Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope

Light sheet microscopy techniques, such as selective plane illumination microscopy (SPIM), are ideally suited for time-lapse imaging of developmental processes lasting several hours to a few days. The success of this promising technology has mainly been limited by the lack of suitable techniques for mounting fragile samples. Embedding zebrafish embryos in agarose, which is common in conventional confocal microscopy, has resulted in severe growth defects and unreliable results. In this study, we systematically quantified the viability and mobility of zebrafish embryos mounted under more suitable conditions. We found that tubes made of fluorinated ethylene propylene (FEP) filled with low concentrations of agarose or methylcellulose provided an optimal balance between sufficient confinement of the living embryo in a physiological environment over 3 days and optical clarity suitable for fluorescence imaging. We also compared the effect of different concentrations of Tricaine on the development of zebrafish and provide guidelines for its optimal use depending on the application. Our results will make light sheet microscopy techniques applicable to more fields of developmental biology, in particular the multiview long-term imaging of zebrafish embryos and other small organisms. Furthermore, the refinement of sample preparation for in toto and in vivo imaging will promote other emerging optical imaging techniques, such as optical projection tomography (OPT).     

Image analysis for understanding embryo development: a bridge from microscopy to biological insights

The digital reconstruction of the embryogenesis of model organisms from 3D+time data is revolutionizing practices in quantitative and integrative Developmental Biology. A manual and fully supervised image analysis of the massive complex data acquired with new microscopy technologies is no longer an option and automated image processing methods are required to fully exploit the potential of imaging data for biological insights. Current developments and challenges in biological image processing include algorithms for microscopy multiview fusion, cell nucleus tracking for quasi-perfect lineage reconstruction, segmentation, and validation methodologies for cell membrane shape identification, single cell gene expression quantification from in situ hybridization data, and multidimensional image registration algorithms for the construction of prototypic models. These tools will be essential to ultimately produce the multilevel in toto reconstruction that combines the cell lineage tree, cells, and tissues structural information and quantitative gene expression data in its spatio-temporal context throughout development.     

Digitizing life at the level of the cell: high-performance laser-scanning microscopy and image analysis for in toto imaging of development

The field of biological imaging is progressing at an amazing rate. Advances in both laser-scanning microscopy and green fluorescent protein (GFP) technology are combining to make possible imaging-based approaches for studying developmental mechanisms that were previously impossible. Modern confocal and multi-photon microscopes are pushing the envelope of speed, sensitivity, spectral resolution, and depth resolution to allow in vivo imaging of whole, live embryos at cellular resolution over extended periods of time. In toto imaging, in which nearly every cell in an embryo or tissue can be tracked through space and time during development, may become a standard technique for small transparent embryos such as zebrafish and early stage chick and mouse embryos. GFP and its spectral variants can be used to mark a wide range of in vivo biological information for in toto imaging including gene expression patterns, mutant phenotypes, and protein subcellular localization patterns. Combining in toto imaging and GFP transgenic approaches on a large scale may usher in an explosion of in vivo, developmental data as has happened in the past several years with genomic data. There are significant challenges that must be met to reach these goals. This paper will discuss the current state-of-the-art, the challenges, and the prospects of in toto imaging in the areas of imaging, image analysis, and informatics.     

Live-cell 3D super-resolution imaging in thick biological samples

We demonstrate three-dimensional (3D) super-resolution live-cell imaging through thick specimens (50-150 μm), by coupling far-field individual molecule localization with selective plane illumination microscopy (SPIM). The improved signal-to-noise ratio of selective plane illumination allows nanometric localization of single molecules in thick scattering specimens without activating or exciting molecules outside the focal plane. We report 3D super-resolution imaging of cellular spheroids.     

Light sheet microscopy for real-time developmental biology

Within only a few short years, light sheet microscopy has contributed substantially to the emerging field of real-time developmental biology. Low photo-toxicity and high-speed multiview acquisition have made selective plane illumination microscopy (SPIM) a popular choice for studies of organ morphogenesis and function in zebrafish, Drosophila, and other model organisms. A multitude of different light sheet microscopes have emerged for the noninvasive imaging of specimens ranging from single molecules to cells, tissues, and entire embryos. In particular, developmental biology can benefit from the ability to watch developmental events occur in real time in an entire embryo, thereby advancing our understanding on how cells form tissues and organs. However, it presents a new challenge to our existing data and image processing tools. This review gives an overview of where we stand as light sheet microscopy branches out, explores new areas, and becomes more specialized.     

Depth-resolved structural imaging by third-harmonic generation microscopy

Third harmonic generation microscopy is shown to be a robust method for obtaining structural information on a variety of biological specimens. Its nature allows depth-resolved imaging of inhomogeneities with virtually no background from surrounding homogeneous media. With an appropriate illumination geometry, third harmonic generation microscopy is shown to be particularly suitable for imaging of biogenic crystals, enabling extraction of the crystal orientation.     

3D-Printed Microwell Arrays for Ciona Microinjection and Timelapse Imaging

Ascidians such as Ciona are close chordate relatives of the vertebrates with small, simple embryonic body plans and small, simple genomes. The tractable size of the embryo offers considerable advantages for in toto imaging and quantitative analysis of morphogenesis. For functional studies, Ciona eggs are considerably more challenging to microinject than the much larger eggs of other model organisms such as zebrafish and Xenopus. One of the key difficulties is in restraining the eggs so that the microinjection needle can be easily introduced and withdrawn. Here we develop and test a device to cast wells in agarose that are each sized to hold a single egg. This injection mold is fabricated by micro-resolution stereolithography with a grid of egg-sized posts that cast corresponding wells in agarose. This 3D printing technology allows the rapid and inexpensive testing of iteratively refined prototypes. In addition to their utility in microinjection, these grids of embryo-sized wells are also valuable for timelapse imaging of multiple embryos.     

R2OBBIE-3D,a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture

While recent imaging techniques provide insights into biological processes from the molecular to the cellular scale, phenotypes at larger scales remain poorly amenable to quantitative analyses. For example, investigations of the biophysical mechanisms generating skin morphological complexity and diversity would greatly benefit from 3D geometry and colour-texture reconstructions. Here, we report on R²OBBIE-3D, an integrated system that combines a robotic arm, a high-resolution digital colour camera, an illumination basket of high-intensity light-emitting diodes and state-of-the-art 3D-reconstruction approaches. We demonstrate that R²OBBIE generates accurate 3D models of biological objects between 1 and 100 cm, makes multiview photometric stereo scanning possible in practical processing times, and enables the capture of colour-texture and geometric resolutions better than 15 μm without the use of magnifying lenses. R²OBBIE has the potential to greatly improve quantitative analyses of phenotypes in addition to providing multiple new applications in, e.g., biomedical science.     

Hybrid framework for feasible modeling of an edge illumination X-ray phase-contrast imaging system at a human scale

Here, we present a hybrid approach for simulating an edge illumination X-ray phase-contrast imaging (EIXPCi) set-up using graphics processor units (GPU) with a high degree of accuracy. In this study, the applicability of pixel, mesh and non-uniform rational B-splines (NURBS) objects to carry out realistic maps of X-ray phase-contrast distribution at a human scale is accounted for by using numerical anthropomorphic phantoms and a very fast and robust simulation framework which integrates total interaction probabilities along selected X-ray paths. We exploit the mathematical and algorithmic properties of NURBS and describe how to represent human scale phantoms in an edge illumination X-ray phase-contrast model. The presented implementation allows the modeling of a variety of physical interactions of x-rays with different mathematically described objects and the recording of quantities, e.g. path integrals, interaction sites and deposited energies. Furthermore, our efficient, scalable and optimized hybrid Monte Carlo and ray-tracing projector can be used in iterative reconstruction algorithms on multi GPU heterogeneous systems. The preliminary results of our innovative approach show the fine performance of an edge illumination X-ray phase-contrast medical imaging system on various human-like soft tissues with noticeably reduced computation time. Our approach to the EIXPCi modeling confirms that building a true imaging system at a human scale should be possible and the simulations presented here aim at its future development.     

Two-dimensional standing wave total internal reflection fluorescence microscopy: superresolution imaging of single molecular and biological specimens

The development of high resolution, high speed imaging techniques allows the study of dynamical processes in biological systems. Lateral resolution improvement of up to a factor of 2 has been achieved using structured illumination. In a total internal reflection fluorescence microscope, an evanescence excitation field is formed as light is total internally reflected at an interface between a high and a low index medium. The <100 nm penetration depth of evanescence field ensures a thin excitation region resulting in low background fluorescence. We present even higher resolution wide-field biological imaging by use of standing wave total internal reflection fluorescence (SW-TIRF). Evanescent standing wave (SW) illumination is used to generate a sinusoidal high spatial frequency fringe pattern on specimen for lateral resolution enhancement. To prevent thermal drift of the SW, novel detection and estimation of the SW phase with real-time feedback control is devised for the stabilization and control of the fringe phase. SW-TIRF is a wide-field superresolution technique with resolution better than a fifth of emission wavelength or approximately 100 nm lateral resolution. We demonstrate the performance of the SW-TIRF microscopy using one- and two-directional SW illumination with a biological sample of cellular actin cytoskeleton of mouse fibroblast cells as well as single semiconductor nanocrystal molecules. The results confirm the superior resolution of SW-TIRF in addition to the merit of a high signal/background ratio from TIRF microscopy.     

Velopharyngeal surgery: a prospective randomized study of pharyngeal flaps and sphincter pharyngoplasties

Residual velopharyngeal insufficiency after palatal repair varies from 10 to 20 percent in most centers. Secondary velopharyngeal surgery to correct residual velopharyngeal insufficiency in patients with cleft palate is a topic frequently discussed in the medical literature. Several authors have reported that varying the operative approach according to the findings of videonasopharyngoscopy and multiview videofluoroscopy significantly improved the success of velopharyngeal surgery. This article compares two surgical techniques for correcting residual velopharyngeal insufficiency, namely pharyngeal flap and sphincter pharyngoplasty. Both techniques were carefully planned according to the findings of videonasopharyngoscopy and multiview videofluoroscopy. Fifty patients with cleft palate and residual velopharyngeal insufficiency were randomly divided into two groups: 25 in group 1 and 25 in group 2. Patients in group 1 were operated on by using a customized pharyngeal flap according to the findings of videonasopharyngoscopy and multiview videofluoroscopy in each case. Those in group 2 received a sphincter pharyngoplasty also customized according to the findings of videonasopharyngoscopy and multiview videofluoroscopy. The median age of the patients in both groups was not significantly different (p > 0.5). The frequency of residual velopharyngeal insufficiency after the individualized velopharyngeal surgery was not significantly different between the patient groups (12 percent versus 16 percent; p > 0.05). It seems that customized pharyngeal flaps and sphincter pharyngoplasties performed according to the findings of videonasopharyngoscopy and multiview videofluoroscopy are safe and reliable procedures for treating residual velopharyngeal insufficiency in cleft palate patients.     

Drosophila pupal macrophages – A versatile tool for combined ex vivo and in vivo imaging of actin dynamics at high resolution

Molecular understanding of actin dynamics requires a genetically traceable model system that allows live cell imaging together with high-resolution microscopy techniques. Here, we used Drosophila pupal macrophages that combine many advantages of cultured cells with a genetic in vivo model system. Using structured illumination microscopy together with advanced spinning disk confocal microscopy we show that these cells provide a powerful system for single gene analysis. It allows forward genetic screens to characterize the regulatory network controlling cell shape and directed cell migration in a physiological context. We knocked down components regulating lamellipodia formation, including WAVE, single subunits of Arp2/3 complex and CPA, one of the two capping protein subunits and demonstrate the advantages of this model system by imaging mutant macrophages ex vivo as well as in vivo upon laser-induced wounding.     

Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy

Live imaging of large biological specimens is fundamentally limited by the short optical penetration depth of light microscopes. To maximize physical coverage, we developed the SiMView technology framework for high-speed in vivo imaging, which records multiple views of the specimen simultaneously. SiMView consists of a light-sheet microscope with four synchronized optical arms, real-time electronics for long-term sCMOS-based image acquisition at 175 million voxels per second, and computational modules for high-throughput image registration, segmentation, tracking and real-time management of the terabytes of multiview data recorded per specimen. We developed one-photon and multiphoton SiMView implementations and recorded cellular dynamics in entire Drosophila melanogaster embryos with 30-s temporal resolution throughout development. We furthermore performed high-resolution long-term imaging of the developing nervous system and followed neuroblast cell lineages in vivo. SiMView data sets provide quantitative morphological information even for fast global processes and enable accurate automated cell tracking in the entire early embryo.     

Studies on ferritin in rat liver and spleen during repeated phlebotomy

1. The ferritin content of liver and spleen in normal and iron-loaded rats decreased during repeated phlebotomy. 2. During increased iron demand, ferritin is degraded in toto. 3. With the ESI and EELS technique the iron distribution was followed in different cell types and cellular compartments. 4. We have demonstrated two methods of iron mobilisation: (a) catabolism of lysosomal ferritin in toto and (b) delivery of ferritin from parenchymal cell into the bile and degradation of ferritin in toto.     

A high-speed multispectral spinning-disk confocal microscope system for fluorescent speckle microscopy of living cells

Fluorescent speckle microscopy (FSM) uses a small fraction of fluorescently labeled subunits to give macromolecular assemblies such as the cytoskeleton fluorescence image properties that allow quantitative analysis of movement and subunit turnover. We describe a multispectral microscope system to analyze the dynamics of multiple cellular structures labeled with spectrally distinct fluorophores relative to one another over time in living cells. This required a high-resolution, highly sensitive, low-noise, and stable imaging system to visualize the small number of fluorophores making up each fluorescent speckle, a means by which to switch between excitation wavelengths rapidly, and a computer-based system to integrate image acquisition and illumination functions and to allow a convenient interface for viewing multispectral time-lapse data. To reduce out-of-focus fluorescence that degrades speckle contrast, we incorporated the optical sectioning capabilities of a dual-spinning-disk confocal scanner. The real-time, full-field scanning allows the use of a low-noise, fast, high-dynamic-range, and quantum-efficient cooled charge-coupled device (CCD) as a detector as opposed to the more noisy photomultiplier tubes used in laser-scanning confocal systems. For illumination, our system uses a 2.5-W Kr/Ar laser with 100-300mW of power at several convenient wavelengths for excitation of few fluorophores in dim FSM specimens and a four-channel polychromatic acousto-optical modulator fiberoptically coupled to the confocal to allow switching between illumination wavelengths and intensity control in a few microseconds. We present recent applications of this system for imaging the cytoskeleton in migrating tissue cells and neurons.     

Inside Front Cover: Uniform light delivery in volumetric optoacoustic tomography (J. Biophotonics 6/2019)

Optimized light delivery allows for single shot whole organ optoacoustic imaging. The authors present an optimized illumination concept for volumetric tomography that utilizes 3D printing in combination with custom‐made optical fiber illumination. The new approach showed a clear advantage over conventional, single‐sided illumination strategies by eliminating the need to correct for illumination variances and resulting in enhancement of the effective field of view, greater penetration depth and significant improvements in the overall image quality. Further details can be found in the article by Benedict Mc Larney, Johannes Rebling, Zhenyue Chen, et al. ( e201800387 )

     

Developing portable widefield fundus camera for teleophthalmology: Technical challenges and potential solutions

A portable, low cost, widefield fundus camera is essential for developing affordable teleophthalmology. However, conventional trans-pupillary illumination used in traditional fundus cameras limits the field of view (FOV) in a snapshot image, and frequently requires pharmacologically pupillary dilation for reliable examination of eye conditions. This minireview summarizes recent developments in alternative illumination approaches for widefield fundus photography. Miniaturized indirect illumination has been used to enable compact design for developing low cost, portable, widefield fundus camera. Contact mode trans-pars-planar illumination has been validated for ultra-widefield fundus imaging of infant eyes. Contact-free trans-pars-planar illumination has been explored for widefield imaging of adult eyes. Trans-palpebral illumination has been also demonstrated in a smartphone-based widefield fundus imager to foster affordable teleophthalmology.     

Carbon dioxide exchange in the needles of the common spruce in southern taiga spruce forests

Dynamics of carbon dioxide exchange in the Common Spruce (Picea abies L.) in relation to environmental factors was monitored during several seasons. Direct linear dependence of photosynthesis rate from the levels of air temperature and illumination was found, and correlation coefficients were 0.860 (p < 0.001) and 0.704 (p < 0.001). It was found that seasonal maximum of net photosynthesis production was attained at temperatures of 23–25°C. A decrease in temperature optimum was associated with reduction of the CO₂ assimilation intensity level. The impact of environmental factors on photosynthesis intensity is discussed in terms of the developed model. Using this model, we demonstrated that temperature and illumination dynamics in toto accounts for 82% of changes in photosynthesis rate. It is the air temperature that exerts the strongest influence on the process of photosynthesis. According to our calculations, the net photosynthesis level was three times higher than the level of respiration. This is indicative of a positive carbon dioxide balance in the needles of the Common Spruce.     

Improving Imaging Contrast of Non-Contacted Plasmonic Lens by Off-Axis Illumination with High Numerical Aperture

Off-axis illumination plasmonic lens (OAIPL) is proposed and demonstrated to improve the imaging contrast in non-contacted application manner. The spatial Fourier components of light transmitted through the nano-patterns are greatly enhanced in the imaging process by shifting the wave vectors with high numerical aperture off-axis illumination. On the other hand, a reflector in the image area helps to tailor the ratio between electric field components in the tangential and normal directions. These two effects resultantly deliver significant improvement of imaging performance, including enhanced resolution, imaging contrast, and elongation of air gap thickness. In comparison to the case of normal illumination, the air gap thickness for 30 and 60 nm half-pitch resolution is extended to 25 and 100 nm by OAIPL with numerical aperture (NA)?=?1.55, respectively.     

Rapid Particle Size Measurement Using 3D Surface Imaging

The present study introduces a new three-dimensional (3D) surface image analysis technique in which white light illumination from different incident angles is used to create 3D surfaces with a photometric approach. The three-dimensional features of the surface images created are then used in the characterization of particle size distributions of granules. This surface image analysis method is compared to sieve analysis and a particle sizing method based on spatial filtering technique with nearly 30 granule batches. The aim is also to evaluate the technique in flowability screening of granular materials. Overall, the new 3D imaging approach allows a rapid analysis of large amounts of sample and gives valuable visual information on the granule surfaces in terms of surface roughness and particle shape.