Sophisticated Optical Systems Research Articles

Enhancing image resolution of confocal fluorescence microscopy with deep learning

Super-resolution optical imaging is crucial to the study of cellular processes. Current super-resolution fluorescence microscopy is restricted by the need of special fluorophores or sophisticated optical systems, or long acquisition and computational times. In this work, we present a deep-learning-based super-resolution technique of confocal microscopy. We devise a two-channel attention network (TCAN), which takes advantage of both spatial representations and frequency contents to learn a more precise mapping from low-resolution images to high-resolution ones. This scheme is robust against changes in the pixel size and the imaging setup, enabling the optimal model to generalize to different fluorescence microscopy modalities unseen in the training set. Our algorithm is validated on diverse biological structures and dual-color confocal images of actin-microtubules, improving the resolution from ~ 230 nm to ~ 110 nm. Last but not least, we demonstrate live-cell super-resolution imaging by revealing the detailed structures and dynamic instability of microtubules.

Dual‐Color Flexible Metasurfaces with Polarization‐Tunable Plasmons in Gold Nanorod Arrays

AbstractOptical metasurfaces have attracted growing attention in plasmonic structural color in recent years due to their supreme performance in display and imaging technologies. However, real‐life applications of optical metasurfaces so far are often hindered by their complex, expensive, and time‐consuming nanofabrication methods, as well as sophisticated optical measurement systems. Herein, a flexible metasurface filter, based on periodic gold nanorods, capable of changing the output color by simple rotation of a linear polarizer is proposed and demonstrated. This phenomenon is enabled by switching of resonance plasmons in the gold nanorods with the polarization of incident light. Subsequent rotation of the input polarizer leads to an output of two distinct colors and their combinations. Moreover, metasurfaces consisting of Au nanorods with different orientations are integrated into a single flexible substrate. Information can be therefore encoded into the orientations of Au nanorods and readily decoded with the color of the metasurface under polarized illumination of white light‐emitting diode without complex optical components.

Structured illumination microscopy using a photonic chip

Structured illumination microscopy (SIM) enables live cell, super-resolution imaging at high speeds. SIM uses sophisticated optical systems to generate pre-determined excitation light patterns, and reconstruction algorithms to enhance the resolution by up to a factor of two. The optical set-up of SIM relies on delicate free-space optics to generate the light patterns, and a high numerical aperture objective lens to project the pattern on the sample. These arrangements are prone to miss-alignment, often with high costs, and with the final resolution-enhancement being limited by the numerical aperture of the collection optics. Here, we present a photonic-chip based total internal reflection fluorescence (TIRF)-SIM that greatly reduces the complexity of the optical setup needed to acquire TIRF-SIM images. This is achieved by taking out the light delivery from the microscope and transferring it to a photonic-chip. The conventional glass slide is replaced by the planar photonic chip, that both holds and illuminates the specimen. The chip is used to create a standing wave interference pattern, which illuminates the sample via evanescent fields. The phase of the interference pattern is controlled by the use of thermo-optical modulation, leaving the footprint of the light illumination path for the SIM system to around 4 by 4 cm$^2$. Furthermore, we show that by the use of the photonic-chip technology, the resolution enhancement of SIM can be increased above that of the conventional approach. In addition, by the separation of excitation and collection light paths the technology opens the possibility to use low numerical objective lenses, without sacrificing on the SIM resolution. Chip-based SIM represents a simple, stable and affordable approach, which could enable widespread penetration of the technique and might also open avenues for high throughput optical super-resolution microscopy.

All-optical control of polarization splitting with a dielectric-clad azobenzene liquid crystal.

We report the design, fabrication, and characterization of an optically switchable polarizing beam splitter with a prism/azobenzene liquid crystal/prism hybrid structure. The beam splitter can operate in the polarization-splitting mode and the non-splitting mode. The switching between the modes is realized by the photoisomerization-induced phase transitions in the azobenzene liquid crystal, featuring all-optical control, bistability, and fast response. Such an active polarization-handling element is highly desirable as it not only simplifies and compacts sophisticated optical systems but also increases the degree of freedom in optical circuit design.

Effective method for fast and detailed analysis of holographic patterns over a large area.

An effective method is proposed that enables one to simultaneously analyze details of numerous holographic grating patterns over a large area. Unlike the conventional approaches relying on sophisticated lighting and optical systems and dark environment, only a flatbed scanner is needed. Thanks to the "rotate-scan" measurement strategy, details of the holographic grating patterns can be obtained, e.g., spatial distribution of the grating patterns, interval and orientation of the grating grooves within each grating pattern, and defects of the holographic patterns. The method has been verified by applications to two holographic papers of different grating intervals and orientations. The measured values agree well with those obtained with a light optical microscope (LOM). The proposed method is applicable to both transparent and reflective holographic materials of broad grating periodicity.

Characterization of optical systems for the ALPS II experiment.

ALPS II is a light shining through a wall style experiment that will use the principle of resonant enhancement to boost the conversion and reconversion probabilities of photons to relativistic WISPs. This will require the use of long baseline low-loss optical cavities. Very high power build up factors in the cavities must be achieved in order to reach the design sensitivity of ALPS II. This necessitates a number of different sophisticated optical and control systems to maintain the resonance and ensure maximal coupling between the laser and the cavity. In this paper we report on the results of the characterization of these optical systems with a 20 m cavity and discuss the results in the context of ALPS II.

Hydrogen sensing via anomalous optical absorption of palladium-based metamaterials

A palladium (Pd)-based optical metamaterial has been designed, fabricated and characterized for its application in hydrogen sensing. The metamaterial can replace Pd thin films in optical transmission schemes for sensing with performances far superior to those of conventional sensors. This artificial material consists of a palladium–alumina metamaterial fabricated using inexpensive and industrial-friendly bottom-up techniques. During the exposure to hydrogen, the system exhibits anomalous optical absorption when compared to the well-known response of Pd thin films, this phenomenon being the key factor for the sensor sensitivity. The exposure to hydrogen produces a large variation in the light transmission through the metamembrane (more than 30% with 4% in volume hydrogen–nitrogen gas mixture at room temperature and atmospheric pressure), thus avoiding the need for sophisticated optical detection systems. An optical homogenization model is proposed to explain the metamaterial response. These results contribute to the development of reliable and low-cost hydrogen sensors with potential applications in the hydrogen economy and industrial processes to name a few, and also open the door to optically study the hydrogen diffusion processes in Pd nanostructures.

Imaging mass spectrometry increased resolution using 2-mercaptobenzothiazole and 2,5-diaminonaphtalene matrices: application to lipid distribution in human colon.

Imaging mass spectrometry is becoming a reference technique in the field of lipidomics, due to its ability to map the distribution of hundreds of species in a single run, along a tissue section. The next frontier is now achieving increasing resolution powers to offer cellular (or even sub-cellular) resolution. Thus, the new spectrometers are equipped with sophisticated optical systems to decrease the laser spot to <30 μm. Here, we demonstrate that by using the correct matrix (i.e., a matrix that maximizes ion detection and forms small crystals) and a careful preparation, it is possible to achieve resolutions of ∼5-10 μm, even with spectrometers equipped with non-optimal optics, which produces laser spots of 50 μm or even larger. As a proof of concept, we present images of distributions of lipids, both in positive and negative ion mode, over human colon endoscopic sections, recorded using 2-mercaptobenzothiazole for positive ion mode and 2,5-diaminonaphtalene for negative ion mode and an LTQ-Orbitrap XL, equipped with a matrix-assisted laser desorption ionization (MALDI) source that produces astigmatic laser spots. Graphical Abstract Imaging mass spectrometry is becoming an invaluable technique to complement traditional histology, but still higher resolutions are required. Here we deal with such issue.

Evaluation of a portable markerless finger position capture device: accuracy of the Leap Motion controller in healthy adults

Although motion analysis is frequently employed in upper limb motor assessment (e.g. visually-guided reaching), they are resource-intensive and limited to laboratory settings. This study evaluated the reliability and accuracy of a new markerless motion capture device, the Leap Motion controller, to measure finger position. Testing conditions that influence reliability and agreement between the Leap and a research-grade motion capture system were examined. Nine healthy young adults pointed to 15 targets on a computer screen under two conditions: (1) touching the target (touch) and (2) 4 cm away from the target (no-touch). Leap data was compared to an Optotrak marker attached to the index finger. Across all trials, root mean square (RMS) error of the Leap system was 17.30 ± 9.56 mm (mean ± SD), sampled at 65.47 ± 21.53 Hz. The % viable trials and mean sampling rate were significantly lower in the touch condition (44% versus 64%, p < 0.001; 52.02 ± 2.93 versus 73.98 ± 4.48 Hz, p = 0.003). While linear correlations were high (horizontal: r2 = 0.995, vertical r2 = 0.945), the limits of agreement were large (horizontal: −22.02 to +26.80 mm, vertical: −29.41 to +30.14 mm). While not as precise as more sophisticated optical motion capture systems, the Leap Motion controller is sufficiently reliable for measuring motor performance in pointing tasks that do not require high positional accuracy (e.g. reaction time, Fitt’s, trails, bimanual coordination).

Introduction to the Series on Computational Approaches to Cardiac Arrhythmias

Of all the cardiac arrhythmias seen in clinical practice, atrial fibrillation (AF) and ventricular tachycardia/fibrillation (VT/VF) are among the leading causes of morbidity and mortality in the developed world. AF is the most common sustained arrhythmia and is associated with an increased risk of stroke, heart failure, dementia, and death.1–3 In developed nations overall prevalence of AF is 0.9% and the number of people affected is projected to more than double over the next 2 decades.3,4 VT/VF is the most important immediate cause of sudden cardiac death (SCD). Incidence of SCD is estimated to be 4 to 5 million cases per year worldwide.5,6 Thus arrhythmias and SCD are among the most significant manifestations of cardiovascular diseases worldwide, but their underlying mechanisms remain elusive. Arrhythmogenic substrates may be established by ischemia, infarction, heart failure and genetic mutations, all of which may cause inflammation, extracellular matrix remodeling, interstitial fibrosis, fatty infiltration, and changes in the 3-dimensional cellular architecture of the working myocardium.7,8 Over the last 17 years, the study of the molecular genetic basis of monogenic cardiac rhythm disorders, together with characterization of functional expression and biophysical properties of mutant channels from patients with inheritable ion channel diseases, has significantly advanced our understanding of the molecular basis of cardiac arrhythmias.9 Yet, this clearly has not been sufficient. Despite such advances, predictable prevention of AF or VF is currently not possible and the development of effective antiarrhythmic pharmacological agents has been extremely difficult. Not all questions related to arrhythmia mechanisms are directly answerable by reductionist experiments such as DNA sequencing or patch clamping. There is a hierarchy of questions whose levels are determined by the generality of the answers sought. Thus the question of what a mutation in an ion …

2-nm narrow band pass f ilter in standard conf iguration evaporate coating machine

High sophisticated optical monitoring systems like the OMS 5000 from Leyboldoptics are commonly used in vacuum coating system to improve the capabilities and reliability of production processes concerning optical performance and repeatability optics. This letter describes a method to perform high end optical filters with additional backside blocking over a wide spectral range. The direct monitoring with intermittent measurement on a large area rotating substrate holder is used to facilitate a narrow band pass filter of 2-nm half bandwidth at 532 nm and high transmittance together with a complex blocking filter to retard disturbing radiation from the ultraviolet (UV) range to the near infrared range. The machine is an ARES 1 350 coating system with basically standard conf iguration. 2013 Chinese Optics Letters.

Integrated precision evaluation method for three-dimensional optical measurement system

An integrated precision evaluation method (IPEM) for evaluating the capabilities of sophisticated optical measurement systems is proposed. The method, which has the advantages of the VDI/VDE2634 guidelines and the Standardization Project for Optical Techniques of Strain measurement procedure, is developed on the basis of three-dimensional (3D) optical measurement technology and statistical principles. The application of the IPEM to a combination of an in-house developed 3D optical measurement system and an in-house developed photogrammetry measurement system is investigated for the case of measuring features on a large-scale waterwheel blade. It is shown that the proposed method is appropriate and feasible for application in manufacturing industries.

Colorimetric immunoassay chip based on gold nanoparticles and gold enhancement

A colorimetric immunoassay chip has been developed based on gold nanoparticles for indicating the antibody–antigen binding activity and gold enhancement for amplifying the specific binding signal. Our investigations showed that the results of immunoassay can be represented by the level of color intensity. They were easily observed by a regular camera or naked eye, which is not needed of sophisticated laboratory equipment. Optimization of experimental conditions was carried out and the colorimetric detection had been compared to the standard chemifluorescent detection. Under the optimized conditions, colorimetric immunoassay chip had been demonstrated to detect different amount of immobilized antigens, i.e., human IgG. The results, i.e., color intensity, were mapped to the concentration of immobilized antigens in a dynamic range of 1–5,000 ng/ml. The proposed detection method does not require any sophisticated optical systems; therefore, it is possible to be miniaturized and integrated into a microfluidic system for developing a portable immunoassay device.

Nano-biosilica from marine diatoms: A brand new material for photonic applications

Several biological organisms, from some sea shells to butterflies, exhibit sophisticated optical systems, which have been developed during the evolution of each species. The diatoms are microscopic algae enclosed between two valves of hydrated amorphous silica. These intricate structures, called frustules, show quite symmetric patterns of micrometric and nanometric pores. Their strong similarity with man-made objects suggests to exploit the optical properties of the frustules in light guiding and optical transducing. We have found very interesting results, both from the experimental and numerical points of view.

Inverse problems in sound radiation of complex structures from measurements in a large acoustic tank

The Laboratory for Structural Acoustics (LSA) at NRL consists of an indoor cylindrical tank (17 m dia. by 15 m deep) filled with ̃ 1 million gallons of deionized water. Key features include: 1) vibration isolation, 2) active temperature control, and 3) anechoic materials. This unique laboratory is instrumented with sophisticated mechanical, electronic and optical systems, that include large workspace in‐water robotic scanners to generate nearfield acoustical holography (NAH) databases. We discuss such a database consisting of the underwater near‐field pressure measured on a two‐dimensional surface conformal to an internally driven complex structure floating at the air‐water interface. Various inverse approaches are discussed to image the normal velocity and intensity of the structure at its interface to the fluid, as well as the total power radiated, revealing mechanisms of radiation related to the internal structure. These inverse approaches consist of the equivalent source method compared with the well established Fourier acoustics methods of NAH. This work was supported by the US Office of Naval Research.

A Challenge for High‐Performance Full‐Field Strain Measurement Systems

Abstract: The advent of digital imaging technology and huge increases in data‐processing power have led to enormous advances in optical techniques for evaluating strain fields. A standardised test material designed for evaluating the capabilities of the most sophisticated optical systems using these techniques is described. The standardised test material presents a significant challenge to optical techniques for full‐field strain evaluation by employing complicated and reproducible strain fields for which analytical solutions are available. The design philosophy and process employed in developing the standardised test material are described and sample results are presented. The relationship between a standardised test material and reference material for calibration is discussed.

Focus on software

Focus on software

Fibre-optical features of a glass sponge.

Some superior technological secrets have come to light from a deep-sea organism. Modern technology cannot yet compete with some of the sophisticated optical systems possessed by biological organisms1,2,3. Here we show that the spicules of the deep-sea 'glass' sponge Euplectella have remarkable fibre-optical properties, which are surprisingly similar to those of commercial telecommunication fibres — except that the spicules themselves are formed under normal ambient conditions and have some technological advantages over man-made versions.

Monte Carlo simulation of polarising cavities

High-reflectivity supermirrors allow for sophisticated neutron optical systems working with multiple reflections (for example polarising cavities and beam splitters). Polarising cavities are highly efficient broad-wavelength band-polariser systems. Beam-splitter polarising cavities, for example, yield a practically ideal separation into one spin “up” and one spin “down” neutron beam, which can supply two different instruments. This later principle was already implemented at BENSC. Monte Carlo simulations were recently done to optimise polarising cavity systems and to search for possible new applications at ESS. Wavelength-dependent polarisation intensities were computed with ESS moderators.

An evaluation of a novel plastic optical fibre sensor for axial strain and bendmeasurements

This paper reports the use of a low cost, intensity-based plastic optical fibresensor for curvature and strain measurements in samples subjected to flexural andtensile loading conditions respectively. This simple and robust sensor exhibits ahigh signal-to-noise ratio and excellent repeatability, rendering the system costeffective for operation in harsh environments. In addition, this inexpensive systemoffers a signal linearity and signal stability comparable to that of an in-fibre Bragggrating sensor and other more sophisticated optical fibre sensor systems. Testresults have shown that the sensor exhibits a highly linear response toaxial strains of up to 1.2% and bending strains up to 0.7% offering astrain resolution of up to 20 microstrain. Findings from a series of cyclictests have demonstrated that the sensor response is highly repeatable,exhibiting only a very small amount of hysteresis. The results also highlightthe possibility of using the sensor for monitoring strain on either thetensile or compressive side/region of a beam subjected to flexural loading.