nwb2bids 0.12.0

Reorganize NWB files into a BIDS directory layout.

nwb2bids

nwb2bids reorganizes NWB (Neurodata Without Borders) files into a BIDS (Brain Imaging Data Structure) directory layout, making your neurophysiology data more accessible and shareable.

Features

• Automatic conversion: Renames NWB files and directories to conform to BIDS conventions
• Metadata extraction: Populates BIDS sidecar TSV & JSON files from NWB metadata
• BEP032 support: Currently supports micro-electrode electrophysiology (extracellular ecephys and intracellular icephys) and associated behavioral events per BEP032

Installation

Install the latest stable release using pip or conda:

# Using pip
pip install nwb2bids

# Using conda
conda install -c conda-forge nwb2bids

Quick Start

Command Line Interface

Convert NWB files to BIDS from the command line:

# Convert files from a directory
nwb2bids convert path/to/nwb/files/

# Specify output directory
nwb2bids convert path/to/nwb/files/ --bids-directory path/to/bids/output/

# Convert multiple sources
nwb2bids convert path/to/directory/ single_file.nwb another_file.nwb

Documentation

For comprehensive information, please visit our full documentation:

📖 nwb2bids.readthedocs.io

The documentation includes:

• User Guide - Detailed usage instructions and advanced features
• Tutorials - Step-by-step examples
• API Reference - Complete function and class documentation
• Developer Guide - Contributing guidelines

Use Cases

nwb2bids was developed to support the DANDI Archive project, enabling researchers to convert neurophysiology datasets from NWB to BIDS format.

Track development with BIDS-Dandisets

The bids-dandisets organization hosts BIDS-formatted versions of datasets from DANDI Archive. You can:

• Browse converted datasets at github.com/bids-dandisets
• Track conversion progress via the dashboard
• Access datasets efficiently using DataLad for version-controlled data management

Contributing

We welcome contributions! Please see our Developer Guide for details on how to contribute.