Physiopy:

[amaiacc]

Project title:
Physiopy: open development solutions for physiology in MRI

Leader:
Stefano Moia

Collaborators:

Topic:
Data visualization, Physiology, Reproducible scientific methods

Project description:
Physiopy is a community developing open science software for physiological files (e.g. vital signs, respiration, eye tracking, skin conductance, ...) handling and processing.Currently maintaining three libraries to format physiological files into BIDS (phys2bids), clean physiological traces and find their peaks (peakdet), and use physiological traces to compute nuisance regressors for fMRI denoising (phys2denoise), this (meta-)project aims to provide challenges for all levels of contributors within physiopy's environment, its three libraries, and its documentation.Collaborators of all levels of experience with git, GitHub, python, and physiology are welcome. Depending on the level of experience, we'll match collaborators and tasks, and help filling gaps and acquire the necessary skills to finish them.

Data to use:
Most tasks do not require data. For those that do, we provide minimal physiological and BOLD fMRI data to work with.

Link to project repository:
https://github.com/physiopy

Goals for Brainhack Donostia 2021:

• Improve physiopy's documentation (e.g. https://github.com/physiopy/physiopy.github.io/issues) [beginner level, no previous experience required].- Extend file support in phys2bids (e.g. Integration of Siemens Product Sequence Filetypes such as ".puls" physiopy/phys2bids#412) [intermediate level, requires minimal knowledge of python programming].- Improve phys2denoise testing suite [intermediate to advanced level, requires knowledge of python programming].- Improve phys2bids testing CI [advanced level, requires knowledge of python programming, bash, and Continuous Integration pipelines].- Improve peakdet manual peak detection GUI [advanced level, requires knowledge of python and matplotlib programming].

First tasks:

Communication channels:
https://mattermost.brainhack.org/brainhack/channels/physiopy

Video channel:
Jitsi

Number of collaborators:
More

Credit to collaborators:
We follow the all-contributors specification in recognising each and all contributions.

Type of project:
Coding methods, Data management, Documentation, Pipeline development, Visualization, literature review

Development status:
Releases existing

Programming languages:
Python, Shell scripting, markdown, if it counts as programming language

Necessary Programming skills level for the project:
None

Necessary git skills level for the project:
None

Modality:
fMRI, physiology

Software suites:
BIDS

Email:
s.moia@bcbl.eu

What will participants learn:
Depending on the task, participants might learn:- git and basic Github (issues, PRs, reviewing, ...)- Continuous Integration and Deployment- use of physiological data in fMRI experiments- python programming