshold	Float	0.5 ms	Refractory period violation threshold
Min SNR	Float	2.0	Minimum signal-to-noise ratio for units
Phy export	Toggle	Off	Export for manual curation in Phy
Save waveforms	Toggle	On	Save spike waveform templates

Outputs

Output	Format	Description
Spike times	NPY	Spike timestamps and unit assignments
Waveform templates	NPY	Average waveform per unit
QC metrics	JSON	SNR, ISI violations, firing rates
NWB output	NWB	Results in Neurodata Without Borders format (optional)
Phy export	TAR.GZ	Files for manual curation in Phy GUI
Sorting summary	PNG	Visual summary of sorting results

Presets

Preset	Sorter	Description
Neuropixels Default	Kilosort4	384 channels, 30kHz, optimized for Neuropixels probes
Quick Sort	MountainSort5	CPU-based, fastest option for small recordings
High Quality	Kilosort4	Full QC metrics + Phy export for manual curation

Compute requirements

Resource	Requirement
GPU	GPU sorters require CUDA-capable GPU. CPU sorters run on CPU only.
Duration	900–1800 seconds depending on recording length and sorter

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