298 results found
Calvarese M, Paie P, Candeo A, et al., 2022, Integrated optical device for Structured Illumination Microscopy, OPTICS EXPRESS, Vol: 30, Pages: 30246-30259, ISSN: 1094-4087
Lightley J, Kumar S, Garcia E, et al., 2022, Robust, single-shot, optical autofocus system utilizing cylindrical lenses to provide high precision and long range of operation
<jats:title>ABSTRACT</jats:title><jats:p>We present a robust, “real-time” optical autofocus system for microscopy that provides high accuracy (<230 nm) and long range (∼130 µm) with a 1.4 numerical aperture oil immersion objective lens. This autofocus can operate in a closed loop, single-shot functionality over a range of ±37.5 µm and can also operate as a 2-step process up to ±68 µm. A real-time autofocus capability is useful for experiments with long image data acquisition times, including single molecule localization microscopy, that may be impacted by defocusing resulting from drift of components, e.g., due to changes in temperature or mechanical drift. It is also vital for automated slide scanning or multiwell plate imaging where the sample may not be in the same horizontal plane for every field of view during the image data acquisition. To realise high precision and long range, we implement orthogonal optical readouts using cylindrical lenses. We demonstrate the performance of this new optical autofocus system with automated multiwell plate imaging and single molecule localisation microscopy and illustrate the benefit of using a superluminescent diode as the autofocus light source.</jats:p>
Garcia E, Lightley J, Kumar S, et 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
Lightley J, Gorlitz F, Kumar S, et al., 2021, Robust deep learning optical autofocus system applied to automated multiwell plate single molecule localization microscopy, JOURNAL OF MICROSCOPY, ISSN: 0022-2720
Qian K, Arichi T, Price A, et 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.
Boland MA, Cohen EAK, Flaxman SR, et 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.
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
Jones 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: 0022-3727
We 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.
Kalita R, Lightley J, Kumar S, et al., 2021, Single-shot quantitative phase contrast using polarisation-resolved differential phase microscopy, ISSN: 1605-7422
We 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.
Lightley J, Görlitz F, Kumar S, et al., 2021, ROBUST OPTICAL AUTOFOCUS SYSTEM UTILIZING NEURAL NETWORKS APPLIED TO AUTOMATED MULTIWELL PLATE STORM MICROSCOPY, ISSN: 1605-7422
We 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.
Kalita 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
Lightley 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
Gong 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.
Wysoczanski R, Baker JR, Fenwick P, et al., 2020, Analysis of defective phagocytosis in COPD using super-resolution microscopy and automated bacterial quantification, Publisher: EUROPEAN RESPIRATORY SOC JOURNALS LTD, ISSN: 0903-1936
Quicke P, Howe CL, Song P, et al., 2020, Subcellular resolution 3D light field imaging with genetically encoded voltage indicators, Neurophotonics, Vol: 7, ISSN: 2329-4248
Significance: Light-field microscopy (LFM) enables high signal-to-noise ratio (SNR) and light efficient volume imaging at fast frame rates. Voltage imaging with genetically encoded voltage indicators (GEVIs) stands to particularly benefit from LFM’s volumetric imaging capability due to high required sampling rates and limited probe brightness and functional sensitivity.Aim: We demonstrate subcellular resolution GEVI light-field imaging in acute mouse brain slices resolving dendritic voltage signals in three spatial dimensions.Approach: We imaged action potential-induced fluorescence transients in mouse brain slices sparsely expressing the GEVI VSFP-Butterfly 1.2 in wide-field microscopy (WFM) and LFM modes. We compared functional signal SNR and localization between different LFM reconstruction approaches and between LFM and WFM.Results: LFM enabled three-dimensional (3-D) localization of action potential-induced fluorescence transients in neuronal somata and dendrites. Nonregularized deconvolution decreased SNR with increased iteration number compared to synthetic refocusing but increased axial and lateral signal localization. SNR was unaffected for LFM compared to WFM.Conclusions: LFM enables 3-D localization of fluorescence transients, therefore eliminating the need for structures to lie in a single focal plane. These results demonstrate LFM’s potential for studying dendritic integration and action potential propagation in three spatial dimensions.
Quicke P, Howe CL, Song P, et al., 2020, Subcellular resolution three-dimensional light-field imaging with genetically encoded voltage indicators, Neurophotonics, Vol: 7, ISSN: 2329-4248
Significance: Light-field microscopy (LFM) enables high signal-to-noise ratio (SNR) and light efficient volume imaging at fast frame rates. Voltage imaging with genetically encoded voltage indicators (GEVIs) stands to particularly benefit from LFM's volumetric imaging capability due to high required sampling rates and limited probe brightness and functional sensitivity. Aim: We demonstrate subcellular resolution GEVI light-field imaging in acute mouse brain slices resolving dendritic voltage signals in three spatial dimensions. Approach: We imaged action potential-induced fluorescence transients in mouse brain slices sparsely expressing the GEVI VSFP-Butterfly 1.2 in wide-field microscopy (WFM) and LFM modes. We compared functional signal SNR and localization between different LFM reconstruction approaches and between LFM and WFM. Results: LFM enabled three-dimensional (3-D) localization of action potential-induced fluorescence transients in neuronal somata and dendrites. Nonregularized deconvolution decreased SNR with increased iteration number compared to synthetic refocusing but increased axial and lateral signal localization. SNR was unaffected for LFM compared to WFM. Conclusions: LFM enables 3-D localization of fluorescence transients, therefore eliminating the need for structures to lie in a single focal plane. These results demonstrate LFM's potential for studying dendritic integration and action potential propagation in three spatial dimensions.
Jones DC, Alexandrov Y, Curry N, et al., 2020, A multidimensional imaging and spectroscopic microscope
We present a multidimensional luminescence microscope for characterisation of emission from defects in diamond. We have applied the photoluminescence, hyperspectral and time-resolved luminescence imaging capabilities of this novel instrument to natural and synthetic diamonds.
Gorlitz F, Wysoczanski R, Kumar S, et al., 2020, Towards easier, faster super-resolved microscopy, Conference on Single Molecule Spectroscopy and Superresolution Imaging XIII, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
Jones DC, Kumar S, Lanigan PMP, et al., 2019, Multidimensional luminescence microscope for imaging defect colour centres in diamond, Methods and Applications in Fluorescence, Vol: 8, ISSN: 2050-6120
We report a multidimensional luminescence microscope providing hyperspectral imaging and time-resolved (luminescence lifetime) imaging for the study of luminescent diamond defects. The instrument includes crossed-polariser white light transmission microscopy to reveal any birefringence that would indicate strain in the diamond lattice. We demonstrate the application of this new instrument to defects in natural and synthetic diamonds including N3, nitrogen and silicon vacancies. Hyperspectral imaging provides contrast that is not apparent in conventional intensity images and the luminescence lifetime provides further contrast.
Quicke 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: 1662-5102
Voltage 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.
Soor 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: 0022-3727
All 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.
Quicke 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: 1662-5102
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.
Munro 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: 1365-2818
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.
Quicke P, Howe CL, Song P, et 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.
Soltan A, Maaskant P, Armstrong N, et al., 2019, Wearable Glasses for Retinal Pigmentiosa Based on Optogenetics, IEEE International Symposium on Circuits and Systems (IEEE ISCAS), Publisher: IEEE, ISSN: 0271-4302
Gorlitz F, Lightley J, Kumar S, et 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
Gorlitz F, Guldbrand S, Runcorn T, et al., 2018, easySLM-STED: stimulated emission depletion microscopy with aberration correction, extended field of view and multiple beam scanning, Journal of Biophotonics, Vol: 11, ISSN: 1864-063X
We demonstrate a simplified set‐up for STED microscopy with a straightforward alignment procedure that uses a single spatial light modulator (SLM) with collinear incident excitation and depletion beams to provide phase modulation of the beam profiles and correction of optical aberrations. We show that this approach can be used to extend the field of view for STED microscopy by correcting chromatic aberration that otherwise leads to walk‐off between the focused excitation and depletion beams. We further show how this arrangement can be adapted to increase the imaging speed through multibeam excitation and depletion. Fine adjustments to the alignment can be accomplished using the SLM only, conferring the potential for automation.
Soltan A, Barrett JM, Maaskant P, et al., 2018, A head mounted device stimulator for optogenetic retinal prosthesis, Journal of Neural Engineering, Vol: 15, ISSN: 1741-2552
Objective. Our main objective is to demonstrate that compact high radiance gallium nitride displays can be used with conventional virtual reality optics to stimulate an optogenetic retina. Hence, we aim to introduce a non-invasive approach to restore vision for people with conditions such as retinitis pigmentosa where there is a remaining viable communication link between the retina and the visual cortex. Approach. We design and implement the headset using a high-density µLED matrix, Raspberry Pi, microcontroller from NXP and virtual reality lens. Then, a test platform is developed to evaluate the performance of the headset and the optical system. Furthermore, image simplification algorithms are used to simplify the scene to be sent to the retina. Moreover, in vivo evaluation of the genetically modified retina response at different light intensity is discussed to prove the reliability of the proposed system. Main results. We demonstrate that in keeping with regulatory guidance, the headset displays need to limit their luminance to 90 kcd m−2. We demonstrate an optical system with 5.75% efficiency which allows for 0.16 mW mm−2 irradiance on the retina within the regulatory guidance, but which is capable of an average peak irradiance of 1.35 mW mm−2. As this is lower than the commonly accepted threshold for channelrhodopsin-2, we demonstrate efficacy through an optical model of an eye onto a biological retina. Significance. We demonstrate a fully functional 8100-pixel headset system including software/hardware which can operate on a standard consumer battery for periods exceeding a 24 h recharge cycle. The headset is capable of delivering enough light to stimulate the genetically modified retina cells and also keeping the amount of light below the regulation threshold for safety.
Quicke P, Reynolds S, Neil M, et al., 2018, High speed functional imaging with source localized multifocal two-photon microscopy, Biomedical Optics Express, Vol: 9, Pages: 3678-3693, ISSN: 2156-7085
Multifocal two-photon microscopy (MTPM) increases imaging speed over single-focus scanning by parallelizing fluorescence excitation. The imaged fluorescence’s susceptibility to crosstalk, however, severely degrades contrast in scattering tissue. Here we present a source-localized MTPM scheme optimized for high speed functional fluorescence imaging in scattering mammalian brain tissue. A rastered line array of beamlets excites fluorescence imaged with a complementary metal-oxide-semiconductor (CMOS) camera. We mitigate scattering-induced crosstalk by temporally oversampling the rastered image, generating grouped images with structured illumination, and applying Richardson-Lucy deconvolution to reassign scattered photons. Single images are then retrieved with a maximum intensity projection through the deconvolved image groups. This method increased image contrast at depths up to 112 μm in scattering brain tissue and reduced functional crosstalk between pixels during neuronal calcium imaging. Source-localization did not affect signal-to-noise ratio (SNR) in densely labeled tissue under our experimental conditions. SNR decreased at low frame rates in sparsely labeled tissue, with no effect at frame rates above 50 Hz. Our non-descanned source-localized MTPM system enables high SNR, 100 Hz capture of fluorescence transients in scattering brain, increasing the scope of MTPM to faster and smaller functional signals.
Kim Y, Warren S, Favero F, et al., 2018, Semi-random multicore fibre design for adaptive multiphoton endoscopy, Optics Express, Vol: 26, Pages: 3661-3673, ISSN: 1094-4087
This paper reports the development, modelling and application of a semi-random multicore fibre (MCF) design for adaptive multiphoton endoscopy. The MCF was constructed from 55 sub-units, each comprising 7 single mode cores, in a hexagonally close-packed lattice where each sub-unit had a random angular orientation. The resulting fibre had 385 single mode cores and was double-clad for proximal detection of multiphoton excited fluorescence. The random orientation of each sub-unit in the fibre reduces the symmetry of the positions of the cores in the MCF, reducing the intensity of higher diffracted orders away from the central focal spot formed at the distal tip of the fibre and increasing the maximum size of object that can be imaged. The performance of the MCF was demonstrated by imaging fluorescently labelled beads with both distal and proximal fluorescence detection and pollen grains with distal fluorescence detection. We estimate that the number of independent resolution elements in the final image – measured as the half-maximum area of the two-photon point spread function divided by the area imaged – to be ~3200.
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