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Accurate EELS background subtraction – an adaptable method in MATLAB

Fung, Kayleigh L.Y.; Fay, Michael W.; Collins, Sean M.; Kepaptsoglou, Demie M.; Skowron, Stephen T.; Ramasse, Quentin M.; Khlobystov, Andrei N.


Kayleigh L.Y. Fung

Sean M. Collins

Demie M. Kepaptsoglou

Stephen T. Skowron

Quentin M. Ramasse


Electron energy-loss spectroscopy (EELS) is a technique that can give useful information on elemental composition and bonding environments. However in practice, the complexity of the background contributions, which can arise from multiple sources, can hamper the interpretation of the spectra. As a result, background removal is both an essential and difficult part of EELS analysis, especially during quantification of elemental composition. Typically, a power law is used to fit the background but this is often not suitable for many spectra such as in the low-loss region (< 50 eV) and when there are overlapping EELS edges. In this article, we present a series of scripts written in MATLAB v. R2019b that aims to provide statistical information on the model used to fit the background, allowing the user to determine the accuracy of background subtraction. The scripts were written for background subtraction of vibrational EELS in the ultralow-loss region near the zero-loss peak but can also be applied to other kinds of EEL spectra. The scripts can use a range of models for fitting, provided by the Curve Fitting Toolbox of MATLAB, and the user is able to precisely define the window for fitting as well as for edge integration. We demonstrate the advantages of using these scripts by comparing their background subtraction of example spectra to the most commonly used software, Gatan Microscopy Suite 3. The example spectra include those containing multiple scattering, multiple overlapping peaks, as well as vibrational EELS. Additionally, a comprehensive guide to using the scripts has been included in the Supplementary Information.


Fung, K. L., Fay, M. W., Collins, S. M., Kepaptsoglou, D. M., Skowron, S. T., Ramasse, Q. M., & Khlobystov, A. N. (2020). Accurate EELS background subtraction – an adaptable method in MATLAB. Ultramicroscopy, 217, Article 113052.

Journal Article Type Article
Acceptance Date Jun 21, 2020
Online Publication Date Jun 25, 2020
Publication Date Oct 1, 2020
Deposit Date Jun 25, 2020
Publicly Available Date Jun 26, 2021
Journal Ultramicroscopy
Print ISSN 0304-3991
Electronic ISSN 1879-2723
Publisher Elsevier
Peer Reviewed Peer Reviewed
Volume 217
Article Number 113052
Keywords Instrumentation; Atomic and Molecular Physics, and Optics; Electronic, Optical and Magnetic Materials
Public URL
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