Kilosort Pipeline

Automated spike sorting pipeline for OpenEphys recordings with Kilosort4 and SpikeInterface.

Installation

uv seems to be simpler and faster alternative to conda. (SpikeInterface's tips on uv)

1. Install uv

Linux:

curl -LsSf https://astral.sh/uv/install.sh | sh

Windows (PowerShell):

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Exit and reopen your terminal after installation.

2. Clone and install in one step

git clone https://github.com/Senzai-Lab/kilosort_pipeline.git
cd kilosort_pipeline
uv sync

3. Activate environment

Linux:

source .venv/bin/activate

Windows (CMD):

.venv\Scripts\activate

---

Using the pipeline

1. Edit config.yaml:

session_name: "session_name"      # timestamp auto-appended
recording_paths:                  # OpenEphys session folders containing structure.oebin file
  - "/path/to/session1"
  - "/path/to/session2"
local_output: "/local/disk"       # path to local SSD
base_output: "/remote/storage"    # path to fsmresfiles

# Optional parameters
target_fs: 1250                   # EEG downsampling (Hz)
save_kwargs:
  n_jobs: 16
  chunk_duration: '2s'
  mp_context: 'spawn'             # for Windows; use 'fork' for macOS/Linux

2. Run pipeline:

# Process all probes
python -m run_pipeline

# Process from common config
python -m run_pipeline --config R:/remote_path/config.yaml

# Process specific probe(s)
python -m run_pipeline --probe ProbeA
python -m run_pipeline --probe ProbeA ProbeB

Output Structure

{local_output}/{session_name}/
├── {session_name}_{timestamp}.log  # Timestamped log file
├── ProbeA/
│   ├── concat/
│   │   └── traces_cached_seg0.raw  # Concatenated binary file
│   ├── eeg/
│   │   └── eeg_data.bin            # Downsampled EEG (if target_fs set)
│   ├── kilosort/                   # Kilosort4 outputs
│   │   ├── spike_times.npy
│   │   ├── spike_clusters.npy
│   │   └── ...
│   └── sync/                       # Synchronized spikes
│       └── spike_times_synced.npy  # Spike times in ADC time scale
└── ProbeB/
    ├── ...