Computational Fluorescence Suppression in Shifted Excitation Raman Spectroscopy

Fiber-based Raman spectroscopy in the context of &lt;italic&gt;in vivo&lt;/italic&gt; 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.</p

Computational Fluorescence Suppression in Shifted Excitation Raman Spectroscopy

Fiber-based Raman spectroscopy in the context of &lt;italic&gt;in vivo&lt;/italic&gt; 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.</p

Datasets for Kufcsak et al Optics Express paper "Time-resolved spectroscopy at 19,000 lines per second using a CMOS SPAD line array enables advanced biophotonics applications"

A SPAD-based line sensor fabricated in 130 nm CMOS technology capable of acquiring time-resolved fluorescence spectra (TRFS) in 8.3 milliseconds is presented. To the best of our knowledge, this is the fastest time correlated single photon counting (TCSPC) TRFS acquisition reported to date. The line sensor is an upgrade to our prior work and incorporates: i) parallelized interface from sensor to surrounding circuitry enabling high line rate to the PC (19,000 lines/s) and ii) novel time-gating architecture where detected photons in the OFF region are rejected digitally after the output stage of the SPAD. The time-gating architecture was chosen to avoid electrical transients on the SPAD high voltage supplies when gating is achieved by excess bias modulation. The time-gate has an adjustable location and time window width allowing the user to focus on time-events of interest. On-chip integrated center-of-mass (CMM) calculations provide efficient acquisition of photon arrivals and direct lifetime estimation of fluorescent decays. Furthermore, any of the SPC, TCSPC and on-chip CMM modes can be used in conjunction with the time-gating. The higher readout rate and versatile architecture greatly empower the user and will allow widespread applications across many techniques and disciplines. Here we focused on 3 examples of TRFS and time-gated Raman spectroscopy: i) kinetics of chlorophyll A fluorescence from an intact leaf; ii) kinetics of a thrombin biosensor FRET probe from quenched to fluorescence states; iii) ex vivo mouse lung tissue autofluorescence TRFS; iv) time-gated Raman spectroscopy of toluene at 3056 cm-1 peak. To the best of our knowledge, we detect spectrally for the first time the fast rise in fluorescence lifetime of chlorophyll A in a measurement over single fluorescent transient.Kufcsak, Andras; Krstajic, Nikola. (2017). Datasets for Kufcsak et al Optics Express paper "Time-resolved spectroscopy at 19,000 lines per second using a CMOS SPAD line array enables advanced biophotonics applications", [dataset]. University of Edinburgh. School of Engineering. http://dx.doi.org/10.7488/ds/2000

Dataset for "Time-resolved spectral-domain optical coherence tomography with CMOS SPAD sensors"

Scripts and raw data used for the manuscript "Time-resolved spectral-domain optical coherence tomography with CMOS SPAD sensors"Kufcsak, Andras; Krstajić, Nikola. (2021). Dataset for "Time-resolved spectral-domain optical coherence tomography with CMOS SPAD sensors", [dataset]. University of Edinburgh. School of Engineering. https://doi.org/10.7488/ds/3020

Supplementary document for Fibre-optic based Exploration of Lung Cancer Autofluorescence using Spectral Fluorescence Lifetime - 6819445.pdf

Supplement materia

Circuits! - Demonstrating the use of optical fibres in biomedical sciences

The Circuits! - project, funded through the The Royal Academy of Engineering Ingenious Grant (ING1617/11/114), demonstrates how research at the intersection of physics, engineering, biology, and medicine can be presented in an interactive and educational way to a non-scientific audience. Respiratory diseases are significant contributors to avoidable morbidity and mortality and have a growing social and economic impact. With the aim of improving lung disease understanding, new techniques in fibre-based optical endomicroscopy have been recently developed. Interdisciplinary research with a focus on prevalent diseases provides a relatable context that can be used to enrich high school education. Here, we present a novel teaching methodology, developed between high school science teachers and researchers, that resembles a bench-to-bedside pathway. The methodology comprises an inexpensive educational tool (< $ 70) adapted from a clinical optical endomicroscopy system and tutorials that cover state-of-the-art research. This data set contains STL files for the 3d printing parts, templates for graphs, an instructional video, teaching material and a detailed description and trouble shooting document for the education tool.Ehrlich, Katjana; Parker, Helen E; McNicholl, Duncan K; Reid, Peter; Reynolds, Mark; Bussiere, Vincent; Crawford, Graham; Deighan, Angela; Garrett, Alice; Kufcsák, András; Norberg, Dominic R; Spennati, Giulia; Szoor-McElhinney, Helen; Jimenez, Melanie. (2019). Circuits! - Demonstrating the use of optical fibres in biomedical sciences, 2017-2019 [dataset]. Circuits!-Team. https://doi.org/10.7488/ds/2587