Published October 28, 2024 | Version v2
Software Open

The osl-ephys Python package for the analysis of electrophysiological data

Creators

  • 1. Oxford Centre for Human Brain Activity, Wellcome Centre for Integrative Neuroimaging, University Department of Psychiatry, Warneford Hospital, Oxford, UK; Centre for Human Brain Health, School of Psychology, University of Birmingham, UK
  • 2. Oxford Centre for Human Brain Activity, Wellcome Centre for Integrative Neuroimaging, University Department of Psychiatry, Warneford Hospital, Oxford, UK

Description

The OHBA Software Library for the analysis of electrophysiology data (osl-ephys) is created by the OHBA Analysis Group, OHBA, University of Oxford, UK. osl-ephys is a Python package for running M/EEG analysis, and it is the successor of the MATLAB OSL package. osl-ephys integrates well-known software packages like MNE-Python and FSL into its own analysis functions and design philosophy.

At the core of osl-ephys sits a configuration user interface, which allows the user to set up a pipeline for processing the data in the most concise way, without losing any flexibility. The config structure is typically on the size of one to two dozen lines of code that capture an entire (pre-) processing pipeline, and can easily be shared for reproducibility and replicability. Moreover, it contains tools for batch and parallel processing, as well as a set of reporting tools for quality control of processed (batch) data.

osl-ephys is under constant development to incorporate new functionalities. The most recent version of osl-ephys can always be found on GitHub; this is also where issue reporting and feature requests take place.

Notes

This research was supported by the National Institute for Health Research (NIHR) Oxford Health Biomedical Research Centre. The Wellcome Centre for Integrative Neuroimaging is supported by core funding from the Wellcome Trust (203139/Z/16/Z). C.G. and M.v.E are supported by the Wellcome Trust (215573/Z/19/Z). A.Q. is supported the MRC (RG94383/RG89702) and by the NIHR Oxford Health Biomedical Research Centre. M.W. is supported by NIHR Oxford Health Biomedical Research Centre, the Wellcome Trust (106183/Z/14/Z and 215573/Z/19/Z), and the New Therapeutics in Alzheimer's Diseases (NTAD) study supported by the MRC and the Dementia Platform UK.

Files

osl-ephys-main.zip

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Additional details

Funding

Exploring the Mechanisms of Distributed Spontaneous Brain Activity. 106183
Wellcome Trust
Integrative imaging of brain structure and function in populations and individuals 215573
Wellcome Trust
Wellcome Centre for Integrative Neuroimaging 203139
Wellcome Trust

References

  • The OHBA Software Library (OSL). https://github.com/OHBA-analysis/osl-core
  • Alexandre Gramfort, Martin Luessi, Eric Larson, Denis A. Engemann, Daniel Strohmeier, Christian Brodbeck, Roman Goj, Mainak Jas, Teon Brooks, Lauri Parkkonen, and Matti S. Hämäläinen. MEG and EEG data analysis with MNE-Python. Frontiers in Neuroscience, 7(267):1–13, 2013. doi:10.3389/fnins.2013.00267.
  • S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004