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drEEM user support

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Urban Wünsch
added an update
Hi,
we've recently pushed an update of the toolbox to fix a compatibility issue with Matlab R2022a. If you updated to this version of Matlab and want to use drEEM, it's important to use the new version of drEEM since you will be unable to access the Matlab documentation while drEEM is on the Matlab path.
Download either via dreem.openfluor.org (Download latest link) or by running "getdreem".
All the best,
Urban
 
Kathleen Murphy
added an update
Our next PARAFAC course will start on January 31st. It will be an online course, with recorded lectures and in-person sessions staged over a 3-week period. Registration via the course webpage will open in November. To express your interest and get updates via email, use this link: https://forms.gle/1jV2NktDr6Rmdbz37
 
Kathleen Murphy
added an update
We are now collecting expressions of interest to participate in an online course on analysing DOM fluorescence data with PARAFAC. It will run over 3 weeks starting in September 2021. More information at the link below. Please submit a survey if you are interested to attend.
 
Urban Wünsch
added an update
Hi,
ever run into trouble with eemreview? You may want to read this and see if the issue goes away with a Maltab update:
Thanks to Yu Kuang and Morimaru Kida for reporting the issue.
 
Kathleen Murphy
added an update
Many practical topics will be covered including: ensuring data quality in fluorescence spectroscopy, checking your instrument, data aquisition and organisation, correcting for inner filter effects, as well as PARAFAC modelling and interpretation.
Registrations close on Monday, Sept 28 and only a small number of seats are still available. Further details on course website https://conferencemanager.events/parafac-2020/about
 
Kathleen Murphy
added an update
Registrations open tomorrow (1st September) at the course website: https://conferencemanager.events/parafac-2020/signup Take advantage of the early bird discount by registering before September 15. Note that participant numbers are limited, and the final date for registration is Sept 28.
 
Kathleen Murphy
added an update
Registration will be possible starting on Tuesday, September 1.
Course fees will be finalised as soon as possible (current estimate is 800 USD + taxes where applicable).
 
Kathleen Murphy
added an update
We are now collecting expressions of interest to participate in an online course on analysing DOM fluorescence data with PARAFAC. It will run over 3 weeks at a date to be decided (between late August and late October, 2020). More information at the link below. Please submit a survey if you would be interested to attend. https://forms.gle/uVLqwwJGTGUjtDdYA
 
Kathleen Murphy
added an update
We are collecting expressions of interest to attend a PARAFAC training workshop in Copenhagen. Tentative dates are early June, 2020. More information at the link below. Please submit a survey if you would be interested to attend. https://forms.gle/HmpA9RDzwvSocgkv5
 
Kathleen Murphy
added an update
I occasionally get asked how to export EEMs that were created or modified with drEEM to individual text files. Here is some code that you could tweak according to needs. Note that some operating systems expect forward slash (/) rather than backslash(\) when specifying file paths. Exporting to csv format is faster than exporting to Excel format, and works on all operating systems.
%export a 3D EEM dataset to individual csv files
Xout=XcRU; %in this example, XcRU is the dataset to be exported
foldername='D:\mymatlab\mydrEEM\eemdata\correctedEEMs'; %the exported files will be saved in this folder
for i=1:Xout.nSample
filename=deblank(char(Xout.filelist{i}));
filename=filename(1:end-5); %this removes unwanted final characters from filename, e.g. .xslx'
eem_i=squeeze(Xout.X(i,:,:)); %3D dataset => 2D matrix
eem_i=[[NaN; Xout.Em] [Xout.Ex'; eem_i]]; % attach Ex and Em to the eem
csvwrite([foldername '\' filename '_corr.csv'],eem_i) %write the eem to a csv file
end
 
Kathleen Murphy
added an update
Hope this is useful to someone. Contact your manufacturer for the latest advice.
 
Kathleen Murphy
added an update
Hope this is useful to someone. Contact the manufacturer for the latest advice.
 
Kathleen Murphy
added an update
Kathleen Murphy
added an update
getting started (3 m 50 s) - http://bit.ly/2wXCdKW
smootheem (9 m 50 s) - http://bit.ly/2IytZOI
splitds (7 m 05 s) - http://bit.ly/2ICxXlo
 
Kathleen Murphy
added a research item
MATLAB mfiles for PARAFAC analysis on fluorescence EEMs. Several minor bug fixes since previous releases.
Kathleen Murphy
added 2 research items
San Francisco Bay dataset used in the drEEM PARAFAC tutorial (see linked publication). The data are corrected and PARAFAC ready.
Simplified, annotated MATLAB code for implementing PARAFAC using the drEEM toolbox (and the N-way toolbox of course, thanks Rasmus!). For a discussion and further details, see the Appendix to our 2013 PARAFAC tutorial in Analytical Methods. Also, see the examples at the bottom of the help for any individual function in drEEM.
Kathleen Murphy
added an update
Some troubleshooting help to be found in this pdf about spectral correction in FDOMcorr and drEEM.
 
Kathleen Murphy
added an update
I am adding some published data and references for quinine sulfate spectra. In the case that you are unsure about which spectral correction factors apply for your fluorometer, these data might be useful to get an indication of spectral bias.
 
Kathleen Murphy
added an update
I am temporarily adding a copy of nprocess.m to this project (compatible with latest MATLAB releases). This update will be deleted as soon as it is confirmed that the file is available via the official NWay website.
 
Kathleen Murphy
added an update
Following recent MATLAB updates, a bug has appeared in an NWAY toolbox function nprocess.m. The drEEM function called normeem.m has stopped working with recent MATLAB releases because it depends on this function .
The error looks like this:
>> Xpre=normeem(Xs)
Not enough input arguments.
Error in nprocess (line 197)
if ~any([1 -1]==reverse)
Error in normeem (line 91)
Xnew.X=nprocess(data.X,[0 0 0],[1 0 0]);
If you have this error, the solution is to download an updated version of nprocess.m from the NWAY toolbox at www.models.life.ku.dk/algorithms. Overwrite the original version of that file which you will find in the embedded NWAY folder at drEEM/nway. You can also choose to update the entire NWAY folder at that location, but if doing so be sure to keep nwayparafac.m since it is not part of the update.
 
Kathleen Murphy
added 4 research items
PARAllel FACtor analysis (PARAFAC) is increasingly used to decompose fluorescence excitation emission matrices (EEMs) into their underlying chemical components. In the ideal case where fluorescence conforms to Beers Law, this process can lead to the mathematical identification and quantification of independently varying fluorophores. However, many practical and analytical hurdles stand between EEM datasets and their chemical interpretation. This article provides a tutorial in the practical application of PARAFAC to fluorescence datasets, demonstrated using a dissolved organic matter (DOM) fluorescence dataset. A new toolbox for MATLAB is presented to support improved visualisation and sensitivity analyses of PARAFAC models in fluorescence spectroscopy.
A method is proposed for automatically determining the upper and lower boundaries of the Raman scatter peak in fluorescence spectroscopy from empirical data. Accurate peak boundaries are needed to calculate accurate Raman peak areas, used for normalizing fluorescence signals to produce data in units that are comparable between instruments. Comparisons of Raman peak boundaries across nine individual instruments (FluoroMax 3 (FM3) fluorometers from HORIBA Jobin Yvon and Cary Eclipse (CE) fluorometers from Varian Inc.) at the excitation wavelength λex = 350 nm reveal consistent results. At 350 nm excitation, the Raman peak was confined by the emission wavelengths of 382–418 nm, with boundaries determined for the FM3 fluorometers deviating by no more than 0.5 nm and 1.5 nm with respect to the start and end of the peak, and CE fluorometers deviating by up to 1.5 nm and 2 nm, respectively. Peak width was a function of fluorometer type and excitation wavelength. For the FM3 instruments, widths increased from approximately 30 nm at λex = 300 nm to 40 nm at λex = 380 nm, while for the CE instruments, peaks were approximately 5–8 nm narrower. Code for implementing the procedure in MATLAB, which allows for the adjustment of input parameters to compensate for noisy data, is provided in the Supplemental Material (available online).