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
    Quicke P, Song C, McKimm EJ, Milosevic MM, Howe CL, Neil M, Schultz SR, Antic SD, Foust AJ, Knopfel Tet al., 2019,

    Single-neuron level one-photon voltage imaging with sparsely targeted genetically encoded voltage indicators

    , Frontiers in Cellular Neuroscience, Vol: 13, ISSN: 1662-5102

    Voltage imaging of many neurons simultaneously at single-cell resolution is hampered by the difficulty of detecting small voltage signals from overlapping neuronal processes in neural tissue. Recent advances in genetically encoded voltage indicator (GEVI) imaging have shown single-cell resolution optical voltage recordings in intact tissue through imaging naturally sparse cell classes, sparse viral expression, soma restricted expression, advanced optical systems, or a combination of these. Widespread sparse and strong transgenic GEVI expression would enable straightforward optical access to a densely occurring cell type, such as cortical pyramidal cells. Here we demonstrate that a recently described sparse transgenic expression strategy can enable single-cell resolution voltage imaging of cortical pyramidal cells in intact brain tissue without restricting expression to the soma. We also quantify the functional crosstalk in brain tissue and discuss optimal imaging rates to inform future GEVI experimental design.
  • Working paper
    Harput S, Christensen-Jeffries K, Ramalli A, Brown J, Zhu J, Zhang G, Leow CH, Toulemonde M, Boni E, Tortoli P, Eckersley RJ, Dunsby C, Tang M-Xet al., 2019,

    3-D super-resolution ultrasound (SR-US) imaging with a 2-D sparse array

    High frame rate 3-D ultrasound imaging technology combined withsuper-resolution processing method can visualize 3-D microvascular structuresby overcoming the diffraction limited resolution in every spatial direction.However, 3-D super-resolution ultrasound imaging using a full 2-D arrayrequires a system with large number of independent channels, the design ofwhich might be impractical due to the high cost, complexity, and volume of dataproduced. In this study, a 2-D sparse array was designed and fabricated with 512elements chosen from a density-tapered 2-D spiral layout. High frame ratevolumetric imaging was performed using two synchronized ULA-OP 256 researchscanners. Volumetric images were constructed by coherently compounding 9-angleplane waves acquired in 3 milliseconds at a pulse repetition frequency of 3000Hz. To allow microbubbles sufficient time to move between consequent compoundedvolumetric frames, a 7-millisecond delay was introduced after each volumeacquisition. This reduced the effective volume acquisition speed to 100 Hz andthe total acquired data size by 3.3-fold. Localization-based 3-Dsuper-resolution images of two touching sub-wavelength tubes were generatedfrom 6000 volumes acquired in 60 seconds. In conclusion, this work demonstratesthe feasibility of 3D super-resolution imaging and super-resolved velocitymapping using a customized 2D sparse array transducer.
  • Journal article
    Munro I, Garcia EAC, Yan M, Guldbrand S, Kumar S, Kwakwa K, Dunsby C, Neil M, French Pet al., 2019,

    Accelerating single molecule localisation microscopy through parallel processing on a high-performance computing cluster

    , Journal of Microscopy, Vol: 273, Pages: 148-160, ISSN: 1365-2818

    Super‐resolved microscopy techniques have revolutionized the ability to study biological structures below the diffraction limit. Single molecule localization microscopy (SMLM) techniques are widely used because they are relatively straightforward to implement and can be realized at relatively low cost, e.g. compared to laser scanning microscopy techniques. However, while the data analysis can be readily undertaken using open source or other software tools, large SMLM data volumes and the complexity of the algorithms used often lead to long image data processing times that can hinder the iterative optimization of experiments. There is increasing interest in high throughput SMLM, but its further development and application is inhibited by the data processing challenges. We present here a widely applicable approach to accelerating SMLM data processing via a parallelized implementation of ThunderSTORM on a high‐performance computing (HPC) cluster and quantify the speed advantage for a four‐node cluster (with 24 cores and 128 GB RAM per node) compared to a high specification (28 cores, 128 GB RAM, SSD‐enabled) desktop workstation. This data processing speed can be readily scaled by accessing more HPC resources. Our approach is not specific to ThunderSTORM and can be adapted for a wide range of SMLM software.
  • Conference paper
    Woodward RI, Kelleher EJR, Runcorn TH, Loranger S, Popa D, Wittwer VJ, Ferrari AC, Popov SV, Kashyap R, Taylor JRet al., 2019,

    Nanosecond to picosecond fiber bragg grating compression of giant-chirped pulses from an ultra-long mode-locked fiber laser
  • Conference paper
    Runcorn TH, Murray RT, Kelleher EJR, Popov SV, Taylor JRet al., 2019,

    Watt-level, Duration-tunable Picosecond Source at 560 nm by Second-harmonic Generation of a Raman Fiber Laser
  • Conference paper
    Thomas GM, Minassian A, Damzen MJ, 2019,

    Directly diode-side-pumped alexandrite slab lasers in the bounce geometry and optical vortex generation
  • Conference paper
    Arbabzadah EA, Kerridge-Johns W, Thomas GM, Minassian A, Damzen MJet al., 2019,

    High efficiency TEM <inf>00</inf> diode end-pumped Alexandrite laser
  • Conference paper
    Teppitaksak A, Thomas GM, Damzen MJ, 2019,

    Gain-switched diode laser seeding of ultra-high-gain Nd: YVO <inf>4</inf> bounce amplifier system as a versatile pulsed laser source
  • Conference paper
    Thipparapu NK, Wang Y, Wang S, Barua P, Sahu JKet al., 2019,

    Bi-doped silica-based fiber amplifier for O-band transmission

    Bismuth (Bi)-doped fibers offer a great potential to develop fiber sources in the 1150-1800nm wavelength region. Here, we review our recent work on Bi-doped fiber amplifiers in the O-band covering from 1300-1360nm.
  • Conference paper
    Petropoulos P, Hong Y, Bottrill K, Taengnoi N, Sakr H, Bradley TD, Thipparapu NK, Wang Y, Umnikov AA, Hayes JR, Jasion GT, Sahu JK, Poletti F, Richardson DJet al., 2019,

    Extending the optical bandwidth of optical communication systems

    This talk discusses the new avenues facilitated through the adoption of ultra-broadband hollow-core optical transmission fibres, paired with amplifiers covering alternative wavelength bands. Transmission experiments using these technologies over an extended optical bandwidth are presented.
  • Conference paper
    Thipparapu NK, Wang Y, Umnikov AA, Barua P, Richardson DJ, Sahu JKet al., 2019,

    High gain Bi-doped all fiber amplifier for O-band DWDM optical fiber communication

    We report a double-pass bismuth-doped fiber amplifier operating in the O-band with a 31dB gain and a 7dB NF for -10dBm input signal. The amplifier power conversion efficiency and gain-coefficient are 11% and 0.06dB/mW, respectively.
  • Conference paper
    Wang Y, Thipparapu NK, Umnikov AA, Barua P, Richardson DJ, Sahu Jet al., 2019,

    Temperature dependent gain and noise figure characteristics of O-band bismuth-doped fibre amplifier

    We report an O-band BDFA gain and NF performance over the temperature-range of -40 to +60oC. A 34dB gain with 5.5dB NF was obtained at 1340nm in a double-pass-BDFA operating at -40oC. The temperature-dependent-gain was decreased by <0.1dB/oC for temperatures above -20oC across 1310-1360nm wavelength-band.
  • Conference paper
    Hong Y, Taengnoi N, Bottrill KRH, Sakr H, Bradley TD, Hayes JR, Jasion GT, Wang Y, Thipparapu NK, Umnikov AA, Sahu JK, Poletti F, Petropoulos P, Richardson DJet al., 2019,

    Dual O+C-band WDM transmission over 1-km hollow core NaNf using an O-band bismuth-doped fibre amplifier

    Amplified transmission of WDM channels over the O- and C-bands is demonstrated using a bismuth-doped fibre amplifier. The transmission medium is an ultra-wide bandwidth nested antiresonant fibre (NANF) offering uniform loss performance across all wavelengths of interest. Comparable performance is obtained across the two bands.
  • Conference paper
    Wang Y, Thipparapu NK, Wang S, Barua P, Richardson DJ, Sahu JKet al., 2019,

    O-band bismuth-doped fiber amplifier and its temperature dependent performance

    , ISSN: 0277-786X

    We report temperature-dependent gain and NF of single-pass and double-pass O-band BDFA from -60 to +80℃. A maximum gain of 41dB, NF 3.8dB was achieved at -60℃ for -23dBm input-signal. The temperature-dependent-gain coefficient was -0.04dB/℃.
  • Conference paper
    Quicke P, Howe CL, Song P, Jadan HV, Dragotti PL, Knöpfel T, Foust AJ, Schultz SR, Neil Met al., 2019,

    Calculation of high numerical aperture lightfield microscope point spread functions

    3D deconvolution of lightfield images enables high resolution reconstruction of sample volumes. Previous point spread function calculations assume low to moderate NA objectives. Here we present a simple vectorial calculation valid for high NA objectives.
  • Conference paper
    Tawy G, Damzen MJ, 2019,

    Tunable and dual wavelength alexandrite laser using the crystal birefringence

    Red-diode-pumped Alexandrite lasers has proven to be an efficient method of generating light in the near infrared with broad tunability from 714 to 818 nm recently demonstrated [1]. Conventionally, tunable Alexandrite lasers have used wavelength selective elements such as birefringent filters or external gratings [1, 2]. In this work wavelength tuning is obtained by exploiting the birefringence of the crystal to use the crystal itself as the wavelength selective element, greatly simplifying the cavity and reducing innecessary loss components.
  • Conference paper
    Tawy G, Wang J, Damzen MJ, 2019,

    Population lensing in alexandrite lasers

    Alexandrite (Cr3+:BeAl2O4) is a vibronic laser at 701-858 nm. Its excellent thermo-mechanical properties and high energy storage make it an ideal high power and high energy Q-switched source with recent development in mJ-level red-diode-pumped Alexandrite oscillators and amplifiers [1-3]. Further power scaling of these systems is limited by thermal lensing which has yet to be addressed in great detail. In this work we present experimental and finite element analysis (FEA) results on the investigation of thermal lensing in a red-diode-pumped Alexandrite laser. Differences in the thermal lensing power for non-lasing and lasing conditions are attributed to a 'population lens' effect. In a separate study stable self-Q-switching (SQS) is observed in an Alexandrite laser cavity containing only the gain medium where the SQS loss mechanism is attributed to the population lens.
  • Conference paper
    Sathian J, Lian W, Minassian A, Damzen MJet al., 2019,

    Brightness-enhanced solid-state light sources: From kaleidoscope effect to uniform illumination

    Luminescent concentrators (LCs) are systems that can increase the brightness of lambertian light sources such as an LED. Applications considered for LED-pumped LCs include laser pumping, general lighting and medical illumination [1-3]. Most studies consider the output power, spectrum and efficiency of the LC system. Here we explore the spatial nature of the output of the LCs under both laser and LED illumination.
  • Conference paper
    Sathian J, Minassian A, Alford NM, Damzen MJet al., 2019,

    Enhancing performance of Ce:YAG luminescent concentrators for high power applications

    High power scaling of an LED pumped luminescent concentrator (LC) can address significant excitation and illumination applications, including laser pumping and medical light therapy [1-3]. However, heat deposited into the luminescent material is critical and was already a serious issue in our prior systems [3] where forced air cooling of the Ce:YAG LC light-guide was employed but limited power and/or duration of operation. Here we report the successful demonstration of a temperature controlled Ce:YAG LC pumped with blue InGaN LEDs.
  • Conference paper
    Sathian J, Tawy G, Sheng X, Minassian A, Damzen MJet al., 2019,

    Compact non-astigmatic alexandrite ring laser with unidirectional single-longitudinal-mode operation

    Progress in single frequency and precise wavelength tunable lasers are essential to address future demands in high resolution spectroscopy, metrology and quantum technology systems. Alexandrite lasers with wide tunability in near-IR spectral region when pumped by low cost red diodes provide a good prospect as a cost effective precision laser source. This was demonstrated in our earlier work [1] using a tunable single-frequency bow-tie cavity with Brewster-cut Alexandrite crystal. The astigmatism of the Brewster cut gain medium and need for angled curved mirrors for astigmatic compensation, whilst being well established [2,3] also places some complexity on the design and can be compromised by astigmatic thermal lensing [1]. Here we report the investigation and successful operation of a non-astigmatic compact design of a unidirectional wavelength tunable Alexandrite ring laser with single frequency operation.
  • Conference paper
    Soltan A, Maaskant P, Armstrong N, Al-Atabany W, Chaudet L, Neil M, Degenaar Pet al., 2019,

    Wearable Glasses for Retinal Pigmentiosa Based on Optogenetics

    , IEEE International Symposium on Circuits and Systems (IEEE ISCAS), Publisher: IEEE, ISSN: 0271-4302
  • Conference paper
    Gorlitz F, Lightley J, Kumar S, Garcia E, Yan M, Wysoczanski R, Alexandrov Y, Baker JR, Barnes PJ, Munro I, Donnelly LE, Dunsby C, Neil MAA, French PMWet al., 2019,

    Automated multiwell plate STORM: towards open source super-resolved high content analysis

    , Conference on Advances in Microscopic Imaging II, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
  • Conference paper
    Harput S, Fong LH, Stanziola A, Zhang G, Toulemonde M, Zhu J, Christensen-Jeffries K, Brown J, Eckersley RJ, Grisan E, Dunsby C, Tang M-Xet al., 2019,

    Super-Resolution Ultrasound Image Filtering with Machine-Learning to Reduce the Localization Error

    , IEEE International Ultrasonics Symposium (IUS), Publisher: IEEE, Pages: 2118-2121, ISSN: 1948-5719
  • Conference paper
    Harput S, Zhang G, Toulemonde M, Zhu J, Christensen-Jeffries K, Brown J, Eckersley RJ, Dunsby C, Tang M-Xet al., 2019,

    Activation and 3D Imaging of Phase-change Nanodroplet Contrast Agents with a 2D Ultrasound Probe

    , IEEE International Ultrasonics Symposium (IUS), Publisher: IEEE, Pages: 2275-2278, ISSN: 1948-5719
  • Conference paper
    Zhang G, Harput S, Shah A, Hernandez-Gil J, Zhu J, Christensen-Jeffries K, Brown J, Long NJ, Eckersley RJ, Dunsby C, Bamber J, Tang M-Xet al., 2019,

    Photoacoustic Super-Resolution Imaging using Laser Activation of Low-Boiling-Point Dye-Coated Nanodroplets in vitro and in vivo

    , IEEE International Ultrasonics Symposium (IUS), Publisher: IEEE, Pages: 944-947, ISSN: 1948-5719
  • Conference paper
    Sathian J, Lian W, Minassian A, Damzen MJet al., 2019,

    Brightness-Enhanced Solid-State Light Sources: From Kaleidoscope Effect to Uniform Illumination

    , Conference on Lasers and Electro-Optics Europe / European Quantum Electronics Conference (CLEO/Europe-EQEC), Publisher: IEEE
  • Conference paper
    Sathian J, Minassian A, Alford NM, Damzen MJet al., 2019,

    Enhancing Performance of Ce:YAG Luminescent Concentrators for High Power Applications

    , Conference on Lasers and Electro-Optics Europe / European Quantum Electronics Conference (CLEO/Europe-EQEC), Publisher: IEEE
  • Conference paper
    Tawy G, Damzen MJ, 2019,

    Tunable and Dual Wavelength Alexandrite Laser Using the Crystal Birefringence

    , Conference on Lasers and Electro-Optics Europe / European Quantum Electronics Conference (CLEO/Europe-EQEC), Publisher: IEEE
  • Conference paper
    Tawy G, Wang J, Damzen MJ, 2019,

    Population Lensing in Alexandrite Lasers

    , Conference on Lasers and Electro-Optics Europe / European Quantum Electronics Conference (CLEO/Europe-EQEC), Publisher: IEEE
  • Conference paper
    Sathian J, Tawy G, Shen X, Minassian A, Damzen MJet al., 2019,

    Compact Non-Astigmatic Alexandrite Ring Laser with Unidirectional Single-Longitudinal-Mode operation

    , Conference on Lasers and Electro-Optics Europe / European Quantum Electronics Conference (CLEO/Europe-EQEC), Publisher: IEEE

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