See a list of publications below or visit the Photonics academic staff page and click on a particular member of staff to access their personal web page, which includes a list of their own publications.
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Journal articleLightley J, Kumar S, Garcia E, et al., 2022,
Robust, single-shot, optical autofocus system utilizing cylindrical lenses to provide high precision and long range of operation
<jats:title>ABSTRACT</jats:title> <jats:p>We present a robust, “real-time” optical autofocus system for microscopy that provides high accuracy (<230 nm) and long range (∼130 µm) with a 1.4 numerical aperture oil immersion objective lens. This autofocus can operate in a closed loop, single-shot functionality over a range of ±37.5 µm and can also operate as a 2-step process up to ±68 µm. A real-time autofocus capability is useful for experiments with long image data acquisition times, including single molecule localization microscopy, that may be impacted by defocusing resulting from drift of components, e.g., due to changes in temperature or mechanical drift. It is also vital for automated slide scanning or multiwell plate imaging where the sample may not be in the same horizontal plane for every field of view during the image data acquisition. To realise high precision and long range, we implement orthogonal optical readouts using cylindrical lenses. We demonstrate the performance of this new optical autofocus system with automated multiwell plate imaging and single molecule localisation microscopy and illustrate the benefit of using a superluminescent diode as the autofocus light source.</jats:p>
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Journal articleChung CH, Li J, Steuer CE, et al., 2022,
Phase II Multi-institutional Clinical Trial Result of Concurrent Cetuximab and Nivolumab in Recurrent and/or Metastatic Head and Neck Squamous Cell Carcinoma.
, Clin Cancer Res, Vol: 28, Pages: 2329-2338PURPOSE: A phase II multi-institutional clinical trial was conducted to determine overall survival (OS) in patients with recurrent and/or metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) treated with a combination of cetuximab and nivolumab. PATIENTS AND METHODS: Patients with R/M HNSCC were treated with cetuximab 500 mg/m2 i.v. on day 14 as a lead-in followed by cetuximab 500 mg/m2 i.v. and nivolumab 240 mg i.v. on day 1 and day 15 of each 28-day cycle. Expression of p16 and programmed cell death-ligand 1 (PD-L1) in archived tumors were determined. Tumor-tissue-modified human papillomavirus (TTMV) DNA was quantified in plasma. RESULTS: Ninety-five patients were enrolled, and 88 patients were evaluable for OS with a median follow-up of 15.9 months. Median OS in the 45 patients who had prior therapy for R/M HNSCC (cohort A) was 11.4 months, with a 1 year OS 50% [90% confidence interval (CI), 0.43-0.57]. Median OS in the 43 patients who had no prior therapy (cohort B) was 20.2 months, with a 1-year OS 66% (90% CI, 0.59-0.71). In the combined cohorts, the p16-negative immunostaining was associated with higher response rate (RR; P = 0.02) but did not impact survival while higher PD-L1 combined positive score was associated with higher RR (P = 0.03) and longer OS (log-rank P = 0.04). In the p16-positive patients, lower median (1,230 copies/mL) TTMV DNA counts were associated with higher RR (P = 0.01) and longer OS compared with higher median (log-rank P = 0.05). CONCLUSIONS: The combination of cetuximab and nivolumab is effective in patients with both previously treated and untreated R/M HNSCC and warrants further evaluation.
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Conference paperFu X, Bhargava A, Bailey S, et al., 2022,
Intra-epithelia cell dynamics shape evolutionary dynamics and selection of therapy resistant clones in lung cancer
, AACR Special Conference - Evolutionary Dynamics in Carcinogenesis and Response to Therapy, Publisher: AMER ASSOC CANCER RESEARCH, ISSN: 0008-5472 -
Journal articleVan de Pette M, Dimond A, Galvao AM, et al., 2022,
Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice
, Nature Communications, Vol: 13, ISSN: 2041-1723Transmission of epigenetic information between generations occurs in nematodes, flies and plants, mediated by specialised small RNA pathways, modified histones and DNA methylation. Similar processes in mammals can also affect phenotype through intergenerational or trans-generational mechanisms. Here we generate a luciferase knock-in reporter mouse for the imprinted Dlk1 locus to visualise and track epigenetic fidelity across generations. Exposure to high-fat diet in pregnancy provokes sustained re-expression of the normally silent maternal Dlk1 in offspring (loss of imprinting) and increased DNA methylation at the somatic differentially methylated region (sDMR). In the next generation heterogeneous Dlk1 mis-expression is seen exclusively among animals born to F1-exposed females. Oocytes from these females show altered gene and microRNA expression without changes in DNA methylation, and correct imprinting is restored in subsequent generations. Our results illustrate how diet impacts the foetal epigenome, disturbing canonical and non-canonical imprinting mechanisms to modulate the properties of successive generations of offspring.
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Conference paperWysoczanski R, Baker JR, Fenwick P, et al., 2022,
Defective Phagocytosis in COPD Macrophages Is Improved by Mitochondrial Antioxidants Without Alteration in Mitochondrial Function
, International Conference of the American-Thoracic-Society, Publisher: AMER THORACIC SOC, ISSN: 1073-449X- Author Web Link
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- Citations: 1
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Journal articleTawy G, Minassian A, Damzen MJ, 2022,
Volume Bragg Grating Locked Alexandrite Laser
, OPTICS, Vol: 3, Pages: 53-59 -
Journal articleHong W, Dunsby C, 2022,
Automatic tube lens design from stock optics for microscope remote-refocusing systems
, Optics Express, Vol: 30, Pages: 4274-4278, ISSN: 1094-4087The remote-refocusing approach of Botcherby et al. [Opt. Lett. 32, 2007 (2007) [CrossRef] ] has been applied widely to 2D and 3D fluorescence microscopes to enable rapid refocusing of the optical system without mechanically perturbing the sample. In order for this approach to operate correctly, it requires that the overall magnification of the first two microscope systems matches the ratio of the refractive indices in sample and intermedia image spaces. However, commercially available tube lenses are not always suitable to produce the desired overall magnification. Therefore, a practical approach to produce tube lenses with low expense and diffraction-limited performance is required. Tube lenses can be formed using a pair of stock achromatic doublets, however, selecting appropriate pairs of achromatic doublets from stock optics is a time-consuming process, as many combinations can be considered. In this paper, we present two software packages (Catalogue Generator and Doublet Selector) developed in MATLAB that use the application programming interface (ZOS-API) to the Zemax OpticStudio optical design software to realise an automatic search of stock achromatic doublets to produce microscope tube lenses with a specified focal length, entrance pupil diameter and maximum design field angle. An algorithm to optimise principal plane positions in versions of OpticStudio before 20.2 was also introduced to enable the use of older software versions. To evaluate the performance of Catalogue Generator and Doublet Selector, we used them to generate ten tube lens designs. All of the software-produced tube lenses have a better optical performance than those using manually selected pairs of stock doublets lenses.
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Conference paperMurray RT, Anderson J, Wei J, et al., 2022,
Wavelength tunable mid-infrared generation in non-critically cut CdSiP2 crystals by cascaded optical parametric generation with a nanosecond 1.064 μm Nd:YAG laser
We demonstrate a method to generate wavelength tunable mid-infrared radiation from 3.7-4.3 μm using a nanosecond 1.064 μm Nd:YAG pump at 10 Hz, employing cascaded optical parametric generation in non-critically cut CdSiP2 crystals.
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Conference paperMurray RT, Anderson J, Wei J, et al., 2022,
Wavelength tunable mid-infrared generation in non-critically cut CdSiP2 crystals by cascaded optical parametric generation with a nanosecond 1.064 µm Nd:YAG laser
We demonstrate a method to generate wavelength tunable mid-infrared radiation from 3.7-4.3 µm using a nanosecond 1.064 µm Nd:YAG pump at 10 Hz, employing cascaded optical parametric generation in non-critically cut CdSiP<inf>2</inf> crystals.
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Conference paperMunj AH, Kerridge-Johns WR, 2022,
Ring Cavity Vortex Laser using a Wedge-Plate Shearing Interferometer
We construct a compact unidirectional Nd:YVO<inf>4</inf> ring laser generating watt-level vortex beam (LG<inf>01</inf>) output with high mode purity (98%) in a single longitudinal mode. This was enabled through a wedge-plate shearing interferometer (WPSI) acting as a Gaussian to LG<inf>01</inf> mode conversion device and output coupler. This compact and cheap device uses off-the-shelf components. The design could be adapted to any gain medium for wavelength versatility.
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Conference paperTawy G, Dorrzapf M, Fang Z, et al., 2022,
Blue-Diode-Pumped Alexandrite Laser
We report a blue-diode-pumped Alexandrite laser operating at 754nm with 0.5W of output laser power with an optical efficiency of 20%. We provide a comparison of blue-diode-pumping to red-diode-pumping to show its potential as a low-cost alternative due to the availability of low-cost high-power blue-diodes. A comparison of the laser characteristics is provided as well as a study of the thermal lensing for blue-diode-pumping for the very first time.
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Conference paperBattle RA, Chandran AM, Runcorn TH, et al., 2022,
Optical parametric amplification seeded by four-wave mixing in photonic crystal fibers
, Conference on Nonlinear Frequency Generation and Conversion - Materials and Devices XXI at SPIE LASE Conference, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X -
Journal articleRamuz M, Diakonov I, Dunsby C, et al., 2022,
MultiFRET: A Detailed Protocol for High-Throughput Multiplexed Ratiometric FRET.
, Methods Mol Biol, Vol: 2483, Pages: 33-59The newly generated software plugin MultiFRET allows for real-time measurements of multiplexed fluorescent biosensors in a near high-throughput fashion. Here we describe a detailed protocol for setup and use of this software for any purpose requiring instant feedback during fluorescence measurement experiments. We further describe its non-primary features including beam splitter misalignment correction, custom calculations through input of simple equations typed in a .txt format, customizable Excel output, and offline bulk analysis of image stacks. Finally, we supply a usage example of a cAMP measurement in cultured rat neonatal cardiomyocytes.
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Conference paperFox MFJ, Bland S, Mangles SPD, et al., 2022,
Expectations of how student views on experimental physics develop during an undergraduate degree
, Physics Education Research Conference (PERC), Publisher: AMER ASSOC PHYSICS TEACHERS, Pages: 182-187, ISSN: 2377-2379 -
Journal articleKalita R, Flanagan W, Lightley J, et al., 2021,
Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast
, JOURNAL OF BIOPHOTONICS, Vol: 14, ISSN: 1864-063X- Cite
- Citations: 10
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Journal articleChandran A, Battle RA, Murray RT, et al., 2021,
Watt-level 743 nm source by second-harmonic generation of a cascaded phosphosilicate Raman fiber amplifier
, Optics Express, Vol: 29, Pages: 41467-41474, ISSN: 1094-4087We demonstrate a nanosecond pulsed 743 nm source through second-harmonic generation of a cascaded phosphosilicate Raman fiber amplifier system operating at 1485 nm. The amplifier is pumped by a 1240 nm phosphosilicate Raman fiber amplifier and seeded with a continuous-wave 1485 nm diode. This 1485 nm light is used for second-harmonic generation in periodically poled lithium niobate. Greater than 1 W of average power is generated at 743 nm with a corresponding pulse energy of 220 nJ at a repetition rate of 5 MHz. The source displays excellent beam quality (M2𝑥,𝑦 ≤ 1.18) with ideal parameters for biomedical imaging applications.
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Journal articleFotiadi AA, Korobko DA, Zolotovskii IO, et al., 2021,
Brillouin-like amplification in rare-earth-doped optical fibers
, OPTICS EXPRESS, Vol: 29, Pages: 40345-40359, ISSN: 1094-4087- Cite
- Citations: 8
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Journal articleGuglielmi L, Heliot C, Kumar S, et al., 2021,
Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways
, NATURE COMMUNICATIONS, Vol: 12- Cite
- Citations: 7
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Journal articleWright T, Sparks H, Paterson C, et al., 2021,
Video-rate remote refocusing through continuous oscillation of a membrane deformable mirror
, Journal of Physics: Photonics, Vol: 3, Pages: 1-14, ISSN: 2515-7647This paper presents the use of a deformable mirror (DM) configured to rapidly refocus a microscope employing a highnumerical aperture objective lens. An Alpao DM97-15 membrane DM was used to refocus a 40×/0.80 NA water-immersionobjective through a defocus range of -50 to 50 m at 26.3 sweeps per second. We achieved imaging with a mean Strehlmetric of > 0.6 over a field of view in the sample of 200×200 m2 over a defocus range of 77 m. We describe anoptimisation procedure where the mirror is swept continuously in order to avoid known problems of hysteresis associatedwith the membrane DM employed. This work demonstrates that a DM-based refocusing system could in the future be used inlight-sheet fluorescence microscopes to achieve video-rate volumetric imaging.
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Conference paperWysoczanski R, Baker J, Fenwick P, et al., 2021,
Image analysis of tissue macrophages to confirm differential phagocytosis between groups by microscopy and automated bacterial quantification
, Publisher: EUROPEAN RESPIRATORY SOC JOURNALS LTD, ISSN: 0903-1936- Author Web Link
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- Citations: 1
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Journal articleGarcia E, Lightley J, Kumar S, et al., 2021,
Application of direct stochastic optical reconstruction microscopy (dSTORM) to the histological analysis of human glomerular disease
, JOURNAL OF PATHOLOGY CLINICAL RESEARCH, Vol: 7, Pages: 438-445- Cite
- Citations: 8
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Journal articleGeberbauer J, Kerridge-Johns W, Damzen M, 2021,
> 30 W vortex LG₀₁ or HG₁₀ laser using a modetransforming output coupler
, Optics Express, Vol: 29, Pages: 29082-29094, ISSN: 1094-4087High-power vortex light generated directly from lasers will help drive theirapplications in material processing, optical manipulation, levitation, particle acceleration, andcommunications, but limited power has been achieved to date. In this work, we demonstraterecord vortex average power of 31.3 W directly from a laser, to the best of our knowledge,using an interferometric mode transforming output coupler to convert a fundamental modeNd:YVO4 laser into a LG01 vortex output. The vortex laser was Q-switched with up to 600 kHzpulse rate with a high slope efficiency of 62.5% and an excellent LG01 modal purity of 95.2%.We further demonstrate > 30W laser power in a high quality HG10 mode by simple adjustmentof the output coupler. Experimental investigations of varying output coupling transmission arecompared with theory. This successful implementation of the interferometric output coupler ina high power system demonstrates the suitability of the mode transforming method for robustturn-key vortex lasers with high efficiency and high modal purity, with scalable power andpulse rate.
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Journal articleLightley J, Gorlitz F, Kumar S, et al., 2021,
Robust deep learning optical autofocus system applied to automated multiwell plate single molecule localization microscopy
, JOURNAL OF MICROSCOPY, ISSN: 0022-2720- Cite
- Citations: 12
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Journal articleQian K, Arichi T, Price A, et al., 2021,
An eye tracking based virtual reality system for use inside magnetic resonance imaging systems
, Scientific Reports, Vol: 11, Pages: 1-17, ISSN: 2045-2322Patients undergoing Magnetic Resonance Imaging (MRI) often experience anxiety and sometimes distress prior to and during scanning. Here a full MRI compatible virtual reality (VR) system is described and tested with the aim of creating a radically different experience. Potential benefits could accrue from the strong sense of immersion that can be created with VR, which could create sense experiences designed to avoid the perception of being enclosed and could also provide new modes of diversion and interaction that could make even lengthy MRI examinations much less challenging. Most current VR systems rely on head mounted displays combined with head motion tracking to achieve and maintain a visceral sense of a tangible virtual world, but this technology and approach encourages physical motion, which would be unacceptable and could be physically incompatible for MRI. The proposed VR system uses gaze tracking to control and interact with a virtual world. MRI compatible cameras are used to allow real time eye tracking and robust gaze tracking is achieved through an adaptive calibration strategy in which each successive VR interaction initiated by the subject updates the gaze estimation model. A dedicated VR framework has been developed including a rich virtual world and gaze-controlled game content. To aid in achieving immersive experiences physical sensations, including noise, vibration and proprioception associated with patient table movements, have been made congruent with the presented virtual scene. A live video link allows subject-carer interaction, projecting a supportive presence into the virtual world.
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Conference paperGarcia E, Lightley J, Kumar S, et al., 2021,
Application of direct stochastic optical reconstruction microscopy (dSTORM) to the histological analysis of human glomerular disease
, Publisher: SPRINGER, Pages: S142-S142, ISSN: 0945-6317 -
Journal articleXiang Y, Seow KLC, Paterson C, et al., 2021,
Multivariate analysis of Brillouin imaging data by supervised and unsupervised learning
, JOURNAL OF BIOPHOTONICS, Vol: 14, ISSN: 1864-063X- Author Web Link
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- Citations: 6
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Journal articleBerk J, Paterson C, Foreman MR, 2021,
Tracking single particles using surface plasmon leakage radiation speckle
, Journal of Lightwave Technology, Vol: 39, Pages: 3950-3960, ISSN: 0733-8724Label free tracking of small bio-particles such as proteins or viruses is of great utility in the study of biological processes, however such experiments are frequently hindered by weak signal strengths and a susceptibility to scattering impurities. To overcome these problems we here propose a novel technique leveraging the enhanced sensitivity of both interferometric detection and the strong field confinement of surface plasmons. Specifically, we show that interference between the field scattered by an analyte particle and a speckle reference field, derived from random scattering of surface plasmons propagating on a rough metal film, enables particle tracking with sub-wavelength accuracy. We present the analytic framework of our technique and verify its robustness to noise through Monte Carlo simulations.
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Journal articleGong H, Guo W, Neil MAA, 2021,
GPU-accelerated real-time reconstruction in Python of three-dimensional datasets from structured illumination microscopy with hexagonal patterns
, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, Vol: 379, ISSN: 1364-503X- Cite
- Citations: 20
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Journal articleBoland MA, Cohen EAK, Flaxman SR, et al., 2021,
Improving axial resolution in Structured Illumination Microscopy using deep learning
, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, Vol: 379, ISSN: 1364-503XStructured Illumination Microscopy is a widespreadmethodology to image live and fixed biologicalstructures smaller than the diffraction limits ofconventional optical microscopy. Using recent advancesin image up-scaling through deep learning models,we demonstrate a method to reconstruct 3D SIMimage stacks with twice the axial resolution attainablethrough conventional SIM reconstructions. We furtherdemonstrate our method is robust to noise & evaluateit against two point cases and axial gratings. Finally,we discuss potential adaptions of the method tofurther improve resolution.
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Journal articleParmar V, Singh S, Kumar S, et al., 2021,
Thermo-physical modeling and experimental validation of core-shell nanoparticle fabrication of nickel-titanium (nitinol) alloy
, Optics and Laser Technology, Vol: 138, ISSN: 0030-3992Nickel-titanium (nitinol) is a biocompatible shape memory alloy with hyperelasticity and biocompatibility property. A three-dimensional heat diffusion model was used in conjunction with phase explosion theory to explain the formation of core-shell nanoparticles of nitinol. The diffusion model was used to evaluate the melt-pool temperature in the ablation region, while the phase explosion theory was used to estimate the thermophysical expansion and subsequent fragmentation of molten and vaporized nitinol. The mathematical parameters were formulated in conjunction with the experimental results of pulsed laser ablation of core-shell nitinol nanoparticles of various sizes. The model was further employed to predict the sizes of the nanoparticles produced at other higher fluences and the results were experimentally validated.
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