trEPR Toolbox

A MATLAB(r) toolbox for preprocessing, display, analysis, and postprocessing of transient (i.e., time-resolved) electron spin resonance spectroscopy (in short: trEPR) data.

The toolbox is fully GUI-based, but all functions are accessible via command line (CLI) as well. Furthermore, the GUI is extensively documented. The toolbox started out in the PhD time of its main author and developer (T. Biskup), became fully GUI-based in about 2010, and got used for over a decade in day-to-day business dealing with trEPR data. The concepts developed towards reproducible research ended up in the Python ASpecD framework for fully-reproducible Analysis of Spectroscopic Data.

Note: While this MATLAB(r) toolbox should still work with current versions of MATLAB(r), you may be interested in the Python package trepr actively being developed and dedicated to fully reproducible data analysis.

Features

• Completely GUI based
• All functions accessible via CLI
• Modular design
• Load diverse data formats
• Display modes: 2D and 1D (x, y)
• Highly configurable display options
• Preprocessing (combine, accumulate)
• Measuring points and distances
• Averaging (with error bars)
• Info GUI for datasets
• Integrated help
• Exporting data
• Exporting display
• Freq. drift and net polarisation analysis
• integrated command line

Installation

Download the toolbox (usually as compressed archive), uncompress (if necessary), start MATLAB(r), change to the folder you have downloaded/uncompressed the toolbox files to, change to the directory internal and call the function trEPRinstall from within the MATLAB(r) command line. This should guide you through the installation process (and add, inter alia, the toolbox to the MATLAB(r) search path). To start using the trEPR toolbox, type trEPRgui at the MATLAB(r) command line and enjoy the GUI.

How to cite

The trEPR toolbox is free software. However, if you use it for your own research, please cite it accordingly:

• Till Biskup, Bernd Paulus, Deborah Meyer. trEPR toolbox (2022). doi:10.5281/zenodo.7395548

  

License

The toolbox is distributed under the GNU Lesser General Public License (LGPL) as published by the Free Software Foundation.

This ensures both, free availability in source-code form and compatibility with the (closed-source and commercial) MATLAB(r) environment.

Authors

• Till Biskup (2007-2022)

  The principal author and main developer of the trEPR toolbox

• Bernd Paulus (2012-13)

  Valuable contributions during his PhD time

• Deborah Meyer (2013-15)

  Valuable contributions during her PhD time

Related projects

There is a number of related MATLAB(r) projects you may be interested in, but have a look at the section with related Python projects as well that are actively being developed.

MATLAB(r) projects

• TSim (Documentation)

  A toolbox for the simulation and fitting of spin-polarised triplet states, using EasySpin for the simulation part, but guiding the user with an extensive CLI and creating well-formatted reports of the results for enhanced reproducibility. Developed by D. Meyer and maintained by T. Biskup.

• common toolbox

  Toolbox providing basic functionality for data analysis. Spiritual predecessor of the ASpecD framework implemented in Python. Each processing and analysis step gets automatically logged with all parameters to ensure reproducibility. Provides basic functionality for installing and configuring as well as standard processing steps.

• epr toolbox

  Toolbox for analysing EPR data (common Toolbox based). Each processing and analysis step gets automatically logged with all parameters to ensure reproducibility. Provides basic functionality and processing steps for EPR spectroscopy.

• cwepr toolbox

  Toolbox for analysing cwEPR data (common Toolbox based). Spiritual predecessor of the cwepr package implemented in Python. Each processing and analysis step gets automatically logged with all parameters to ensure reproducibility. Focusses particularly on automating the pre-processing and representation of data.

• TA toolbox

  Toolbox for preprocessing, display, analysis, and postprocessing of transient absorption (flash photolysis) data. Similarly to the trEPR toolbox, the TA toolbox is fully GUI-based, but all functions are accessible via command line (CLI) as well. Furthermore, the GUI is extensively documented.

Python projects

• ASpecD framework

  A Python framework for the analysis of spectroscopic data focussing on reproducibility and good scientific practice, developed by T. Biskup.

• trEPR package

  Python package for processing and analysing time-resolved electron paramagnetic resonance (trEPR) data, developed by J. Popp, currently developed and maintained by M. Schröder and T. Biskup.

• cwepr package

  Python package for processing and analysing continuous-wave electron paramagnetic resonance (cw-EPR) data, originally implemented by P. Kirchner, developed and maintained by M. Schröder and T. Biskup.

• FitPy

  Python framework for the advanced fitting of models to spectroscopic data focussing on reproducibility, developed by T. Biskup.