Light-sheet fluorescence microscopy for quantitative biology

Imaging the Renal Microcirculation in Cell Therapy

Renal microvascular rarefaction plays a pivotal role in progressive kidney disease. Therefore, modalities to visualize the microcirculation of the kidney will increase our understanding of disease mechanisms and consequently may provide new approaches for evaluating cell-based therapy. At the moment, however, clinical practice is lacking non-invasive, safe, and efficient imaging modalities to monitor renal microvascular changes over time in patients suffering from renal disease. To emphasize the importance, we summarize current knowledge of the renal microcirculation and discussed the involvement in progressive kidney disease. Moreover, an overview of available imaging techniques to uncover renal microvascular morphology, function, and behavior is presented with the associated benefits and limitations. Ultimately, the necessity to assess and investigate renal disease based on in vivo readouts with a resolution up to capillary level may provide a paradigm shift for diagnosis and therapy in the field of nephrology.

Cerebrovascular development: mechanisms and experimental approaches

The cerebral vasculature plays a central role in human health and disease and possesses several unique anatomic, functional and molecular characteristics. Despite their importance, the mechanisms that determine cerebrovascular development are less well studied than other vascular territories. This is in part due to limitations of existing models and techniques for visualisation and manipulation of the cerebral vasculature. In this review we summarise the experimental approaches used to study the cerebral vessels and the mechanisms that contribute to their development.

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

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

Visualizing three-dimensional fungal growth using light sheet fluorescence microscopy

The evaluation of morphology is fundamental to comprehend how fungi grow, develop, and interact with the environment. Although fungal growth has been extensively studied associated to two-dimensional geometries, lack of appropriate experimental tools has limited exploration of the complex three-dimensional (3D) structures exhibited by mycelia in more general contexts. In this paper, we report the construction of a light-sheet fluorescence microscope (LSFM) capable of performing time-lapse visualization of 3D biological structures (4D microscopy), and the use of this instrument to follow the dynamics of fungal growth. LSFM uses scanning of selective plane illumination and digital reconstruction to provide 3D images of the specimen. We describe the optical, electronic, and computational means to implement two-color LSFM, and provide detailed procedures for aligning and testing the setup. We successfully demonstrate use of both autofluorescence and specific tagging to image Trichoderma atroviride and Neurospora crassa strains growing in liquid media, over extended times (~12 h) and volumes (~400 × 1500 × 800 μm³) at single-hypha resolution. The excellent image contrast provided by LSFM enables us to visualize the dynamics of mycelial architecture, interactions among hyphae, and measure rates of 3D apical extension. Altogether, our work shows a powerful imaging tool to perform 3D morphological analysis of fungi, from hyphae to mycelium.

Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis

BACKGROUND

Organoids are morphologically heterogeneous three-dimensional cell culture systems and serve as an ideal model for understanding the principles of collective cell behaviour in mammalian organs during development, homeostasis, regeneration, and pathogenesis. To investigate the underlying cell organisation principles of organoids, we imaged hundreds of pancreas and cholangiocarcinoma organoids in parallel using light sheet and bright-field microscopy for up to 7 days.

RESULTS

We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation, and degeneration and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation, and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright-field microscopy analysis of entire cultures.

CONCLUSION

Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying the core regulatory principles of organoid morphogenesis.

Deep Learning for Biospectroscopy and Biospectral Imaging: State-of-the-Art and Perspectives

With the advances in instrumentation and sampling techniques, there is an explosive growth of data from molecular and cellular samples. The call to extract more information from the large data sets has greatly challenged the conventional chemometrics method. Deep learning, which utilizes very large data sets for finding hidden features therein and for making accurate predictions for a wide range of applications, has been applied in an unbelievable pace in biospectroscopy and biospectral imaging in the recent 3 years. In this Feature, we first introduce the background and basic knowledge of deep learning. We then focus on the emerging applications of deep learning in the data preprocessing, feature detection, and modeling of the biological samples for spectral analysis and spectroscopic imaging. Finally, we highlight the challenges and limitations in deep learning and the outlook for future directions.

Detecting Differences of Fluorescent Markers Distribution in Single Cell Microscopy: Textural or Pointillist Feature Space?

We consider the detection of change in spatial distribution of fluorescent markers inside cells imaged by single cell microscopy. Such problems are important in bioimaging since the density of these markers can reflect the healthy or pathological state of cells, the spatial organization of DNA, or cell cycle stage. With the new super-resolved microscopes and associated microfluidic devices, bio-markers can be detected in single cells individually or collectively as a texture depending on the quality of the microscope impulse response. In this work, we propose, via numerical simulations, to address detection of changes in spatial density or in spatial clustering with an individual (pointillist) or collective (textural) approach by comparing their performances according to the size of the impulse response of the microscope. Pointillist approaches show good performances for small impulse response sizes only, while all textural approaches are found to overcome pointillist approaches with small as well as with large impulse response sizes. These results are validated with real fluorescence microscopy images with conventional resolution. This, a priori non-intuitive result in the perspective of the quest of super-resolution, demonstrates that, for difference detection tasks in single cell microscopy, super-resolved microscopes may not be mandatory and that lower cost, sub-resolved, microscopes can be sufficient.

Application of Airy beam light sheet microscopy to examine early neurodevelopmental structures in 3D hiPSC-derived human cortical spheroids

BACKGROUND

The inability to observe relevant biological processes in vivo significantly restricts human neurodevelopmental research. Advances in appropriate in vitro model systems, including patient-specific human brain organoids and human cortical spheroids (hCSs), offer a pragmatic solution to this issue. In particular, hCSs are an accessible method for generating homogenous organoids of dorsal telencephalic fate, which recapitulate key aspects of human corticogenesis, including the formation of neural rosettes-in vitro correlates of the neural tube. These neurogenic niches give rise to neural progenitors that subsequently differentiate into neurons. Studies differentiating induced pluripotent stem cells (hiPSCs) in 2D have linked atypical formation of neural rosettes with neurodevelopmental disorders such as autism spectrum conditions. Thus far, however, conventional methods of tissue preparation in this field limit the ability to image these structures in three-dimensions within intact hCS or other 3D preparations. To overcome this limitation, we have sought to optimise a methodological approach to process hCSs to maximise the utility of a novel Airy-beam light sheet microscope (ALSM) to acquire high resolution volumetric images of internal structures within hCS representative of early developmental time points.

RESULTS

Conventional approaches to imaging hCS by confocal microscopy were limited in their ability to image effectively into intact spheroids. Conversely, volumetric acquisition by ALSM offered superior imaging through intact, non-clarified, in vitro tissues, in both speed and resolution when compared to conventional confocal imaging systems. Furthermore, optimised immunohistochemistry and optical clearing of hCSs afforded improved imaging at depth. This permitted visualization of the morphology of the inner lumen of neural rosettes.

CONCLUSION

We present an optimized methodology that takes advantage of an ALSM system that can rapidly image intact 3D brain organoids at high resolution while retaining a large field of view. This imaging modality can be applied to both non-cleared and cleared in vitro human brain spheroids derived from hiPSCs for precise examination of their internal 3D structures. This process represents a rapid, highly efficient method to examine and quantify in 3D the formation of key structures required for the coordination of neurodevelopmental processes in both health and disease states. We posit that this approach would facilitate investigation of human neurodevelopmental processes in vitro.

3D imaging using scanning diffractometry

Imaging of cells is a challenging problem as they do not appreciably change the intensity of the illuminating light. Interferometry-based methods to do this task suffer from high sensitivity to environmental vibrations. We introduce scanning diffractometry as a simple non-contact and vibration-immune methodology for quantitative phase imaging. Fresnel diffractometry by a phase step has led to several applications such as high-precision measurements of displacement. Additional scanning may lead to 3D imaging straightforwardly. We apply the technique to acquire 3D images of holographic grating, red blood cell, neuron, and sperm cell. Either visibility of the diffraction fringes or the positions of extrema may be used for phase change detection. The theoretical analysis through the Fresnel diffraction from one-dimensional phase step is presented and the experimental results are validated with digital holographic microscopy. The presented technique can be suggested to serve as a robust device for 3D phase imaging and biomedical measurements.

Volume holographic optical element for light sheet fluorescence microscopy

Three-dimensional (3D) imaging of living organisms requires fine optical sectioning and high-speed image acquisition, which can be achieved by light sheet fluorescence microscopy (LSFM). However, orthogonal illumination and detection arms in the LSFM system make it bulky. Here, we propose and demonstrate the application of a volume holographic optical element (photopolymer-based volume holographic grating) for designing a compact LSFM system, called a volume holographic LSFM (VHLSFM). Using the VHLSFM, we performed in vivo imaging of Caenorhabditis elegans (C. elegans) and observed high-contrast optically sectioned fluorescence images of the oocytes and embryonic development in real time for 3D imaging.

Nuclear crowding and nonlinear diffusion during interkinetic nuclear migration in the zebrafish retina

An important question in early neural development is the origin of stochastic nuclear movement between apical and basal surfaces of neuroepithelia during interkinetic nuclear migration. Tracking of nuclear subpopulations has shown evidence of diffusion - mean squared displacements growing linearly in time - and suggested crowding from cell division at the apical surface drives basalward motion. Yet, this hypothesis has not yet been tested, and the forces involved not quantified. We employ long-term, rapid light-sheet and two-photon imaging of early zebrafish retinogenesis to track entire populations of nuclei within the tissue. The time-varying concentration profiles show clear evidence of crowding as nuclei reach close-packing and are quantitatively described by a nonlinear diffusion model. Considerations of nuclear motion constrained inside the enveloping cell membrane show that concentration-dependent stochastic forces inside cells, compatible in magnitude to those found in cytoskeletal transport, can explain the observed magnitude of the diffusion constant.

Tissue culture, genetic transformation, interaction with beneficial microbes, and modern bio-imaging techniques in alfalfa research

Current research needs to be more focused on agronomical plants to effectively utilize the knowledge obtained from model plant species. Efforts to improve legumes have long employed common breeding tools. Recently, biotechnological approaches facilitated the development of improved legumes with new traits, allowing them to withstand climatic changes and biotic stress. Owing to its multiple uses and profits, alfalfa (Medicago sativa L.) has become a prominent forage crop worldwide. This review provides a comprehensive research summary of tissue culture-based genetic transformation methods, which could be exploited for the development of transgenic alfalfa with agronomically desirable traits. Moreover, advanced bio-imaging approaches, including cutting-edge microscopy and phenotyping, are outlined here. Finally, characterization and the employment of beneficial microbes should help to produce biotechnologically improved and sustainable alfalfa cultivars.

MAGIC: Live imaging of cellular division in plant seedlings using lightsheet microscopy

Imaging technologies have been used to understand plant genetic and developmental processes, from the dynamics of gene expression to tissue and organ morphogenesis. Although the field has advanced incredibly in recent years, gaps remain in identifying fine and dynamic spatiotemporal intervals of target processes, such as changes to gene expression in response to abiotic stresses. Lightsheet microscopy is a valuable tool for such studies due to its ability to perform long-term imaging at fine intervals of time and at low photo-toxicity of live vertically oriented seedlings. In this chapter, we describe a detailed method for preparing and imaging Arabidopsis thaliana seedlings for lightsheet microscopy via a Multi-Sample Imaging Growth Chamber (MAGIC), which allows simultaneous imaging of at least four samples. This method opens new avenues for acquiring imaging data at a high temporal resolution, which can be eventually probed to identify key regulatory time points and any spatial dependencies of target developmental processes.

Investigating Optimal Time Step Intervals of Imaging for Data Quality through a Novel Fully-Automated Cell Tracking Approach

Computer-based fully-automated cell tracking is becoming increasingly important in cell biology, since it provides unrivalled capacity and efficiency for the analysis of large datasets. However, automatic cell tracking’s lack of superior pattern recognition and error-handling capability compared to its human manual tracking counterpart inspired decades-long research. Enormous efforts have been made in developing advanced cell tracking packages and software algorithms. Typical research in this field focuses on dealing with existing data and finding a best solution. Here, we investigate a novel approach where the quality of data acquisition could help improve the accuracy of cell tracking algorithms and vice-versa. Generally speaking, when tracking cell movement, the more frequent the images are taken, the more accurate cells are tracked and, yet, issues such as damage to cells due to light intensity, overheating in equipment, as well as the size of the data prevent a constant data streaming. Hence, a trade-off between the frequency at which data images are collected and the accuracy of the cell tracking algorithms needs to be studied. In this paper, we look at the effects of different choices of the time step interval (i.e., the frequency of data acquisition) within the microscope to our existing cell tracking algorithms. We generate several experimental data sets where the true outcomes are known (i.e., the direction of cell migration) by either using an effective chemoattractant or employing no-chemoattractant. We specify a relatively short time step interval (i.e., 30 s) between pictures that are taken at the data generational stage, so that, later on, we may choose some portion of the images to produce datasets with different time step intervals, such as 1 min, 2 min, and so on. We evaluate the accuracy of our cell tracking algorithms to illustrate the effects of these different time step intervals. We establish that there exist certain relationships between the tracking accuracy and the time step interval associated with experimental microscope data acquisition. We perform fully-automatic adaptive cell tracking on multiple datasets, to identify optimal time step intervals for data acquisition, while at the same time demonstrating the performance of the computer cell tracking algorithms.

An accurate and universal approach for short-exposure-time microscopy image enhancement

Fluorescence microscopy imaging has become an essential technique in the biology and biomedical science which can provide comprehensive visualization of many biological processes, and the exposure time is one of the most critical parameters for fluorescence microscopy imaging. Short-exposure-time (SET) imaging overcomes the limitations of photo-bleaching and photo-toxicity, allowing comprehensive visualization of the biological processes. Unfortunately, SET images deteriorate the signal to noise ratio and the image quality when compared with the long-exposure-time (LET) images. Therefore, we introduce a data-driven microscopy image enhancement network (MIEN) to improve the quality of SET microscopy images without requiring any manual intervention, facilitating the production of high-resolution and high contrast images. The universal property and accuracy of the proposed network are validated on 38,500 real fluorescence microscopy images, which contain different object contents and are collected from various exposure time ratios and fluorescence microscopes platforms. Experimental results demonstrate that the proposed MIEN model is effective to enhance the quality of SET fluorescence microscopy images, and can be used to observe delicate changes in cells, tissues and organs with low photo-bleaching and photo-toxicity.

Anatomy and Physiology of Macaque Visual Cortical Areas V1, V2, and V5/MT: Bases for Biologically Realistic Models

The cerebral cortex of primates encompasses multiple anatomically and physiologically distinct areas processing visual information. Areas V1, V2, and V5/MT are conserved across mammals and are central for visual behavior. To facilitate the generation of biologically accurate computational models of primate early visual processing, here we provide an overview of over 350 published studies of these three areas in the genus Macaca, whose visual system provides the closest model for human vision. The literature reports 14 anatomical connection types from the lateral geniculate nucleus of the thalamus to V1 having distinct layers of origin or termination, and 194 connection types between V1, V2, and V5, forming multiple parallel and interacting visual processing streams. Moreover, within V1, there are reports of 286 and 120 types of intrinsic excitatory and inhibitory connections, respectively. Physiologically, tuning of neuronal responses to 11 types of visual stimulus parameters has been consistently reported. Overall, the optimal spatial frequency (SF) of constituent neurons decreases with cortical hierarchy. Moreover, V5 neurons are distinct from neurons in other areas for their higher direction selectivity, higher contrast sensitivity, higher temporal frequency tuning, and wider SF bandwidth. We also discuss currently unavailable data that could be useful for biologically accurate models.

Accelerated Stimulated Raman Projection Tomography by Sparse Reconstruction From Sparse-View Data

OBJECTIVE

Stimulated Raman projection tomography (SRPT), a recently developed label-free volumetric chemical imaging technology, has been reported to quantitatively reconstruct the distribution of chemicals in a three-dimensional (3D) complex system. The current image reconstruction scheme used in SRPT is based on a filtered back projection (FBP) algorithm that requires at least 180 angular-dependent projections to rebuild a reasonable SRPT image, resulting in a long total acquisition time. This is a big limitation for longitudinal studies on live systems.

METHODS

We present a sparse-view data-based sparse reconstruction scheme, in which sparsely sampled projections at 180 degrees were used to reconstruct the volumetric information. In the scheme, the simultaneous algebra reconstruction technique (SART), combined with total variation regularization, was used for iterative reconstruction. To better describe the projection process, a pixel vertex driven model (PVDM) was developed to act as projectors, whose performance was compared with those of the distance driven model (DDM).

RESULTS

We evaluated our scheme with numerical simulations and validated it for SRPT by mapping lipid contents in adipose cells. Simulation results showed that the PVDM performed better than the DDM in the case of using sparse-view data. Our scheme could maintain the quality of the reconstructed images even when the projection number was reduced to 15. The cell-based experimental results demonstrated that the proposed scheme can improve the imaging speed of the current FBP-based SRPT scheme by a factor of 9-12 without sacrificing discernible imaging details.

CONCLUSION

Our proposed scheme significantly reduces the total acquisition time required for SRPT at a speed of one order of magnitude faster than the currently used scheme. This significant improvement in imaging speed would potentially promote the applicability of SRPT for imaging living organisms.

Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big

The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale.

Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila

Mosaic analysis provides a means to probe developmental processes in situ by generating loss-of-function mutants within otherwise wildtype tissues. Combining these techniques with quantitative microscopy enables researchers to rigorously compare RNA or protein expression across the resultant clones. However, visual inspection of mosaic tissues remains common in the literature because quantification demands considerable labor and computational expertise. Practitioners must segment cell membranes or cell nuclei from a tissue and annotate the clones before their data are suitable for analysis. Here, we introduce Fly-QMA, a computational framework that automates each of these tasks for confocal microscopy images of Drosophila imaginal discs. The framework includes an unsupervised annotation algorithm that incorporates spatial context to inform the genetic identity of each cell. We use a combination of real and synthetic validation data to survey the performance of the annotation algorithm across a broad range of conditions. By contributing our framework to the open-source software ecosystem, we aim to contribute to the current move toward automated quantitative analysis among developmental biologists.

Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy

As the general population ages, more people are affected by eye diseases, such as retinopathies. It is therefore critical to improve imaging of eye disease mouse models. Here, we demonstrate that 1) rapid, quantitative 3D and 4D (time lapse) imaging of cellular and subcellular processes in the mouse eye is feasible, with and without tissue clearing, using light-sheet fluorescent microscopy (LSFM); 2) flat-mounting retinas for confocal microscopy significantly distorts tissue morphology, confirmed by quantitative correlative LSFM-Confocal imaging of vessels; 3) LSFM readily reveals new features of even well-studied eye disease mouse models, such as the oxygen-induced retinopathy (OIR) model, including a previously unappreciated ‘knotted’ morphology to pathological vascular tufts, abnormal cell motility and altered filopodia dynamics when live-imaged. We conclude that quantitative 3D/4D LSFM imaging and analysis has the potential to advance our understanding of the eye, in particular pathological, neurovascular, degenerative processes.

Eye diseases affect millions of people worldwide and can have devasting effects on people’s lives. To find new treatments, scientists need to understand more about how these diseases arise and how they progress. This is challenging and progress has been held back by limitations in current techniques for looking at the eye. Currently, the most commonly used method is called confocal imaging, which is slow and distorts the tissue. Distortion happens because confocal imaging requires that thin slices of eye tissue from mice used in experiments are flattened on slides; this makes it hard to accurately visualize three-dimensional structures in the eye.

New methods are emerging that may help. One promising method is called light-sheet fluorescent microscopy (or LSFM for short). This method captures three-dimensional images of the blood vessels and cells in the eye. It is much faster than confocal imaging and allows scientists to image tissues without slicing or flattening them. This could lead to more accurate three-dimensional images of eye disease.

Now, Prahst et al. show that LSFM can quickly produce highly detailed, three-dimensional images of mouse retinas, from the smallest parts of cells to the entire eye. The technique also identified new features in a well-studied model of retina damage caused by excessive oxygen exposure in young mice. Previous studies of this model suggested the disease caused blood vessels in the eye to balloon, hinting that drugs that shrink blood vessels would help. But using LSFM, Prahst et al. revealed that these blood vessels actually take on a twisted and knotted shape. This suggests that treatments that untangle the vessels rather than shrink them are needed.

The experiments show that LSFM is a valuable tool for studying eye diseases, that may help scientists learn more about how these diseases arise and develop. These new insights may one day lead to better tests and treatments for eye diseases.

Early developmental plasticity of lateral roots in response to asymmetric water availability

Root branching is influenced by the soil environment and exhibits a high level of plasticity. We report that the radial positioning of emerging lateral roots is influenced by their hydrological environment during early developmental stages. New lateral root primordia have both a high degree of flexibility in terms of initiation and development angle towards the available water. Our observations reveal how the external hydrological environment regulates lateral root morphogenesis.

Single-Virus Tracking: From Imaging Methodologies to Virological Applications

Uncovering the mechanisms of virus infection and assembly is crucial for preventing the spread of viruses and treating viral disease. The technique of single-virus tracking (SVT), also known as single-virus tracing, allows one to follow individual viruses at different parts of their life cycle and thereby provides dynamic insights into fundamental processes of viruses occurring in live cells. SVT is typically based on fluorescence imaging and reveals insights into previously unreported infection mechanisms. In this review article, we provide the readers a broad overview of the SVT technique. We first summarize recent advances in SVT, from the choice of fluorescent labels and labeling strategies to imaging implementation and analytical methodologies. We then describe representative applications in detail to elucidate how SVT serves as a valuable tool in virological research. Finally, we present our perspectives regarding the future possibilities and challenges of SVT.

Fast quantitative time lapse displacement imaging of endothelial cell invasion

In order to unravel rapid mechano-chemical feedback mechanisms in sprouting angiogenesis, we combine selective plane illumination microscopy (SPIM) and tailored image registration algorithms - further referred to as SPIM-based displacement microscopy - with an in vitro model of angiogenesis. SPIM successfully tackles the problem of imaging large volumes while upholding the spatial resolution required for the analysis of matrix displacements at a subcellular level. Applied to in vitro angiogenic sprouts, this unique methodological combination relates subcellular activity - minute to second time scale growing and retracting of protrusions - of a multicellular systems to the surrounding matrix deformations with an exceptional temporal resolution of 1 minute for a stack with multiple sprouts simultaneously or every 4 seconds for a single sprout, which is 20 times faster than with a conventional confocal setup. Our study reveals collective but non-synchronised, non-continuous activity of adjacent sprouting cells along with correlations between matrix deformations and protrusion dynamics.

Optical sectioning and high resolution visualization of trabecular meshwork using Bessel beam assisted light sheet fluorescence microscopy

Glaucoma, one of the leading causes of blindness, is an eye disease caused by irregularities in the ocular aqueous outflow system causing an elevated intraocular pressure. High resolution imaging of the aqueous outflow system comprising trabecular meshwork is immensely valuable to vision analysts and clinicians in comprehending the disease state for the efficacious analysis and treatment of glaucoma. Currently available ocular imaging devices are unable to deliver high resolution images for the visualization of the trabecular meshwork. A method to obtain high resolution (sub-micrometer) images of the trabecular meshwork using Bessel-Gauss beam scanned light sheet fluorescence microscopy is presented and the optical sectioning capability of this technique to obtain three-dimensional volumetric images of the trabecular meshwork of an intact eye without any physical dissection is demonstrated. Figure: Three-dimensional visualization of trabecular meshwork of porcine eye.

Fast 3-D Imaging of Brain Organoids With a New Single-Objective Planar-Illumination Two-Photon Microscope

Human inducible pluripotent stem cells (hiPSCs) hold a large potential for disease modeling. hiPSC-derived human astrocyte and neuronal cultures permit investigations of neural signaling pathways with subcellular resolution. Combinatorial cultures, and three-dimensional (3-D) embryonic bodies (EBs) enlarge the scope of investigations to multi-cellular phenomena. The highest level of complexity, brain organoids that-in many aspects-recapitulate anatomical and functional features of the developing brain permit the study of developmental and morphological aspects of human disease. An ideal microscope for 3-D tissue imaging at these different scales would combine features from both confocal laser-scanning and light-sheet microscopes: a micrometric optical sectioning capacity and sub-micrometric spatial resolution, a large field of view and high frame rate, and a low degree of invasiveness, i.e., ideally, a better photon efficiency than that of a confocal microscope. In the present work, we describe such an instrument that uses planar two-photon (2P) excitation. Its particularity is that-unlike two- or three-lens light-sheet microscopes-it uses a single, low-magnification, high-numerical aperture objective for the generation and scanning of a virtual light sheet. The microscope builds on a modified Nipkow-Petráň spinning-disk scheme for achieving wide-field excitation. However, unlike the Yokogawa design that uses a tandem disk, our concept combines micro lenses, dichroic mirrors and detection pinholes on a single disk. This new design, advantageous for 2P excitation, circumvents problems arising with the tandem disk from the large wavelength difference between the infrared excitation light and visible fluorescence. 2P fluorescence excited by the light sheet is collected with the same objective and imaged onto a fast sCMOS camera. We demonstrate 3-D imaging of TO-PRO3-stained EBs and of brain organoids, uncleared and after rapid partial transparisation with triethanolamine formamide (RTF) and we compare the performance of our instrument to that of a confocal laser-scanning microscope (CLSM) having a similar numerical aperture. Our large-field 2P-spinning disk microscope permits one order of magnitude faster imaging, affords less photobleaching and permits better depth penetration than a confocal microscope with similar spatial resolution.

Next-generation imaging of the skeletal system and its blood supply

Bone is organized in a hierarchical 3D architecture. Traditionally, analysis of the skeletal system was based on bone mass assessment by radiographic methods or on the examination of bone structure by 2D histological sections. Advanced imaging technologies and big data analysis now enable the unprecedented examination of bone and provide new insights into its 3D macrostructure and microstructure. These technologies comprise ex vivo and in vivo methods including high-resolution computed tomography (CT), synchrotron-based imaging, X-ray microscopy, ultra-high-field magnetic resonance imaging (MRI), light-sheet fluorescence microscopy, confocal and intravital two-photon imaging. In concert, these techniques have been used to detect and quantify a novel vascular system of trans-cortical vessels in bone. Furthermore, structures such as the lacunar network, which harbours and connects osteocytes, become accessible for 3D imaging and quantification using these methods. Next-generation imaging of the skeletal system and its blood supply are anticipated to contribute to an entirely new understanding of bone tissue composition and function, from macroscale to nanoscale, in health and disease. These insights could provide the basis for early detection and precision-type intervention of bone disorders in the future.

Light sheet microscopy for histopathology applications

Light sheet microscopy (LSM) is an evolving optical imaging technique with a plane illumination for optical sectioning and volumetric imaging spanning cell biology, embryology, and in vivo live imaging. Here, we focus on emerging biomedical applications of LSM for tissue samples. Decoupling of the light sheet illumination from detection enables high-speed and large field-of-view imaging with minimal photobleaching and phototoxicity. These unique characteristics of the LSM technique can be easily adapted and potentially replace conventional histopathological procedures. In this review, we cover LSM technology from its inception to its most advanced technology; in particular, we highlight the human histopathological imaging applications to demonstrate LSM's rapid diagnostic ability in comparison with conventional histopathological procedures. We anticipate that the LSM technique can become a useful three-dimensional imaging tool for assessing human biopsies in the near future.

Structural and functional imaging of large and opaque plant specimens

Three- and four-dimensional imaging techniques are a prerequisite for spatially resolving the form-structure-function relationships in plants. However, choosing the right imaging method is a difficult and time-consuming process as the imaging principles, advantages and limitations, as well as the appropriate fields of application first need to be compared. The present study aims to provide an overview of three imaging methods that allow for imaging opaque, large and thick (>5 mm, up to several centimeters), hierarchically organized plant samples that can have complex geometries. We compare light microscopy of serial thin sections followed by 3D reconstruction (LMTS3D) as an optical imaging technique, micro-computed tomography (µ-CT) based on ionizing radiation, and magnetic resonance imaging (MRI) which uses the natural magnetic properties of a sample for image acquisition. We discuss the most important imaging principles, advantages, and limitations, and suggest fields of application for each imaging technique (LMTS, µ-CT, and MRI) with regard to static (at a given time; 3D) and dynamic (at different time points; quasi 4D) structural and functional plant imaging.

Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution

Caenorhabditis elegans (C. elegans) stands out as the only organism in which the challenge of understanding the cellular origins of an entire nervous system can be observed, with single cell resolution, in vivo. Here, we present an integrated protocol for the examination of neurodevelopment in C. elegans embryos. Our protocol combines imaging, lineaging and neuroanatomical tracing of single cells in developing embryos. We achieve long-term, four-dimensional (4D) imaging of living C. elegans embryos with nearly isotropic spatial resolution through the use of Dual-view Inverted Selective Plane Illumination Microscopy (diSPIM). Nuclei and neuronal structures in the nematode embryos are imaged and isotropically fused to yield images with resolution of ~330 nm in all three dimensions. These minute-by-minute high-resolution 4D data sets are then analyzed to correlate definitive cell-lineage identities with gene expression and morphological dynamics at single-cell and subcellular levels of detail. Our protocol is structured to enable modular implementation of each of the described steps and enhance studies on embryogenesis, gene expression, or neurodevelopment.

High-resolution 3D imaging of fixed and cleared organoids

In vitro 3D organoid systems have revolutionized the modeling of organ development and diseases in a dish. Fluorescence microscopy has contributed to the characterization of the cellular composition of organoids and demonstrated organoids' phenotypic resemblance to their original tissues. Here, we provide a detailed protocol for performing high-resolution 3D imaging of entire organoids harboring fluorescence reporters and upon immunolabeling. This method is applicable to a wide range of organoids of differing origins and of various sizes and shapes. We have successfully used it on human airway, colon, kidney, liver and breast tumor organoids, as well as on mouse mammary gland organoids. It includes a simple clearing method utilizing a homemade fructose-glycerol clearing agent that captures 3D organoids in full and enables marker quantification on a cell-by-cell basis. Sample preparation has been optimized for 3D imaging by confocal, super-resolution confocal, multiphoton and light-sheet microscopy. From organoid harvest to image analysis, the protocol takes 3 d.

A practical guide to adaptive light-sheet microscopy

We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detection focal planes in living specimens. Our protocol enables researchers to introduce adaptive imaging capabilities in an existing light-sheet microscope or use our SiMView microscope blueprint to set up a new adaptive multiview light-sheet microscope. The protocol describes (i) the mechano-optical implementation of the adaptive imaging hardware, including technical drawings for all custom microscope components; (ii) the algorithms and software library for automated adaptive imaging, including the pseudocode and annotated source code for all software modules; and (iii) the execution of adaptive imaging experiments, as well as the configuration and practical use of the AutoPilot framework. Setup of the adaptive imaging hardware and software takes 1-2 weeks each. Previous experience with light-sheet microscopy and some familiarity with software engineering and building of optical instruments are recommended. Successful implementation of the protocol recovers near diffraction-limited performance in many parts of typical multicellular organisms studied with light-sheet microscopy, such as fruit fly and zebrafish embryos, for which resolution and signal strength are improved two- to fivefold.

Three-Dimensional Quantitative Co-Mapping of Pulmonary Morphology and Nanoparticle Distribution with Cellular Resolution in Nondissected Murine Lungs

Deciphering biodistribution, biokinetics, and biological effects of nanoparticles (NPs) in entire organs with cellular resolution remains largely elusive due to the lack of effective imaging tools. Here, light sheet fluorescence microscopy in combination with optical tissue clearing was validated for concomitant three-dimensional mapping of lung morphology and NP biodistribution with cellular resolution in nondissected ex vivo murine lungs. Tissue autofluorescence allowed for label-free, quantitative morphometry of the entire bronchial tree, acinar structure, and blood vessels. Co-registration of fluorescent NPs with lung morphology revealed significant differences in pulmonary NP distribution depending on the means of application (intratracheal instillation and ventilator-assisted aerosol inhalation under anesthetized conditions). Inhalation exhibited a more homogeneous NP distribution in conducting airways and acini indicated by a central-to-peripheral (C/P) NP deposition ratio of unity (0.98 ± 0.13) as compared to a 2-fold enhanced central deposition (C/P = 1.98 ± 0.37) for instillation. After inhalation most NPs were observed in the proximal part of the acini as predicted by computational fluid dynamics simulations. At cellular resolution patchy NP deposition was visualized in bronchioles and acini, but more pronounced for instillation. Excellent linearity of the fluorescence intensity-dose response curve allowed for accurate NP dosimetry and revealed ca. 5% of the inhaled aerosol was deposited in the lungs. This single-modality imaging technique allows for quantitative co-registration of tissue architecture and NP biodistribution, which could accelerate elucidation of NP biokinetics and bioactivity within intact tissues, facilitating both nanotoxicology studies and the development of nanomedicines.

Universal light-sheet generation with field synthesis

We introduce Field Synthesis, a theorem that can be used to synthesize any scanned or dithered light-sheet, including those used in lattice light-sheet microscopy (LLSM), from an incoherent superposition of one-dimensional intensity distributions. This user-friendly and modular approach offers a drastically simplified optical design, higher light-throughput, simultaneous multicolor illumination, and a 100% spatial duty cycle that provides biological imaging with low rates of photobleaching.

A network of trans-cortical capillaries as mainstay for blood circulation in long bones

Closed circulatory systems (CCS) underlie the function of vertebrate organs, but in long bones their structure is unclear, although they constitute the exit route for bone marrow (BM) leukocytes. To understand neutrophil emigration from BM, we studied the vascular system of murine long bones. Here we show that hundreds of capillaries originate in BM, cross murine cortical bone perpendicularly along the shaft and connect to the periosteal circulation. Structures similar to these trans-cortical-vessels (TCVs) also exist in human limb bones. TCVs express arterial or venous markers and transport neutrophils. Furthermore, over 80% arterial and 59% venous blood passes through TCVs. Genetic and drug-mediated modulation of osteoclast count and activity leads to substantial changes in TCV numbers. In a murine model of chronic arthritic bone inflammation, new TCVs develop within weeks. Our data indicate that TCVs are a central component of the CCS in long bones and may represent an important route for immune cell export from the BM.

Light-sheet microscopy with length-adaptive Bessel beams

In light-sheet microscopy, a confined layer in the focal plane of the detection objective is illuminated from the side. The illumination light-sheet usually has a constant beam length independent of the shape of the biological object. Since the thickness and the length of the illumination light-sheet are coupled, a tradeoff between resolution, contrast and field of view has to be accepted. Here we show that scanned Bessel beams enable object adapted tailoring of the light-sheet defined by its beam length and position. The individual beam parameters are obtained from automatic object shape estimation by low-power laser light scattered at the object. Using Arabidopsis root tips, cell clusters and zebrafish tails, we demonstrate that Bessel beam light-sheet tailoring leads to a 50% increase in image contrast and a 50% reduction in photobleaching. Light-sheet tailoring requires only binary amplitude modulation, therefore allowing a real time illumination adaptation with little technical effort in the future.

Expansion Light Sheet Microscopy Resolves Subcellular Structures in Large Portions of the Songbird Brain

Expansion microscopy and light sheet imaging (ExLSM) provide a viable alternative to existing tissue clearing and large volume imaging approaches. The analysis of intact volumes of brain tissue presents a distinct challenge in neuroscience. Recent advances in tissue clearing and light sheet microscopy have re-addressed this challenge and blossomed into a plethora of protocols with diverse advantages and disadvantages. While refractive index matching achieves near perfect transparency and allows for imaging at large depths, the resolution of cleared brains is usually limited to the micrometer range. Moreover, the often long and harsh tissue clearing protocols hinder preservation of native fluorescence and antigenicity. Here we image large expanded brain volumes of zebra finch brain tissue in commercially available light sheet microscopes. Our expansion light sheet microscopy (ExLSM) approach presents a viable alternative to many clearing and imaging methods because it improves on tissue processing times, fluorophore compatibility, and image resolution.

Light-sheet fluorescence expansion microscopy: fast mapping of neural circuits at super resolution

The goal of understanding the architecture of neural circuits at the synapse level with a brain-wide perspective has powered the interest in high-speed and large field-of-view volumetric imaging at subcellular resolution. Here, we developed a method combining tissue expansion and light-sheet fluorescence microscopy to allow extended volumetric super resolution high-speed imaging of large mouse brain samples. We demonstrate the capabilities of this method by performing two color fast volumetric super resolution imaging of mouse CA1 and dentate gyrus molecular-, granule cell-, and polymorphic layers. Our method enables an exact evaluation of granule cell and neurite morphology within the context of large cell ensembles spanning several orders of magnitude in resolution. We found that imaging a brain region of 1    mm 3 in super resolution using light-sheet fluorescence expansion microscopy is about 17-fold faster than imaging the same region by a current state-of-the-art high-resolution confocal laser scanning microscope.

Choosing the right microscope to image mitosis in zebrafish embryos: A practical guide

Tissue growth and organismal development require orchestrated cell proliferation. To understand how cell division guides development, it is important to explore mitosis at the tissue-wide, cellular, and subcellular scale. At the tissue level this includes determining a tissue's mitotic index, at the cellular level the tracing of cell lineages, and at the subcellular level the characterization of intracellular components. These different tasks can be addressed by different imaging approaches (e.g., laser-scanning confocal, spinning disk confocal, and light-sheet fluorescence microscopy). Here, we summarize three protocols for exploring different facets of mitosis in developing zebrafish embryos. Zebrafish embryos are transparent and their rapid external development greatly facilitates the study of cellular processes and developmental dynamics using microscopy. A critical step in all imaging studies of mitosis in development is to choose the most suitable microscope for each scientific question. This choice is important in order to ensure a balance between the required temporal and spatial resolution and minimal phototoxicity that could otherwise perturb the process of interest. The use of different microscopy techniques, best suited for the purpose of each experiment, thus permits to generate a comprehensive and unbiased view on how mitosis influences development.

EyeCi: Optical clearing and imaging of immunolabeled mouse eyes using light-sheet fluorescence microscopy

Immunofluorescent imaging is an indispensable technique to study morphology and molecular aspects in tissues. Classical approaches make it necessary to cut physical sections of tissue samples to overcome the limited penetration depth of light, restricting the available information to two dimensions. Recent advances in tissue-clearing techniques enable imaging of fluorescently labeled organs and entire organisms on a cellular level in three dimensions without the need of sectioning. Volume imaging of immunolabeled and cleared tissues started a new era of systems biology, because these techniques provide information on connectivity and circuits, especially in structures with projections in three dimensions such as vascular or nervous systems. The variety of published clearing protocols allows the imaging of every organ with a single exception: the eye. Whole-eye clearing approaches were unsuccessful so far due to the strong pigmentation of the retinal pigment epithelium. Here, we present a new protocol that combines a highly effective melanin bleaching step with solvent-based clearing, termed EyeCi. The protocol is compatible with immunolabeling as demonstrated by the visualization of ocular and retinal vasculature in the intact mouse eye by means of light-sheet fluorescence microscopy. This novel protocol is rapid (1 week) and inexpensive, hence allowing high-throughput, high resolution analysis of vascular architecture of healthy and diseased eyes, in its native, three-dimensional organization within intact eyeballs. Volume imaging of whole cleared eyeballs further enables three-dimensional surface reconstruction and automated quantification of choroidal and retinal vasculature extending ocular imaging to a global level. Thus, EyeCi represents an extension to state-of-the-art light microscopy techniques and is potentially suitable for the investigation of vascular leakage or neovascularization processes.

Photonic crystal enhanced fluorescence immunoassay on diatom biosilica

Fluorescence biosensing is one of the most established biosensing methods, particularly fluorescence spectroscopy and microscopy. These are two highly sensitive techniques but require high-grade electronics and optics to achieve the desired sensitivity. Efforts have been made to implement these methods using consumer grade electronics and simple optical setups for applications such as point-of-care diagnostics, but the sensitivity inherently suffers. Sensing substrates, capable of enhancing fluorescence are thus needed to achieve high sensitivity for such applications. In this paper, we demonstrate a photonic crystal-enhanced fluorescence immunoassay biosensor using diatom biosilica, which consists of silica frustules with sub-100 nm periodic pores. Utilizing the enhanced local optical field, the Purcell effect and increased surface area from the diatom photonic crystals, we create ultrasensitive immunoassay biosensors that can significantly enhance fluorescence spectroscopy as well as fluorescence imaging. Using standard antibody-antigen-labeled antibody immunoassay protocol, we experimentally achieved 100× and 10× better detection limit with fluorescence spectroscopy and fluorescence imaging respectively. The limit of detection of the mouse IgG goes down to 10^-16 M (14 fg/mL) and 10^-15 M (140 fg/mL) for the two respective detection modalities, virtually sensing a single mouse IgG molecule on each diatom frustule. The effectively enhanced fluorescence imaging in conjunction with the simple hot-spot counting analysis method used in this paper proves the great potential of diatom fluorescence immunoassay for point-of-care biosensing.

Three-dimensional imaging of the developing human fetal urogenital-genital tract: Indifferent stage to male and female differentiation

Recent studies in our lab have utilized three imaging techniques to visualize the developing human fetal urogenital tract in three dimensions: optical projection tomography, scanning electron microscopy and lightsheet fluorescence microscopy. We have applied these technologies to examine changes in morphology and differential gene expression in developing human external genital specimens from the ambisexual stage (<9 weeks fetal age) to well-differentiated male and female organs (>13 weeks fetal age). This work outlines the history and function of each of these three imaging modalities, our methods to prepare specimens for each and the novel findings we have produced thus far. We believe the images in this paper of human fetal urogenital organs produced using lightsheet fluorescence microscopy are the first published to date.

Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis

Embryogenesis relies on instructions provided by spatially organized signaling molecules known as morphogens. Understanding the principles behind morphogen distribution and how cells interpret locally this information remains a major challenge in developmental biology. Here, we introduce morphogen-age measurements as a novel approach to test models of morphogen gradient formation. Using a tandem fluorescent timer as a protein age sensor, we find a gradient of increasing age of Bicoid along the anterior-posterior axis in the early Drosophila embryo. Quantitative analysis of the protein age distribution across the embryo reveals that the synthesis-diffusion-degradation model is the most likely model underlying Bicoid gradient formation, and rules out other hypotheses for gradient formation. Moreover, we show that the timer can detect transitions in the dynamics associated with syncytial cellularization. Our results provide new insight into Bicoid gradient formation and demonstrate how morphogen-age information can complement knowledge about movement, abundance, and distribution, which should be widely applicable to other systems.

Multiscale imaging of plant development by light-sheet fluorescence microscopy

Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.

Microscopy in Infectious Disease Research-Imaging Across Scales

A comprehensive understanding of host-pathogen interactions requires quantitative assessment of molecular events across a wide range of spatiotemporal scales and organizational complexities. Due to recent technical developments, this is currently only achievable with microscopy. This article is providing a general perspective on the importance of microscopy in infectious disease research, with a focus on new imaging modalities that promise to have a major impact in biomedical research in the years to come. Every major technological breakthrough in light microscopy depends on, and is supported by, advancements in computing and information technologies. Bioimage acquisition and analysis based on machine learning will pave the way toward more robust, automated and objective implementation of new imaging modalities and in biomedical research in general. The combination of novel imaging technologies with machine learning and near-physiological model systems promises to accelerate discoveries and breakthroughs in our understanding of infectious diseases, from basic research all the way to clinical applications.

Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations

In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.

Light sheet theta microscopy for rapid high-resolution imaging of large biological samples

BACKGROUND

Advances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy approaches to image large samples quantitatively and at high resolution. While light sheet microscopy (LSM), with its high planar imaging speed and low photo-bleaching, can be effective, scaling up to larger imaging volumes has been hindered by the use of orthogonal light sheet illumination.

RESULTS

To address this fundamental limitation, we have developed light sheet theta microscopy (LSTM), which uniformly illuminates samples from the same side as the detection objective, thereby eliminating limits on lateral dimensions without sacrificing the imaging resolution, depth, and speed. We present a detailed characterization of LSTM, and demonstrate its complementary advantages over LSM for rapid high-resolution quantitative imaging of large intact samples with high uniform quality.

CONCLUSIONS

The reported LSTM approach is a significant step for the rapid high-resolution quantitative mapping of the structure and function of very large biological systems, such as a clarified thick coronal slab of human brain and uniformly expanded tissues, and also for rapid volumetric calcium imaging of highly motile animals, such as Hydra, undergoing non-isomorphic body shape changes.