PhysioPy - peak detection toolbox for physiological signals

Title

PhysioPy - peakdet

Leaders

Roza G. Bayrak (@rgbayrak) roza.g.bayrak@vanderbilt.edu

Collaborators

Stefano Moia (@smoia), Lars Kasper (@mrikasper), David Romero

Brainhack Global 2022 Event

Brainhack Physiopy

Project Description

peakdet aims to provide a set of tools that will work with a variety of input data to reproducibly generate analysis-ready physiological data.

peakdet is designed for use in the reproducible processing and analysis of physiological data, like those collected from respiratory belts, pulse photoplethysmography (PPG), or electrocardiogram (ECG/EKG) monitors.

What makes your project special and exciting? Physiological monitoring is a key component of understanding physiological sources of signal variance in fMRI data. Monitoring physiology during scanning is critical to enable the characterization of a given subject’s physiologic state at the time of the scan, and to track variations in physiology throughout the scan. With these data, we can more accurately model how these factors manifest in the fMRI signal time series.

How to get started?
Join our Slack channel!

Where to find key resources?
Documentation: https://peakdet.readthedocs.io/en/latest/

Link to project repository/sources

Documentation: https://peakdet.readthedocs.io/en/latest/
Github: https://github.com/physiopy/peakdet

Goals for Brainhack Global

• Pipeline comparison
• Integrate with NeuroKit and learn from PhysIO Toolbox
• QC

Good first issues

• Compare existing pipelines to peakdet pipeline
• Create a data folder structure for dev
• Run existing pipelines on your data, on example data
• Minimal changes to repo - good first github issue!
• Update documentation - clarify usage, describe methods (advanced physio knowledge)
• Refactor code (advanced python)

Communication channels

Slack!

Skills

• Python: Basic (there is no skill level requirement but advanced programming experience would be helpful)
• Physiological Signal Knowledge: Basic

Onboarding documentation

No response

What will participants learn?

This is going to be an exercise in testing, understanding and documenting. You will learn:

• to visualize and process physiological time-series data
• to contribute to an Open Source project and collaborate on Github

Data to use

See the issues!

Number of collaborators

more

Credit to collaborators

We’re looking for code contributors, but any suggestion/bug report is welcome! Feel free to open issues!

This project follows the all-contributors specification. Contributions of any kind welcome!

Image

Type

documentation, pipeline_development, visualization

Development status

1_basic structure

Topic

physiology

Tools

other

Programming language

Matlab, Python

Modalities

other

Git skills

0_no_git_skills, 1_commit_push, 2_branches_PRs

Anything else?

No response

Things to do after the project is submitted and ready to review.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.