Towards quantifying biomarkers for respiratory distress in preterm infants: Machine learning on mid infrared spectroscopy of lipid mixtures.

Neonatal respiratory distress syndrome (nRDS) is a challenging condition to diagnose which can lead to delays in receiving appropriate treatment. Mid infrared (IR) spectroscopy is capable of measuring the concentrations of two diagnostic nRDS biomarkers, lecithin (L) and sphingomyelin (S) with the potential for point of care (POC) diagnosis and monitoring. The effects of varying other lipid species present in lung surfactant on the mid IR spectra used to train machine learning models are explored. This study presents a lung lipid model of five lipids present in lung surfactant and varies each in a systematic approach to evaluate the ability of machine learning models to predict the lipid concentrations, the L/S ratio and to quantify the uncertainty in the predictions using the jackknife + -after-bootstrap and variant bootstrap methods. We establish the L/S ratio can be determined with an uncertainty of approximately ±0.3 mol/mol and we further identify the 5 most prominent wavenumbers associated with each machine learning model.

Multiframe-based non-local means denoising for Raman spectra.

A method for denoising Raman spectra is presented in this paper. The approach is based on the principle that the original signal can be restored by averaging pixels based on structure similarity. Similarity searching and averaging are not limited to the neighbouring pixels but extended throughout the entire signal range across different frames. This approach is distinguished from the conventional single-frame neighbour pixel-based filtering. The effectiveness and robustness of the proposed method are demonstrated through denoising simulated and experimental Raman data sets with fixed denoising parameters. Several denoised results and statistical indicators are presented for the simulated data. Recovery of the experimental Raman spectrum from our newly developed cost-effective waveguide-enhanced Raman spectroscopy system is also presented and compared to the spectrum from a conventional expensive Raman microscope for the same analyte.

Grating-incoupled waveguide-enhanced Raman sensor.

We report a waveguide-enhanced Raman spectroscopy (WERS) platform with alignment-tolerant under-chip grating input coupling. The demonstration is based on a 100-nm thick planar (slab) tantalum pentoxide (Ta2O5) waveguide and the use of benzyl alcohol (BnOH) and its deuterated form (d7- BnOH) as reference analytes. The use of grating couplers simplifies the WERS system by providing improved translational alignment tolerance, important for disposable chips, as well as contributing to improved Raman conversion efficiency. The use of non-volatile, non-toxic BnOH and d7-BnOH as chemical analytes results in easily observable shifts in the Raman vibration lines between the two forms, making them good candidates for calibrating Raman systems. The design and fabrication of the waveguide and grating couplers are described, and a discussion of further potential improvements in performance is presented.

Bi-frequency operation in a membrane external-cavity surface-emitting laser.

We report on the achievement of continuous wave bi-frequency operation in a membrane external-cavity surface-emitting laser (MECSEL), which is optically pumped with up to 4 W of 808 nm pump light. The presence of spatially specific loss of the intra-cavity high reflectivity mirror allows loss to be controlled on certain transverse cavity modes. The regions of spatially specific loss are defined through the removal of Bragg layers from the surface of the cavity high reflectivity mirror in the form of crosshair patterns with undamaged central regions, which are created using a laser ablation system incorporating a digital micromirror device (DMD). By aligning the laser cavity mode with the geometric centre of the loss patterns, the laser simultaneously operated on two Hermite-Gaussian spatial modes: the fundamental HG00 and the higher order HG11 mode. We demonstrate bi-frequency operation over a range of pump powers and sizes of spatial loss features, with a wavelength separation of approximately 5 nm centred at 1005 nm.

Coherent waveguide laser arrays in semiconductor quantum well membranes.

Coherent laser arrays compatible with silicon photonics are demonstrated in a waveguide geometry in epitaxially grown semiconductor membrane quantum well lasers transferred on substrates of silicon carbide and oxidised silicon; we record lasing thresholds as low as 60 mW of pump power. We study the emission of single lasers and arrays of lasers in the sub-mm range. We are able to create waveguide laser arrays with modal widths of approximately 5 - 10 µm separated by 10 - 20 µm, using real and reciprocal space imaging we study their emission characteristics and find that they maintain their mutual coherence while operating on either single or multiple longitudinal modes per lasing cavity.

Artificial neural networks for material parameter extraction in terahertz time-domain spectroscopy.

Terahertz time-domain spectroscopy (THz-TDS) is a proven technique whereby the complex refractive indices of materials can be obtained without requiring the use of the Kramers-Kronig relations, as phase and amplitude information can be extracted from the measurement. However, manual pre-processing of the data is still required and the material parameters require iterative fitting, resulting in complexity, loss of accuracy and inconsistencies between measurements. Alternatively approximations can be used to enable analytical extraction but with a considerable sacrifice of accuracy. We investigate the use of machine learning techniques for interpreting spectroscopic THz-TDS data by training with large data sets of simulated light-matter interactions, resulting in a computationally efficient artificial neural network for material parameter extraction. The trained model improves on the accuracy of analytical methods that need approximations while being easier to implement and faster to run than iterative root-finding methods. We envisage neural networks can alleviate many of the common hurdles involved in analyzing THz-TDS data such as phase unwrapping, time domain windowing, slow computation times, and extraction accuracy at the low frequency range.

Prediction of Neonatal Respiratory Distress Biomarker Concentration by Application of Machine Learning to Mid-Infrared Spectra.

The authors of this study developed the use of attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) combined with machine learning as a point-of-care (POC) diagnostic platform, considering neonatal respiratory distress syndrome (nRDS), for which no POC currently exists, as an example. nRDS can be diagnosed by a ratio of less than 2.2 of two nRDS biomarkers, lecithin and sphingomyelin (L/S ratio), and in this study, ATR-FTIR spectra were recorded from L/S ratios of between 1.0 and 3.4, which were generated using purified reagents. The calibration of principal component (PCR) and partial least squares (PLSR) regression models was performed using 155 raw baselined and second derivative spectra prior to predicting the concentration of a further 104 spectra. A three-factor PLSR model of second derivative spectra best predicted L/S ratios across the full range (R2: 0.967; MSE: 0.014). The L/S ratios from 1.0 to 3.4 were predicted with a prediction interval of +0.29, -0.37 when using a second derivative spectra PLSR model and had a mean prediction interval of +0.26, -0.34 around the L/S 2.2 region. These results support the validity of combining ATR-FTIR with machine learning to develop a point-of-care device for detecting and quantifying any biomarker with an interpretable mid-infrared spectrum.

The Effect of Haematocrit on Measurement of the Mid-Infrared Refractive Index of Plasma in Whole Blood.

Recent advances suggest that miniaturised mid-infrared (MIR) devices could replace more time-consuming, laboratory-based techniques for clinical diagnostics. This work uses Fourier transform infrared spectroscopy to show that the MIR complex refractive index of whole blood varies across a range of haematocrit. This indicates that the use of an evanescent measurement is not sufficient to optically exclude the cellular content of blood in the MIR, as previously assumed. Here, spectral refractive index data is presented in two ways. First, it is given as whole blood with varying haematocrit. Second, it is given as the percentage error that haematocrit introduces to plasma. The maximum error in the effective plasma refractive index due to the haematocrit of healthy adults was 0.25% for the real part n and 11% for the imaginary part k. This implies that calibration measurements of haematocrit can be used to account for errors introduced by the cellular content, enabling plasma spectra and analyte concentrations to be indirectly calculated from a whole blood sample. This methodological advance is of clinical importance as plasma concentration of analytes such as drugs can be determined using MIR without the preprocessing of whole blood.

Study of waveguide background at visible wavelengths for on-chip nanoscopy.

On-chip super-resolution optical microscopy is an emerging field relying on waveguide excitation with visible light. Here, we investigate two commonly used high-refractive index waveguide platforms, tantalum pentoxide (Ta2O5) and silicon nitride (Si3N4), with respect to their background with excitation in the range 488-640 nm. The background strength from these waveguides were estimated by imaging fluorescent beads. The spectral dependence of the background from these waveguide platforms was also measured. For 640 nm wavelength excitation both the materials had a weak background, but the background increases progressively for shorter wavelengths for Si3N4. We further explored the effect of the waveguide background on localization precision of single molecule localization for direct stochastic optical reconstruction microscopy (dSTORM). An increase in background for Si3N4 at 488 nm is shown to reduce the localization precision and thus the resolution of the reconstructed images. The localization precision at 640nm was very similar for both the materials. Thus, for shorter wavelength applications Ta2O5 is preferable. Reducing the background from Si3N4 at shorter wavelengths via improved fabrication will be worth pursuing.

Waveguide Enhanced Raman Spectroscopy for Biosensing: A Review.

Waveguide enhanced Raman spectroscopy (WERS) utilizes simple, robust, high-index contrast dielectric waveguides to generate a strong evanescent field, through which laser light interacts with analytes residing on the surface of the waveguide. It offers a powerful tool for the direct identification and reproducible quantification of biochemical species and an alternative to surface enhanced Raman spectroscopy (SERS) without reliance on fragile noble metal nanostructures. The advent of low-cost laser diodes, compact spectrometers, and recent progress in material engineering, nanofabrication techniques, and software modeling tools have made realizing portable and cheap WERS Raman systems with high sensitivity a realistic possibility. This review highlights the latest progress in WERS technology and summarizes recent demonstrations and applications. Following an introduction to the fundamentals of WERS, the theoretical framework that underpins the WERS principles is presented. The main WERS design considerations are then discussed, and a review of the available approaches for the modification of waveguide surfaces for the attachment of different biorecognition elements is provided. The review concludes by discussing and contrasting the performance of recent WERS implementations, thereby providing a future roadmap of WERS technology where the key opportunities and challenges are highlighted.

Optimized design for grating-coupled waveguide-enhanced Raman spectroscopy.

We report a new design optimization process for planar photonic waveguides applied to waveguide-enhanced Raman spectroscopy (WERS) that combines the optimization of both the surface intensity performance and the grating coupling efficiency. We consider the impact of film thickness on the grating coupling efficiency of two materials with different refractive indices, namely tantalum pentoxide (Ta2O5) and silicon (Si). We propose a new figure-of-merit (FOM) that takes into account both the coupling efficiency and surface intensity dependence for Raman excitation on the film thickness. Our study shows that the optimum surface-sensitive waveguide thickness is thinner than the optimum coupling efficiency thickness for both material systems. As an example, for a tantalum pentoxide waveguide operating at 785 nm, our optimization strategy proposes a 20% increase in waveguide core thickness relative to the optimum surface-sensitive thickness to achieve the best performance in WERS applications.

Supercontinuum generation in tantalum pentoxide waveguides for pump wavelengths in the 900 nm to 1500 nm spectral region.

We characterize the spectral broadening performance in silica clad and unclad Tantalum pentoxide (Ta2O5) waveguides as a function of the input pulse central wavelength and polarization, sweeping over a wavelength range from 900 nm to 1500 nm, with an average incident power of 110 mW. The waveguides are 0.7 µm high and between 2.2 and 3.2 µm wide, and the SiO2 top cladding layer is 2 µm thick. We model the dispersion of the higher order spatial modes, and use numerical simulations based on the generalized nonlinear Schrödinger equation to analyze the nonlinear behaviour of the spatial modes within the waveguides as well as the dispersive effects observed in the experiments. We achieve octave spanning supercontinuum with an average power of 175 mW incident on the waveguide at 1000 nm pump wavelength.

Ge on Si waveguide mid-infrared absorption spectroscopy of proteins and their aggregates.

Specific proteins and their aggregates form toxic amyloid plaques and neurofibrillary tangles in the brains of people suffering from neurodegenerative diseases such as Alzheimer's and Parkinson's. It is important to study these conformational changes to identify and differentiate these diseases at an early stage so that timely medication is provided to patients. Mid-infrared spectroscopy can be used to monitor these changes by studying the line-shapes and the relative absorbances of amide bands present in proteins. This work focusses on the spectroscopy of the protein, Bovine Serum Albumin as an exemplar, and its aggregates using germanium on silicon waveguides in the 1900-1000 cm-1 (5.3-10.0 µm) spectral region.

Perspective on Thin Film Waveguides for on-Chip Mid-Infrared Spectroscopy of Liquid Biochemical Analytes.

Miniaturized spectrometers offering low cost, low reagent consumption, high throughput, sensitivity and automation are the future of sensing and have significant applications in environmental monitoring, food safety, biotechnology, pharmaceuticals, and healthcare. Midinfrared (MIR) spectroscopy employing complementary metal oxide semiconductor (CMOS) compatible thin film waveguides and microfluidics shows great promise toward highly integrated and robust detection tools and liquid handling. This perspective provides an overview of the emergence of thin film optical waveguides used for evanescent field sensing of liquid chemical and biological samples for MIR absorption spectroscopy. The state of the art of new material and waveguide systems used for spectroscopic measurements in the MIR is presented. An outlook on the advantages and future of waveguide-based MIR spectroscopy for application in clinical settings for point-of-care biochemical analysis is discussed.

Monolithically-integrated cytometer for measuring particle diameter in the extracellular vesicle size range using multi-angle scattering.

Size measurement of extracellular vesicles is hampered by the high cost and measurement uncertainty of conventional flow cytometers which is mainly due to the use of non-specialised free space optics. Integrated cytometry, where the optics and fluidics are embedded in a monolithic chip shows promise for the production of low cost, micro-flow cytometers dedicated for extracellular vesicle (EV) analysis with improved size measurement accuracy and precision. This research demonstrates a unique integrated cytometer for sub-micron particle size measurement using multi-angle scattering analysis. A combination of three technologies is used: (i) Dean-based hydrodynamic focussing to deliver a tight sample core stream to the analysis region, (ii) integrated waveguides with multimode interference devices to focus a narrow excitation beam onto the sample stream, and (iii) an angular array of collection waveguides to measure particle scattering distribution and calculate diameter. Low index 200 nm liposomes could be detected and polystyrene size standards as small as 400 nm diameter could be measured with an uncertainty of ±21 nm (1/2 IQR) demonstrating a first step on the path to high performance integrated cytometry of EVs.

FCMPASS Software Aids Extracellular Vesicle Light Scatter Standardization.

The study of extracellular vesicles (EVs) is a rapidly growing field due to their great potential in many areas of clinical medicine including diagnostics, prognostics, theranostics, and therapeutics. Flow cytometry is currently one of the most popular methods of analyzing EVs due to it being a high-throughput, multiparametric technique, that is readily available in the majority of research labs. Despite its wide use, few commercial flow cytometers are designed specifically for the detection of EVs. Many flow cytometers used for EV analysis are working at their detection limits and are unable to detect the majority of EVs. Currently, very little standardization exists for EV flow cytometry, which is an issue because flow cytometers vary considerably in the way they collect scattered or fluorescent light from particles being interrogated. This makes published research hard to interpret, compare, and in some cases, impossible to reproduce. Here we demonstrate a method of flow cytometer light scatter standardization, utilizing flow cytometer postacquisition analysis software (FCMPASS ). FCMPASS is built upon Mie theory and enables the approximation of flow cytometer geometric parameters either by analyzing beads of known diameter and refractive index or by inputting the collection angle if known. The software is then able to create a scatter-diameter curve and scatter-refractive index curve that enables researchers to convert scattering data and instrument sensitivity into standardized units. Furthermore, with the correct controls, light scatter data can be converted to diameter distributions or refractive index distributions. FCMPASS therefore offers a freely available and ergonomic method of standardizing and further extending EV characterization using flow cytometry.

Optical biosensors based on refractometric sensing schemes: A review.

Biosensor technology is an active field of research and development presenting rapid progress in recent decades, and the subfield of optical biosensors based on refractometric sensing schemes has developed dramatically during this time. This review focuses on advances in the refractometric sensing-based guided-wave optical biosensors particularly in the last two decades. It starts with a concise discussion on the underlying principles of label-free refractometric biosensor. Subsequently, advances in biosensor design, especially the transducer configuration and the integration of the sensing device are reviewed, highlighting the challenges and efforts dedicated to improving this technology. Various surface functionalization strategies designed to produce well-defined and reproducible surface properties are introduced for evaluation. Refractometric sensing scheme-based optical biosensors have found versatile applications varying from environmental monitoring and food safety to clinical diagnostics, together with advances in these applications and others are described. This paper concludes with a brief discussion on the outlook for integrating biosensors with emerging technologies.

High index contrast photonic platforms for on-chip Raman spectroscopy.

Nanophotonic waveguide enhanced Raman spectroscopy (NWERS) is a sensing technique that uses a highly confined waveguide mode to excite and collect the Raman scattered signal from molecules in close vicinity of the waveguide. The most important parameters defining the figure of merit of an NWERS sensor include its ability to collect the Raman signal from an analyte, i.e. "the Raman conversion efficiency" and the amount of "Raman background" generated from the guiding material. Here, we compare different photonic integrated circuit (PIC) platforms capable of on-chip Raman sensing in terms of the aforementioned parameters. Among the four photonic platforms under study, tantalum oxide and silicon nitride waveguides exhibit high signal collection efficiency and low Raman background. In contrast, the performance of titania and alumina waveguides suffers from a strong Raman background and a weak signal collection efficiency, respectively.

Waveguide Absorption Spectroscopy of Bovine Serum Albumin in the Mid-Infrared Fingerprint Region.

Protein sensing in biological fluids provides important information to diagnose many clinically relevant diseases. Mid-infrared (MIR) absorption spectroscopy of bovine serum albumin (BSA) is experimentally demonstrated on a germanium on silicon (GOS) waveguide in the 1900-1000 cm-1 (5.3-10.0 µm) region of the MIR. GOS waveguides were shown to guide light up to a wavelength of 12.9 µm. The waveguide absorption spectrum of water, showing molecular bending vibrations, was obtained experimentally and compared with a theoretical model showing good agreement. Measurement of a concentration series of BSA protein in phosphate buffered saline (PBS) from 0.1 mg/mL to 100 mg/mL was performed on the waveguide using filter paper as a flow strip, and the amide I, II, and III peaks were observed and quantified.

Chalcogenide glass waveguides with paper-based fluidics for mid-infrared absorption spectroscopy.

We demonstrate the integration of paper fluidics with mid-infrared (MIR) chalcogenide waveguides to introduce liquid samples to the waveguide evanescent field for analysis. Spectroscopy of model analytes (water and isopropyl alcohol) having well-defined mid-IR absorptions, on a ZnSe rib waveguide fabricated on silicon, is demonstrated in the wavelength range of 2.6-3.7 µm, showing their O-H and C-H stretching absorptions. The results are compared with a theoretical waveguide model, achieving good agreement. It is concluded that the presence of paper in the evanescent field does not interfere with the waveguide measurements, opening up opportunities to combine low-cost paper-based fluidics and integrated photonic technologies.