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.
Results
- Showing results for:
- Reset all filters
Search results
-
Journal articleZhu J, Rowland E, Harput S, et al., 2019,
3D super-resolution ultrasound imaging of rabbit lymph node vasculature in vivo using microbubbles
, Radiology, Vol: 291, Pages: 642-650, ISSN: 0033-8419Background: Variations in lymph node (LN) microcirculation can be indicative of metastasis. Identifying and quantifying metastatic LNs remains essential for prognosis and treatment planning but a reliable non-invasive imaging technique is lacking. 3D super-resolution (SR) ultrasound has shown potential to noninvasively visualize microvascular networks in vivo.Purpose: To study the feasibility of 3D SR ultrasound imaging of rabbit lymph node (LN) microvascular structure and blood flow using microbubbles.Materials and Methods: In vivo studies were carried out to image popliteal LNs of two healthy male New Zealand White rabbits aged 6-8 weeks. 3D high frame rate contrast enhanced ultrasound was achieved by mechanically scanning a linear imaging probe. Individual microbubbles were identified, localized, and tracked to form 3D SR images and super-resolved velocity maps. Acoustic sub-aperture processing (ASAP)was used to improve image contrast and generateenhanced power Doppler (PD) and color Doppler (CD) images. Vessel size and blood flow velocity distributions were evaluated and assessed by Student’s paired t-test. Results:SR images revealed micro-vessels in the rabbitLN, with branches clearly resolved when separated by 30 μm, which is less than half of the acoustic wavelength and not resolvable by power or color Doppler. The apparent size distribution of most vessels in the SR images was below 80 μm and agrees with micro-CT data whereas most of those detected by Doppler techniques were larger than 80 μm. The blood flow velocity distribution indicated that most of the blood flow in the rabbit popliteal LN was at velocities lower than 5mm/s. Conclusion: 3D super-resolution ultrasound imaging using microbubbles allows non-invasive and non-ionizing visualization and quantification of rabbit lymph node microvascular structures and blood flow dynamics with resolution below the wave diffraction limit.
-
Journal articleThipparapu NK, Wang Y, Wang S, et al., 2019,
Bi-doped fiber amplifiers and lasers [Invited]
, OPTICAL MATERIALS EXPRESS, Vol: 9, Pages: 2446-2465, ISSN: 2159-3930 -
Journal articleGuo W, Kumar S, Gorlitz F, et al., 2019,
Automated fluorescence lifetime imaging high content analysis of Förster resonance energy transfer between endogenously-labeled kinetochore proteins in live budding yeast cells
, Slas Technology, Vol: 24, Pages: 308-320, ISSN: 2472-6303We describe an open-source automated multiwell plate fluorescence lifetime imaging (FLIM) methodology to read out Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) labeling endogenous kinetochore proteins (KPs) in live budding yeast cells. The low copy number of many KPs and their small spatial extent present significant challenges for the quantification of donor fluorescence lifetime in the presence of significant cellular autofluorescence and photobleaching. Automated FLIM data acquisition was controlled by µManager and incorporated wide-field time-gated imaging with optical sectioning to reduce background fluorescence. For data analysis, we used custom MATLAB-based software tools to perform kinetochore foci segmentation and local cellular background subtraction and fitted the fluorescence lifetime data using the open-source FLIMfit software. We validated the methodology using endogenous KPs labeled with mTurquoise2 FP and/or yellow FP and measured the donor fluorescence lifetimes for foci comprising 32 kinetochores with KP copy numbers as low as ~2 per kinetochore under an average labeling efficiency of 50%. We observed changes of median donor lifetime ≥250 ps for KPs known to form dimers. Thus, this FLIM high-content analysis platform enables the screening of relatively low-copy-number endogenous protein–protein interactions at spatially confined macromolecular complexes.
-
Journal articleZhang G, Harput S, Hu H, et al., 2019,
Fast acoustic wave sparsely activated localization microscopy (fast-AWSALM): ultrasound super-resolution using plane-wave activation of nanodroplets
, IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, Vol: 66, Pages: 1039-1046, ISSN: 0885-3010Localization-based ultrasound super-resolution imaging using microbubble contrast agents and phase-change nano-droplets has been developed to visualize microvascular structures beyond the diffraction limit. However, the long data acquisition time makes the clinical translation more challenging. In this study, fast acoustic wave sparsely activated localization microscopy (fast-AWSALM) was developed to achieve super-resolved frames with sub-second temporal resolution, by using low-boiling-point octafluoropropane nanodroplets and high frame rate plane waves for activation, destruction, as well as imaging. Fast-AWSALM was demonstrated on an in vitro microvascular phantom to super-resolve structures that could not be resolved by conventional B-mode imaging. The effects of the temperature and mechanical index on fast-AWSALM was investigated. Experimental results show that sub-wavelength micro-structures as small as 190 lm were resolvable in 200 ms with plane-wave transmission at a center frequency of 3.5 MHz and a pulse repetition frequency of 5000 Hz. This is about a 3.5 fold reduction in point spread function full-width-half-maximum compared to that measured in conventional B-mode, and two orders of magnitude faster than the recently reported AWSALM under a non-flow/very slow flow situations and other localization based methods. Just as in AWSALM, fast-AWSALM does not require flow, as is required by current microbubble based ultrasound super resolution techniques. In conclusion, this study shows the promise of fast-AWSALM, a super-resolution ultrasound technique using nanodroplets, which can generate super-resolution images in milli-seconds and does not require flow.
-
Conference paperChandran AM, Runcorn TH, Murray RT, et al., 2019,
620 nm source by second harmonic generation of a phosphosilicate raman fiber amplifier
, Conference on Lasers and Electro-Optics (CLEO), Publisher: IEEE, ISSN: 2160-9020We demonstrate a nanosecond-pulsed 620 nm source through frequency doubling a 1240 nm phosphosilicate Raman fiber amplifier. The source emits up to 213 mW of average power, and is repetition rate and pulse duration tunable.
-
Journal articleQuicke P, Song C, McKimm EJ, et al., 2019,
Corrigendum: Single-neuron level one-photon voltage imaging with sparsely targeted genetically encoded voltage indicators
, Frontiers in Cellular Neuroscience, Vol: 13, ISSN: 1662-5102Voltage imaging of many neurons simultaneously at single-cell resolution is hampered bythe difficulty of detecting small voltage signals from overlapping neuronal processes inneural tissue. Recent advances in genetically encoded voltage indicator (GEVI) imaginghave shown single-cell resolution optical voltage recordings in intact tissue throughimaging naturally sparse cell classes, sparse viral expression, soma restricted expression,advanced optical systems, or a combination of these. Widespread sparse and strongtransgenic GEVI expression would enable straightforward optical access to a denselyoccurring cell type, such as cortical pyramidal cells. Here we demonstrate that a recentlydescribed sparse transgenic expression strategy can enable single-cell resolution voltageimaging of cortical pyramidal cells in intact brain tissue without restricting expression tothe soma. We also quantify the functional crosstalk in brain tissue and discuss optimalimaging rates to inform future GEVI experimental design.
-
Journal articleThipparapu NK, Wang Y, Umnikov AA, et al., 2019,
40 dB gain all fiber bismuth-doped amplifier operating in the O-band
, OPTICS LETTERS, Vol: 44, Pages: 2248-2251, ISSN: 0146-9592 -
Journal articleWu P-J, Masouleh MI, Paterson C, et al., 2019,
Detection of proteoglycan loss from articular cartilage using Brillouin microscopy, with applications to osteoarthritis
, Biomedical Optics Express, Vol: 10, Pages: 2457-2466, ISSN: 2156-7085The degeneration of articular cartilage (AC) occurs in osteoarthritis (OA), which is a leading cause of pain and disability in middle-aged and older people. The early disease-related changes in cartilage extra-cellular matrix (ECM) start with depletion of proteoglycan (PG), leading to an increase in tissue hydration and permeability. These early compositional changes are small (<10%) and hence difficult to register with conventional non-invasive imaging technologies (magnetic resonance and ultrasound imaging). Here we apply Brillouin microscopy for detecting changes in the mechanical properties and composition of porcine AC. OA-like degradation is mimicked by enzymatic tissue digestion, and we compare Brillouin microscopy measurements against histological staining of PG depletion over varying digestion times and enzyme concentrations. The non-destructive nature of Brillouin imaging technology opens new avenues for creating minimally invasive arthroscopic devices for OA diagnostics and therapeutic monitoring.
-
Conference paperChandran AM, Runcorn TH, Tmurray R, et al., 2019,
620nm Source by Second Harmonic Generation of a Phosphosilicate Raman Fiber Amplifier
We demonstrate a nanosecond-pulsed 620 nm source through frequency doubling a 1240 nm phosphosilicate Raman fiber amplifier. The source emits up to 213 mW of average power, and is repetition rate and pulse duration tunable.
-
Conference paperThipparapu NK, Wang Y, Umnikov AA, et 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.
-
Journal articleKerridge-Johns W, Geberbauer JWT, Damzen M, 2019,
Vortex laser by transforming Gaussian mode with an interferometric output coupler
, Optics Express, Vol: 27, Pages: 11642-11650, ISSN: 1094-4087Generation of vortex beams directly from the laser source can be limited in power and efficiency, or to specific pump sources and gain media. Here, we propose a new high power and high efficiency vortex laser methodology with interferometric mode transformation as output coupling, which uses high power handling and low loss optics that have wavelength versatility. Experimental demonstration is made in a diode-pumped Nd:YVO4 laser using an imbalanced Sagnac interferometer as output coupler producing high quality vortex output beams (M2 = 2.07) with fully selectable control of handedness whilst the intracavity mode is maintained as a fundamental Gaussian. Vortex output power >3W is produced with only small reduction in efficiency compared to the equivalent TEM00 laser. Continuous variation of vortex output coupling transmission and the quality of the vortex is investigated experimentally showing good agreement with theory. This work reveals a new approach to high power structured laser radiation direct from the source through interferometric spatial mode transformations.
-
Journal articleGratus J, Kinsler P, McCall M, 2019,
Evaporating black-holes, wormholes, and vacuum polarisation: must they always conserve charge?
, Foundations of Physics, Vol: 49, Pages: 330-350, ISSN: 0015-9018A careful examination of the fundamentals of electromagnetic theory showsthat due to the underlying mathematical assumptions required for Stokes’ Theorem,global charge conservation cannot be guaranteed in topologically non-trivial space-times. However, in order to break the charge conservation mechanism we must alsoallow the electromagnetic excitation fieldsD,Hto possess a gauge freedom, just asthe electromagnetic scalar and vector potentialsφandAdo. This has implicationsfor the treatment of electromagnetism in spacetimes where black holes both form andthen evaporate, as well as extending the possibilities for treating vacuum polarisation.Using this gauge freedom ofD,Hwe also propose an alternative to the acceptednotion that a charge passing through a wormhole necessarily leads to an additional(effective) charge on the wormhole’s mouth.
-
Journal articleGouveia RM, Lepert G, Gupta S, et al., 2019,
Assessment of corneal substrate biomechanics and its effect on epithelial stem cell maintenance and differentiation
, NATURE COMMUNICATIONS, Vol: 10, ISSN: 2041-1723- Author Web Link
- Cite
- Citations: 79
-
Journal articleBrown J, Christensen-Jeffries K, Harput S, et al., 2019,
Investigation of microbubble detection methods for super-resolution imaging of microvasculature
, IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, Vol: 66, Pages: 676-691, ISSN: 0885-3010Ultrasound super-resolution techniques use the response of microbubble contrast agents (MBs) to visualize the microvasculature. Techniques that localize isolated bubble signals first require detection algorithms to separate the MB and tissue responses. This work explores the three main MB detection techniques for super-resolution of microvasculature. Pulse inversion (PI), differential imaging (DI) and singular value decomposition (SVD) filtering were compared in terms of the localization accuracy, precision and contrast to tissue ratio (CTR). MB responses were simulated based on the properties of Sonovue™ and using the Marmottant model. Non-linear propagation through tissue was modelled using the k-Wave software package. For the parameters studied, the results show that PI is most appropriate for low frequency applications, but also most dependent on transducer bandwidth. SVD is preferable for high frequency acquisition where localization precision on the order of a few microns is possible. PI is largely independent of flow direction and speed compared to SVD and DI, so is appropriate for visualizing the slowest flows and tortuous vasculature. SVD is unsuitable for stationary MBs and can introduce a localization error on the order of hundreds of microns over the speed range 0- 2 mm/s and flow directions from lateral (parallel to probe) to axial (perpendicular to probe). DI is only suitable for flow rates > 0.5 mm/s or as flow becomes more axial. Overall, this study develops a MB and tissue non-linear simulation platform to improve understanding of how different MB detection techniques can impact the super-resolution process and explores some of the factors influencing the suitability of each.
-
Journal articleChen L, Li G, Tang L, et al., 2019,
Hyperspectral scanning laser optical tomography
, Journal of Biophotonics, Vol: 12, ISSN: 1864-063XIn order to study physical relationships within tissue volumes or even organism-level systems, the spatial distribution of multiple fluorescent markers needs to be resolved efficiently in three dimensions. Here, rather than acquiring discrete spectral images sequentially using multiple emission filters, a hyperspectral scanning laser optical tomography system is developed to obtain hyperspectral volumetric data sets with 2-nm spectral resolution of optically transparent mesoscopic (millimeter-centimeter) specimens. This is achieved by acquiring a series of point-scanning hyperspectral extended depth of field images at different angles and subsequently tomographically reconstructing the 3D intensity distribution for each wavelength. This technique is demonstrated to provide robust measurements via the comparison of spectral and intensity profiles of fluorescent bead phantoms. Due to its enhanced spectral resolving ability, this technique is also demonstrated to resolve largely overlapping fluorophores, as demonstrated by the 3D fluorescence hyperspectral reconstruction of a dual-labeled mouse thymus gland sample and the ability to distinguish tumorous and normal tissues of an unlabeled mouse intestine sample.
-
Journal articleSoor N, Quicke P, Howe C, et al., 2019,
All-optical crosstalk-free manipulation and readout of Chronos-expressing neurons
, Journal of Physics D: Applied Physics, Vol: 52, Pages: 1-10, ISSN: 0022-3727All optical neurophysiology allows manipulation and readout of neural network activity with single-cell spatial resolution and millisecond temporal resolution. Neurons can be made to express proteins that actuate transmembrane currents upon light absorption, enabling optical control of membrane potential and action potential signalling. In addition, neurons can be genetically or synthetically labelled with fluorescent reporters of changes in intracellular calcium concentration or membrane potential. Thus, to optically manipulate and readout neural activity in parallel, two spectra are involved: the action spectrum of the actuator, and the absorption spectrum of the fluorescent reporter. Due to overlap in these spectra, previous all-optical neurophysiology paradigms have been hindered by spurious activation of neuronal activity caused by the readout light. Here, we pair the blue-green absorbing optogenetic actuator, Chronos, with a deep red-emitting fluorescent calcium reporter CaSiR-1. We show that cultured Chinese hamster ovary cells transfected with Chronos do not exhibit transmembrane currents when illuminated with wavelengths and intensities suitable for exciting one-photon CaSiR-1 fluorescence. We then demonstrate crosstalk-free, high signal-to-noise ratio CaSiR-1 red fluorescence imaging at 100 frames s−1 of Chronos-mediated calcium transients evoked in neurons with blue light pulses at rates up to 20 Hz. These results indicate that the spectral separation between red light excited fluorophores, excited efficiently at or above 640 nm, with blue-green absorbing opsins such as Chronos, is sufficient to avoid spurious opsin actuation by the imaging wavelengths and therefore enable crosstalk-free all-optical neuronal manipulation and readout.
-
Conference paperMathur V, Mathur A, Kumar S, 2019,
A comparative study of soft computing paradigms for automatic humour detection in Tweets
, Pages: 975-979Humour has been an integral entity of human life with its lingual, social and psychological aspects. Due to its vast applications and increasing popularity on social media platforms, enabling computers to process humour has become very crucial. Therefore, we intent to aid task of computational analysis of humour by employing deep learning and machine learning techniques for humour detection. We use micro-blogging website twitter, being an abundant source of humorous content, as the focus of this study. We created a symmetrically distributed dataset containing 4000 funny and plain tweets and applied seven supervised classification algorithms to perform the task of detecting tweets, which contain humour. Accuracy, recall and precision have been used as the metrics of performance.
-
Journal articleGratus J, Kinsler P, McCall MW, 2019,
Maxwell's (D, H) excitation fields: lessons from permanent magnets
, EUROPEAN JOURNAL OF PHYSICS, Vol: 40, ISSN: 0143-0807 -
Journal articleBoriskina SV, Greanya V, Weir K, 2019,
Biomimetic photonics
, JOURNAL OF OPTICS, Vol: 21, ISSN: 2040-8978 -
Journal articleQuicke P, Song C, McKimm EJ, et al., 2019,
Single-neuron level one-photon voltage imaging with sparsely targeted genetically encoded voltage indicators
, Frontiers in Cellular Neuroscience, Vol: 13, ISSN: 1662-5102Voltage 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 paperHarput S, Christensen-Jeffries K, Ramalli A, et 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 articleMunro I, Garcia EAC, Yan M, et 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: 1365-2818Super‐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 paperWoodward RI, Kelleher EJR, Runcorn TH, et al., 2019,
Nanosecond to picosecond fiber bragg grating compression of giant-chirped pulses from an ultra-long mode-locked fiber laser
-
Conference paperRuncorn TH, Murray RT, Kelleher EJR, et al., 2019,
Watt-level, Duration-tunable Picosecond Source at 560 nm by Second-harmonic Generation of a Raman Fiber Laser
-
Conference paperThomas GM, Minassian A, Damzen MJ, 2019,
Directly diode-side-pumped alexandrite slab lasers in the bounce geometry and optical vortex generation
- Cite
- Citations: 1
-
Conference paperArbabzadah EA, Kerridge-Johns W, Thomas GM, et al., 2019,
High efficiency TEM <inf>00</inf> diode end-pumped Alexandrite laser
-
Conference paperTeppitaksak 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 paperThipparapu NK, Wang Y, Wang S, et 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 paperPetropoulos P, Hong Y, Bottrill K, et 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 paperThipparapu NK, Wang Y, Umnikov AA, et 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.
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.