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
    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
    Ahmad H, Aidit SN, Samion MZ, Wang S, Wang Y, Sahu JKet al., 2021,

    Tunable Dual-Wavelength Bismuth Fiber Laser With 37.8-GHz Frequency Spacing

    , JOURNAL OF LIGHTWAVE TECHNOLOGY, Vol: 39, Pages: 6617-6623, ISSN: 0733-8724
  • 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
    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
  • 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.
  • 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
    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
    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
    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

    Structured 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.
  • Journal article
    Ahmad H, Azri MFM, Aidit SN, Yusoff N, Zamzuri AK, Samion MZ, Wang S, Wang Y, Sahu JKet al., 2021,

    1.3 μm passively Q-Switched bismuth doped fiber laser using Nb<inf>2</inf>C saturable absorber

    , Optical Materials, Vol: 116, ISSN: 0925-3467

    A tunable passively Q-switched fiber laser operating at 1.3 μm was demonstrated using bismuth-doped fiber (BDF) as the gain medium and using niobium carbide (Nb2C) as the saturable absorber (SA). The Nb2C was prepared using the solution casting method, and then fabricated into a film form for ease of integration into the laser cavity. Stable Q-switched pulses were observed as the pump power was increased from 820 to 1037 mW, generating pulses with increasing repetition rates from 10.1 kHz to 13.8 kHz and decreasing pulse widths from 17.54 to 7.58 μs. The all-fiber laser had a center wavelength at 1314 nm with a broad 3-dB bandwidth of 8.35 nm. The maximum output power and pulse energy of the Q-switched laser were 0.74 mW and 53.7 nJ, respectively. The laser was stable when tested for its long-term stability, where the peak frequency remained consistent at 13.8 kHz and the SNRs were maintained to be more than 60 dB throughout the entire test period. To the best of our knowledge, this is the first demonstration for a passively Q-switched fiber laser operating at 1.3 μm wavelength region using BDF as the gain medium.
  • Conference paper
    Wang Y, Thipparapu NK, Richardson DJ, Sahu JKet al., 2021,

    High Gain Bi-Doped Fiber Amplifier Operating in the E-band with a 3-dB Bandwidth of 40nm

    We report a double-pass bismuth-doped fiber amplifier operating in the E-band providing 38dB gain with 6dB NF for -23dBm input signal at 1430nm. The amplifier 3-dB bandwidth and temperature-dependent-gain coefficient are 40nm and -0.006dB/, respectively.
  • Conference paper
    Hong Y, Bottrill KRH, Wang Y, Thipparapu NK, Sahu JK, Petropoulos P, Richardson DJet al., 2021,

    O+E-band Transmission over 50-km SMF using A Broadband Bismuth Doped Fibre Amplifier

    Ultra-wideband (UWB) transmission over single-mode fibres (SMFs) is an attractive route in optical transmission, since it allows the available low-loss bandwidth offered in conventional silica SMFs to be utilised more efficiently [1] - [3]. However, data transmission beyond a single span over wavelengths outside the erbium gain band remains challenging, primarily because of the lack of suitable optical amplifiers. Recently, the emergence of bismuth-doped fibre amplifiers (BDFAs) has shown considerable potential for amplified high-speed data communications outside the C+L-bands [4] - [8]. An exciting recent work has reported the development of a BDFA exhibiting a 115nm gain bandwidth, covering the range 1345-1460nm [8]. In this paper, we demonstrate the first data transmission experiment utilising this BDFA as a booster amplifier, and we study its performance across this entire gain band.
  • Conference paper
    Thipparapu NK, Alam S, Wang Y, Shankar P, Richardson DJ, Sahu JKet al., 2021,

    Tunable Actively Mode-locked Bi-doped O-band Fibre Laser

    Widely tunable pulsed fibre laser sources in the O-band (1260-1360nm) are of interest in a variety of fields including spectroscopy, optical communication, time-resolved measurements, and optical system diagnostics [1]. Furthermore, major constituents of biological tissues such as water, oxyhemoglobin, and melanin exhibit minimum optical loss windows in the 1300nm band pointing to applications in medicine [2]. Bi-doped phoshosilicate fibres (BPSFs) have recently been investigated as a promising medium to develop new wavelength lasers and amplifiers in the O-band [3]. They exhibit broad emission spectra which is an important characteristic for developing widely tunable pulsed laser sources [4]. However, to the best of our knowledge, there are no reports of tunable pulsed Bi-doped fibre lasers around 1300nm. Here, we demonstrate an actively tunable mode-locked Bi-doped fibre laser (ML-BDFL) operating in the wavelength region from 1300-1370nm.
  • 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
    Gratus J, Kinsler P, McCall MW, 2021,

    Temporary Singularities and Axions: An Analytic Solution that Challenges Charge Conservation

    , ANNALEN DER PHYSIK, Vol: 533, ISSN: 0003-3804
  • Journal article
    Hong Y, Bottrill KRH, Taengnoi N, Thipparapu NK, Wang Y, Sahu JK, Richardson DJ, Petropoulos Pet al., 2021,

    Numerical and experimental study on the impact of chromatic dispersion on O-band direct-detection transmission

    , APPLIED OPTICS, Vol: 60, Pages: 4383-4390, ISSN: 1559-128X
  • Journal article
    Cannon T, Lagarto J, Dyer B, Garcia Castano E, Kelly D, Peters N, Lyon A, French P, Dunsby Cet al., 2021,

    Characterisation of NADH fluorescence properties under one-photon excitation with respect to temperature, pH and binding to lactate dehydrogenase

    , Optical Society of America Continuum, Vol: 4, Pages: 1610-1625

    Reduced nicotinamide adenine dinucleotide (NADH) is the principal electron donor in glycolysis and oxidative metabolism and is thus recognized as a key biomarker for probing metabolic state. While the fluorescence characteristics of NADH have been investigated extensively, there are discrepancies in the published data due to diverse experimental conditions, instrumentation and microenvironmental parameters that can affect NADH fluorescence. Using a cuvette-based time-resolved spectrofluorimeter employing one-photon excitation at 375 nm, we characterized the fluorescence intensity, lifetime, spectral response, anisotropy and time-resolved anisotropy of NADH in aqueous solution under varying microenvironmental conditions, namely temperature, pH, and binding to lactate dehydrogenase (LDH). Our results demonstrate how temperature, pH, and binding partners each impact the fluorescence signature of NADH and highlight the complexity of the fluorescence data when different parameters produce competing effects. We hope that the data presented in this study will provide a reference for potential sources of variation in experiments measuring NADH fluorescence.
  • Journal article
    Taengnoi N, Bottrill KRH, Hong Y, Wang Y, Thipparapu NK, Sahu JK, Petropoulos P, Richardson DJet al., 2021,

    Experimental characterization of an o-band bismuth-doped fiber amplifier

    , OPTICS EXPRESS, Vol: 29, Pages: 15345-15355, ISSN: 1094-4087
  • Journal article
    Murray RT, Chandran AM, Battle RA, Runcorn TH, Schunemann PG, Zawilski KT, Guha S, Taylor JRet al., 2021,

    Seeded optical parametric generation in CdSiP2 pumped by a Raman fiber amplifier at 124  µm

    , Optics Letters, Vol: 46, Pages: 2039-2039, ISSN: 0146-9592

    We report a seeded optical parametric generator (OPG) producing tunable radiation from 4.2–4.6 µm. The seeded OPG employs a 13 mm long CdSiP2 (CSP) crystal cut for non-critical phase-matching, pumped by a nanosecond-pulsed, MHz repetition rate Raman fiber amplifier system at 1.24 µm. A filtered, continuous-wave fiber supercontinuum source at 1.72 µm is used as the seed. The source generates up to 0.25 W of mid-infrared (MIR) idler power with a total pump conversion of 42% (combined signal and idler).
  • Journal article
    Kerridge-Johns WR, Jaillot J-B, Damzen MJ, 2021,

    Sampling a vortex from a Gaussian beam using a wedge-plate shearing interferometer

    , Applied Optics, Vol: 60, Pages: 3510-3510, ISSN: 1559-128X

    Many vortex-generation techniques have been developed to address a range of potential applications, exploiting their unique amplitude and phase profiles and their possession of orbital angular momentum. In this work, we present what may be the simplest method of vortex beam generation, requiring only a wedged optic: the wedge-plate shearing interferometer (WPSI). We show that the WPSI can reflect a first order Laguerre–Gaussian vortex beam (LG01) with a theoretical purity of >99% from an input fundamental Gaussian beam, with 98% LG01 purity experimentally demonstrated. We demonstrate 1% power conversion with a route to 14%. The monolithic WPSI is a simple, compact, and highly stable device, which can operate at any wavelength that the material is transparent to. We anticipate that it will be useful where sampling a robust, high-purity vortex beam from a Gaussian laser beam is required, including low-cost vortex generation for metrology or education.
  • Conference paper
    Dvinskikh L, Harding S, Sparks H, Gorelik J, MacLeod K, Dunsby Cet al., 2021,

    High speed imaging of calcium dynamics in cardiomyocytes with a flexible light-sheet fluorescence microscope

    , Biophotonics Congress 2021
  • Journal article
    Collart C, Ciccarelli A, Ivanovitch K, Rosewell I, Kumar S, Kelly G, Edwards A, Smith JCet al., 2021,

    The migratory pathways of the cells that form the endocardium, dorsal aortae, and head vasculature in the mouse embryo

    , BMC DEVELOPMENTAL BIOLOGY, Vol: 21, ISSN: 1471-213X
  • Journal article
    Ahmad H, Aidit SN, Ooi SI, Samion MZ, Wang S, Wang Y, Sahu JK, Zamzuri AKet al., 2021,

    1.3 µm dissipative soliton resonance generation in Bismuth doped fiber laser.

    , Sci Rep, Vol: 11

    In this work, a Figure-9 (F9) bismuth-doped fiber laser (BiDFL) operating in the dissipative soliton resonance (DSR) regime is presented. The 1338 nm laser used a BiDF as the active gain medium, while a nonlinear amplifying loop mirror (NALM) in an F9 configuration was employed to obtain high energy mode-locked pulses. The wave breaking-free rectangular pulse widened significantly in the time domain with the increase of the pump power while maintaining an almost constant peak power of 0.6 W. At the maximum pump power, the mode-locked laser delivered a rectangular-shaped pulse with a duration of 48 ns, repetition rate of 362 kHz and a radio-frequency signal-to-noise ratio of more than 60 dB. The maximum output power was recorded at around 11 mW with a corresponding pulse energy of 30 nJ. This is, to the best of the author's knowledge, the highest mode-locked pulse energy obtained at 1.3 μm as well as the demonstration of an NALM BiDFL in a F9 configuration.
  • Journal article
    Codescu M-A, Weiß M, Brehm M, Kornilov O, Sebastiani D, Nibbering ETJet al., 2021,

    Switching between Proton Vacancy and Excess Proton Transfer Pathways in the Reaction between 7-Hydroxyquinoline and Formate

    , The Journal of Physical Chemistry A, Vol: 125, Pages: 1845-1859, ISSN: 1089-5639

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