Installation

Basic Install

Install SpikeLab from source using pip:

pip install spikelab

Optional Extras

SpikeLab keeps most dependencies optional so the core library stays lightweight. Install only what you need:

Extra	Command	Includes
io	pip install spikelab[io]	pandas (KiloSort cluster info)
ml	pip install spikelab[ml]	scikit-learn, umap-learn, networkx, python-louvain
neo	pip install spikelab[neo]	neo, quantities, pynwb
ibl	pip install spikelab[ibl] (+ pip install git+https://github.com/int-brain-lab/paper-brain-wide-map.git)	ONE-api (query and load IBL Brain-Wide Map datasets); brainwidemap is not on PyPI and must be installed separately from its git repo
numba	pip install spikelab[numba]	numba (JIT-compiled analysis functions)
s3	pip install spikelab[s3]	boto3 (Amazon S3 access)
gplvm	pip install spikelab[gplvm]	poor-man-gplvm, jax, jaxlib, jaxopt, optax
spike-sorting	pip install spikelab[spike-sorting]	spikeinterface, natsort, six, pandas
kilosort4	pip install spikelab[kilosort4]	kilosort (PyTorch + CUDA must be installed separately)
batch-jobs	pip install spikelab[batch-jobs]	pydantic, PyYAML, Jinja2, kubernetes
mcp	pip install spikelab[mcp]	mcp (Model Context Protocol server)
all	pip install spikelab[all]	Everything above plus dev and docs dependencies

Development Install

To install from source in editable mode (for contributing or local development):

git clone https://github.com/braingeneers/spikelab.git
cd spikelab/SpikeLab
pip install -e ".[dev]"

This installs the package in development mode along with testing tools (pytest, pytest-asyncio, black).