physiopy: open development solutions for physiology in MRI

The physiopy contributors:

Daniel Alcalá, Apoorva Ayyagari, Roza G. Bayrak, Katie Bottenhorn, Molly Bright, Catie Chang,
César Caballero-Gaudes, Inés Chavarría, Niall Duncan, Elizabeth DuPre, Inês Esteves, Vicente Ferrer,
Sarah Goodale, Soichi Hayashi, Vittorio Iacovella, Tomas Lenc, François Lespinasse, Ryan Lim, Neville Magielse,
Ross Markello, Mary Miedema, Stefano Moia, Robert Oostenveld, Marie-Eve Picard, Joana Pinto,
David Romero-Bascones, Taylor Salo, Rachael Stickland, Mi Xue Tan, Eneko Uruñuela, Hao-Ting Wang,
Merel van der Thiel, Kristina Zvolanek, & Marcel Zwiers.

physiopy

MRI-related physiology is still a niche → we need more researchers and clinicians to become interested in the topic. Sharing physiological data following the concepts of Open (Science) Data could improve the exposition of this topic

*Open Source Software Development is the idea of developing a software publicly, sharing it from the beginning of the development, fostering a democratic community of contributors in support of the project, using version control and software testing.

One aim of physiopy is to ease this process using a Community driven, BIDS-based, Open Development* approach.

physiopy's libraries

Raw data

BIDSification

physiological data preprocessing

phys. denoising

phys. imaging

Data acquisition

Process description

physiopy's libraries

Raw data

phys2bids

peakdet

phys2denoise

phys. imaging

Data acquisition

physiopy's documentation

physioQC

Project 1: BIDS support and BIDS App!

Add automatic I/O for BIDS (derivatives) formats
Containerise Physiopy's apps (Docker, Apptainer)

Skills recommended:

git/Github [basics]
Docker / Singularity/Apptainer

Skills acquired:

All of the above
physio data interaction

Join us over on Github
and @ building H8!

GitHub: https://github.com/physiopy

Today

Tomorrow

BIDSifying physiological data: phys2bids

physiopy/phys2bids is our flagship repository, introduced in December 2019.

Its aim is reorganising physiological recordings into BIDS format, and it currently supports AcqKnowledge (BIOPAC), Labchart (ADInstruments), Spike2, and GE files.