drEEM toolbox for MATLAB

About the Horiba Aqualog SampleQ automatic processing & exporting feature

Fri, 20 Mar 2026 00:00:00 +0000

Background

Many laboratories focussing on Dissolved Organic Matter (DOM) are using a Horiba Aqualog for their absorbance and fluorescence measurements. Judging by the workshops we host, it is the most-used instrument in the community. Amongst the users of the instrument, quite a few use it in connection with an autosampler or by using the SampleQ feature. I myself like the SampleQ feature and use it extensively whenever it makes sense (i.e. makes my life easier). This post addresses the functionality to automate processing and export. I argue that this particular instrument-software feature should be avoided in its current form if you’re planning to do anything but a quick inspection of your measurements.

The issues

Have you ever used this feature? Don’t know? Well, if your files end in ABS.dat or PEM.dat, then you have used this feature yourself. Ok, but what are the issues?

Lack of FAIRness

The files produced by the software’s SampleQ functionality all end in the same file patterns. And they all contain either absorbance data or fluorescence data. But no descriptions beyond that. Wavelength and data; that’s it. Good, that makes them easy to import. But Imagine you retrieve those files i some weeks, months, or years. Or you inherit the files from a group member that left for another job. But without their extensive lab notebook. Can you tell from the files how they were processed (blanks, IFEs, normalization, scatter)? Spoiler: No you can’t. Well, you can guess. But in some cases, it is hard to tell. And do you want to guess if you’re trying to reuse these data in a project?

For example, you won’t be able to tell if the blanks were good (if those got subtracted) or if your scatter excision settings were adequate (if you decided to cut scatter). We run PARAFAC workshops on a regular basis and see contaminated blanks every time. In the end you’ll wonder why your PARAFAC components look strange and settle for a model with few components because it’s the only stable model. But how frustrating is it that you never had a chance to get more components in the first place because your automatically subtracted blank was contaminated? Not to mention that your fluorescence intensities are offset due to that contaminated blank. Not great for global comparisons.

As authors of a toolbox in MATLAB, we often get criticism for supporting a software with closed-source code with expensive licensing policies. But the drEEM toolbox code is open and documented and it documents in great detail when and how a step was performed. The same cannot be said of the features you use in the SampleQ functionality because the files don’t show the information. But all of this functionality can be implemented using open source software. I argue that you can and should use drEEM or staRdom instead of sampleQ.

Lack of consistency in the exported files

We receive support requests from users with SampleQ-type files on a somewhat regular basis. File imports fail and the obvious culprit is the importing software toolbox, not the exporing instrument software, right?

With drEEM-2, we tried to simplify the topic of data import. We use the newer MATLAB functions (readmatrix, or readtable) that are quite smart in finding the boundaries of your files. You used to have to provide this information (“A1..B189”). But when you reuse scripts, these inputs are easy to overlook and will import strange scans if you changed resolution or wavelength coverage.

The import functions of drEEM-2 look at the first file in sequence, identify the boundaries, and then check all subsequent files for their boundaries. If there are mismatches, files will be excluded from the import to catch errors preemptively. Que the SampleQ functionality: During the processing, it will sometimes identify measurements as having produced non-sense data (e.g. absorbance too high). It will then decide to export empty cells. Not necessarily a problem, right? Except this often happens at the edges of your measurements, e.g. at short excitation. The import scripts then get confused by the empty cells and MATLAB has a hard time automatically detecting the file boundaries. End result: You see an error during the import and get frustrated. It’s the first step with this new unknown toolbox and an error right at the start is, well, not a strong start.

The solution

Don’t use the automatic export function to produce processed ABS.dat or *PEM.dat files. Instead, only produce the *.ogw files. These can be opened in the software or even Origin Pro if you don’t have the AquaLog software on hand. You can export these measurements using the more reliable “Export HJY data” function. If you read in these files, you can use the default options of importeems and importabsorbance, and I have yet to spot errors other than the occasional mismatch in the wavelength coverage that comes from using different settings.

Using this HJY export function, you blanks are always paired with your sample, and the processing is completely left to you, the expert. You’ll produce better processed EEMs and CDOM spectra and the drEEM toolbox will automatically document everything for you. We’re working hard on improving features that increase FAIRness and you’ll future-proof your own analysis pipeline by opting this way.

drEEM version 2 update

Tue, 02 Sep 2025 00:00:00 +0000

We’ve been keeping a monthly update schedule to iron out some small bugs and improve the functionality of drEEM-2. The September update (version 2.25.09) mainly fixes some inconsistencies with the toolbox’s custom documentation. Otherwise, internal reorganization of files that improve the future stability of the toolbox.

Download as always via MATLAB File Exchange. If you’re interested in details, the changelog is here.

We are very actively developing new features for the toolbox now that a stable basis is there.

The update-check feature is now fully working and will notify users about updates when they become available!

Happy PARAFACing! Urban

drEEM version 2 released!

Thu, 31 Jul 2025 00:00:00 +0000

The first release of the new drEEM toolbox version 2 is now published.

I want to try it but…

Don’t worry, it’s super easy to try the new toolbox! You can try it out using Matlab online (see below). You don’t even need to have MATLAB installed on your own computer. Trying it out doesn’t even require a payed license (just a free MathWorks account).

How do I get the toolbox?

What’s changed?

The toolbox is much easier to use with many graphical user interfaces, function input help, meaningful error messages, and nicely formatted documentation.

While many functions have changed, the toolbox comes with a guide and many examples that you can use to get friendly with the new way of doing things.

drEEM upgrade!

Mon, 14 Jul 2025 00:00:00 +0000

It’s been a while since the last significant update of drEEM. Today, we’re happy to share that a completely overhauled drEEM toolbox is publicly available for download! Why upgrade?

It’s free (as always!)
Most tasks are have been reduced to one line of code.
GUI support for tasks that are vital for producing good data
Easy export of data for open data publishing.
Standardized dataset objects and because of that: Much, much more meaningful error messages!
If you like object-oriented programming, you’ll love this update!
Many, many more improvements and new features.

For the moment, the toolbox is available on Gitlab but there is no formal release version yet. Feel free to download and test.

Newsletter offering

Wed, 27 Mar 2024 00:00:00 +0000

We have added an option to sign up for newsletters to allow users to receive updates and announcements regarding our toolbox. Sign up by clicking on the Newsletter link in the header of the toolbox website!

Bug fix in drEEM

Tue, 19 Apr 2022 00:00:00 +0000

we’ve recently pushed an update of the toolbox to fix a new compatibility issue with Matlab R2022a. If you updated to this version and want to use drEEM, it’s important to update drEEM as well since you will be unable to access the Matlab documentation while drEEM is on the Matlab path.

You can download v0.6.5 here.

To update (if drEEM is already installed), simply execute getdreem without providing any input to the function. getdreem downloads the newest release and installs it properly. This will only work on drEEM v0.6.0 or newer.

The changes are as follows:

v0.6.5

Modifications:
- associatemetadata: Bugfix, suppress error message when metadata table contains more entries than the dataset itself.
- N-Way toolbox: Removed incompatible file info.xml to prevent error messages when accessing any documentation in Matlab (since R2022a). Renamed contents.m to prevent similar issues.

Course announcement: Parallel Factor Analysis for DOM fluorescence

Tue, 16 Nov 2021 00:00:00 +0000

Register now for our 2022 online PARAFAC course

Are you interested in learning more about PARAFAC analysis of organic matter fluorescence datasets? We are running our online course Parallel Factor Analysis for DOM fluorescence between January 31st and February 25th 2022.

For general information on the course, head over to our course website. If you’re missing important information, just send us an email.

Registrations start on November 17th 2021 and end on January 17th 2022. We’re offering an early-bird discount until December 15th 2021. Take a look at the course website for more information.

If you are a student, you can obtain credits for your participation through Chalmers University of Technology (link to course page).

Common issue for drEEM 0.6.x with older Matlab

Fri, 05 Mar 2021 00:00:00 +0000

When using eemreview (v0.5 or older) with Matlab R2018b (or older), you may come across this string of error messages when hitting the “spectra” button:

Dot indexing is not supported for variables of this type. 

Error in ginput>setupFcn (line 221) 
    initialState.toolbarVisible{1} = tb.Visible; 

Error in ginput (line 60) 
    initialState = setupFcn(fig); 

Error in eemreview>init_exemmview (line 362) 
[x,y]=ginput(1); 

Error using uiwait (line 81) 
Error while evaluating UIControl Callback.

This error originates in a Matlab-internal function that produces the error and we have therefore no control over fixing the issue. But there is good news – it is only an issue for older Matlab versions. When we verify a release of the drEEM toolbox, we use the latest Matlab version at the time. The issue above is solved with a Matlab update to the latest version. We highly recommend updating Matlab regularly, especially when switching to a newer version of drEEM.

Bug fix in drEEM

Fri, 09 Oct 2020 00:00:00 +0000

Yet another minor update ironing out bugs. You can download v0.6.2 here.

To update, simply execute getdreem without providing any input to the function. getdreem downloads the newest release and installs it properly. This will only work on drEEM v0.6.0 or newer.

The changes are as follows:

v0.6.2

Modifications:
- outliertest: Fixed R2020b compatibility and spelling mistake.
- handlescatter: Fixed behaviour for selective scatter excision & interpolation.
- checkdataset: Fixed displaying message when no models are in the structure.
- splitanalysis: Fixed a bug in the non-parallel function execution (thanks to Morimaru Kida)

Minor update to drEEM

Thu, 01 Oct 2020 00:00:00 +0000

After the release of v0.6.0, we’ve ironed out some minor bugs in drEEM and released a new version. You can download v0.6.1 here.

To update from 0.6.0, simply execute getdreem without providing any input to the function. getdreem downloads the newest release and installs it properly.

The changes are as follows:

Modifications:

splitanalysis: Bugfix in input argument parsing. Now works as documented. 0.6.0 had it and constraints switched.
handlescatter: Bugfix. Smoothing now works as expected (previously interpolation was done for all types and ignored the user input in opt.interpolate).
modelout & modeloutmac: Bugfix in drEEM version reporting & .Smooth handling. Support for handlescatter added (no error message as in 0.6.0)
assembledataset: Added .i as a standard field to the function output to ensure compatibility with checkdataset

New

modelexport: Based on modelout, but works faster and is platform independent. This function may require Matlab R2019a or newer to work properly.

drEEM toolbox for MATLAB

About the Horiba Aqualog SampleQ automatic processing & exporting feature

drEEM version 2 update

drEEM version 2 released!

I want to try it but…

How do I get the toolbox?

What’s changed?

Read more here:

drEEM upgrade!

Newsletter offering

Bug fix in drEEM

v0.6.5

Course announcement: Parallel Factor Analysis for DOM fluorescence

Register now for our 2022 online PARAFAC course

Common issue for drEEM 0.6.x with older Matlab

Bug fix in drEEM

v0.6.2

Minor update to drEEM