High-speed 1-frame/ms scanning confocal microscope with a microlens and Nipkow disks

Extremely high spatiotemporal resolution microscopy for live cell imaging by single photon counting, noise elimination, and a novel restoration algorithm based on probability calculation

Optical microscopy is essential for direct observation of dynamic phenomena in living cells. According to the classic optical theories, the images obtained through light microscopes are blurred for about half the wavelength of light, and therefore small structures below this "diffraction limit" were thought unresolvable by conventional optical microscopy. In reality, accurately obtained optical images contain complete information about the observed objects. Temporal resolution is also important for the observation of dynamic phenomena. A challenge exists here to overcome the trade-off between the time required for measurement and the accuracy of the measurement. The present paper describes a concrete methodology for reconstructing the structure of an observed object, based on the information contained in the image obtained by optical microscopy. It is realized by accurate single photon counting, complete noise elimination, and a novel restoration algorithm based on probability calculation. This method has been implemented in the Super-resolution Confocal Live Imaging Microscopy (SCLIM) we developed. The new system named SCLIM2M achieves unprecedented high spatiotemporal resolution. We have succeeded in capturing sub-diffraction-limit structures with millisecond-level dynamics of organelles and vesicles in living cells, which were never observed by conventional optical microscopy. Actual examples of the high-speed and high-resolution 4D observation of living cells are presented.

Micro-Scale Particle Tracking: From Conventional to Data-Driven Methods

Micro-scale positioning techniques have become essential in numerous engineering systems. In the field of fluid mechanics, particle tracking velocimetry (PTV) stands out as a key method for tracking individual particles and reconstructing flow fields. Here, we present an overview of the micro-scale particle tracking methodologies that are predominantly employed for particle detection and flow field reconstruction. It covers various methods, including conventional and data-driven techniques. The advanced techniques, which combine developments in microscopy, photography, image processing, computer vision, and artificial intelligence, are making significant strides and will greatly benefit a wide range of scientific and engineering fields.

Programmable high-speed confocal reflectance microscopy enabled by a digital micromirror device

The digital micromirror device (DMD) has been used to achieve parallel scanning in confocal microscopy significantly increasing acquisition speed. However, for confocal reflectance imaging, such an approach is limited to mostly surface imaging due to strong backreflections coming from the DMD that can dominate the signal recorded on a camera. Here, we report on an optical configuration that uses separate areas of DMD to generate multiple spots and pinholes and thereby prevents backreflections from the DMD from reaching the camera. We thus demonstrate confocal imaging of weakly reflecting objects, such as a pollen grain sample.

Polarized structured illumination microscopy using polarization gratings for optical sectioning

In this investigation, we describe polarized structured illumination microscopy based on polarization gratings to generate a stable polarized illumination pattern in an extensive area. The visibility of the illumination pattern is immediately calculated by using a polarizing pixelated camera, and the 3D surface profile of the specimen can be successfully reconstructed. Moreover, a polarization grating pair was used to reasonably eliminate the unexpected pattern caused by the polarization grating itself. To experimentally characterize the system performance, a step height standard specimen was measured. Moreover, the axial response for the visibility of the illumination pattern was discussed with the consideration of the spectral bandwidth of the source and the spatial coherence of incident light.

Direct Imaging of Local pH Reveals Bubble-Induced Mixing in a CO2 Electrolyzer

Electrochemical CO2 reduction poses a promising pathway to produce hydrocarbon chemicals and fuels without relying on fossil fuels. Gas diffusion electrodes allow high selectivity for desired carbon products at high current density by ensuring a sufficient CO2 mass transfer rate to the catalyst layer. In addition to CO2 mass transfer, the product selectivity also strongly depends on the local pH at the catalyst surface. In this work, we directly visualize for the first time the two-dimensional (2D) pH profile in the catholyte channel of a gas-fed CO2 electrolyzer equipped with a bipolar membrane. The pH profile is imaged with operando fluorescence lifetime imaging microscopy (FLIM) using a pH-sensitive quinolinium-based dye. We demonstrate that bubble-induced mixing plays an important role in the Faradaic efficiency. Our concentration measurements show that the pH at the catalyst remains lower at -100 mA cm-2 than at -10 mA cm-2, implying that bubble-induced advection outweighs the additional OH- flux at these current densities. We also prove that the pH buffering effect of CO2 from the gas feed and dissolved CO2 in the catholyte prevents the gas diffusion electrode from becoming strongly alkaline. Our findings suggest that gas-fed CO2 electrolyzers with a bipolar membrane and a flowing catholyte are promising designs for scale-up and high-current-density operation because they are able to avoid extreme pH values in the catalyst layer.

3D microscopy in industrial measurements

Quality control is essential to ensure the performance and yield of microdevices in industrial processing and manufacturing. In particular, 3D microscopy can be considered as a separate branch of microscopic instruments and plays a pivotal role in monitoring processing quality. For industrial measurements, 3D microscopy is mainly used for both the inspection of critical dimensions to ensure the design performance and detection of defects for improving the yield of microdevices. However, with the progress of advanced manufacturing technology and the increasing demand for high-performance microdevices, 3D microscopy has ushered in new challenges and development opportunities, such as breakthroughs in diffraction limit, 3D characterisation and calibrations of critical dimensions, high-precision detection and physical property determination of defects, and application of artificial intelligence. In this review, we provide a comprehensive survey about the state of the art and challenges in 3D microscopy for industrial measurements, and provide development ideas for future research. By describing techniques and methods with their advantages and limitations, we provide guidance to researchers and developers about the most suitable technique available for their intended industrial measurements.

Resolution and uniformity improvement of parallel confocal microscopy based on microlens arrays and a spatial light modulator

In traditional fluorescence microscopy, it is hard to achieve a large uniform imaging field with high resolution. In this manuscript, we developed a confocal fluorescence microscope combining the microlens array with spatial light modulator to address this issue. In our system, a multi-spot array generated by a spatial light modulator passes through the microlens array to form an optical probe array. Then multi-spot adaptive pixel-reassignment method for image scanning microscopy (MAPR-ISM) will be introduced in this parallelized imaging to improve spatial resolution. To generate a uniform image, we employ an optimized double weighted Gerchberg-Saxton algorithm (ODWGS) using signal feedback from the camera. We have built a prototype system with a FOV of 3.5 mm × 3.5 mm illuminated by 2500 confocal points. The system provides a lateral resolution of ∼0.82 µm with ∼1.6 times resolution enhancement after ISM processing. And the nonuniformity across the whole imaging field is 3%. Experimental results of fluorescent beads, mouse brain slices and melanoma slices are presented to validate the applicability and effectiveness of our system.

Three-dimensional wide-field fluorescence microscopy for transcranial mapping of cortical microcirculation

Wide-field fluorescence imaging is an indispensable tool for studying large-scale biodynamics. Limited space-bandwidth product and strong light diffusion make conventional implementations incapable of high-resolution mapping of fluorescence biodistribution in three dimensions. We introduce a volumetric wide-field fluorescence microscopy based on optical astigmatism combined with fluorescence source localization, covering 5.6×5.6×0.6 mm3 imaging volume. Two alternative configurations are proposed exploiting multifocal illumination or sparse localization of point emitters, which are herein seamlessly integrated in one system. We demonstrate real-time volumetric mapping of the murine cortical microcirculation at capillary resolution without employing cranial windows, thus simultaneously delivering quantitative perfusion information across both brain hemispheres. Morphological and functional changes of cerebral vascular networks are further investigated after an acute ischemic stroke, enabling cortex-wide observation of concurrent collateral recruitment events occurring on a sub-second scale. The reported technique thus offers a wealth of unmatched possibilities for non- or minimally invasive imaging of biodynamics across scales.

Multifocal confocal microscopy using a volume holographic lenslet array illuminator

Multifocal illumination can improve image acquisition time compared to single point scanning in confocal microscopy. However, due to an increase in the system complexity, obtaining uniform multifocal illumination throughout the field of view with conventional methods is challenging. Here, we propose a volume holographic lenslet array illuminator (VHLAI) for multifocal confocal microscopy. To obtain uniform array illumination, a super Gaussian (SG) beam has been incorporated through VHLAI with an efficiency of 43%, and implemented in a confocal microscope. The design method for a photo-polymer based volume holographic beam shaper is presented and its advantages are thoroughly addressed. The proposed system can significantly improve image acquisition time without sacrificing the quality of the image. The performance of the proposed multifocal confocal microscopy was compared with wide-field images and also evaluated by measuring optically sectioned microscopic images of fluorescence beads, florescence pollen grains, and biological samples. The proposed multifocal confocal system generates images faster without any changes in scanning devices. The present method may find important applications in high-speed multifocal microscopy platforms.

A Model of Discovery: The Role of Imaging Established and Emerging Non-mammalian Models in Neuroscience

Rodents have been the dominant animal models in neurobiology and neurological disease research over the past 60 years. The prevalent use of rats and mice in neuroscience research has been driven by several key attributes including their organ physiology being more similar to humans, the availability of a broad variety of behavioral tests and genetic tools, and widely accessible reagents. However, despite the many advances in understanding neurobiology that have been achieved using rodent models, there remain key limitations in the questions that can be addressed in these and other mammalian models. In particular, in vivo imaging in mammals at the cell-resolution level remains technically difficult and demands large investments in time and cost. The simpler nervous systems of many non-mammalian models allow for precise mapping of circuits and even the whole brain with impressive subcellular resolution. The types of non-mammalian neuroscience models available spans vertebrates and non-vertebrates, so that an appropriate model for most cell biological questions in neurodegenerative disease likely exists. A push to diversify the models used in neuroscience research could help address current gaps in knowledge, complement existing rodent-based bodies of work, and bring new insight into our understanding of human disease. Moreover, there are inherent aspects of many non-mammalian models such as lifespan and tissue transparency that can make them specifically advantageous for neuroscience studies. Crispr/Cas9 gene editing and decreased cost of genome sequencing combined with advances in optical microscopy enhances the utility of new animal models to address specific questions. This review seeks to synthesize current knowledge of established and emerging non-mammalian model organisms with advances in cellular-resolution in vivo imaging techniques to suggest new approaches to understand neurodegeneration and neurobiological processes. We will summarize current tools and in vivo imaging approaches at the single cell scale that could help lead to increased consideration of non-mammalian models in neuroscience research.

Versatile, do-it-yourself, low-cost spinning disk confocal microscope

Confocal microscopy is an invaluable tool for 3D imaging of biological specimens, however, accessibility is often limited to core facilities due to the high cost of the hardware. We describe an inexpensive do-it-yourself (DIY) spinning disk confocal microscope (SDCM) module based on a commercially fabricated chromium photomask that can be added on to a laser-illuminated epifluorescence microscope. The SDCM achieves strong performance across a wide wavelength range (∼400-800 nm) as demonstrated through a series of biological imaging applications that include conventional microscopy (immunofluorescence, small-molecule stains, and fluorescence in situ hybridization) and super-resolution microscopy (single-molecule localization microscopy and expansion microscopy). This low-cost and simple DIY SDCM is well-documented and should help increase accessibility to confocal microscopy for researchers.

Vision chromatic confocal sensor based on a geometrical phase lens

A vison chromatic confocal sensor used to monitor the location of a measured point is proposed and experimentally verified. To induce chromatic aberration of the sensor, a geometrical phase lens is adopted and is also used as a beam splitter. Near the geometrical phase lens, a focused beam is used for the chromatic confocal sensor, and a diverging beam is used for imaging of the specimen. In the experiment, the performance of the proposed system was verified with regard to distance sensing and the capability of monitoring the measured points. The measuring range was approximately 10 mm, and the repeatability was 0.4 µm when a geometrical phase lens with a 75 mm focal length was used.

Harnessing non-destructive 3D pathology

High-throughput methods for slide-free three-dimensional (3D) pathological analyses of whole biopsies and surgical specimens offer the promise of modernizing traditional histology workflows and delivering improvements in diagnostic performance. Advanced optical methods now enable the interrogation of orders of magnitude more tissue than previously possible, where volumetric imaging allows for enhanced quantitative analyses of cell distributions and tissue structures that are prognostic and predictive. Non-destructive imaging processes can simplify laboratory workflows, potentially reducing costs, and can ensure that samples are available for subsequent molecular assays. However, the large size of the feature-rich datasets that they generate poses challenges for data management and computer-aided analysis. In this Perspective, we provide an overview of the imaging technologies that enable 3D pathology, and the computational tools-machine learning, in particular-for image processing and interpretation. We also discuss the integration of various other diagnostic modalities with 3D pathology, along with the challenges and opportunities for clinical adoption and regulatory approval.

Full-field fluorescence lifetime dual-comb microscopy using spectral mapping and frequency multiplexing of dual-comb optical beats

Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool for quantitative fluorescence imaging because fluorescence lifetime is independent of concentration of fluorescent molecules or excitation/detection efficiency and is robust to photobleaching. However, since most FLIMs are based on point-to-point measurements, mechanical scanning of a focal spot is needed for forming an image, which hampers rapid imaging. Here, we demonstrate scan-less full-field FLIM based on a one-to-one correspondence between two-dimensional (2D) image pixels and frequency-multiplexed radio frequency (RF) signals. A vast number of dual-comb optical beats between dual optical frequency combs are effectively adopted for 2D spectral mapping and high-density frequency multiplexing in the RF region. Bimodal images of fluorescence amplitude and lifetime are obtained with high quantitativeness from amplitude and phase spectra of fluorescence RF comb modes without the need for mechanical scanning. The parallelized FLIM will be useful for rapid quantitative fluorescence imaging in life science.

Cortex-wide microcirculation mapping with ultrafast large-field multifocal illumination microscopy

The recently introduced large-field multifocal illumination (LMI) fluorescence microscopy technique opened new possibilities for transcranial observations of mouse brain dynamics with a unique combination of capillary level resolution and centimeter-scale field-of-view (FOV). Here we report on a new acceleration scheme for LMI based on raster scan of a lattice pattern combined with a parallel camera exposure scheme, which attains 200 Hz frame rate over 12 × 12 mm² FOV with 7.5 μm spatial resolution. We demonstrate real-time transcranial in vivo tracking of particles and imaging of microcirculation across the entire mouse cortex, thus corroborating the superb spatiotemporal resolution performance of LMI unattainable with other techniques. Potential applications include investigations into cerebrovascular function, cell tracking, as well as large-scale functional neuroimaging.

Homogeneous multifocal excitation for high-throughput super-resolution imaging

Super-resolution microscopies have become an established tool in biological research. However, imaging throughput remains a main bottleneck in acquiring large datasets required for quantitative biology. Here we describe multifocal flat illumination for field-independent imaging (mfFIFI). By integrating mfFIFI into an instant structured illumination microscope (iSIM), we extend the field of view (FOV) to >100 × 100 µm² while maintaining high-speed, multicolor, volumetric imaging at double the diffraction-limited resolution. We further extend the effective FOV by stitching adjacent images for fast live-cell super-resolution imaging of dozens of cells. Finally, we combine our flat-fielded iSIM with ultrastructure expansion microscopy to collect three-dimensional (3D) images of hundreds of centrioles in human cells, or thousands of purified Chlamydomonas reinhardtii centrioles, per hour at an effective resolution of ~35 nm. Classification and particle averaging of these large datasets enables 3D mapping of posttranslational modifications of centriolar microtubules, revealing differences in their coverage and positioning.

Optimizing the performance of multiline-scanning confocal microscopy

Line-scanning confocal microscopy provides high imaging speed and moderate optical sectioning strength, which makes it a useful tool for imaging various biospecimens ranging from living cells to fixed tissues. Conventional line-scanning systems have only used a single excitation line and slit, and thus have not fully exploited benefits of parallelization. Here we investigate the optical performance of multi-line scanning confocal microscopy (mLS) by employing a digital micro-mirror that provides programmable patterns of the illumination beam and the detection slit. Through experimental results and optical simulations, we assess the depth discrimination of mLS under different optical parameters and compare it with multi-point systems such as scanning disk confocal microscopy (SDCM). Under the same illumination duty cycle, we find that mLS has better optical sectioning than SDCM at a high degree of parallelization. The optimized mLS provides a low photobleaching rate and video-rate imaging while its optical sectioning is similar to single line-scanning confocal microscopy.

Fluorescence imaging with tailored light

Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from super-resolution imaging to long-term real-time observation of living organisms. In this review, we discuss current fluorescence imaging techniques in terms of the use of tailored or structured light for the sample illumination and fluorescence detection, providing a clear overview of their working principles and capabilities.

Multi-line fluorescence scanning microscope for multi-focal imaging with unlimited field of view

Confocal scanning microscopy is the de facto standard modality for fluorescence imaging. Point scanning, however, leads to a limited throughput and makes the technique unsuitable for fast multi-focal scanning over large areas. We propose an architecture for multi-focal fluorescence imaging that is scalable to large area imaging. The design is based on the concept of line scanning with continuous 'push broom' scanning. Instead of a line sensor, we use an area sensor that is tilted with respect to the optical axis to acquire image data from multiple depths inside the sample simultaneously. A multi-line illumination where the lines span a plane conjugate to the tilted sensor is created by means of a diffractive optics design, implemented on a spatial light modulator. In particular, we describe a design that uses higher order astigmatism to generate focal lines of substantially constant peak intensity along the lines. The proposed method is suitable for fast 3D image acquisition with unlimited field of view, it requires no moving components except for the sample scanning stage, and provides intrinsic alignment of the simultaneously scanned focal slices. As proof of concept, we have scanned 9 focal slices simultaneously over an area of 36 mm² at 0.29 µm pixel size in object space. The projected ultimate throughput that can be realized with the proposed architecture is in excess of 100 Mpixel/s.

Visible-wavelength two-photon excitation microscopy with multifocus scanning for volumetric live-cell imaging

Two-photon excitation microscopy is one of the key techniques used to observe three-dimensional (3-D) structures in biological samples. We utilized a visible-wavelength laser beam for two-photon excitation in a multifocus confocal scanning system to improve the spatial resolution and image contrast in 3-D live-cell imaging. Experimental and numerical analyses revealed that the axial resolution has improved for a wide range of pinhole sizes used for confocal detection. We observed the 3-D movements of the Golgi bodies in living HeLa cells with an imaging speed of 2 s per volume. We also confirmed that the time-lapse observation up to 8 min did not cause significant cell damage in two-photon excitation experiments using wavelengths in the visible light range. These results demonstrate that multifocus, two-photon excitation microscopy with the use of a visible wavelength can constitute a simple technique for 3-D visualization of living cells with high spatial resolution and image contrast.

Low-photobleaching line-scanning confocal microscopy using dual inclined beams

Confocal microscopy is an indispensable tool for biological imaging due to its high resolution and optical sectioning capability. However, its slow imaging speed and severe photobleaching have largely prevented further applications. Here, we present dual inclined beam line-scanning (LS) confocal microscopy. The reduced excitation intensity of our imaging method enabled a 2-fold longer observation time of fluorescence compared to traditional LS microscopy while maintaining a good sectioning capability and single-molecule sensitivity. We characterized the performance of our method and applied it to subcellular imaging and three-dimensional single-molecule RNA imaging in mammalian cells.

High-speed color three-dimensional measurement based on parallel confocal detection with a focus tunable lens

Reflectance confocal microscopy is a widely used optical imaging technique for non-destructive three-dimensional (3D) surface measurement. In confocal microscopy, a stack of two-dimensional (2D) images along the axial position is used for 3D reconstruction. This means the speed of 3D volumetric acquisition is limited by the beam scanning and the mechanical axial scanning. To achieve fast volumetric imaging, simultaneous multiple point scanning by parallelizing the beam instead of transverse point scanning can be considered, using a pinhole array. Previously, we developed a direct-view confocal microscope with a focus tunable lens (FTL) to produce a monochrome 3D surface profile of a sample without any mechanical scanning. Here, we report a high-speed color 3D measurement method based on parallel confocal detection. The proposed method produces a color 3D image of an object by acquiring 180 2D color images with an acquisition time of 1 second. We also visualized the color information of the object by overlaying the color obtained with a color area detector and a white LED illumination on top of the 3D surface profile. In addition, we designed an improved optical system to reduce artifacts caused by internal reflections and developed a new algorithm for noise-resistant 3D measurements. The feasibility of the proposed non-contact high-speed color 3D measurement for use in industrial or biomedical fields was demonstrated by imaging the color 3D shapes of various specimens. We anticipate that this technology can be utilized in various fields, where rapid 3D surface profiles with color information are required.

Full-field microsurface profilometry using image correlation without vertical scanning

A full-field microprofilometry involving innovative image correlation was developed for profile measurement without vertical scanning. High-speed optical inspection has become critical for confirming precise dimensions in semiconductor fabrication such as microbumping in 3D stacked ICs and precision manufacturing. A digital micromirror device (DMD) is designed to serve as a point-light-source array in a quasiconfocal optical configuration and perform lateral scanning to minimize signal crosstalk between neighboring testing points. More importantly, multiple diffractive images are detected and measured with a prebuilt depth-correlated database to extract the height information of a tested surface. A 100-nm repeatability can be realized in the absence of a detector pinhole and without vertical scanning, thus achieving high-speed submicrometer-scale surface profilometry.

High-speed polarized low coherence scanning interferometry based on spatial phase shifting

In this investigation, we describe polarized low coherence scanning interferometry (PLCSI) to enhance the measurement speed based on the spatial phase shifting technique by using a polarized CMOS camera. In every scanning step, the visibility of the correlogram can be directly extracted by spatial phase shifting. PLCSI does not need any scanning conditions such as a scanning step size smaller than that determined by the Nyquist sampling limit and equidistant scanning step, which restrict the measurement speed of the typical low coherence scanning interferometry (LCSI). The measurement data can also be significantly reduced due to the larger scanning step size. PLCSI can be comparable to confocal scanning microscopy in the view of monitoring visibilities. In the experiments, three types of specimens such as a plane mirror, a concave mirror, and a step height specimen were measured by PLCSI with various scanning step sizes, and it was confirmed that the surface profiles were successfully reconstructed. Moreover, the compensation technique of the surface profile, precisely determined by the phase information, was also discussed.

Speckle-structured illumination for 3D phase and fluorescence computational microscopy

High-content biological microscopy targets high-resolution imaging across large fields-of-view, often achieved by computational imaging approaches. Previously, we demonstrated 2D multimodal high-content microscopy via structured illumination microscopy (SIM) with resolution > 2 × the diffraction limit, using speckle illumination from Scotch tape. In this work, we extend the method to 3D by leveraging the fact that the speckle illumination is in fact a 3D structured pattern. We use both a coherent and an incoherent imaging model to develop algorithms for joint retrieval of the 3D super-resolved fluorescent and complex-field distributions of the sample. Our reconstructed images resolve features beyond the physical diffraction-limit set by the system's objective and demonstrate 3D multimodal imaging with ∼ 0.6 × 0.6 × 6   μ m3 resolution over a volume of ∼ 314 × 500 × 24   μ m3.

Modern Laser Scanning Confocal Microscopy

Since its commercialization in the late 1980's, confocal laser scanning microscopy (CLSM) has since become one of the most prevalent fluorescence microscopy techniques for three-dimensional structural studies of biological cells and tissues. The flexibility of the approach has enabled its application in a diverse array of studies, from the fast imaging of dynamic processes in living cells, to meticulous morphological analyses of tissues, and co-localization of protein expression patterns. In this chapter, we introduce the principles of confocal microscopy and discuss how the approach has become a mainstay in the biological sciences. We describe the components of a CLSM system and assess how modern implementations of the approach have further expanded the use of the technique. Finally, we briefly outline some practical considerations to take into account when acquiring data using a CLSM system. © 2018 by John Wiley & Sons, Inc.

Aberration correction considering curved sample surface shape for non-contact two-photon excitation microscopy with spatial light modulator

In this paper, excitation light wavefront modulation is performed considering the curved sample surface shape to demonstrate high-quality deep observation using two-photon excitation microscopy (TPM) with a dry objective lens. A large spherical aberration typically occurs when the refractive index (RI) interface between air and the sample is a plane perpendicular to the optical axis. Moreover, the curved sample surface shape and the RI mismatch cause various aberrations, including spherical ones. Consequently, the fluorescence intensity and resolution of the obtained image are degraded in the deep regions. To improve them, we designed a pre-distortion wavefront for correcting the aberration caused by the curved sample surface shape by using a novel, simple optical path length difference calculation method. The excitation light wavefront is modulated to the pre-distortion wavefront by a spatial light modulator incorporated in the TPM system before passing through the interface, where the RI mismatch occurs. Thus, the excitation light is condensed without aberrations. Blood vessels were thereby observed up to an optical depth of 2,000 μm in a cleared mouse brain by using a dry objective lens.

Spectrally encoded coherence tomography and reflectometry: Simultaneous en face and cross-sectional imaging at 2 gigapixels per second

Non-invasive biological imaging is crucial for understanding in vivo structure and function. Optical coherence tomography (OCT) and reflectance confocal microscopy are two of the most widely used optical modalities for exogenous contrast-free, high-resolution, three-dimensional imaging in non-fluorescent scattering tissues. However, sample motion remains a critical barrier to raster-scanned acquisition and reconstruction of wide-field anatomically accurate volumetric datasets. We introduce spectrally encoded coherence tomography and reflectometry (SECTR), a high-speed, multimodality system for simultaneous OCT and spectrally encoded reflectance (SER) imaging. SECTR utilizes a robust system design consisting of shared optical relays, scanning mirrors, swept laser and digitizer to achieve the fastest reported in vivo multimodal imaging rate of 2 gigapixels per second. Our optical design and acquisition scheme enable spatiotemporally co-registered acquisition of OCT cross-sections simultaneously with en face SER images for multivolumetric mosaicking. Complementary axial and lateral translation and rotation are extracted from OCT and SER data, respectively, for full volumetric estimation of sample motion with micron spatial and millisecond temporal resolution.

Virtual phase conjugation based optical tomography for single-shot three-dimensional imaging

We propose a virtual phase conjugation (VPC) based optical tomography (VPC-OT) for realizing single-shot optical tomographic imaging systems. Using a computer-based numerical beam propagation, the VPC combines pre-modulation and post-demodulation of the probe beam's wavefront, which provides an optical sectioning capability for resolving the depth coordinates. In VPC-OT, the physical optical microscope system and VPC are coupled using digital holography. Therefore, in contrast to conventional optical tomographic imaging (OTI) systems, this method does not require additional elements such as low-coherence light sources or confocal pinholes. It is challenging to obtain single-shot three-dimensional (3D) tomographic images using a conventional OTI system; however, this can be achieved using VPC-OT, which employs both digital holography and computer based numerical beam propagation. In addition, taking into account that VPC-OT is based on a complex amplitude detection using digital holography, this method allows us to simultaneously obtain quantitative phase contrast images. Using an objective lens with a numerical aperture (NA) of 0.8, we demonstrate a single-shot 3D imaging of frog blood cells with a depth resolution of 0.94 μm.

High-speed spinning disks on flexible threads

A common spinning toy, called “buzzer”, consists of a perforated disk and flexible threads. Despite of its simple construction, a buzzer can effectively transfer translational motions into high-speed rotations. In the present work, we find that the disk can be spun by hand at an extremely high rotational speed, e.g., 200,000 rpm, which is much faster than the previously reported speed of any manually operated device. We explore, both experimentally and theoretically, the detailed mechanics and potential applications of such a thread–disk system. The theoretical prediction, validated by experimental measurements, can help design and optimize the system for, e.g., easier operation and faster rotation. Furthermore, we investigate the synchronized motion of multiple disks spinning on a string. Distinctly different twist waves can be realized by the multi-disk system, which could be exploited in the control of mechanical waves. Finally, we develop two types of manually-powered electric generators based on the thread–disk system. The high-speed rotation of the rotors enables a pulsed high current, which holds great promise for potential applications in, for instance, generating electricity and harvesting energy from ocean waves and other rhythmic translational motions.

Quantitative Reflection Imaging for the Morphology and Dynamics of Live Aplysia californica Pedal Ganglion Neurons Cultured on Nanostructured Plasmonic Crystals

We describe a reflection imaging system that consists of a plasmonic crystal, a common laboratory microscope, and band-pass filters for use in the quantitative imaging and in situ monitoring of live cells and their substrate interactions. Surface plasmon resonance (SPR) provides a highly sensitive method to monitor changes in physicochemical properties occurring at metal-dielectric interfaces. Polyelectrolyte thin films deposited using the layer-by-layer (LBL) self-assembly method provide a reference system for calibrating the reflection contrast changes that occur when the polyelectrolyte film thickness changes and provide insight into the optical responses that originate from the multiple plasmonic features supported by this imaging system. Finite-difference time-domain (FDTD) simulations of the optical responses measured experimentally from the polyelectrolyte reference system are used to provide a calibration of the optical system for subsequent use in quantitative studies investigating live cell dynamics in cultures supported on a plasmonic crystal substrate. Live Aplysia californica pedal ganglion neurons cultured in artificial seawater were used as a model system through which to explore the utility of this plasmonic imaging technique. Here, the morphology of cellular peripheral structures ≲80 nm in thickness were quantitatively analyzed, and the dynamics of their trypsin-induced surface detachment were visualized. These results illustrate the capacities of this system for use in investigations of the dynamics of ultrathin cellular structures within complex bioanalytical environments.

Measurement of bacterial capture and phagosome maturation of Kupffer cells by intravital microscopy

It is central to the field of bacterial pathogenesis to define how bacteria are killed by phagocytic cells. During phagocytosis, the microbe is localized to the phagolysosome where crucial defense mechanisms such as acidification and production of reactive oxygen species (ROS) are initiated. This process has extensively been studied in vitro, however many resident tissue phagocytes will phenotypically change upon isolation from their natural environment. Therefore, interrogation of phagocytosis and phagosomal function of cells in the context of their natural tissue environment enhances our understanding of the biological process in vivo. This article outlines a real-time intravital microscopy protocol that utilizes fluorescent dyes to study the process of phagocytosis, which reveals acidification and oxidation of individual bacteria inside host cells of living animals. The novelty of this technique exists in use of bacteria that are covalently labelled with the fluorescent dyes Oxyburst and pHrodo, which respectively report on oxidation or acidification. Intravital microscopy is applied to visualize the uptake and subsequent oxidation or acidification of reporter bacteria in the organ of interest. Fluorescently labelled antibodies can be used to counter stain for host immune cells such as neutrophils and macrophages, along with reference stains to identify all bacteria. Although these assays were originally developed to assess the uptake and survival ofStaphylococcus aureusin liver resident macrophages (Kupffer cells), this protocol may be adapted to investigate any bacterium-host cell interaction.

The α-β circular scanning with large range and low noise

A circular-route scanning method called α-β circular scanning is proposed and realized using sinusoidal signals with a constant phase difference of π/2. Experiments show that the circular scanning range of α-β circular scanning is 57% greater than the rectangular scanning range of raster scanning within an effective optical field of view. Moreover, the scanning speed is improved by 7.8% over raster scanning because the whole sine signal is utilized in α-β circular scanning whereas the flyback area of the saw-tooth signal needs to be discarded in raster scanning. The maximum scanning acceleration decreases by a factor of 44, drastically decreasing the high noise, which should considerably elongate the lifetime of the galvanometers while inhibiting internal vibration. The proposed α-β circular scanning technique could be used in scanning imaging, optical tweezers and laser-beam fabrication.

Structured illumination microscopy with unknown patterns and a statistical prior

Structured illumination microscopy (SIM) improves resolution by down-modulating high-frequency information of an object to fit within the passband of the optical system. Generally, the reconstruction process requires prior knowledge of the illumination patterns, which implies a well-calibrated and aberration-free system. Here, we propose a new algorithmic self-calibration strategy for SIM that does not need to know the exact patterns a priori, but only their covariance. The algorithm, termed PE-SIMS, includes a pattern-estimation (PE) step requiring the uniformity of the sum of the illumination patterns and a SIM reconstruction procedure using a statistical prior (SIMS). Additionally, we perform a pixel reassignment process (SIMS-PR) to enhance the reconstruction quality. We achieve 2× better resolution than a conventional widefield microscope, while remaining insensitive to aberration-induced pattern distortion and robust against parameter tuning.

A virtually imaged defocused array (VIDA) for high-speed 3D microscopy

We report a method to capture a multifocus image stack based on recording multiple reflections generated by imaging through a custom etalon. The focus stack is collected in a single camera exposure and consequently the information needed for 3D reconstruction is recorded in the camera integration time, which is only 100 µs. We have used the VIDA microscope to temporally resolve the multi-lobed 3D morphology of neutrophil nuclei as they rotate and deform through a microfluidic constriction. In addition, we have constructed a 3D imaging flow cytometer and quantified the nuclear morphology of nearly a thousand white blood cells flowing at a velocity of 3 mm per second. The VIDA microscope is compact and simple to construct, intrinsically achromatic, and the field-of-view and stack number can be easily reconfigured without redesigning diffraction gratings and prisms.

Design methodology for a confocal imaging system using an objective microlens array with an increased working distance

In this study, a design methodology for a multi-optical probe confocal imaging system was developed. To develop an imaging system that has the required resolving power and imaging area, this study focused on a design methodology to create a scalable and easy-to-implement confocal imaging system. This system overcomes the limitations of the optical complexities of conventional multi-optical probe confocal imaging systems and the short working distance using a micro-objective lens module composed of two microlens arrays and a telecentric relay optical system. The micro-objective lens module was fabricated on a glass substrate using backside alignment photolithography and thermal reflow processes. To test the feasibility of the developed methodology, an optical system with a resolution of 1 μm/pixel using multi-optical probes with an array size of 10 × 10 was designed and constructed. The developed system provides a 1 mm × 1 mm field of view and a sample scanning range of 100 μm. The optical resolution was evaluated by conducting sample tests using a knife-edge detecting method. The measured lateral resolution of the system was 0.98 μm.

High-speed 3-D measurement with a large field of view based on direct-view confocal microscope with an electrically tunable lens

We propose a new structure of confocal imaging system based on a direct-view confocal microscope (DVCM) with an electrically tunable lens (ETL). Since it has no mechanical moving parts to scan both the lateral (x-y) and axial (z) directions, the DVCM with an ETL allows for high-speed 3-dimensional (3-D) imaging. Axial response and signal intensity of the DVCM were analyzed theoretically according to the pinhole characteristics. The system was designed to have an isotropic spatial resolution of 20 µm in both lateral and axial direction with a large field of view (FOV) of 10 × 10 mm. The FOV was maintained according to the various focal shifts as a result of an integrated design of an objective lens with the ETL. The developed system was calibrated to have linear focal shift over a range of 9 mm with an applied current to the ETL. The system performance of 3-D volume imaging was demonstrated using standard height specimens and a dental plaster.

Visualizing the Tumor Microenvironment of Liver Metastasis by Spinning Disk Confocal Microscopy

Intravital microscopy has evolved into an invaluable technique to study the complexity of tumors by visualizing individual cells in live organisms. Here, we describe a method for employing intravital spinning disk confocal microscopy to picture high-resolution tumor-stroma interactions in real time. We depict in detail the surgical procedures to image various tumor microenvironments and different cellular components in the liver.

Spirally-patterned pinhole arrays for long-term fluorescence cell imaging

Fluorescence cell imaging using a fluorescence microscope is an extensively used technique to examine the cell nucleus, internal structures, and other cellular molecules with fluorescence response time and intensity. However, it is difficult to perform high resolution cell imaging for a long period of time with this technique due to necrosis and apoptosis depending on the type and subcellular location of the damage caused by phototoxicity. A large number of studies have been performed to resolve this problem, but researchers have struggled to meet the challenge between cellular viability and image resolution. In this study, we employ a specially designed disc to reduce cell damage by controlling total fluorescence exposure time without deterioration of the image resolution. This approach has many advantages such as, the apparatus is simple, cost-effective, and easily integrated into the optical pathway through a conventional fluorescence microscope.

Single nucleotide polymorphism detection using gold nanoprobes and bio-microfluidic platform with embedded microlenses

The use of microfluidics platforms combined with the optimal optical properties of gold nanoparticles has found plenty of application in molecular biosensing. This paper describes a bio-microfluidic platform coupled to a non-cross-linking colorimetric gold nanoprobe assay to detect a single nucleotide polymorphism associated with increased risk of obesity fat-mass and obesity-associated (FTO) rs9939609 (Carlos et al., 2014). The system enabled significant discrimination between positive and negative assays using a target DNA concentration of 5 ng/µL below the limit of detection of the conventionally used microplate reader (i.e., 15 ng/µL) with 10 times lower solution volume (i.e., 3 µL). A set of optimization of our previously reported bio-microfluidic platform (Bernacka-Wojcik et al., 2013) resulted in a 160% improvement of colorimetric analysis results. Incorporation of planar microlenses increased 6 times signal-to-loss ratio reaching the output optical fiber improving by 34% the colorimetric analysis of gold nanoparticles, while the implementation of an optoelectronic acquisition system yielded increased accuracy and reduced noise. The microfluidic chip was also integrated with a miniature fiber spectrometer to analyze the assays' colorimetric changes and also the LEDs transmission spectra when illuminating through various solutions. Furthermore, by coupling an optical microscope to a digital camera with a long exposure time (30 s), we could visualise the different scatter intensities of gold nanoparticles within channels following salt addition. These intensities correlate well to the expected difference in aggregation between FTO positive (none to small aggregates) and negative samples (large aggregates).

Frequency- and spectrally-encoded confocal microscopy

We describe a three-dimensional microscopy technique based on spectral and frequency encoding. The method employs a wavelength-swept laser to illuminate a specimen with a spectrally-dispersed line focus that sweeps over the specimen in time. The spatial information along each spectral line is further mapped into different modulation frequencies. Spectrally-resolved detection and subsequent Fourier analysis of the back-scattered light from the specimen therefore enable high-speed, scanner-free imaging of the specimen with a single-element photodetector. High-contrast, three-dimensional imaging capability of this method is demonstrated by presenting images of various materials and biological specimens.

Spectrally encoded slit confocal microscopy using a wavelength-swept laser

We present an implementation of spectrally encoded slit confocal microscopy. The method employs a rapid wavelength-swept laser as the light source and illuminates a specimen with a line focus that scans through the specimen as the wavelength sweeps. The reflected light from the specimen is imaged with a stationary line scan camera, in which the finite pixel height serves as a slit aperture. This scanner-free operation enables a simple and cost-effective implementation in a small form factor, while allowing for the three-dimensional imaging of biological samples.

Live cell imaging of intracellular Salmonella enterica

During the intracellular phase of the pathogenic lifestyle, Salmonella enterica massively alters the endosomal system of its host cells. Two hallmarks are the remodeling of phagosomes into the Salmonella-containing vacuole (SCV) as a replicative niche, and the formation of tubular structures, such as Salmonella-induced filaments (SIFs). To study the dynamics and the fate of these Salmonella-specific compartments, live cell imaging (LCI) is a method of choice. In this chapter, we compare currently used microscopy techniques and focus on considerations and requirements specific for LCI. Detailed protocols for LCI of Salmonella infection with either confocal laser scanning microscopy (CLSM) or spinning disk confocal microscopy (SDCM) are provided.

Rapid microstructure characterization of polymer thin films with 2D-array multifocus Raman microspectroscopy

Multifocus Raman imaging is one of the fast-imaging alternatives to the conventional single point mapping technique.

Tracking protein dynamics with photoconvertible Dendra2 on spinning disk confocal systems

Understanding the dynamic properties of cellular proteins in live cells and in real time is essential to delineate their function. In this context, we introduce the Fluorescence Recovery After Photobleaching-Photoactivation unit (Andor) combined with the Nikon Eclipse Ti E Spinning Disk (Andor) confocal microscope as an advantageous and robust platform to exploit the properties of the Dendra2 photoconvertible fluorescent protein (Evrogen) and analyse protein subcellular trafficking in living cells. A major advantage of the spinning disk confocal is the rapid acquisition speed, enabling high temporal resolution of cellular processes. Furthermore, photoconversion and imaging are less invasive on the spinning disk confocal as the cell exposition to illumination power is reduced, thereby minimizing photobleaching and increasing cell viability. We have tested this commercially available platform using experimental settings adapted to track the migration of fast trafficking proteins such as UBC9, Fibrillarin and have successfully characterized their differential motion between subnuclear structures. We describe here step-by-step procedures, with emphasis on cellular imaging parameters, to successfully perform the dynamic imaging and photoconversion of Dendra2-fused proteins at high spatial and temporal resolutions necessary to characterize the trafficking pathways of proteins.

Non-contact high-frequency ultrasound microbeam stimulation for studying mechanotransduction in human umbilical vein endothelial cells

We describe how contactless high-frequency ultrasound microbeam stimulation (HFUMS) is capable of eliciting cytoplasmic calcium (Ca(2+)) elevation in human umbilical vein endothelial cells. The cellular mechanotransduction process, which includes cell sensing and adaptation to the mechanical micro-environment, has been studied extensively in recent years. A variety of tools for mechanical stimulation have been developed to produce cellular responses. We developed a novel tool, a highly focused ultrasound microbeam, for non-contact cell stimulation at a microscale. This tool, at 200 MHz, was applied to human umbilical vein endothelial cells to investigate its potential to elicit an elevation in cytoplasmic Ca(2+) levels. It was found that the response was dose dependent, and moreover, extracellular Ca(2+) and cytoplasmic Ca(2+) stores were involved in the Ca(2+) elevation. These results suggest that high-frequency ultrasound microbeam stimulation is potentially a novel non-contact tool for studying cellular mechanotransduction if the acoustic pressures at such high frequencies can be quantified.