Computational Fluorescence Suppression in Shifted Excitation Raman Spectroscopy

Nia C. Jenkins; Katjana Ehrlich; Andras Kufcsak; Stephanos Yerolatsitis; Susan Fernandes; Irene Young; Katie Hamilton; Harry A.C. Wood; Tom Quinn; Vikki Young; Ahsan R. Akram; James M. Stone; Robert R. Thomson; Keith Finlayson; Kevin Dhaliwal; Sohan Seth

doi:10.1109/TBME.2023.3243866

Computational Fluorescence Suppression in Shifted Excitation Raman Spectroscopy

Nia C. Jenkins, Katjana Ehrlich, Andras Kufcsak, Stephanos Yerolatsitis, Susan Fernandes, Irene Young, Katie Hamilton, Harry A.C. Wood, Tom Quinn, Vikki Young, Ahsan R. Akram, James M. Stone, Robert R. Thomson, Keith Finlayson, Kevin Dhaliwal, Sohan Seth

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Abstract

Fiber-based Raman spectroscopy in the context of <italic>in vivo</italic> biomedical application suffers from the presence of background fluorescence from the surrounding tissue that might mask the crucial but inherently weak Raman signatures. One method that has shown potential for suppressing the background to reveal the Raman spectra is shifted excitation Raman spectroscopy (SER). SER collects multiple emission spectra by shifting the excitation by small amounts and uses these spectra to computationally suppress the fluorescence background based on the principle that Raman spectrum shifts with excitation while fluorescence spectrum does not. We introduce a method that utilizes the spectral characteristics of the Raman and fluorescence spectra to estimate them more effectively, and compare this approach against existing methods on real world datasets.

Original language	English
Pages (from-to)	2374-2383
Number of pages	10
Journal	IEEE Transactions on biomedical engineering
Volume	70
Issue number	8
Early online date	10 Feb 2023
DOIs	https://doi.org/10.1109/TBME.2023.3243866
Publication status	Published - 31 Aug 2023

Bibliographical note

The authors thank the BioResource for access to tissue (NHS
Lothian BioResource, Scotland Research Ethics Service, reference
15/ES/0094). NCJ was supported through the University of Edinburgh
funding award. JMS, SY and HACW are supported through an
EPSRC fellowship (EP/S001123/1). SF is supported through an
MRC fellowship (MR/R017794/1). ARA is supported by a CRUK
Clinician Scientist Fellowship (A24867). NCJ and SS are with the
School of Informatics, University of Edinburgh, 10 Crichton Street,
Edinburgh, EH8 9AB, UK. (e-mails: {njenkin3,sohan.seth}@ed.ac.uk).
KE, AK, SF, IY, KH, TQ, VY, ARA, RRT, KF, KD, and SS are
with the Translational Healthcare Technology Group, Centre for
Inflammation Research, Queen’s Medical Research Institute,
University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16
4TJ, UK. (e-mails: {Katjana.Ehrlich,A.Kufcsak,Susan.Fernandes,
iyoung3 K.Hamilton,tquinn,Vikki.Young,Ahsan.Akram,Keith.Finlayson,
Kev.Dhaliwal}@ed.ac.uk). SY, HACW. and JMS are with
the Centre for Photonics and Photonic Materials, University
of Bath, Claverton Down, Bath, BA2 7AY, UK. (emails:
{S.Yerolatsitis,H.Wood,J.M.Stone}@bath.ac.uk). RRT is with Scottish
Universities Physics Alliance (SUPA), Institute of Photonics and
Quantum Science, Heriot-Watt University, Edinburgh, EH144AS, UK.
(email: [email protected]).

Funding

The work of Nia C. Jenkins was supported by the University of Edinburgh. The work of James M. Stone, Stephanos Yerolatsitis, and Harry A. C. Wood was supported by EPSRC fellowship under Grant EP/S001123/1. The work of Susan Fernandes was supported by MRC fellowship under Grant MR/R017794/1. The work of Ahsan R. Akram was supported by the CRUK Clinician Scientist Fellowship under Grant A24867. The authors thank the BioResource for access to tissue (NHS Lothian BioResource, Scotland Research Ethics Service, reference 15/ES/0094).

Funders	Funder number
Medical Research Council	MR/R017794/1
Engineering and Physical Sciences Research Council	EP/S001123/1
Cancer Research UK	A24867, 15/ES/0094
University of Edinburgh

Keywords

Biomedical
fluorescence
lung tissue
machine learning
optical fiber
raman spectroscopy
regularization
shifted excitation
smoothness
sparsity

ASJC Scopus subject areas

Biomedical Engineering

Access to Document

10.1109/TBME.2023.3243866

Computational_Fluorescence_Suppression_in_Shifted_Excitation_Raman_Spectroscopy
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Cite this

Jenkins, N. C., Ehrlich, K., Kufcsak, A., Yerolatsitis, S., Fernandes, S., Young, I., Hamilton, K., Wood, H. A. C., Quinn, T., Young, V., Akram, A. R., Stone, J. M., Thomson, R. R., Finlayson, K., Dhaliwal, K., & Seth, S. (2023). Computational Fluorescence Suppression in Shifted Excitation Raman Spectroscopy. IEEE Transactions on biomedical engineering, 70(8), 2374-2383. https://doi.org/10.1109/TBME.2023.3243866

Jenkins, NC, Ehrlich, K, Kufcsak, A, Yerolatsitis, S, Fernandes, S, Young, I, Hamilton, K, Wood, HAC, Quinn, T, Young, V, Akram, AR, Stone, JM, Thomson, RR, Finlayson, K, Dhaliwal, K & Seth, S 2023, 'Computational Fluorescence Suppression in Shifted Excitation Raman Spectroscopy', IEEE Transactions on biomedical engineering, vol. 70, no. 8, pp. 2374-2383. https://doi.org/10.1109/TBME.2023.3243866

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abstract = "Fiber-based Raman spectroscopy in the context of in vivo biomedical application suffers from the presence of background fluorescence from the surrounding tissue that might mask the crucial but inherently weak Raman signatures. One method that has shown potential for suppressing the background to reveal the Raman spectra is shifted excitation Raman spectroscopy (SER). SER collects multiple emission spectra by shifting the excitation by small amounts and uses these spectra to computationally suppress the fluorescence background based on the principle that Raman spectrum shifts with excitation while fluorescence spectrum does not. We introduce a method that utilizes the spectral characteristics of the Raman and fluorescence spectra to estimate them more effectively, and compare this approach against existing methods on real world datasets.",

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author = "Jenkins, {Nia C.} and Katjana Ehrlich and Andras Kufcsak and Stephanos Yerolatsitis and Susan Fernandes and Irene Young and Katie Hamilton and Wood, {Harry A.C.} and Tom Quinn and Vikki Young and Akram, {Ahsan R.} and Stone, {James M.} and Thomson, {Robert R.} and Keith Finlayson and Kevin Dhaliwal and Sohan Seth",

note = "The authors thank the BioResource for access to tissue (NHS Lothian BioResource, Scotland Research Ethics Service, reference 15/ES/0094). NCJ was supported through the University of Edinburgh funding award. JMS, SY and HACW are supported through an EPSRC fellowship (EP/S001123/1). SF is supported through an MRC fellowship (MR/R017794/1). ARA is supported by a CRUK Clinician Scientist Fellowship (A24867). NCJ and SS are with the School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh, EH8 9AB, UK. (e-mails: {njenkin3,sohan.seth}@ed.ac.uk). KE, AK, SF, IY, KH, TQ, VY, ARA, RRT, KF, KD, and SS are with the Translational Healthcare Technology Group, Centre for Inflammation Research, Queen{\textquoteright}s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK. (e-mails: {Katjana.Ehrlich,A.Kufcsak,Susan.Fernandes, iyoung3 K.Hamilton,tquinn,Vikki.Young,Ahsan.Akram,Keith.Finlayson, Kev.Dhaliwal}@ed.ac.uk). SY, HACW. and JMS are with the Centre for Photonics and Photonic Materials, University of Bath, Claverton Down, Bath, BA2 7AY, UK. (emails: {S.Yerolatsitis,H.Wood,J.M.Stone}@bath.ac.uk). RRT is with Scottish Universities Physics Alliance (SUPA), Institute of Photonics and Quantum Science, Heriot-Watt University, Edinburgh, EH144AS, UK. (email: [email protected]). ",

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AU - Hamilton, Katie

AU - Wood, Harry A.C.

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AU - Stone, James M.

AU - Thomson, Robert R.

AU - Finlayson, Keith

AU - Dhaliwal, Kevin

AU - Seth, Sohan

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AB - Fiber-based Raman spectroscopy in the context of in vivo biomedical application suffers from the presence of background fluorescence from the surrounding tissue that might mask the crucial but inherently weak Raman signatures. One method that has shown potential for suppressing the background to reveal the Raman spectra is shifted excitation Raman spectroscopy (SER). SER collects multiple emission spectra by shifting the excitation by small amounts and uses these spectra to computationally suppress the fluorescence background based on the principle that Raman spectrum shifts with excitation while fluorescence spectrum does not. We introduce a method that utilizes the spectral characteristics of the Raman and fluorescence spectra to estimate them more effectively, and compare this approach against existing methods on real world datasets.

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Computational Fluorescence Suppression in Shifted Excitation Raman Spectroscopy

Abstract

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

Access to Document

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Fellowship - Next Generation Endoscopes

Cite this

Computational Fluorescence Suppression in Shifted Excitation Raman Spectroscopy

Abstract

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Projects

Fellowship - Next Generation Endoscopes

Cite this