Publications

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 article
    Kinsler P, McCall MW, Oulton RF, Clark ASet al., 2022,

    The surprising persistence of time-dependent quantum entanglement

    , NEW JOURNAL OF PHYSICS, Vol: 24, ISSN: 1367-2630
  • Journal article
    Darling C, Davis SPX, Kumar S, French PMW, McGinty Jet al., 2022,

    Single-shot optical projection tomography for high-speed volumetric imaging of dynamic biological samples

    , JOURNAL OF BIOPHOTONICS, ISSN: 1864-063X
  • Journal article
    Coney AT, Beecher S, Damzen MJ, Elder Iet al., 2022,

    High-energy Q-switched Nd:YAG oscillator and amplifier development for large-mode, low-alignment sensitivity applications

    , LASER PHYSICS LETTERS, Vol: 19, ISSN: 1612-2011
  • Journal article
    Chung CH, Li J, Steuer CE, Bhateja P, Johnson M, Masannat J, Poole MI, Song F, Hernandez-Prera JC, Molina H, Wenig BM, Kumar S, Kuperwasser C, Stephens PJ, Farinhas JM, Shin DM, Kish JA, Muzaffar J, Kirtane K, Rocco JW, Schell MJ, Saba NF, Bonomi Met 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: 2329-2338

    PURPOSE: 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.
  • Journal article
    Fisher A, Van de Pette M, Dimond A, Galvao AM, Millership SJ, To W, Prodani C, McNamara G, Bruno L, Sardini A, Webster Z, McGinty Jet al., 2022,

    Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice

    , Nature Communications, ISSN: 2041-1723
  • Journal article
    Fisher A, Van de Pette M, Dimond A, Galvao AM, Millership SJ, To W, Prodani C, McNamara G, Bruno L, Sardini A, Webster Z, McGinty J, French PMW, Uren AG, Castillo-Fernandez J, Watkinson W, Ferguson-Smith AC, Merkenschlager M, John RM, Kelsey Get al., 2022,

    Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice

    , Nature Communications, ISSN: 2041-1723
  • Journal article
    Hong W, Dunsby C, 2022,

    Automatic tube lens design from stock optics for microscope remote-refocusing systems

    , Optics Express, Vol: 30, Pages: 4274-4278, ISSN: 1094-4087

    The 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.
  • Journal article
    Lee H, Berk J, Webster A, Kim D, Foreman MRet al., 2022,

    Label-free detection of single nanoparticles with disordered nanoisland surface plasmon sensor.

    , Nanotechnology, Vol: 33, Pages: 1-11, ISSN: 0957-4484

    We report sensing of single nanoparticles using disordered metallic nanoisland substrates supporting surface plasmon polaritons (SPPs). Speckle patterns arising from leakage radiation of elastically scattered SPPs provides a unique fingerprint of the scattering microstructure at the sensor surface. Experimental measurements of the speckle decorrelation are presented and shown to enable detection of sorption of individual gold nanoparticles and polystyrene beads. Our approach is verified through bright-field and fluorescence imaging of particles adhering to the nanoisland substrate.
  • Journal article
    Byrnes N, Foreman MR, 2022,

    Polarisation statistics of vector scattering matrices from the circular orthogonal ensemble

    , Optics Communications, Vol: 503, Pages: 1-6, ISSN: 0030-4018

    We study the polarisation properties of random𝑁×𝑁scattering matrices distributed according to the circularorthogonal ensemble. We interpret 2×2 sub-blocks of the scattering matrix as Jones matrices and study theirstatistical properties. Using the polar decomposition, we derive probability density functions for retardanceand diattenuation from scattering matrices of arbitrary size and in the limit𝑁→∞.
  • Conference paper
    Battle RA, Chandran AM, Runcorn TH, Mussot A, Kudlinski A, Murray RT, Taylor JRet 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 article
    Ramuz M, Diakonov I, Dunsby C, Gorelik Jet al., 2022,

    MultiFRET: A Detailed Protocol for High-Throughput Multiplexed Ratiometric FRET.

    , Methods Mol Biol, Vol: 2483, Pages: 33-59

    The 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.
  • Journal article
    Chandran A, Battle RA, Murray RT, Runcorn T, Taylor JRet 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: 1094-4087

    We 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.
  • Journal article
    Fotiadi AA, Korobko DA, Zolotovskii IO, Taylor JRet al., 2021,

    Brillouin-like amplification in rare-earth-doped optical fibers

    , OPTICS EXPRESS, Vol: 29, Pages: 40345-40359, ISSN: 1094-4087
  • Journal article
    Guglielmi L, Heliot C, Kumar S, Alexandrov Y, Gori I, Papaleonidopoulou F, Barrington C, East P, Economou AD, French PMW, McGinty J, Hill CSet al., 2021,

    Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways

    , NATURE COMMUNICATIONS, Vol: 12
  • Journal article
    Wright T, Sparks H, Paterson C, Dunsby Cet al., 2021,

    Video-rate remote refocusing through continuous oscillation of a membrane deformable mirror

    , Journal of Physics: Photonics, Vol: 3, Pages: 1-14, ISSN: 2515-7647

    This 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.
  • Journal article
    Kalita R, Flanagan W, Lightley J, Kumar S, Alexandrov Y, Garcia E, Hintze M, Barkoulas M, Dunsby C, French PMWet al., 2021,

    Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast

    , JOURNAL OF BIOPHOTONICS, Vol: 14, ISSN: 1864-063X
  • Conference paper
    Wysoczanski R, Baker J, Fenwick P, Dunsby C, French P, Barnes P, Donnelly Let 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
  • Journal article
    Geberbauer 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: 1094-4087

    High-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.
  • Journal article
    Lightley J, Gorlitz F, Kumar S, Kalita R, Kolbeinsson A, Garcia E, Alexandrov Y, Bousgouni V, Wysoczanski R, Barnes P, Donnelly L, Bakal C, Dunsby C, Neil MAA, Flaxman S, French PMWet al., 2021,

    Robust deep learning optical autofocus system applied to automated multiwell plate single molecule localization microscopy

    , JOURNAL OF MICROSCOPY, ISSN: 0022-2720
  • Journal article
    Qian K, Arichi T, Price A, Dall'Orso S, Eden J, Noh Y, Rhode K, Burdet E, Neil M, Edwards AD, Hajnal JVet al., 2021,

    An eye tracking based virtual reality system for use inside magnetic resonance imaging systems

    , Scientific Reports, Vol: 11, Pages: 1-17, ISSN: 2045-2322

    Patients 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.
  • Journal article
    Berk J, Foreman MR, 2021,

    Role of multiple scattering in single particle perturbations in absorbing random media

    , Physical Review Research, Vol: 3, Pages: 1-14, ISSN: 2643-1564

    Speckle patterns produced by disordered scattering systems exhibit asensitivity to addition of individual particles which can be used for sensingapplications. Using a coupled dipole model we investigate how multiplescattering can enhance field perturbations arising in such random scatteringbased sensors. Three distinct families of multiple scattering paths are shownto contribute and the corresponding complex enhancement factors derived.Probability distributions of individual enhancement factors over the complexplane are characterised numerically within the context of surface plasmonpolariton scattering in which absorption is shown to play an important role. Weshow that enhancements become more strongly dependent on individual scattererproperties when absorption losses are larger, however, amplitude enhancements$\sim 10^2$, comparable to low loss surface plasmons, are achievable throughsensor optimisation. Approximate analytic expressions for the complex meanenhancements are also found, which agree well with simulations when loopcontributions are negligible.
  • Journal article
    Gratus J, Seviour R, Kinsler P, Jaroszynski DAet al., 2021,

    Temporal boundaries in electromagnetic materials

    , NEW JOURNAL OF PHYSICS, Vol: 23, ISSN: 1367-2630
  • Conference paper
    Garcia E, Lightley J, Kumar S, Kalita R, Gorlitz F, Alexandrov Y, Cook T, Dunsby C, Neil M, Roufosse C, French Pet 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 article
    Berk J, Foreman MR, 2021,

    Theory of multiple scattering enhanced single particle plasmonic sensing

    , ACS Photonics, Vol: 8, Pages: 2227-2233, ISSN: 2330-4022

    Methods to increase the light scattered from small particles can help improve the sensitivity of many sensing techniques. Here, we investigate the role multiple scattering plays in perturbing the scattered signal when a particle is added to a random scattering environment. Three enhancement factors, parametrizing the effect of different classes of multiple scattering trajectories on the field perturbation, are introduced and their mean amplitudes explored numerically in the context of surface plasmon polariton scattering. We demonstrate that there exists an optimum scatterer density at which the sensitivity enhancement is maximized, with factors on the order of 102 achievable. Dependence of the enhancement factors on scatterer properties are also studied.
  • Journal article
    Xiang Y, Seow KLC, Paterson C, Torok Pet al., 2021,

    Multivariate analysis of Brillouin imaging data by supervised and unsupervised learning

    , JOURNAL OF BIOPHOTONICS, Vol: 14, ISSN: 1864-063X
  • Journal article
    Berk 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: 0733-8724

    Label 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.
  • Journal article
    Boland MA, Cohen EAK, Flaxman SR, Neil MAAet 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: 1364-503X
  • Journal article
    Gong 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
  • Journal article
    Parmar V, Singh S, Kumar S, Vijaya Prakash G, Kalyanasundaram Det 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: 0030-3992

    Nickel-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.
  • Journal article
    Garcia E, Lightley J, Kumar S, Kalita R, Gorlitz F, Alexandrov Y, Cook T, Dunsby C, Neil MAA, Roufosse CA, French PMWet 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

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