Skip to content

Welcome to biosigIO

PyPI version Tests codecov

biosigIO is a Python package for biosignal import/export and manipulation across modalities (EEG, EMG, iEEG, MEG, and behavioral/marker streams). It provides a unified Recording interface for working with data from many acquisition systems and archives and exporting it to standardized and serving formats with harmonized metadata.

Why biosigIO?

Working with biosignal data across multiple recording systems can be challenging due to:

  • Different file formats
  • Varied metadata structures
  • Inconsistent channel naming
  • Diverse sampling rates and filtering

biosigIO simplifies this process by providing a standardized interface for loading, manipulating, and exporting biosignal data regardless of the original source.

Key Features

  • Multi-system support:
  • EEGLAB set files (supported)
  • Delsys Trigno (supported)
  • OTB Systems (supported)
  • EDF/BDF(+) (supported, including annotations)
  • WFDB (supported, including annotations)
  • XDF/Lab Streaming Layer (supported, multi-stream)
  • MEG: .fif and CTF .ds via MNE (supported; meg extra)
  • BrainVision .vhdr via MNE (supported; meg extra)
  • Proprietary electrophysiology via python-neo: Intan, Blackrock, Spike2, Plexon, Micromed, Neuralynx (supported; neo extra)
  • Generic CSV (supported with auto-detection)

  • Noraxon (planned)

  • Intelligent import:

  • Automatic file format detection
  • Format-specific metadata extraction
  • Handling of specialized CSV formats
  • Automatic annotation/event loading (WFDB, EDF+/BDF+, and EEGLAB .set) into the events table, embedded back on EDF+/BDF+ export and carried in the Parquet/Arrow/Zarr serialization formats

  • LSL timestamp preservation for XDF files (for synchronization)

  • Intelligent export:

  • Automatic determination of EDF/BDF format based on signal quality
  • Smart handling of precision requirements
  • BIDS-compatible metadata formatting

  • Annotation export (EDF+/BDF+)

  • Serialization & serving (see Serialization & Serving):

  • Parquet and Arrow/Feather: lossless columnar round-trip (analytics, fast IPC); arrow extra

  • Zarr: cloud-native serving store (viewing, inference, and training from one store), a derived downsampled copy; zarr extra

  • Data manipulation:

  • Channel selection
  • Metadata handling
  • Event/Annotation handling (access, add)
  • Basic signal visualization
  • Raw data access and modification

Quick Example

from biosigio import Recording

# Load data with automatic format detection, will issue an error to indicate use of the `trigno` importer
rec = Recording.from_file('data.csv')  # Format detected from file extension

# Load data with explicit importer
rec = Recording.from_file('data.csv', importer='trigno')

# Plot specific channels
rec.plot_signals(['EMG1', 'EMG2'])

# Export to EDF/BDF (format automatically determined)
rec.to_edf('output.edf')  # Extension will be added if not provided

Documentation Structure

This documentation is organized as follows:

  • User Guide: Step-by-step instructions for using biosigIO
  • Data Formats: Details about supported input/output formats
  • API Reference: Complete documentation of classes and methods
  • Examples: Practical examples for various use cases

License

This project is licensed under the BSD 3-Clause License.