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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Conference paperDvinskikh L, Harding S, Sparks H, et al., 2021,
High speed imaging of calcium dynamics in cardiomyocytes with a flexible light-sheet fluorescence microscope
, Biophotonics Congress 2021 -
Journal articleCollart C, Ciccarelli A, Ivanovitch K, et 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- Cite
- Citations: 4
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Journal articleCodescu M-A, Weiß M, Brehm M, et 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 -
Conference paperMurray RT, Chandran AM, Battle RA, et al., 2021,
Seeded optical parametric generation in CdSiP2 pumped by a nanosecond pulsed, MHz repetition rate Raman fiber amplifier at 1.24 µm
, Nonlinear Frequency Generation and Conversion: Materials and Devices XX, Publisher: SPIE, Pages: 1-10We report a CdSiP2 (CSP) based seeded optical parametric generator (OPG), emitting sub-nanosecond duration, 3 MHz repetition rate, wavelength tunable mid-infrared (MIR) light at 4.2-4.6 μm. We generate up to 0.25 W at 4.2 μm with a total pump conversion efficiency of 42%. The OPG is pumped by a 1.24 μm Raman fiber amplifier system. This is the first demonstration of pumping CSP with a Raman fiber source in this region, and we show that Raman fiber sources in the near-infrared (NIR) are ideal pump sources for non-critically phasematched (NCPM) CSP devices. Pumping CSP at 1.24 μm permits the use of NCPM whilst decreasing the negative effects of both two-photon absorption and linear absorption losses, when compared to conventional 1 μm pumping. This offers a potential advantage for MIR power scaling of CSP parametric devices due to a reduced thermal load in the crystal from residual pump absorption. The OPG is seeded with a continuous-wave fiber supercontinuum source emitting radiation in the 1.7 μm region, to lower the threshold pump intensity required for efficient conversion. NCPM and temperature tuning of the crystal allow for simple wavelength tuning of the idler radiation. We report on laser damage induced by elevated crystal temperatures, which we propose is linked to the decrease in CSP bandgap energy with increasing temperature.
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Journal articleKondo H, Ratcliffe CDH, Hooper S, et al., 2021,
Single-cell resolved imaging reveals intra-tumor heterogeneity in glycolysis, transitions between metabolic states, and their regulatory mechanisms
, CELL REPORTS, Vol: 34, ISSN: 2211-1247- Author Web Link
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- Citations: 54
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Journal articleJones DC, Alexandrov Y, Curry N, et al., 2021,
Multidimensional spectroscopy and imaging of defects in synthetic diamond: excitation-emission-lifetime luminescence measurements with multiexponential fitting and phasor analysis
, Journal of Physics D: Applied Physics, Vol: 54, Pages: 1-13, ISSN: 0022-3727We report the application of phasor analysis and nonlinear iterative fitting to complex spatial and spectroscopic luminescence decay data obtained from multidimensional microscopy of a CVD diamond grown on a HPHT substrate. This spectral and lifetime-resolved analysis enabled spatial mapping of variations in concentrations of nitrogen vacancy (NV) defects in both charge states and the quenching of NV− defects, as well as the identification of SiV− luminescence. These imaging and spectroscopic modalities may be important for reliable fabrication of quantum devices based on such defects in diamond, which will require well-defined and characterised quantum electronic properties.
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Conference paperDeepak MD, Karthik P, Kumar SS, et al., 2021,
Comparative Study of Feature Extraction Using Different Transform Techniques in Frequency Domain
, Pages: 2835-2846, ISSN: 1876-1100The compressed sensing is a mathematical approach of reconstructing a signal that is acquired from the dimensionally reduced data coefficients/less number of samples, i.e., less than the Niquist rate. The data coefficients are high-frequency components and low-frequency components. The high-frequency components are due to the rapid changes in the images (edges) and low-frequency correspond are due to slow varying information (continuous surface). The idea is to retain only low-frequency components, i.e., the significant components that constitute the compressed signal. This compressed signal is the sparse signal which is so helpful during medical scenario. During the Medical Resonance Imaging (MRI) scans, the patient undergoes many kinds difficulties like uncomfortness, patients are afraid of the scanning devices, he/she cannot be stable or changing his body positions slightly. Due to all these reasons, there can be a chance of acquiring only the less number of samples during the process of MRI scan. Even though the numbers of samples is less than the Nyquist rate, the reconstruction is possible by using the compressed sensing technique. The work has been carried out in the frequency domain to achieve the sparsity. The comparative study is done on percentage of different levels of sparsity of the signal. This can be verified by using peak signal-to-noise ratio (PSNR), root mean square error (RMSE), and structural similarity (SSIM) methods which are calculated between the reference image and the reconstructed image.
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Conference paperGratus J, Kinsler P, McCall MW, 2021,
D and H cannot exist: Axions, topology and global charge conservation
, Pages: 719-720The excitation fields D and H cannot be directly measured and have a gauge freedom. Admitting this freedom opens many possibilities, concerning the axionic response, which have direct application. We show a simple scenario which due to topological reasons is impossible using D and H. It can be used to model periodic lattices which have non zero total charge and show that an evaporated black hold can break charge conservation. We reflect on the nature of a homogeneous axionic response.
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Conference paperTawy G, Minassian A, Damzen MJ, 2021,
8.5W linear and 3.6W Ring TEM00 diode-pumped alexandrite lasers
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Conference paperGeberbauer JWT, Kerridge-Johns WR, Damzen MJ, 2021,
>30 W vortex laser using vortex output coupler
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Conference paperChandran AM, Battle RA, Murray RT, et al., 2021,
743 nm Source by SHG of a Cascaded Phosphosilicate Raman Fiber Amplifier
We demonstrate a nanosecond-pulsed 743 nm source by second harmonic generation of a cascaded phosphosilicate Raman fiber amplifier operating at 1485 nm. The source emits >1 W of 743 nm average power at a 5 MHz repetition rate.
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Conference paperKalita R, Lightley J, Kumar S, et al., 2021,
Single-shot quantitative phase contrast using polarisation-resolved differential phase microscopy
, ISSN: 1605-7422We present a robust, low-cost single-shot implementation of differential phase microscopy utilising a polarisation-sensitive camera to simultaneously acquire 4 images from which the phase gradients and quantitative phase image can be calculated.
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Conference paperLightley J, Görlitz F, Kumar S, et al., 2021,
ROBUST OPTICAL AUTOFOCUS SYSTEM UTILIZING NEURAL NETWORKS APPLIED TO AUTOMATED MULTIWELL PLATE STORM MICROSCOPY
, ISSN: 1605-7422We present a robust, low-cost neural network-based optical autofocus system that can operate over a range of ±100µm with submicron precision, enabling automated high-content super-resolved imaging with a 1.3 NA objective lens.
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Conference paperDarling C, Davis SPX, Kumar S, et al., 2021,
Single-Shot Volumetric Imaging Using Optical Projection Tomography
, ISSN: 1605-7422We present a single-shot volumetric imaging method, utilising optical projection tomography. We record projections simultaneously, implementing compressive sensing and machine learning to record up to 70 (camera limited) 1x1x1.9mm volumes/second.
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Journal articleKumar S, Bhuyan MK, Iwahori Y, 2021,
Multi-level uncorrelated discriminative shared Gaussian process for multi-view facial expression recognition
, Visual Computer, Vol: 37, Pages: 143-159, ISSN: 0178-2789In multi-view facial expression recognition, discriminative shared Gaussian process latent variable model (DS-GPLVM) gives better performance than that of linear and nonlinear multi-view learning-based methods. However, Laplacian-based prior used in DS-GPLVM only captures topological structure of data space without considering the inter-class separability of the data, and hence the obtained latent space is suboptimal. So, we propose a multi-level uncorrelated DS-GPLVM (ML-UDSGPLVM) model which searches a common uncorrelated discriminative latent space learned from multiple observable spaces. A novel prior is proposed, which not only depends on the topological structure of the intra-class data, but also on the local-between-class-scatter-matrix of the data onto the latent manifold. The proposed approach employs an hierarchical framework, in which, expressions are first divided into three sub-categories. Subsequently, each of the sub-categories are further classified to identify the constituent basic expressions. Experimental results show that the proposed method outperforms state-of-the-art methods in many instances.
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Conference paperSparks H, Almagro J, Behrens A, et al., 2021,
Dual-view oblique plane microscopy
Dual-view Oblique Plane Microscopy (dOPM) enables single-objective multi-view light-sheet fluorescence microscopy. This talk introduces the dOPM concept and demonstrates optical resolution performance with exemplar 3D datasets of fluorescence bead samples and fixed multicellular spheroids.
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Conference paperMurray RT, Chandran AM, Battle RA, et al., 2021,
CdSiP2 based mid-infrared optical parametric sources pumped with Raman fiber amplifiers
CdSiP<inf>2</inf> (CSP) is a nonlinear optical semiconductor which can phasematch pump wavelengths throughout the near-infrared (NIR) to generate mid-infrared (MIR) light through parametric three-wave mixing. In this work, we investigate the unique combination of NIR Raman fiber amplifiers around 1.24 µm and non-critical phasematching in CSP, to demonstrate tunable sources in the 4-5 µm MIR region.
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Journal articleHimabindu DD, Kumar SP, 2021,
A Survey on Computer Vision Architectures for Large Scale Image Classification using Deep Learning
, International Journal of Advanced Computer Science and Applications, Vol: 12, Pages: 105-120, ISSN: 2158-107XThe advancement in deep learning is increasing day-by-day from image classification to language understanding tasks. In particular, the convolution neural networks are revived and shown their performance in multiple fields such as natural language understanding, signal processing, and computer vision. The property of translational invariance for convolutions has made a huge advantage in the field of computer vision to extract feature invariances appropriately. When these convolutions trained using back-propagation tend to prove their results ability to outperform existing machine vision techniques by overcoming the various hand-engineered machine vision models. Hence, a clear understanding of current deep learning methods is crucial. These convolution neural networks have proven to show their performance by attaining state-of-the-art performance in computer vision over years when applied on humongous data. Hence in this survey, we detail a set of state-of-the-art models in image classification evolved from the birth of convolutions to present ongoing research. Each state-of-the-art model evolved in the successive year is illustrated with architecture schema, implementation details, parametric tuning and their performance. It is observed that the neural architecture construction i.e. a supervised approach for an image classification problem is evolved as data construction with cautious augmentations i.e., a self-supervised approach. A detailed evolution from neural architecture construction to augmentation construction is illustrated by provided appropriate suggestions to improve the performance. Additionally, the implementation details and the appropriate source for the execution and reproducibility of results are tabulated.
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Conference paperGeberbauer JWT, Kerridge-Johns WR, Damzen MJ, 2021,
>30 W vortex laser using vortex output coupler
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Conference paperTawy G, Minassian A, Damzen MJ, 2021,
8.5W linear and 3.6W Ring TEM<inf>00</inf> diode-pumped alexandrite lasers
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Conference paperBerk J, Paterson C, Foreman MR, 2021,
Tracking using surface plasmon leakage radiation speckle
An approach capable of label-free sensing and tracking of single nanoscale particles using interference between light scattered from the particle and a plasmon leakage radiation speckle field is introduced. Simulations show nanometre level tracking accuracy.
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Conference paperGeberbauer JWT, Kerridge-Johns WR, Damzen MJ, 2021,
>30 W Vortex Laser Using Vortex Output Coupler
, Conference on Lasers and Electro-Optics Europe / European Quantum Electronics Conference (CLEO/Europe-EQEC), Publisher: IEEE -
Journal articleJones B, McGlone ER, Fang Z, et al., 2021,
Genetic and biased agonist-mediated reductions in β-arrestin recruitment prolong cAMP signalling at glucagon family receptors
, Journal of Biological Chemistry, Vol: 296, Pages: 1-15, ISSN: 0021-9258Receptors for the peptide hormones glucagon-like peptide-1 (GLP-1R), glucose-dependent insulinotropic polypeptide (GIPR) and glucagon (GCGR) are important regulators of insulin secretion and energy metabolism. GLP-1R agonists have been successfully deployed for the treatment of type 2 diabetes, but it has been suggested that their efficacy is limited by target receptor desensitisation and downregulation due to recruitment of β-arrestins. Indeed, recently described GLP-1R agonists with reduced β-arrestin-2 recruitment have delivered promising results in preclinical and clinical studies. We therefore aimed to determine if the same phenomenon could apply to the closely related GIPR and GCGR. In HEK293 cells depleted of both β-arrestin isoforms the duration of G protein-dependent cAMP/PKA signalling was increased in response to the endogenous ligand for each receptor. Moreover, in wild-type cells, “biased” GLP-1, GCG and GIP analogues with selective reductions in β-arrestin-2 recruitment led to reduced receptor endocytosis and increased insulin secretion over a prolonged stimulation period, although the latter effect was only seen at high agonist concentrations. Biased GCG analogues increased the duration of cAMP signalling, but this did not lead to increased glucose output from hepatocytes. Our study provides a rationale for development of GLP-1R, GIPR and GCGR agonists with reduced β-arrestin recruitment, but further work is needed to maximally exploit this strategy for therapeutic purposes.
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Conference paperLightley J, Gorlitz F, Kumar S, et al., 2021,
ROBUST OPTICAL AUTOFOCUS SYSTEM UTILIZING NEURAL NETWORKS APPLIED TO AUTOMATED MULTIWELL PLATE STORM MICROSCOPY
, European Conferences on Biomedical Optics - Advances in Microscopic Imaging III, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X -
Conference paperDarling C, Davis SPX, Kumar S, et al., 2021,
Single-Shot Volumetric Imaging Using Optical Projection Tomography
, European Conferences on Biomedical Optics - Advances in Microscopic Imaging III, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X- Author Web Link
- Cite
- Citations: 1
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Conference paperKalita R, Lightley J, Kumar S, et al., 2021,
Single-shot quantitative phase contrast using polarisation-resolved differential phase microscopy
, European Conferences on Biomedical Optics - Advances in Microscopic Imaging III, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X -
Journal articleConey A, Damzen M, 2021,
High-energy diode-pumped alexandrite amplifier development with applications in satellite-based lidar
, Journal of the Optical Society of America B: Optical Physics, Vol: 38, Pages: 209-219, ISSN: 0740-3224Efficient, wavelength-tunable diode-pumped alexandrite laser systems offer the potential for a more versatile, satellite-based lidar source compared to fixed wavelength Nd:YAG systems and non-space compliant lamp-pumped alexandrite. In this paper, we develop a strategy to enable the high-energy operation required for atmospheric lidar based on an efficient diode-pumped Master-Oscillator Power-Amplifier (MOPA) system design. A novel multi-pass ‘diamond’ slab amplifier geometry is introduced alongside the experimental results of the world’s first diode-pumped alexandrite amplifier producing a gain of 2.13 in a demonstration system. A diode-pumped Q-switched alexandrite oscillator is presented with a record-highest pulse energy of 3.80 mJ. Detailed optimisation of a two-stage amplifier design is studied numerically and maximised with temperature, wavelength and pump pulse duration to produce 50 mJ pulse energy. This forms part of an optimised alexandrite MOPA design capable of high pulse energy, showing the future potential of diode pumped alexandrite for satellite-based atmospheric lidar.
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Conference paperTawy G, Minassian A, Damzen MJ, 2021,
8.5W Linear and 3.6W Ring TEM<sub>00</sub> Diode-Pumped Alexandrite Lasers
, Conference on Lasers and Electro-Optics Europe / European Quantum Electronics Conference (CLEO/Europe-EQEC), Publisher: IEEE -
SoftwareGong H, Wenjun G, Neil M, 2020,
HexSimProcessor
This repository is for the publication: "GPU-accelerated real-time reconstruction in Python of three-dimensional datasets from structured illumination microscopy with hexagonal patterns". It includes: raw data from experiments and simulations, the code for generating the simulated data, and the code for post-processing the raw data.
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Conference paperTewari S, Agrawal U, Verma S, et al., 2020,
Ensemble model for COVID-19 detection from chest X-ray scans using image segmentation, fuzzy color and stacking approaches
Coronavirus is a virus of RNA-type that can infect both humans and animal and causes a wide variety of respiratory infections. In humans, it also causes pneumonia. Since coronavirus has been declared a pandemic, Reverse Transcription Polymerase Chain Reaction (RT-PCR) has been the standard method for detection but is a time consuming operation and due to sudden surge in demand it has a high cost. In this study, coronavirus was detected from X-ray scans of chest using a deep learning model consisting of fuzzy image enhancement, offline data augmentation, image segmentation and classification through Convolutional Neural Network. For training and classification, an ensembeled model consisting of the features of VGG-16, ResNet-50 and MobileNetV2 was built and optimized with bayesian optimization. The proposed model achieved an overall accuracy of 96.34%. The precision, recall and F1-Score for COVID-19 class was 100%, 96% and 98% respectively.
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