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BEADS: Baseline Estimation And Denoising w/ Sparsity (chromatogram signals)

version 1.7 (327 KB) by

Remove baseline, background or drift and random noise from positive and sparse chromatographic peaks

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The BEADS toolbox jointly addresses the problem of simultaneous baseline correction and noise reduction, for positive and sparse signals arising in analytical chemistry (Raman, infrared, XRD, etc.), here applied to gas chromatography signals. The baseline is similar to slow-varying trends, instrumental drifts or background offset. The proposed baseline filtering algorithm is based on modeling the series of chromatogram peaks as mostly positive, sparse with sparse derivatives, and on modeling the baseline as a low-pass signal. A convex optimization problems formulated so as to encapsulate these non-parametric models. To account for the positivity of chromatogram peaks, an asymmetric penalty function, similar to a regularized l1 norm is utilized. A robust, computationally efficient, iterative algorithm is developed that is guaranteed to converge to the unique optimal solution. It implements the method published in the paper "Chromatogram baseline estimation and denoising using sparsity (BEADS)", by Xiaoran Ning, Ivan W. Selesnick, Laurent Duval, in Chemometrics and Intelligent Laboratory Systems, December 2014, http://dx.doi.org/10.1016/j.chemolab.2014.09.014
The ZIP file contains two Matlab functions:
* a demonstration script (example.m);
* the main function (beads.m),
and an html readme help.
BEADS has since been used in 1D and 2D (GCxGC) chromatography, Raman spectroscopy, high-resolution mass spectrometry for astronomical hyperspectral data, electroencephalogram (EEG), electrocardiogram (ECG) and arabic script analysis.

Comments and Ratings (14)

kai zhang

It is an excellent tool - works very well ones you figure out parameters. Would be much better with more extensive documentation.

how can I choose fc,d,r,amp,lam0,lam1.lam2 values for NIRS data in BEADS TOOLBOX?can u upload a video about BEADS TOOLBOX?
Thank you

Laurent Duval

@Yigal Barkan thank you very much for sharing the data and the parameters, it will help me provide more hints

Laurent Duval

@Mariam Alharthi I do appreciate our exchange and the nice and original use of BEADS

Yigal Barkan

@Laurent Duval

Hi again.
Regarding my X-ray diffraction pattern back removal, I thought I'd share the parameters I used:

beads_parm.fc = 0.01;
beads_parm.d = 1;
beads_parm.r = 6;
beads_parm.amp = 0.5;
beads_parm.lam0 = 0.5* beads_parm.amp;
beads_parm.lam1 = 5* beads_parm.amp;
beads_parm.lam2 = 4* beads_parm.amp;

Here are links to two diffractograms I used this parameterization for:
Synthetic Calcite:
https://drive.google.com/file/d/0BwbffeOK2JyMamhnV280MlFuLUU/view?usp=sharing
Synthetic Aragonite:
https://drive.google.com/file/d/0BwbffeOK2JyMbmIxNU56aGczcFE/view?usp=sharing

Thanks a lot for this code! Let me know when you write the documentation.
Cheers, Y.

amazing code, it helps me lots.

thank you so much.

Mustafa UNAL

Laurent Duval

@Yigal Barkan Thanks for the questions. They provide me with directions for parameter choice prediction

Yigal Barkan

@Laurent Duval
I agree with Ole, I just looked at the documentation and came here for answers.
here are my initial Qs:
d: How do I choose d? is 1 or 2 the polynomial order? please give examples when to use what.
fc: what do you mean by cycles/sample? how should I choose it?
r,lam0, lam1, lam2: don't know where to start with these.

I am about to use the toolbox for background removal of X-ray diffraction patterns. Then do a peak based quantitative analysis of a mixture.

Thanks for the toolbox, I Bet you'll get the documentation ready in no time.

Cheers,
Yigal.

Laurent Duval

@Ole Kjos This is an issue I would like to improve on in the coming weeks, with a few rules of thumb. Could you share the type of signals you are dealing with?

Ole Kjos

Great tool, but a bit under documented for regular use. I really struggle to adjust parameters and tune the toolbox to optimal performance on my data. The published paper is to advanced for me to understand and relate to the actual toolbox parameters, and in the example the user input parameters (lam0,lam1,lam2, rc, r and d) is poorly explained.

Google have given me some vague idea, but I would have preferred that the authors wrote 2-3 lines for each parameter giving me some indication on which effect the parameters will have (filtering high frequency noise, adjusting baseline shape, effecting peak identification etc.) as that would make it easier to use the toolbox without understanding every detail about the mathematics behind it.

Laurent Duval

Thank you a lot for your nice feedback. I am very glad it is helpful for your research. The frequency is typically easy to fix in my application. How do your signals look like?

Jie YANG

Dear writer,
Thank you for sharing. I am very glad to obtian this toolbox. It's very helpful to my current research. But I have a problem with this script that I have no idea how to set value for fc. Could you please tell me in detail. I will very appreciate if you send email to my Email address: busyyangjie@outlook.com

BR
YANG.Jie

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