Vespa

Versatile Simulation Pulses and Analysis - Python tools for Magnetic Resonance Spectroscopy

• Contact: Brian J. Soher, vespa@briansoher.com

• Bug Reports: vespa.bugs@gmail.com

• Licence: BSD, specifically a "three-clause" BSD license

• Vespa can be installed via PyPI (see the Vespa-Suite package).

• This repository is primarity for contributing towards development.

• For more Installation, User Manuals, and Technical Information see Github Pages:

  https://vespa-mrs.github.io/vespa.io/

Overview

Vespa is an integrated, open source, open development platform for magnetic resonance spectroscopy (MRS) research. It contains four software applications, written in Python, called:

1. Pulse - for RF pulse design
2. Simulation - allows spectral simulation and prototyping
3. DataSim - an application for creating synthetic MRS data sets
4. Analysis - interactive spectral data processing and analysis

These applications can be run separately, but can also communicate via a shared database of objects/results. Integration allows one application to use the output from another as input. For example, Simulation can make use of an RF pulse designed in Pulse to create a more realistic MR simulation.

The Vespa project addresses previous software limitations such as: non-standard data access, closed source and multiple language software (that complicate algorithm extension), and a lack of integration between programs.

Acknowledgements

This work has been supported by NIH grants: R01 EB008387, R01 EB000207, R01 NS080816 and R01 EB000822

Citation

If you publish material that makes use of Vespa, please cite the following publication:

Soher B, Semanchuk P, Todd D, Ji X, Deelchand D, Joers J, Oz G and Young K. Vespa: Integrated applications for RF pulse design, spectral simulation and MRS data analysis. Magn Reson Med. 2023;1-16. epub doi: 10.1002/mrm.29686

Background

The Vespa package is an extensive redesign of three previous MRS software tools:

• MatPulse (Pulse) - software for RF pulse design written in Matlab,
• GAVA/Gamma (Simulation) - software for spectral simulation code in IDL
• IDL_Vespa (Analysis) - spectral data processing and analysis code in IDL

Thanks to the NIH (grant number 1R01EB008387-01A1) for funding the maintenance and extension of these separate applications into a combined environment based entirely on the Python language.

Compatibility

Vespa has been tested and is certified to run on the following systems: Windows, Macintosh OSX, and Linux. However, it should run on any system that supports Python and wxpython. As of version 1.0.0, Vespa now runs under Python 3.7 and later.