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  • Journal article
    Darling C, Kumar S, Alexandrov Y, de Faye J, Almagro Santiago J, Rýdlová A, Bugeon L, Dallman MJ, Behrens AJ, French PMW, McGinty Jet al., 2024,

    Optical projection tomography implemented for accessibility and low cost (OPTImAL)

    , Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol: 382, ISSN: 1364-503X

    Optical projection tomography (OPT) is a three-dimensional mesoscopic imaging modality that can use absorption or fluorescence contrast, and is widely applied to fixed and live samples in the mm-cm scale. For fluorescence OPT, we present OPT implemented for accessibility and low cost, an open-source research-grade implementation of modular OPT hardware and software that has been designed to be widely accessible by using low-cost components, including light-emitting diode (LED) excitation and cooled complementary metal-oxide-semiconductor (CMOS) cameras. Both the hardware and software are modular and flexible in their implementation, enabling rapid switching between sample size scales and supporting compressive sensing to reconstruct images from undersampled sparse OPT data, e.g. to facilitate rapid imaging with low photobleaching/phototoxicity. We also explore a simple implementation of focal scanning OPT to achieve higher resolution, which entails the use of a fan-beam geometry reconstruction method to account for variation in magnification. This article is part of the Theo Murphy meeting issue 'Open, reproducible hardware for microscopy'.

  • Journal article
    Hansen-Shearer J, Yan J, Lerendegui M, Huang B, Toulemonde M, Riemer K, Tan Q, Tonko J, Weinberg PD, Dunsby C, Tang M-Xet al., 2024,

    Ultrafast 3-D Transcutaneous Super Resolution Ultrasound Using Row-Column Array Specific Coherence-Based Beamforming and Rolling Acoustic Sub-aperture Processing: In Vitro, in Rabbit and in Human Study

    , ULTRASOUND IN MEDICINE AND BIOLOGY, Vol: 50, Pages: 1045-1057, ISSN: 0301-5629
  • Journal article
    Lerendegui M, Yan J, Stride E, Dunsby C, Tang M-Xet al., 2024,

    Understanding the effects of microbubble concentration on localization accuracy in super-resolution ultrasound imaging

    , PHYSICS IN MEDICINE AND BIOLOGY, Vol: 69, ISSN: 0031-9155
  • Journal article
    Dent LG, Curry N, Sparks H, Bousgouni V, Maioli V, Kumar S, Munro I, Butera F, Jones I, Arias-Garcia M, Rowe-Brown L, Dunsby C, Bakal Cet al., 2024,

    Environmentally dependent and independent control of 3D cell shape

    , CELL REPORTS, Vol: 43, ISSN: 2211-1247
  • Journal article
    Riemer K, Tan Q, Morse S, Bau L, Toulemonde M, Yan J, Zhu J, Wang B, Taylor L, Lerendegui M, Wu Q, Stride E, Dunsby C, Weinberg PD, Tang M-Xet al., 2024,

    3D Acoustic Wave Sparsely Activated Localization Microscopy With Phase Change Contrast Agents

    , INVESTIGATIVE RADIOLOGY, Vol: 59, Pages: 379-390, ISSN: 0020-9996
  • Journal article
    Zeng H-J, Xue W-Z, Murray RT, Cui C, Wang L, Pan Z, Loiko P, Mateos X, Yuan F, Zhang G, Griebner U, Petrov V, Chen Wet al., 2024,

    In-band pumped Kerr-lens mode-locked Tm,Ho-codoped calcium aluminate laser

    , OPTICS EXPRESS, Vol: 32, Pages: 16083-16089, ISSN: 1094-4087
  • Journal article
    Lerendegui M, Riemer K, Papageorgiou G, Wang B, Lachlan A, Chavignon A, Zhang T, Couture O, Huang P, Ashikuzzaman M, Dencks S, Dunsby C, Helfield B, Jensen ØA, Lisson T, Lowerison MR, Rivaz H, Samir AE, Schmitz G, Schoen S, Ruud VS, Pengfei S, Stevens T, Yan J, Sboros V, Tang Met al., 2024,

    ULTRA-SR challenge: assessment of UltrasoundLocalization and TRacking Algorithms for Super-Resolution Imaging

    , IEEE Transactions on Medical Imaging, ISSN: 0278-0062

    With the widespread interest and uptake of super-resolution ultrasound (SRUS) through localization and tracking of microbubbles, also known as ultrasound localization microscopy (ULM), many localization and tracking algorithms have been developed. ULM can image many centimeters into tissue in-vivo and track microvascular flow non-invasively with sub-diffraction resolution. In a significant community effort, we organized a challenge, Ultrasound Localization and TRacking Algorithms for Super-Resolution (ULTRA-SR). The aims of this paper are threefold: to describe the challenge organization, data generation, and winning algorithms; to present the metrics and methods for evaluating challenge entrants; and to report results and findings of the evaluation. Realistic ultrasound datasets containing microvascular flow for different clinical ultrasound frequencies were simulated, using vascular flow physics, acoustic field simulation and nonlinear bubble dynamics simulation. Based on these datasets, 38 submissions from 24 research groups were evaluated against ground truth using an evaluation framework with six metrics, three for localization and three for tracking. In-vivo mouse brain and human lymph node data were also provided, and performance assessed by an expert panel. Winning algorithms are described and discussed. The publicly available data with ground truth and the defined metrics for both localization and tracking present a valuable resource for researchers to benchmark algorithms and software, identify optimized methods/software for their data, and provide insight into the current limits of the field. In conclusion, Ultra-SR challenge has provided benchmarking data and tools as well as direct comparison and insights for a number of the state-of-the art localization and tracking algorithms.

  • Journal article
    Temel T, Murray RT, Wang L, Chen W, Schirrmacher A, Battle RA, Petrov Vet al., 2024,

    Narrowband-seeded PPLN non-resonant optical parametric oscillator

    , OPTICAL MATERIALS EXPRESS, Vol: 14, ISSN: 2159-3930
  • Journal article
    Xiao H, Jiang X, Damzen MJ, 2024,

    Transient pump-probe analysis of pump-induced lensing in laser amplifiers

    , Optics Express, Vol: 32, Pages: 12783-12799, ISSN: 1094-4087

    Understanding of pump-induced lensing in laser amplifiers is essential for the optimized design of high-power lasers with high spatial quality, but there is usually incomplete knowledge of the interplay between thermal and population induced lensing mechanisms, lensing under lasing and non-lasing conditions, and transient lensing effects under pulsed operation. This paper provides quantitative insight of pump-induced lensing effects by using experimental transient pump-probe measurements in an alexandrite laser amplifier end-pumped by a short pulse pump beam with Gaussian spatial intensity distribution. Lensing results are presented showing a large difference in lensing under both non-lasing and lasing conditions and distinction of the population lens and thermal lens contributions from their different response time. Different pump beam sizes are used to show the variation of the relative strength of the lensing mechanisms. Comparison of experimental results with the analytical transient theory developed in this paper for the Gaussian pump beam gives excellent agreement and quantitative information on the thermal and population contributions to the amplifier lens. This paper provides a methodology for quantitative investigation of pump-induced lensing in general laser amplifier systems, and potentially other classes of optical materials with residual optical absorption.

  • Conference paper
    Codescu M-A, Murray JM, Zawilski KT, Schunemann PG, Murray RT, Guha Set al., 2024,

    Optical Parametric Generation in Non-Critically Cut CdSiP2 with a Nanosecond 1.064 μm Nd:YAG Laser

    , Optica High-Brightness Sources and Light-Driven Interactions Congress
  • Journal article
    Temel T, Murray RT, Wang L, Chen W, Schirrmacher A, Divliansky IB, Mhibik O, Glebov LB, Petrov Vet al., 2024,

    Energy scaling of a narrowband, periodically poled LiNbO3, nanosecond, nonresonant optical parametric oscillator

    , APPLIED OPTICS, Vol: 63, Pages: 1811-1814, ISSN: 1559-128X
  • Journal article
    Bharadwaj A, Kalita R, Kumar A, Sarma A, Jaganathan BG, Kumar S, Gorlitz F, Lightley J, Dunsby C, Neil M, Hollick C, Graham J, French PMW, Boruah BRet al., 2024,

    A cost-effective, modular, research-grade optical microscope

    , CURRENT SCIENCE, Vol: 126, Pages: 244-254, ISSN: 0011-3891
  • Conference paper
    Murray JM, Codescu M-A, Zawilski KT, Schunemann PG, Murray R, Guha Set al., 2024,

    Optical Parametric Generation in Non-Critically Cut CdSiP2 with a Nanosecond 1.064 μm Nd:YAG Laser

    , Optica High-Brightness Sources and Light-Driven Interactions Congress
  • Conference paper
    Murray RT, Battle RA, Simon D, Xiang Y, Robinson K, Azevedo Magalhães SF, Wang Y, Runcorn TH, Takats Zet al., 2024,

    Visualizing Metabolites at the Cellular Level: Advancements in 3 Micron Laser Desorption Mass Spectrometry Imaging

    , ISSN: 1605-7422

    By combining high beam quality picosecond pulsed optical parametric amplifiers at 2.94 µm with Rapid Evaportive Ionisation Mass Spectrometry (REIMS), we have demonstrated record spatial pixel resolutions for ambient mass spectrometry (MS) imaging of < 10 µm. In this contribution, we introduce our work in this area, demonstrating the platform workflow and highlighting recent results of metabolic imaging at the single cell resolution level.

  • Conference paper
    Bottrill KRH, Taengnoi N, Wang Y, Sahu JK, Petropoulos Pet al., 2024,

    1200km Coherent O-band Transmission using In-line BDFAs and Standard Single-mode Fibre

    We demonstrate a record 1200km reach O-band transmission of a 22.5GBd dual-pol QPSK signal using a recirculating loop with in-line BDFA amplification and 50km spans of standard single-mode fibre.

  • Conference paper
    Runcorn TH, Murray RT, Taylor JR, 2024,

    Multi-watt red nanosecond frequency-doubled Raman-shifted fiber laser

    , Conference on Nonlinear Frequency Generation and Conversion - Materials and Devices XXIII, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
  • Conference paper
    Krawczyk B, Kudlinski A, Battle RA, Murray RT, Runcorn THet al., 2024,

    Enhancement of four-wave mixing via stimulated emission in a Yb-doped photonic crystal fiber

    , Conference on Fiber Lasers XXI - Technology and Systems, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
  • Journal article
    Paie P, Calisesi G, Candeo A, Comi A, Sala F, Ceccarelli F, De Luigi A, Veglianese P, Muhlberger K, Fokine M, Valentini G, Osellame R, Neil M, Bassi A, Bragheri Fet al., 2023,

    Structured-light-sheet imaging in an integrated optofluidic platform

    , LAB ON A CHIP, Vol: 24, Pages: 34-46, ISSN: 1473-0197
  • Journal article
    Liang M, Minassian A, Damzen MJ, 2023,

    High-energy acousto-optic Q-switched alexandrite laser with wavelength tunable fundamental and UV second harmonic generation

    , Optics Express, Vol: 31, Pages: 42428-42438, ISSN: 1094-4087

    We investigate high-energy mJ-class diode-pumped acousto-optic (AO) Q-switched alexandrite lasers with broad tunability at both the fundamental near-IR wavelength range and second harmonic generation (SHG) in the UV wavelength range. An AO Q-switched alexandrite laser with continuous-wave diode-pumping has been operated at up to 10 kHz and producing pulse energy of 700 µJ at repetition rate of 1 kHz. With pulsed double-pass diode-pumping, we demonstrate higher pulse energy of 2.6 mJ. With wavelength tuning, this laser system demonstrated broad fundamental tuning range from 719 to 787 nm with diffraction-limited beam quality (M2 = 1.05). By external cavity second harmonic generation in a Type-I LBO crystal, pulse energy of 0.66 mJ is generated at 375 nm and with UV tuning range from 361 to 391 nm. To our knowledge, this is the first demonstration of AO Q-switched alexandrite laser with broad wavelength tuning in the near-IR and UV wavelength ranges and shows its excellent potential as a pulsed source for future applications.

  • Journal article
    Ahmad H, Roslan NA, Zaini MKA, Samion MZ, Reduan SA, Wang Y, Wang S, Sahu JK, Yasin Met al., 2023,

    Generation of multiwavelength bismuth-doped fiber laser based on all-fiber Lyot filter

    , Optical Fiber Technology, Vol: 81, ISSN: 1068-5200

    A stable multiwavelength fiber laser was proposed and demonstrated using a bismuth-doped fiber together with an all-fiber Lyot filter. The proposed multiwavelength bismuth-doped fiber laser (BDFL) spectrum can generate up to 21 output channels between 1309.88 nm and 1313.69 nm by carefully adjusting two polarization controllers (PCs). The multiwavelength BDFL shows good stability over time with a signal-to-noise ratio (SNR) of 48.69 dB, contributing to the average power fluctuations of 0.6 dB and wavelength drift of less than 0.1 nm in the laser output. In addition, the multiwavelength BDFL exhibits a free spectral range (FSR) of about 0.192 nm and a frequency bandwidth of 33.45 GHz. The characteristics of the multiwavelength BDFL can be observed by varying the pump power of the pump source, lasing output at different lengths of polarization maintaining fiber (PMF), and the generation in multiwavelengths using additional single mode-fiber (SMF).

  • Journal article
    Zeng H, Xue W, Murray RT, Chen W, Pan Z, Wang L, Cui C, Loiko P, Mateos X, Griebner U, Petrov Vet al., 2023,

    Continuous-Wave and Mode-Locked Operation of an In-Band Pumped Tm,Ho,Lu:CaGdAlO<sub>4</sub> Laser

    , APPLIED SCIENCES-BASEL, Vol: 13
  • Journal article
    Koufidis SFR, Mccall MW, 2023,

    Wavelength-independent Bragg-like reflection in uniaxial bi-anisotropic media

    , JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, Vol: 40, Pages: 2829-2841, ISSN: 0740-3224
  • Journal article
    Hong W, Sparks H, Dunsby C, 2023,

    Alignment and characterisation of remote-refocusingsystems

    , Applied Optics, Vol: 62, Pages: 7431-7440, ISSN: 1559-128X

    The technique of remote refocusing is used in optical microscopy to provide rapid axial scanning without mechanically perturbing the sample and in techniques such as oblique plane microscopy that build on remote refocusing to image a tilted plane within the sample. The magnification between the pupils of the primary (O1) and secondary (O2) microscope objectives of the remote-refocusing system has been shown previously by Mohanan and Corbett [J. Microsc. 288, 95 (2022) [CrossRef] ] to be crucial in obtaining the broadest possible remote-refocusing range. In this work, we performed an initial alignment of a remote-refocusing system and then studied the effect of axial misalignments of O1 and O2, axial misalignment of the primary tube lens (TL1) relative to the secondary tube lens (TL2), lateral misalignments of TL2, and changes in the focal length of TL2. For each instance of the setup, we measured the mean point spread function FWHMxy of 100 nm fluorescent beads and the normalized bead integrated fluorescence signal, and we calculated the axial and lateral distortion of the system; all of these quantities were mapped over the remote-refocusing range and as a function of lateral image position. This allowed us to estimate the volume over which diffraction-limited performance is achieved and how this changes with the alignment of the system.

  • Journal article
    Lightley J, Kumar S, Lim MQ, Garcia E, Goerlitz F, Alexandrov Y, Parrado T, Hollick C, Steele E, Rossmann K, Graham J, Broichhagen J, Mcneish IA, Roufosse CA, Neil MAA, Dunsby C, French PMWet al., 2023,

    <i>openFrame</i>: A modular, sustainable, open microscopy platform with single-shot, dual-axis optical autofocus module providing high precision and long range of operation

    , JOURNAL OF MICROSCOPY, ISSN: 0022-2720
  • Journal article
    Koufidis SF, Koutserimpas TT, McCall MW, 2023,

    Temporal analog of Bragg gratings

    , OPTICS LETTERS, Vol: 48, Pages: 4500-4503, ISSN: 0146-9592
  • Journal article
    Tawy G, Davidson NP, Churchill G, Damzen MJ, Smith PGR, Gates JC, Gawith CBEet al., 2023,

    Temperature-tunable UV generation using an Alexandrite laser and PPLN waveguides

    , OPTICS EXPRESS, Vol: 31, Pages: 22757-22765, ISSN: 1094-4087
  • Journal article
    Taylor JR, 2023,

    Early optical soliton research at Imperial College London

    , OPTICS COMMUNICATIONS, Vol: 536, ISSN: 0030-4018
  • Journal article
    Codescu M-A, Kunze T, Weiß M, Brehm M, Kornilov O, Sebastiani D, Nibbering ETJet al., 2023,

    Ultrafast Proton Transfer Pathways Mediated by Amphoteric Imidazole

    , The Journal of Physical Chemistry Letters, Vol: 14, Pages: 4775-4785, ISSN: 1948-7185
  • Journal article
    Smith M, Sparks H, Almagro J, Chaigne A, Behrens A, Dunsby C, Salbreux Get al., 2023,

    Active mesh and neural network pipeline for cell aggregate segmentation

    , Biophysical Journal, Vol: 122, Pages: 1586-1599, ISSN: 0006-3495

    Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology due to improvements in capacity and accuracy of microscopy techniques. Here, we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary gland organoids imaged over 24 h with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin that implements active mesh deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction.

  • Journal article
    Riemer K, Toulemonde M, Yan J, Lerendegui M, Stride E, Weinberg PD, Dunsby C, Tang M-Xet al., 2023,

    Fast and selective super-resolution ultrasound in vivo with acoustically activated nanodroplets

    , IEEE Transactions on Medical Imaging, Vol: 42, Pages: 1056-1067, ISSN: 0278-0062

    Perfusion by the microcirculation is key to the development, maintenance and pathology of tissue. Its measurement with high spatiotemporal resolution is consequently valuable but remains a challenge in deep tissue. Ultrasound Localization Microscopy (ULM) provides very high spatiotemporal resolution but the use of microbubbles requires low contrast agent concentrations, a long acquisition time, and gives little control over the spatial and temporal distribution of the microbubbles. The present study is the first to demonstrate Acoustic Wave Sparsely-Activated Localization Microscopy (AWSALM) and fast-AWSALM for in vivo super-resolution ultrasound imaging, offering contrast on demand and vascular selectivity. Three different formulations of acoustically activatable contrast agents were used. We demonstrate their use with ultrasound mechanical indices well within recommended safety limits to enable fast on-demand sparse activation and destruction at very high agent concentrations. We produce super-localization maps of the rabbit renal vasculature with acquisition times between 5.5 s and 0.25 s, and a 4-fold improvement in spatial resolution. We present the unique selectivity of AWSALM in visualizing specific vascular branches and downstream microvasculature, and we show super-localized kidney structures in systole (0.25 s) and diastole (0.25 s) with fast-AWSALM outdoing microbubble based ULM. In conclusion, we demonstrate the feasibility of fast and selective measurement of microvascular dynamics in vivo with subwavelength resolution using ultrasound and acoustically activatable nanodroplet contrast agents.

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