> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biom.science/llms.txt
> Use this file to discover all available pages before exploring further.

# SpikeInterface — Spike Sorting

> Automated spike sorting with 7 sorter backends.

# 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          |