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swepy

A basic user interface to load and analyse shear wave elastography scans.

https://github.com/oseynnes/swepy

Science Score: 44.0%

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Repository

A basic user interface to load and analyse shear wave elastography scans.

Basic Info
  • Host: GitHub
  • Owner: oseynnes
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 59.2 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created over 4 years ago · Last pushed 12 months ago
Metadata Files
Readme License Citation

README.md

Documentation

Swepy is a basic user interface to load and analyse shear wave elastography files recorded with Hologic Supersonic machines.

The script works with DICOM files and is optimised for Mach30 machines but should work with other machines from the Mach range. Scans from Aixplorer machines also seem to be compatible but have not yet been tested thoroughly.

The analysis currently consists in a graphical preview of the elastography measurements for each frame (violin plots), and calculations of mean and median values. Results can be exported to a csv or xlsx file.

NB: For now, the analysis only works for cine loops.

Dependencies

The scripts run with Python 3.8. All package dependencies are listed in requirements.txt.

Get started

  • Clone this repository
  • Install dependencies
  • Run the swepy/start.py file to start the user interface
  • Load a DICOM file containing an image sequence (generally a video clip, takes a few seconds)
  • Enter the following parameters found on the image frame:
    • acquisition frequency of SWE frames (SWE fhz parameter)
    • maximal scale value (max. scale parameter, in kPa or m/s)

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  • (optional) Change ROI size or shape
  • Press Analyse
  • Find results preview and export interface in the Results tab.

  • Export to a csv or xlsx file

Acknowledgements

I am grateful to Neil Cronin (University of Jyväskylä) for his input early in the project.
I also thank Valentin Doguet, Antoine Nordez and Aurélie Sarcher (Nantes Université) for sharing their experience and views, based on the development or utilisation of the excellent ElastoGUI.

Citation

swepy is a project developed at the Norwegian School of Sport Sciences. If needed, this code can be referenced from the cff file of this repository, or as follows: @software{Seynnes_swepy_2023, author = {Seynnes, Olivier}, license = {MIT}, month = apr, title = {{swepy}}, url = {https://github.com/oseynnes/swepy}, year = {2023} }

Owner

  • Login: oseynnes
  • Kind: user

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: swepy
message: Analysis tool for shear wave elastography scans
type: software
authors:
  - given-names: Olivier
    family-names: Seynnes
    email: oliviers@nih.no
    orcid: 'https://orcid.org/0000-0002-1289-246X'
    affiliation: Norwegian School of Sport Sciences
repository-code: 'https://github.com/oseynnes/swepy'
license: MIT
date-released: '2023-04-24'

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