physiopy: open development solutions for physiology in MRI
The physiopy contributors:
Daniel Alcalá, Apoorva Ayyagari, Katie Bottenhorn, Molly Bright, César Caballero-Gaudes, Inés Chavarría, Vicente Ferrer, Soichi Hayashi, Vittorio Iacovella, François Lespinasse, Ross Markello, Stefano Moia, Robert Oostenveld, David Romero-Bascones, Taylor Salo, Rachael Stickland, Eneko Uruñuela, Merel van der Thiel, & Kristina Zvolanek.
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
physiopy's main aims translate into three core components:
- A BIDSificator, phys2bids
- (Pre)processing tools for physiological data based on BIDS
- A documentation that introduces users to the world of physiological data
Improving physiopy's documentation
Project 1: Improve physiopy's documentation
Skills required:
- None!
Skills recommended:
- git/Github
- MarkDown
- reStructuredText
Skills acquired:
- git/Github [basic]
- MarkDown
- physiologial denoising techniques
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 supports AcqKnowledge (BIOPAC) and Labchart (ADInstruments) files.
Project 2: Extend support for filetypes in phys2bids (Siemens MRI data)
Skills required:
- python [basics]
Skills recommended:
- git/Github
- Continuous Integration
Skills acquired:
- git/Github
- Continuous Integration
- physio data interaction
Denoising fMRI data: phys2denoise
physiopy/phys2denoise is our second repository, introduced in May 2020.
Its aim is creating denoising regressors for fMRI from physiological recordings.
Project 3: Write testing functions for phys2denoise
Skills required:
- python [basics]
Skills recommended:
- git/Github
- pytest
Skills acquired:
- git/Github
- Continuous Integration
- pytest
Preprocess physio data: peakdet
physiopy/peakdet was "donated" by its maintaner, Ross Markello, and is currently maintained by physiopy.
Its aim is denoising physiological data and detect peaks in the signal.
Project 4: Improve peakdet's GUI
Skills required:
- python
- matplotlib GUI development
Skills recommended:
- git/Github
- pytest
Skills acquired:
- git/Github
- Continuous Integration
- pytest
physiopy
Bonus project: Design logos!
physiopy
phys2bids
Credit to Daniel Alcala'
Join us over Mattermost and/or Gathertown!
Mattermost channel: ~physiopy
GitHub: https://github.com/physiopy
That's all folks!
Thanks to...
... the physiopy contributors
... the tedana community!
...you for the (sustained) attention!
BHD2021 physiopy
By Stefano Moia
