Pipeline for the removal of hardware related artifacts and background noise for Raman spectroscopy

Christian J. F. Bertens; Shuo Zhang; Roel J. Erckens; Frank J. H. M. van den Biggelaar; Tos T. J. M. Berendschot; Carroll A. B. Webers; Rudy M. M. A. Nuijts; Marlies Gijs

doi:10.1016/j.mex.2020.100883

Pipeline for the removal of hardware related artifacts and background noise for Raman spectroscopy

Christian J. F. Bertens (Corresponding author), Shuo Zhang, Roel J. Erckens, Frank J. H. M. van den Biggelaar, Tos T. J. M. Berendschot, Carroll A. B. Webers, Rudy M. M. A. Nuijts, Marlies Gijs

Medical Image Analysis

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Abstract

Raman spectroscopy is a real-time, non-contact, and non-destructive technique able to obtain information about the composition of materials, chemicals, and mixtures. It uses the energy transfer properties of molecules to detect the composition of matter. Raman spectroscopy is mainly used in the chemical field because background fluorescence and instrumental noise affect biological (in vitro and in vivo) measurements. In this method, we describe how hardware related artifacts and fluorescence background can be corrected without affecting signal of the measurement. First, we applied manual correction for cosmic ray spikes, followed by automated correction to reduce fluorescence and hardware related artifacts based on a partial 5 ^th degree polynomial fitting and Tophat correction. Along with this manuscript we provide a MatLab ^Ⓡ script for the automated correction of Raman spectra. • “Polynomial_Tophat_background_subtraction _methods.m” offers an automated method for the removal of hardware related artifacts and fluorescence signals in Raman spectra. • “Polynomial_Tophat_background_subtraction _methods.m” provides a modifiable MatLab file adjustable for multipurpose spectroscopy analysis. • We offer a standardized method for Raman spectra processing suitable for biological and chemical applications for modular confocal Raman spectroscopes.

Original language	English
Article number	100883
Number of pages	13
Journal	MethodsX
Volume	7
DOIs	https://doi.org/10.1016/j.mex.2020.100883
Publication status	Published - 2020

Funding

This research was performed under the framework of the Chemelot Institute for Science and Technology (InSciTe). MatlabⒸ script: “Polynomial_Tophat_background_subtraction _methods.m”

Funders	Funder number
Chemelot Institute for Science and Technology (InSciTe)

Keywords

Raman spectroscopy
Ketorolac tromethamine
Data processing
Rabbits
Ophthalmology
Partial 5 degree polynomial fitting, and Tophat filtering according to: Perez-Pueyo, R., M.J. Soneira, and S. Ruiz-Moreno, Morphology-based automated baseline removal for Raman spectra of artistic pigments. Appl Spectrosc, 2010. 64(6): p. 595–600.

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title = "Pipeline for the removal of hardware related artifacts and background noise for Raman spectroscopy",

abstract = "Raman spectroscopy is a real-time, non-contact, and non-destructive technique able to obtain information about the composition of materials, chemicals, and mixtures. It uses the energy transfer properties of molecules to detect the composition of matter. Raman spectroscopy is mainly used in the chemical field because background fluorescence and instrumental noise affect biological (in vitro and in vivo) measurements. In this method, we describe how hardware related artifacts and fluorescence background can be corrected without affecting signal of the measurement. First, we applied manual correction for cosmic ray spikes, followed by automated correction to reduce fluorescence and hardware related artifacts based on a partial 5 th degree polynomial fitting and Tophat correction. Along with this manuscript we provide a MatLab Ⓡ script for the automated correction of Raman spectra. • “Polynomial_Tophat_background_subtraction _methods.m” offers an automated method for the removal of hardware related artifacts and fluorescence signals in Raman spectra. • “Polynomial_Tophat_background_subtraction _methods.m” provides a modifiable MatLab file adjustable for multipurpose spectroscopy analysis. • We offer a standardized method for Raman spectra processing suitable for biological and chemical applications for modular confocal Raman spectroscopes. ",

keywords = "Raman spectroscopy, Ketorolac tromethamine, Data processing, Rabbits, Ophthalmology, Partial 5 degree polynomial fitting, and Tophat filtering according to: Perez-Pueyo, R., M.J. Soneira, and S. Ruiz-Moreno, Morphology-based automated baseline removal for Raman spectra of artistic pigments. Appl Spectrosc, 2010. 64(6): p. 595–600.",

author = "Bertens, {Christian J. F.} and Shuo Zhang and Erckens, {Roel J.} and {van den Biggelaar}, {Frank J. H. M.} and Berendschot, {Tos T. J. M.} and Webers, {Carroll A. B.} and Nuijts, {Rudy M. M. A.} and Marlies Gijs",

year = "2020",

doi = "10.1016/j.mex.2020.100883",

language = "English",

volume = "7",

journal = "MethodsX",

issn = "2215-0161",

publisher = "Elsevier",

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TY - JOUR

T1 - Pipeline for the removal of hardware related artifacts and background noise for Raman spectroscopy

AU - Bertens, Christian J. F.

AU - Zhang, Shuo

AU - Erckens, Roel J.

AU - van den Biggelaar, Frank J. H. M.

AU - Berendschot, Tos T. J. M.

AU - Webers, Carroll A. B.

AU - Nuijts, Rudy M. M. A.

AU - Gijs, Marlies

PY - 2020

Y1 - 2020

N2 - Raman spectroscopy is a real-time, non-contact, and non-destructive technique able to obtain information about the composition of materials, chemicals, and mixtures. It uses the energy transfer properties of molecules to detect the composition of matter. Raman spectroscopy is mainly used in the chemical field because background fluorescence and instrumental noise affect biological (in vitro and in vivo) measurements. In this method, we describe how hardware related artifacts and fluorescence background can be corrected without affecting signal of the measurement. First, we applied manual correction for cosmic ray spikes, followed by automated correction to reduce fluorescence and hardware related artifacts based on a partial 5 th degree polynomial fitting and Tophat correction. Along with this manuscript we provide a MatLab Ⓡ script for the automated correction of Raman spectra. • “Polynomial_Tophat_background_subtraction _methods.m” offers an automated method for the removal of hardware related artifacts and fluorescence signals in Raman spectra. • “Polynomial_Tophat_background_subtraction _methods.m” provides a modifiable MatLab file adjustable for multipurpose spectroscopy analysis. • We offer a standardized method for Raman spectra processing suitable for biological and chemical applications for modular confocal Raman spectroscopes.

AB - Raman spectroscopy is a real-time, non-contact, and non-destructive technique able to obtain information about the composition of materials, chemicals, and mixtures. It uses the energy transfer properties of molecules to detect the composition of matter. Raman spectroscopy is mainly used in the chemical field because background fluorescence and instrumental noise affect biological (in vitro and in vivo) measurements. In this method, we describe how hardware related artifacts and fluorescence background can be corrected without affecting signal of the measurement. First, we applied manual correction for cosmic ray spikes, followed by automated correction to reduce fluorescence and hardware related artifacts based on a partial 5 th degree polynomial fitting and Tophat correction. Along with this manuscript we provide a MatLab Ⓡ script for the automated correction of Raman spectra. • “Polynomial_Tophat_background_subtraction _methods.m” offers an automated method for the removal of hardware related artifacts and fluorescence signals in Raman spectra. • “Polynomial_Tophat_background_subtraction _methods.m” provides a modifiable MatLab file adjustable for multipurpose spectroscopy analysis. • We offer a standardized method for Raman spectra processing suitable for biological and chemical applications for modular confocal Raman spectroscopes.

KW - Raman spectroscopy

KW - Ketorolac tromethamine

KW - Data processing

KW - Rabbits

KW - Ophthalmology

KW - Partial 5 degree polynomial fitting, and Tophat filtering according to: Perez-Pueyo, R., M.J. Soneira, and S. Ruiz-Moreno, Morphology-based automated baseline removal for Raman spectra of artistic pigments. Appl Spectrosc, 2010. 64(6): p. 595–600.

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M3 - Article

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SN - 2215-0161

VL - 7

JO - MethodsX

JF - MethodsX

M1 - 100883

ER -

Pipeline for the removal of hardware related artifacts and background noise for Raman spectroscopy

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Keywords

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