Open-sourced Raman spectroscopy data processing package implementing a baseline removal algorithm validated from multiple datasets acquired in human tissue and biofluids

Guillaume Sheehy; Fabien Picot; Frédérick Dallaire; Katherine J. Ember; Tien Nguyen; Kevin Petrecca; Dominique Trudel; Frédéric Leblond

doi:10.1117/1.JBO.28.2.025002

21 February 2023 Open-sourced Raman spectroscopy data processing package implementing a baseline removal algorithm validated from multiple datasets acquired in human tissue and biofluids

Guillaume Sheehy, Fabien Picot, Frédérick Dallaire, Katherine J. Ember, Tien Nguyen, Kevin Petrecca, Dominique Trudel, Frédéric Leblond

Author Affiliations +

Journal of Biomedical Optics, Vol. 28, Issue 2, 025002 (February 2023). https://doi.org/10.1117/1.JBO.28.2.025002

Abstract

Significance

Standardized data processing approaches are required in the field of bio-Raman spectroscopy to ensure information associated with spectral data acquired by different research groups, and with different systems, can be compared on an equal footing.

Aim

An open-sourced data processing software package was developed, implementing algorithms associated with all steps required to isolate the inelastic scattering component from signals acquired using Raman spectroscopy devices. The package includes a novel morphological baseline removal technique (BubbleFill) that provides increased adaptability to complex baseline shapes compared to current gold standard techniques. Also incorporated in the package is a versatile tool simulating spectroscopic data with varying levels of Raman signal-to-background ratios, baselines with different morphologies, and varying levels of stochastic noise.

Results

Application of the BubbleFill technique to simulated data demonstrated superior baseline removal performance compared to standard algorithms, including iModPoly and MorphBR. The data processing workflow of the open-sourced package was validated in four independent in-human datasets, demonstrating it leads to inter-systems data compatibility.

Conclusions

A new open-sourced spectroscopic data pre-processing package was validated on simulated and real-world in-human data and is now available to researchers and clinicians for the development of new clinical applications using Raman spectroscopy.

CC BY: © The Authors. Published by SPIE under a Creative Commons Attribution 4.0 International License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.

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Guillaume Sheehy, Fabien Picot, Frédérick Dallaire, Katherine J. Ember, Tien Nguyen, Kevin Petrecca, Dominique Trudel, and Frédéric Leblond "Open-sourced Raman spectroscopy data processing package implementing a baseline removal algorithm validated from multiple datasets acquired in human tissue and biofluids," Journal of Biomedical Optics 28(2), 025002 (21 February 2023). https://doi.org/10.1117/1.JBO.28.2.025002

Received: 21 October 2022; Accepted: 30 January 2023; Published: 21 February 2023

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