An AI-powered assistant for spike sorting and neural data analysis

SpikeAgent is a web-based AI assistant that streamlines the spike sorting pipeline — from raw neural recordings to curated spike trains. It integrates with SpikeInterface and leverages large language models (OpenAI, Anthropic, Google Gemini) to automate spike sorting, quality control, and data curation.

• Python 3.11+ (recommended via conda)
• At least one API key from OpenAI, Anthropic, or Google

git clone https://github.com/arnaumarin/SpikeAgent.git
cd SpikeAgent
conda create -n spikeagent python=3.11 -y
conda activate spikeagent
pip install -e .

# Pull the image
docker pull ghcr.io/arnaumarin/spikeagent-cpu:latest

# Run (mount your data directories as needed)
docker run --rm -p 8501:8501 --env-file .env \
  -v /path/to/your/data:/path/to/your/data \
  ghcr.io/arnaumarin/spikeagent-cpu:latest

For GPU support (required for Kilosort4):

docker build -f dockerfiles/Dockerfile.gpu -t spikeagent:gpu .
docker run --rm --gpus all -p 8501:8501 --env-file .env spikeagent:gpu

Create a .env file in the project root with at least one key:

OPENAI_API_KEY=sk-...
# and/or
ANTHROPIC_API_KEY=sk-ant-...
# and/or
GOOGLE_API_KEY=...

conda activate spikeagent
spikeagent

The app will open in your browser at http://localhost:8501.

The tutorials/ directory contains Jupyter notebooks demonstrating key workflows:

• vlm_noise_rejection_tutorial.ipynb — AI-assisted spike curation using vision-language models (classifying units, quality control via waveforms and autocorrelograms)
• vlm_merge_simple_tutorial.ipynb — Automated merge analysis using crosscorrelograms, amplitude distributions, and PCA clustering

SpikeAgent can be tested with publicly available datasets:

• Neuropixels 2.0 chronic recordings in mice
• AutoSort flexible electrode recordings

If you use SpikeAgent in your work, please cite:

Lin, Z., Marin-Llobet, A., Baek, J., He, Y., Lee, J., Wang, W., ... & Liu, J. (2025). Spike sorting AI agent. Preprint at bioRxiv. https://doi.org/10.1101/2025.02.11.637754

Buccino, A. P., Hurwitz, C. L., Garcia, S., Magland, J., Siegle, J. H., Hurwitz, R., & Hennig, M. H. (2020). SpikeInterface, a unified framework for spike sorting. eLife, 9, e61834.

MIT