drEEM toolbox

Processing and analysis of ultraviolet-visible absorbance and fluorescence spectra.

drEEM aids the import, processing, and analysis of ultraviolet-visible absorbance and fluorescence spectra. Particular focus is on FAIR data policies. The toolbox is particularly useful for the chemometric analysis of excitation-emission matrices (EEMs) of dissolved organic matter (DOM). Spectral properties of chromophoric DOM can also be determined easily.

Installation

1. Via browser outside MATLAB: hit "Open in MATLAB online" or "Download". Double click on the .mltbx file to install the toolbox after download.
2. From within MATLAB: In the home tab, open the Add-Ons Explorer, search for "drEEM toolbox" and click "Add".

If you have older versions of drEEM installed, you will see a warning or error message telling you to remove these from the path. You should follow this advice to make sure you're actually benefitting from the newest version.

Required Add-Ons

1. Statistics and Machine Learning Toolbox is required, but only to calculate exponential CDOM slopes. Such fits are used to to calculate the long wavelength range CDOM slope and to extrapolate CDOM absorbance data in cases where the measured fluorescence emission exceeds the coverage of absorbance data. If you don't require these features, drEEM will run fine without the toolbox.

Recommended Add-Ons

1. Parallel Processing Toolbox (optional) to benefit from multi-core CPUs when fitting PARAFAC models. Even without it, drEEM-2 is 5x faster than previous versions.
2. PLS_toolbox (optional) to use the latest PARAFAC algorithms. However, this requires PLS_toolbox to be purchased and installed. This toolbox is by no means required since drEEM ships with the free N-Way toolbox.

Getting started

After installation, a guide to get you started will be displayed. drEEM is based on object-oriented programming, so you call methods (functions) by refering to a toolbox object. You get started by initializing the toolbox:

tbx=drEEMtoolbox;
tbx.importwizard % This would open the data import GUI
tbx.doc("drEEM")

• To see which methods are available, type `tbx.` followed by hitting the TAB key to get a list of method suggestions.
• For orientation, method names generally refer to an action and an object, e.g. importeems, fitparafac, subtractblanks, splitdataset, etc.
• Type doc drEEM to see the documentation (highly recommended).
• Video tutorials on drEEM

Additional external resources

drEEM ships with several functions provided by external sources:

1. N-Way toolbox by Rasmus Bro
2. inpaint_nans by John D'Errico
3. crameri colormaps by Fabio Crameri & Chad Greene

Please respect the licenses of these resources when redistributing this software.

Further reading (peer-reviewed publications)

• PARAFAC tutorial paper (2013)
• The N-Way toolbox publication
• OpenFluor database publication

Further watching on multiway analysis

• Lecture series on multiway analysis

Questions, comments , suggestions?

Email the main developer: [e-mail]