Ab initio study of defect interactions between the negatively charged nitrogen vacancy centre and the carbon self-interstitial in diamond

Fabrication techniques for nitrogen-vacancy centres in diamond require the creation of Frenkel defects (vacancy-interstitial pairs) the components of which can interact with formed NV centres affecting their photophysical properties. Here we use Density Functional Theory simulations of inter-defect electronic and strain interactions to explore how the NV centre and carbon self-interstitial interact in different configurations. We find that hybridization occurs between the NV centre e-orbitals and the carbon self-interstitial when an interstitial is present on the vacancy side of the NV centre. We propose that this phenomenon may explain the fluorescence blinking of NV centres observed during annealing. This article is part of the Theo Murphy meeting issue 'Diamond for quantum applications'.

Universal adaptive optics for microscopy through embedded neural network control

The resolution and contrast of microscope imaging is often affected by aberrations introduced by imperfect optical systems and inhomogeneous refractive structures in specimens. Adaptive optics (AO) compensates these aberrations and restores diffraction limited performance. A wide range of AO solutions have been introduced, often tailored to a specific microscope type or application. Until now, a universal AO solution - one that can be readily transferred between microscope modalities - has not been deployed. We propose versatile and fast aberration correction using a physics-based machine learning assisted wavefront-sensorless AO control (MLAO) method. Unlike previous ML methods, we used a specially constructed neural network (NN) architecture, designed using physical understanding of the general microscope image formation, that was embedded in the control loop of different microscope systems. The approach means that not only is the resulting NN orders of magnitude simpler than previous NN methods, but the concept is translatable across microscope modalities. We demonstrated the method on a two-photon, a three-photon and a widefield three-dimensional (3D) structured illumination microscope. Results showed that the method outperformed commonly-used modal-based sensorless AO methods. We also showed that our ML-based method was robust in a range of challenging imaging conditions, such as 3D sample structures, specimen motion, low signal to noise ratio and activity-induced fluorescence fluctuations. Moreover, as the bespoke architecture encapsulated physical understanding of the imaging process, the internal NN configuration was no-longer a "black box", but provided physical insights on internal workings, which could influence future designs.

Zwitterion-doped liquid crystal speckle reducers for immersive displays and vectorial imaging

Lasers possess many attractive features (e.g., high brightness, narrow linewidth, well-defined polarization) that make them the ideal illumination source for many different scientific and technological endeavors relating to imaging and the display of high-resolution information. However, their high-level of coherence can result in the formation of noise, referred to as speckle, that can corrupt and degrade images. Here, we demonstrate a new electro-optic technology for combatting laser speckle using a chiral nematic liquid crystal (LC) dispersed with zwitterionic dopants. Results are presented that demonstrate when driven at the optimum electric field conditions, the speckle noise can be reduced by >90% resulting in speckle contrast (C) values of C = 0.07, which is approaching that required to be imperceptible to the human eye. This LC technology is then showcased in an array of different display and imaging applications, including a demonstration of speckle reduction in modern vectorial laser-based imaging.

Laser-Written Tunable Liquid Crystal Aberration Correctors

In this Article, we present a series of novel laser-written liquid crystal (LC) devices for aberration control for applications in beam shaping or aberration correction through adaptive optics. Each transparent LC device can correct for a chosen aberration mode with continuous greyscale tuning up to a total magnitude of more than 2π radians phase difference peak to peak at a wavelength of λ = 660 nm. For the purpose of demonstration, we present five different devices for the correction of five independent Zernike polynomial modes (although the technique could readily be used to manufacture devices based on other modes). Each device is operated by a single electrode pair tuned between 0 and 10 V. These devices have potential as a low-cost alternative to spatial light modulators for applications where a low-order aberration correction is sufficient and transmissive geometries are required.

Deflectometry based calibration of a deformable mirror for aberration correction and remote focusing in microscopy

Adaptive optics (AO) techniques enhance the capability of optical microscopy through precise control of wavefront modulations to compensate phase aberrations and improves image quality. However, the aberration correction is often limited due to the lack of dynamic range in existing calibration methods, such as interferometry or Shack-Hartmann (SH) wavefront sensors. Here, we use deflectometry (DF) as a calibration method for a deformable mirror (DM) to extend the available range of aberration correction. We characterised the dynamic range and accuracy of the DF-based calibration of DMs depending on the spatial frequency of the test pattern used in DF. We also demonstrated the capability of large magnitude phase control for remote-focusing over a range larger than was possible with SH sensing.

Wavefront-sensorless adaptive optics with a laser-free spinning disk confocal microscope

Adaptive optics is being applied widely to a range of microscopies in order to improve imaging quality in the presence of specimen-induced aberrations. We present here the first implementation of wavefront-sensorless adaptive optics for a laser-free, aperture correlation, spinning disk microscope. This widefield method provides confocal-like optical sectioning through use of a patterned disk in the illumination and detection paths. Like other high-resolution microscopes, its operation is compromised by aberrations due to refractive index mismatch and variations within the specimen. Correction of such aberrations shows improved signal level, contrast and resolution.

On-chip beam rotators, adiabatic mode converters, and waveplates through low-loss waveguides with variable cross-sections

Photonics integrated circuitry would benefit considerably from the ability to arbitrarily control waveguide cross-sections with high precision and low loss, in order to provide more degrees of freedom in manipulating propagating light. Here, we report a new method for femtosecond laser writing of optical-fiber-compatible glass waveguides, namely spherical phase-induced multicore waveguide (SPIM-WG), which addresses this challenging task with three-dimensional on-chip light control. Fabricating in the heating regime with high scanning speed, precise deformation of cross-sections is still achievable along the waveguide, with shapes and sizes finely controllable of high resolution in both horizontal and vertical transversal directions. We observed that these waveguides have high refractive index contrast of 0.017, low propagation loss of 0.14 dB/cm, and very low coupling loss of 0.19 dB coupled from a single-mode fiber. SPIM-WG devices were easily fabricated that were able to perform on-chip beam rotation through varying angles, or manipulate the polarization state of propagating light for target wavelengths. We also demonstrated SPIM-WG mode converters that provide arbitrary adiabatic mode conversion with high efficiency between symmetric and asymmetric nonuniform modes; examples include circular, elliptical modes, and asymmetric modes from ppKTP (periodically poled potassium titanyl phosphate) waveguides which are generally applied in frequency conversion and quantum light sources. Created inside optical glass, these waveguides and devices have the capability to operate across ultra-broad bands from visible to infrared wavelengths. The compatibility with optical fiber also paves the way toward packaged photonic integrated circuitry, which usually needs input and output fiber connections.

Dynamic phase measurement of fast liquid crystal phase modulators

We present dynamic time-resolved measurements of a multi-pixel analog liquid crystal phase modulator driven at a 1 kHz frame rate. A heterodyne interferometer is used to interrogate two pixels independently and simultaneously, to deconvolve phase modulation with a wide bandwidth. The root mean squared optical phase error within a 30 Hz to 25 kHz bandwidth is <0.5° and the crosstalk rejection is 50 dB. Measurements are shown for a custom-built device with a flexoelectro-optic chiral nematic liquid crystal. However, the technique is applicable to many different types of optical phase modulators and spatial light modulators.

Single-mode sapphire fiber Bragg grating

Sapphire optical fiber has the ability to withstand ultrahigh temperatures and high radiation, but it is multimoded which prevents its use in many sensing applications. Problematically, Bragg gratings in such fiber exhibit multiple reflection peaks with a fluctuating power distribution. In this work, we write single-mode waveguides with Bragg gratings in sapphire using a novel multi-layer depressed cladding design in the 1550 nm telecommunications waveband. The Bragg gratings have a narrow bandwidth (<0.5 nm) and have survived annealing at 1000°C. The structures are inscribed with femtosecond laser direct writing, using adaptive beam shaping with a non-immersion objective. A single-mode sapphire fiber Bragg grating is created by writing a waveguide with a Bragg grating within a 425 µm diameter sapphire optical fiber, providing significant potential for accurate remote sensing in ultra-extreme environments.

Democratising “Microscopi”: a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork

Commercial fluorescence microscope stands and fully automated XYZt fluorescence imaging systems are generally beyond the limited budgets available for teaching and outreach. We have addressed this problem by developing “Microscopi”, an accessible, affordable, DIY automated imaging system that is built from 3D printed and commodity off-the-shelf hardware, including electro-mechanical, computer and optical components. Our design features automated sample navigation and image capture with a simple web-based graphical user interface, accessible with a tablet or other mobile device. The light path can easily be switched between different imaging modalities. The open source Python-based control software allows the hardware to be driven as an integrated imaging system. Furthermore, the microscope is fully customisable, which also enhances its value as a learning tool. Here, we describe the basic design and demonstrate imaging performance for a range of easily sourced specimens.

Generalised adaptive optics method for high-NA aberration-free refocusing in refractive-index-mismatched media

Phase aberrations are introduced when focusing by a high-numerical aperture (NA) objective lens into refractive-index-mismatched (RIM) media. The axial focus position in these media can be adjusted through either optical remote-focusing or mechanical stage translation. Despite the wide interest in remote-focusing, no generalised control algorithm using Zernike polynomials has been presented that performs independent remote-focusing and RIM correction in combination with mechanical stage translation. In this work, we thoroughly review derivations that model high-NA defocus and RIM aberration. We show through both numerical simulation and experimental results that optical remote-focusing using an adaptive device and mechanical stage translation are not optically equivalent processes, such that one cannot fully compensate for the other without additional aberration compensation. We further establish new orthogonal modes formulated using conventional Zernike modes and discuss its device programming to control high-NA remote-focusing and RIM correction as independent primary modes in combination with mechanical stage translation for aberration-free refocusing. Numerical simulations are performed, and control algorithms are validated experimentally by fabricating graphitic features in diamond using direct laser writing.

Repeated imaging through a multimode optical fiber using adaptive optics

Multimode optical fibers (MMF) have shown considerable potential for minimally invasive diffraction-limited fluorescence imaging of deep brain regions owing to their small size. They also look to be suitable for imaging across long time periods, with repeated measurements performed within the same brain region, which is useful to assess the role of synapses in normal brain function and neurological disease. However, the approach is not without challenge. Prior to imaging, light propagation through a MMF must be characterized in a calibration procedure. Manual repositioning, as required for repeated imaging, renders this calibration invalid. In this study, we provide a two-step solution to the problem consisting of (1) a custom headplate enabling precise reinsertion of the MMF implant achieving low-quality focusing and (2) sensorless adaptive optics to correct translational shifts in the MMF position enabling generation of high-quality imaging foci. We show that this approach achieves fluorescence imaging after repeated removal and reinsertion of a MMF.

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses “Python-Microscope” (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging.

Laser induced forward transfer isolating complex-shaped cell by beam shaping

Beam shaping techniques have been widely used in holographic optical tweezers to accurately manipulate tiny particles and hologram optimization algorithms have also been widely reported to improve the optical trapping performance. In this paper, we presented a beam shaping laser induced forward transfer (BS-LIFT) technique to isolate complex-shaped cells. To do this, we built up a BS-LIFT instrument which combined beam shaping methods and laser induced forward transfer using liquid-crystal-on-silicon spatial light modulator. The laser beam was modulated into multiple desired points at the focal plane employing the Gerchberg-Saxton (GS) algorithm. Feasibility was verified through transferring various samples. To our knowledge, this is the first demonstration of BS-LIFT applied to the transfer complex-shaped cells. We successfully transferred cells whose size ranged from 1 µm to 100 µm. Our design will provide a novel approach for the application of this beam shaping technique and the isolation of single cells with variable shapes.

Shrinking multiplexed orbital angular momentum to the nanoscale

Orbital angular momentum interactions at the nanoscale have remained elusive because the phase structure becomes unresolved. Now researchers have shown how to overcome this with tightly focused beams, demonstrating a record-high six-dimensional encoding in an ultra-dense nanoscale volume.

Extended range and aberration-free autofocusing via remote focusing and sequence-dependent learning

Rapid autofocusing over long distances is critical for tracking 3D topological variations and sample motion in real time. Taking advantage of a deformable mirror and Shack-Hartmann wavefront sensor, remote focusing can permit fast axial scanning with simultaneous correction of system-induced aberrations. Here, we report an autofocusing technique that combines remote focusing with sequence-dependent learning via a bidirectional long short term memory network. A 120 µm autofocusing range was achieved in a compact reflectance confocal microscope both in air and in refractive-index-mismatched media, with similar performance under arbitrary-thickness liquid layers up to 1 mm. The technique was validated on sample types not used for network training, as well as for tracking of continuous axial motion. These results demonstrate that the proposed technique is suitable for real-time aberration-free autofocusing over a large axial range, and provides unique advantages for biomedical, holographic and other related applications.

Python-Microscope - a new open-source Python library for the control of microscopes

Custom-built microscopes often require control of multiple hardware devices and precise hardware coordination. It is also desirable to have a solution that is scalable to complex systems and that is translatable between components from different manufacturers. Here we report Python-Microscope, a free and open-source Python library for high-performance control of arbitrarily complex and scalable custom microscope systems. Python-Microscope offers simple to use Python-based tools, abstracting differences between physical devices by providing a defined interface for different device types. Concrete implementations are provided for a range of specific hardware, and a framework exists for further expansion. Python-Microscope supports the distribution of devices over multiple computers while maintaining synchronisation via highly precise hardware triggers. We discuss the architectural features of Python-Microscope that overcome the performance problems often raised against Python and demonstrate the different use cases that drove its design: integration with user-facing projects, namely the Microscope-Cockpit project; control of complex microscopes at high speed while using the Python programming language; and use as a microscope simulation tool for software development.

Polarisation optics for biomedical and clinical applications: a review

Many polarisation techniques have been harnessed for decades in biological and clinical research, each based upon measurement of the vectorial properties of light or the vectorial transformations imposed on light by objects. Various advanced vector measurement/sensing techniques, physical interpretation methods, and approaches to analyse biomedically relevant information have been developed and harnessed. In this review, we focus mainly on summarising methodologies and applications related to tissue polarimetry, with an emphasis on the adoption of the Stokes-Mueller formalism. Several recent breakthroughs, development trends, and potential multimodal uses in conjunction with other techniques are also presented. The primary goal of the review is to give the reader a general overview in the use of vectorial information that can be obtained by polarisation optics for applications in biomedical and clinical research.

Three-dimensional adaptive optical nanoscopy for thick specimen imaging at sub-50-nm resolution

Understanding cellular organization demands the best possible spatial resolution in all three dimensions. In fluorescence microscopy, this is achieved by 4Pi nanoscopy methods that combine the concepts of using two opposing objectives for optimal diffraction-limited 3D resolution with switching fluorescent molecules between bright and dark states to break the diffraction limit. However, optical aberrations have limited these nanoscopes to thin samples and prevented their application in thick specimens. Here we have developed an improved iso-stimulated emission depletion nanoscope, which uses an advanced adaptive optics strategy to achieve sub-50-nm isotropic resolution of structures such as neuronal synapses and ring canals previously inaccessible in tissue. The adaptive optics scheme presented in this work is generally applicable to any microscope with a similar beam path geometry involving two opposing objectives to optimize resolution when imaging deep in aberrating specimens.

Democratising "Microscopi": a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork

Commercial fluorescence microscope stands and fully automated XYZt fluorescence imaging systems are generally beyond the limited budgets available for teaching and outreach. We have addressed this problem by developing "Microscopi", an accessible, affordable, DIY automated imaging system that is built from 3D printed and commodity off-the-shelf hardware, including electro-mechanical, computer and optical components. Our design features automated sample navigation and image capture with a simple web-based graphical user interface, accessible with a tablet or other mobile device. The light path can easily be switched between different imaging modalities. The open source Python-based control software allows the hardware to be driven as an integrated imaging system. Furthermore, the microscope is fully customisable, which also enhances its value as a learning tool. Here, we describe the basic design and demonstrate imaging performance for a range of easily sourced specimens.

3D super-resolution deep-tissue imaging in living mice

Stimulated emission depletion (STED) microscopy enables the three-dimensional (3D) visualization of dynamic nanoscale structures in living cells, offering unique insights into their organization. However, 3D-STED imaging deep inside biological tissue is obstructed by optical aberrations and light scattering. We present a STED system that overcomes these challenges. Through the combination of two-photon excitation, adaptive optics, red-emitting organic dyes, and a long-working-distance water-immersion objective lens, our system achieves aberration-corrected 3D super-resolution imaging, which we demonstrate 164 µm deep in fixed mouse brain tissue and 76 µm deep in the brain of a living mouse.

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses “Python-Microscope” (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging.

Volumetric two-photon fluorescence imaging of live neurons using a multimode optical fiber

Multimode optical fibers (MMFs), combined with wavefront control methods, have achieved minimally invasive in vivo imaging of neurons in deep-brain regions with diffraction-limited spatial resolution. Here, we report a method for volumetric two-photon fluorescence imaging with a MMF-based system requiring a single transmission matrix measurement. Central to this method is the use of a laser source able to generate both continuous wave light and femtosecond pulses. The chromatic dispersion of pulses generated an axially elongated excitation focus, which we used to demonstrate volumetric imaging of neurons and their dendrites in live rat brain slices through a 60 µm core MMF.

Practical sensorless aberration estimation for 3D microscopy with deep learning

Estimation of optical aberrations from volumetric intensity images is a key step in sensorless adaptive optics for 3D microscopy. Recent approaches based on deep learning promise accurate results at fast processing speeds. However, collecting ground truth microscopy data for training the network is typically very difficult or even impossible thereby limiting this approach in practice. Here, we demonstrate that neural networks trained only on simulated data yield accurate predictions for real experimental images. We validate our approach on simulated and experimental datasets acquired with two different microscopy modalities and also compare the results to non-learned methods. Additionally, we study the predictability of individual aberrations with respect to their data requirements and find that the symmetry of the wavefront plays a crucial role. Finally, we make our implementation freely available as open source software in Python.

Microscope-AOtools: a generalised adaptive optics implementation

Aberrations arising from sources such as sample heterogeneity and refractive index mismatches are constant problems in biological imaging. These aberrations reduce image quality and the achievable depth of imaging, particularly in super-resolution microscopy techniques. Adaptive optics (AO) technology has been proven to be effective in correcting for these aberrations, thereby improving the image quality. However, it has not been widely adopted by the biological imaging community due, in part, to difficulty in set-up and operation of AO. The methods for doing so are not novel or unknown, but new users often waste time and effort reimplementing existing methods for their specific set-ups, hardware, sample types, etc. Microscope-AOtools offers a robust, easy-to-use implementation of the essential methods for set-up and use of AO elements and techniques. These methods are constructed in a generalised manner that can utilise a range of adaptive optics elements, wavefront sensing techniques and sensorless AO correction methods. Furthermore, the methods are designed to be easily extensible as new techniques arise, leading to a streamlined pipeline for new AO technology and techniques to be adopted by the wider microscopy community.

Trimming laser-written waveguides through overwriting

Femtosecond laser direct writing is widely used to create waveguide circuits for optical processing in applications including communications, astrophotonics, simulation and quantum information processing. The properties of these waveguide circuits can be sensitive to the fabrication conditions, meaning that noticeable variability can be present in nominally identical manufactured components. One potential solution to this problem is the use of device trimming, whereby additional laser fabrication is applied to optimise the optical properties of a device based upon measurement feedback. We show how this approach can be used in the manufacture of directional couplers by overwriting the laser-written structure to alter the coupling ratios.

Photonic Topological Mode Bound to a Vortex

We report the observation of a mode associated with a topological defect in the bulk of a 2D photonic material by introducing a vortex distortion to a hexagonal lattice analogous to graphene. The observed modes lie midgap at zero energy and are closely related to Majorana bound states in superconducting vortices. This is the first experimental demonstration of the Jackiw-Rossi model [R. Jackiw and P. Rossi, Nucl. Phys. B190, 681 (1981)NUPBBO0550-321310.1016/0550-3213(81)90044-4].

Compact and contactless reflectance confocal microscope for neurosurgery

Visual guidance at the cellular level during neurosurgical procedures is essential for complete tumour resection. We present a compact reflectance confocal microscope with a 20 mm working distance that provided <1.2 µm spatial resolution over a 600 µm × 600 µm field of view in the near-infrared region. A physical footprint of 200 mm × 550 mm was achieved using only standard off-the-shelf components. Theoretical performance of the optical design was first evaluated via commercial Zemax software. Then three specimens from rodents: fixed brain, frozen calvaria and live hippocampal slices, were used to experimentally assess system capability and robustness. Results show great potential for the proposed system to be translated into use as a next generation label-free and contactless neurosurgical microscope.

Deconvolution for multimode fiber imaging: modeling of spatially variant PSF

Focusing light through a step-index multimode optical fiber (MMF) using wavefront control enables minimally-invasive endoscopy of biological tissue. The point spread function (PSF) of such an imaging system is spatially variant, and this variation limits compensation for blurring using most deconvolution algorithms as they require a uniform PSF. However, modeling the spatially variant PSF into a series of spatially invariant PSFs re-opens the possibility of deconvolution. To achieve this we developed svmPSF: an open-source Java-based framework compatible with ImageJ. The approach takes a series of point response measurements across the field-of-view (FOV) and applies principal component analysis to the measurements' co-variance matrix to generate a PSF model. By combining the svmPSF output with a modified Richardson-Lucy deconvolution algorithm, we were able to deblur and regularize fluorescence images of beads and live neurons acquired with a MMF, and thus effectively increasing the FOV.

CryoSIM: super-resolution 3D structured illumination cryogenic fluorescence microscopy for correlated ultrastructural imaging

Rapid cryopreservation of biological specimens is the gold standard for visualizing cellular structures in their true structural context. However, current commercial cryo-fluorescence microscopes are limited to low resolutions. To fill this gap, we have developed cryoSIM, a microscope for 3D super-resolution fluorescence cryo-imaging for correlation with cryo-electron microscopy or cryo-soft X-ray tomography. We provide the full instructions for replicating the instrument mostly from off-the-shelf components and accessible, user-friendly, open-source Python control software. Therefore, cryoSIM democratizes the ability to detect molecules using super-resolution fluorescence imaging of cryopreserved specimens for correlation with their cellular ultrastructure.

Multi-scale sensorless adaptive optics: application to stimulated emission depletion microscopy

Sensorless adaptive optics is commonly used to compensate specimen-induced aberrations in high-resolution fluorescence microscopy, but requires a bespoke approach to detect aberrations in different microscopy techniques, which hinders its widespread adoption. To overcome this limitation, we propose using wavelet analysis to quantify the loss of resolution due to the aberrations in microscope images. By examining the variations of the wavelet coefficients at different scales, we are able to establish a multi-valued image quality metric that can be successfully deployed in different microscopy techniques. To corroborate our arguments, we provide experimental verification of our method by performing aberration correction experiments in both confocal and STED microscopy using three different specimens.

Electrically-tunable positioning of topological defects in liquid crystals

Topological defects are a consequence of broken symmetry in ordered systems and are important for understanding a wide variety of phenomena in physics. In liquid crystals (LCs), defects exist as points of discontinuous order in the vector field that describes the average orientation of the molecules in space and are crucial for explaining the fundamental behaviour and properties of these mesophases. Recently, LC defects have also been explored from the perspective of technological applications including self-assembly of nanomaterials, optical-vortex generation and in tunable plasmonic metamaterials. Here, we demonstrate the fabrication and stabilisation of electrically-tunable defects in an LC device using two-photon polymerisation and explore the dynamic behaviour of defects when confined by polymer structures laser-written in topologically discontinuous states. We anticipate that our defect fabrication technique will enable the realisation of tunable, 3D, reconfigurable LC templates towards nanoparticle self-assembly, tunable metamaterials and next-generation spatial light modulators for light-shaping.

Defects in liquid crystals (LCs) find application in self-assembly of nanomaterials, optical-vortex generation and in tunable plasmonic metamaterials but methods for flexible and tailored fabrication of defects are scarce. Here, the authors demonstrate fabrication and stabilisation of electrically-tunable defects in an LC device using two-photon polymerisation, revealing interesting electro-optic behaviour.

Adaptive optics in laser processing

Adaptive optics are becoming a valuable tool for laser processing, providing enhanced functionality and flexibility for a range of systems. Using a single adaptive element, it is possible to correct for aberrations introduced when focusing inside the workpiece, tailor the focal intensity distribution for the particular fabrication task and/or provide parallelisation to reduce processing times. This is particularly promising for applications using ultrafast lasers for three-dimensional fabrication. We review recent developments in adaptive laser processing, including methods and applications, before discussing prospects for the future.

Active compensation of extrinsic polarization errors using adaptive optics

We present a scheme for active compensation of complex extrinsic polarization perturbations introduced into an optical system. Imaging polarimeter is used to measure the polarization state across a beam profile and a liquid crystal spatial light modulator controls the polarization of the input beam. A sequence of measurements permits determination of the birefringence properties of a perturbing specimen. The necessary correction is calculated and fed back to the polarization modulator to compensate for the polarization perturbation. The system capabilities are demonstrated on a range of birefringent specimens.

High precision automated alignment procedure for two-mirror telescopes

A significant challenge in the production of Earth observation satellites is the precise alignment of the telescope optical components. We have developed a strategy to perform automated alignment of two-mirror telescopes for use in a realistic factory-based setting. A Ritchey-Chrétien telescope was used as an example. The secondary mirror was mounted on a high precision hexapod and its misalignment inferred from the Zernike coefficients for tilt, defocus, and coma, as measured by a phase-shifting interferometer. The required corrections to the position of the secondary mirror were implemented using an integral controller and alignment was achieved within minutes, compared to within days when using a manual alignment process. The Zernike coefficient for each aberration was reduced to within one standard deviation of the fluctuations due to residual instability (48 nm).

Complex vectorial optics through gradient index lens cascades

Graded index (GRIN) lenses are commonly used for compact imaging systems. It is not widely appreciated that the ion-exchange process that creates the rotationally symmetric GRIN lens index profile also causes a symmetric birefringence variation. This property is usually considered a nuisance, such that manufacturing processes are optimized to keep it to a minimum. Here, rather than avoiding this birefringence, we understand and harness it by using GRIN lenses in cascade with other optical components to enable extra functionality in commonplace GRIN lens systems. We show how birefringence in the GRIN cascades can generate vector vortex beams and foci, and how it can be used advantageously to improve axial resolution. Through using the birefringence for analysis, we show that the GRIN cascades form the basis of a new single-shot Müller matrix polarimeter with potential for endoscopic label-free cancer diagnostics. The versatility of these cascades opens up new technological directions.

The manufacturing process for GRIN lenses causes a symmetric birefringence variation which is considered a deficiency. Here, the authors show how this birefringence can generate vector vortex beams and form the basis of a Müller matrix polarimeter with potential for endoscopic label-free cancer diagnostics.

Adaptive optics allows STED-FCS measurements in the cytoplasm of living cells

Fluorescence correlation spectroscopy in combination with super-resolution stimulated emission depletion microscopy (STED-FCS) is a powerful tool to investigate molecular diffusion with sub-diffraction resolution. It has been of particular use for investigations of two dimensional systems like cell membranes, but has so far seen very limited applications to studies of three-dimensional diffusion. One reason for this is the extreme sensitivity of the axial (z) STED depletion pattern to optical aberrations. We present here an adaptive optics-based correction method that compensates for these aberrations and allows STED-FCS measurements in the cytoplasm of living cells.

Calibration of a phase-only spatial light modulator for both phase and retardance modulation

Liquid crystal spatial light modulators (SLMs) are usually configured and calibrated for phase modulation. However, as they are variable retarders, they also have application as polarization modulators. We show that conventional phase-only calibrations are insufficient for this purpose, and a separate retardance calibration is needed. To overcome this shortcoming we report a simple Twyman-Green interferometer-based setup to realize SLM phase and retardance calibration. For phase calibration, we identify the non-linear, spatially variant response to the drive voltage of the SLM using fringe analysis and both horizontally and vertically polarized incident light. For retardance calibration, we use incident light polarized at 45° and assess the intensity variation. The methods presented are compatible with in situ calibration of SLMs.

Component-wise testing of laser-written integrated coupled-mode beam splitters

Photonic integrated circuits (PICs) are important enabling technologies for the developments of areas such as quantum information processing (QIP). Coupled-mode integrated beam splitters (IBS) are widely used in many PICs, so direct and accurate testing of individual IBSs inside a PIC is increasingly desirable, as the development of PICs for QIP is scaled up. Here we demonstrate a solution for component-wise testing of coupled-mode IBSs without limitations on component location and PIC architectures. The method is based on the imaging of an individual IBS with a custom-built multifunctional adaptive optical microscope, combined with the calculation of its beam-splitting ratio through numerical modelling.

Dynamic response of large tilt-angle flexoelectro-optic liquid crystal modulators

We present here the first time-resolved tilt-angle and retardance measurements for large-tilt (>45°) flexoelectro-optic liquid crystal modulators. These devices have potential for next generation fast switching (>1 kHz), 0-2π analog phase spatial light modulators (SLMs), with applications in optical beamsteering, microscopy and micromachining. The chiral nematic device used consisted of a mixture of CBC7CB and the chiral dopant R5011 in a nominally 5 µm-thick cell, aligned in the uniform lying helix mode. As the device is dynamically switched over angles of ± 54°, retardance changes of up to 0.17λ are observed. Furthermore, the time-resolved measurements reveal an asymmetry in the tilt in the optic-axis depending on the polarity of the applied electric field. The change in the optic-axis exhibits a pattern dependence, whereby it is determined by both the pulse history and the applied field. This pattern dependence results in tilt-angle errors of up to 8.8°, which could manifest as phase errors as large as 35.2° in potential SLMs. These time domain measurements may allow correction of these deterministic errors, to realize practical devices.

Focusing light in biological tissue through a multimode optical fiber: refractive index matching

Controlling light propagation through a step-index multimode optical fiber (MMF) has several important applications, including biological imaging. However, little consideration has been given to the coupling of fiber and tissue optics. In this Letter, we characterized the effects of tissue-induced light distortions, in particular those arising from a mismatch in the refractive index of the pre-imaging calibration and biological media. By performing the calibration in a medium matching the refractive index of the brain, optimal focusing ability was achieved, as well as a gain in focus uniformity within the field-of-view. These changes in illumination resulted in a 30% improvement in spatial resolution and intensity in fluorescence images of beads and live brain tissue. Beyond refractive index matching, our results demonstrate that sample-induced aberrations can severely deteriorate images from MMF-based systems.

Fast and low loss flexoelectro-optic liquid crystal phase modulator with a chiral nematic reflector

In this paper, we demonstrate a flexoelectro-optic liquid crystal phase-only device that uses a chiral nematic reflector to achieve full 2π phase modulation. This configuration is found to be very tolerant to imperfections in the chiral nematic reflector provided that the flexoelectro-optic LC layer fulfils the half-wave condition. Encouragingly, the modulation in the phase, which operates at kHz frame rates, is also accompanied by low amplitude modulation. The configuration demonstrated herein is particularly promising for the development of next-generation liquid crystal on silicon spatial light modulators.

Laser Writing of Scalable Single Color Centers in Silicon Carbide

Single photon emitters in silicon carbide (SiC) are attracting attention as quantum photonic systems ( Awschalom et al. Nat. Photonics 2018 , 12 , 516 - 527 ; Atatüre et al. Nat. Rev. Mater. 2018 , 3 , 38 - 51 ). However, to achieve scalable devices, it is essential to generate single photon emitters at desired locations on demand. Here we report the controlled creation of single silicon vacancy (V_Si) centers in 4H-SiC using laser writing without any postannealing process. Due to the aberration correction in the writing apparatus and the nonannealing process, we generate single V_Si centers with yields up to 30%, located within about 80 nm of the desired position in the transverse plane. We also investigated the photophysics of the laser writing V_Si centers and concluded that there are about 16 photons involved in the laser writing V_Si center process. Our results represent a powerful tool in the fabrication of single V_Si centers in SiC for quantum technologies and provide further insights into laser writing defects in dielectric materials.

IsoSense: frequency enhanced sensorless adaptive optics through structured illumination

We present IsoSense, a wavefront sensing method that mitigates sample dependency in image-based sensorless adaptive optics applications in microscopy. Our method employs structured illumination to create additional high spatial frequencies in the image through custom illumination patterns. This improves the reliability of image quality metric calculations and enables sensorless wavefront measurement even in samples with sparse spatial frequency content. We demonstrate the feasibility of IsoSense for aberration correction in a deformable-mirror-based structured illumination super-resolution fluorescence microscope.

Investigation of structural mechanisms of laser-written waveguide formation through third-harmonic microscopy

The mechanisms of laser-induced modification of transparent materials are complex combinations of different processes that depend on the material itself and a range of processing parameters. As such, the mechanisms are still subject to ongoing study. We use a custom-built adaptive third-harmonic generation (THG) microscope to study those mechanisms. New femtosecond-laser-written phenomena are revealed through this method of imaging. This Letter, together with previous reports by Miyamoto Opt. Express24, 25718 (2016)OPEXFF1094-408710.1364/OE.24.025718 and Fernandez J. Phys. D48, 155101 (2015)JPAPBE0022-372710.1088/0022-3727/48/15/155101 suggest that the distribution of the generated plasma during writing is responsible for the newly revealed phenomena.

Quasi-simultaneous multiplane calcium imaging of neuronal circuits

Two-photon excitation fluorescence microscopy is widely used to study the activity of neuronal circuits. However, the fast imaging is typically constrained to a single lateral plane for a standard microscope design. Given that cortical neuronal networks in a mouse brain are complex three-dimensional structures organised in six histologically defined layers which extend over many hundreds of micrometres, there is a strong demand for microscope systems that can record neuronal signalling in volumes. Henceforth, we developed a quasi-simultaneous multiplane imaging technique combining an acousto-optic deflector and static remote focusing to provide fast imaging of neurons from different axial positions inside the cortical layers without the need for mechanical disturbance of either the objective lens or the specimen. The hardware and the software are easily adaptable to existing two-photon microscopes. Here, we demonstrated that our imaging method can record, at high speed and high image contrast, the calcium dynamics of neurons in two different imaging planes separated axially with the in-focus and the refocused planes 120 µm and 250 µm below the brain surface respectively.

Femtosecond fiber Bragg grating fabrication with adaptive optics aberration compensation

We present fiber Bragg gratings (FBGs) fabricated using adaptive optics aberration compensation for the first time to the best of our knowledge. The FBGs are fabricated with a femtosecond laser by the point-by-point method using an air-based objective lens, removing the requirement for immersion oil or ferrules. We demonstrate a general phase correction strategy that can be used for accurate fabrication at any point in the fiber cross-section. We also demonstrate a beam-shaping approach that nullifies the aberration when focused inside a central fiber core. Both strategies give results which are in excellent agreement with coupled-mode theory. An extremely low wavelength polarization sensitivity of 4 pm is reported.

Ultrafast laser writing quill effect in low loss waveguide fabrication regime

The quill effect is a laser writing phenomenon in which different fabrication effects occur, depending upon the direction of laser translation. It has not yet, to our knowledge, been studied in the low-loss-waveguide (LLW) writing regime, probably due to its very weak visibility under conventional transmission microscope in that regime. In this report, with the help of adaptive third harmonic generation microscopy, we reveal the quill effect in the LLW writing regime and show its influences on the properties of laser-written photonic integrated components, in terms of polarization-related properties in fused silica and beam-splitting ratios of three-waveguide-coupler in borosilicate glass.