bilab 0.1.1

A data API for the Brain Interfacing Laboratory

BIL Data Python API

This repository contains the public-facing Python API for accessing and analyzing neural data from the Brain Interfacing Laboratory. The public deposition is at the Stanford Digital Repository (SDR).

Installation

pip install bilab

Data Availability

The bil package is an API for interacting with publicly deposited data. In that directory, each recording session has its own identifier under the data directory. For instance, "U201130_01" is the first session by subject U on 2020-11-30.

Not all data types are available for all sessions.

Public datasets are deposited incrementally. The API contains methods for signals that will raise a FileNotFoundError if those signals have not been published.

Quickstart

See demo/md/quickstart.md.

from bil.api import get

# Initialize a study using a session ID
# Data will be fetched over HTTPS from the Stanford Digital Repository
study = get("U201130_01", download_dir="my_data")

# Access trial metadata
print(f"Number of trials: {len(study)}")
df = study.df

# Get a span of data for the first trial
# This is an accessor for a continuous segment of time
span = study.spans[0]

# Retrieve LFP data from that period of time from the Utah array in motor cortex
# This well get deposited in my_data/U201130_01
lfp = span.lfp(region="m1")  # (96, T) ndarray

Development

For development, clone the repository and install the additional dev dependencies:

pip install -e ".[dev]"

Alternatively, uv can be used to pull the latest uv.lock into a virtual environment:

uv sync --all-extras

Finally, configure pre-commit hooks:

pre-commit install