Optical sectioning deep inside live embryos by selective plane illumination microscopy

High-resolution light-sheet microscopy for whole-cell sub-cellular dynamics

Research in the areas of organelle dynamics, cytoskeletal interactions, membrane protrusions, and cell motility relies heavily on live-cell imaging. These structures continuously move about in complex patterns and imaging them live at sufficient temporal resolutions as well as for durations long enough to extract significant number of events is an absolute necessity. Capturing most of the sub-cellular dynamics in whole cell volumes was beyond reach due to the lack of balance between reduced photo-toxicity, time resolution, and the required spatial resolution in dominant imaging modalities like point scanning confocal and spinning disc confocal microscopy. In the last few years, a plethora of light-sheet geometries have emerged, pushing the limits of measurements. In this review, we will focus on a subset of light-sheet modalities that are most suited to studying live, sub-cellular dynamics in whole-cell volumes.

Transcription Factor Dynamics: One Molecule at a Time

Cells must tightly regulate their gene expression programs and yet rapidly respond to acute biochemical and biophysical cues within their environment. This information is transmitted to the nucleus through various signaling cascades, culminating in the activation or repression of target genes. Transcription factors (TFs) are key mediators of these signals, binding to specific regulatory elements within chromatin. While live-cell imaging has conclusively proven that TF-chromatin interactions are highly dynamic, how such transient interactions can have long-term impacts on developmental trajectories and disease progression is still largely unclear. In this review, we summarize our current understanding of the dynamic nature of TF functions, starting with a historical overview of early live-cell experiments. We highlight key factors that govern TF dynamics and how TF dynamics, in turn, affect downstream transcriptional bursting. Finally, we conclude with open challenges and emerging technologies that will further our understanding of transcriptional regulation.

Gentle label-free nonlinear optical imaging relaxes linear-absorption-mediated triplet

Sample health is critical for live-cell fluorescence microscopy and has promoted light-sheet microscopy that restricts its ultraviolet-visible excitation to one plane inside a three-dimensional sample. It is thus intriguing that laser-scanning nonlinear optical microscopy, which similarly restricts its near-infrared excitation, has not broadly enabled gentle label-free molecular imaging. We hypothesize that intense near-infrared excitation induces phototoxicity via linear absorption of intrinsic biomolecules with subsequent triplet buildup, rather than the commonly assumed mechanism of nonlinear absorption. Using a reproducible phototoxicity assay based on the time-lapse elevation of auto-fluorescence (hyper-fluorescence) from a homogeneous tissue model (chicken breast), we provide strong evidence supporting this hypothesis. Our study justifies a simple imaging technique, e.g., rapidly scanned sub-80-fs excitation with full triplet-relaxation, to mitigate this ubiquitous linear-absorption-mediated phototoxicity independent of sample types. The corresponding label-free imaging can track freely moving C. elegans in real-time at an irradiance up to one-half of water optical breakdown.

Efficient compressed sensing reconstruction for 3D fluorescence microscopy using OptoMechanical Modulation Tomography (OMMT) with a 1+2D regularization

OptoMechanical Modulation Tomography (OMMT) exploits compressed sensing to reconstruct high resolution microscopy volumes from fewer measurement images compared to exhaustive section sampling in conventional light sheet microscopy. Nevertheless, the volumetric reconstruction process is computationally expensive, making it impractically slow to use on large-size images, and prone to generating visual artefacts. Here, we propose a reconstruction approach that uses a 1+2D Total Variation (TV1+2) regularization that does not generate such artefacts and is amenable to efficient implementation using parallel computing. We evaluate our method for accuracy and scaleability on simulated and experimental data. Using a high quality, but computationally expensive, Plug-and-Play (PnP) method that uses the BM4D denoiser as a benchmark, we observe that our approach offers an advantageous trade-off between speed and accuracy.

Education in microscopy: taking a closer look with Jennifer Waters

Jennifer Waters (Nikon Imaging Center, Harvard Medical School, MA, USA) spoke to Ebony Torrington (Future Science Group, London, UK) about her career in microscopy and the importance of education. Jennifer is the Director of the Nikon Imaging Center (NIC) at Harvard Medical School and a Chan Zuckerberg Initiative (CZI) Imaging Scientist. She was trained in cell biology and microscopy by Ted Salmon at University of North Carolina (UNC) at Chapel Hill (NC, USA), where her research focused on mitosis and cell cycle regulation. Jennifer's main focus today, in addition to running the NIC, is developing light microscopy educational resources.

Scattered-light-sheet microscopy with sub-cellular resolving power

Since its first demonstration over 100 years ago, scattering-based light-sheet microscopy has recently re-emerged as a key modality in label-free tissue imaging and cellular morphometry; however, scattering-based light-sheet imaging with subcellular resolution remains an unmet target. This is because related approaches inevitably superimpose speckle or granular intensity modulation on to the native subcellular features. Here, we addressed this challenge by deploying a time-averaged pseudo-thermalized light-sheet illumination. While this approach increased the lateral dimensions of the illumination sheet, we achieved subcellular resolving power after image deconvolution. We validated this approach by imaging cytosolic carbon depots in yeast and bacteria with increased specificity, no staining, and ultralow irradiance levels. Overall, we expect this scattering-based light-sheet microscopy approach will advance single, live cell imaging by conferring low-irradiance and label-free operation towards eradicating phototoxicity.

In Vivo Imaging Sheds Light on the Susceptibility and Permissivity of Carassius auratus to Cyprinid Herpesvirus 2 According to Developmental Stage

Cyprinid herpesvirus 2 (CyHV-2) is a virus that causes mass mortality in economically important Carassius spp. However, there have been no comprehensive studies into host susceptibility or permissivity with respect to developmental stage, and the major portal of viral entry into the host is still unclear. To help bridge these knowledge gaps, we developed the first ever recombinant strain of CyHV-2 expressing bioluminescent and fluorescent reporter genes. Infection of Carassius auratus hosts with this recombinant by immersion facilitated the exploitation of various in vivo imaging techniques to establish the spatiotemporal aspects of CyHV-2 replication at larval, juvenile, and adult developmental stages. While less susceptible than later developmental stages, larvae were most permissive to CyHV-2 replication, leading to rapid systemic infection and high mortality. Permissivity to CyHV-2 decreased with advancing development, with adults being the least permissive and, thus, also exhibiting the least mortality. Across all developmental stages, the skin was the most susceptible and permissive organ to infection at the earliest sampling points post-infection, indicating that it represents the major portal of entry into these hosts. Collectively these findings provide important fundamental insights into CyHV-2 pathogenesis and epidemiology in Carassius auratus with high relevance to other related economically important virus-host models.

Mesoscopic Oblique Plane Microscopy via Light-sheet Mirroring

Understanding the intricate interplay and inter-connectivity of biological processes across an entire organism is important in various fields of biology, including cardiovascular research, neuroscience, and developmental biology. Here, we present a mesoscopic oblique plane microscope (OPM) that enables whole organism imaging with high speed and subcellular resolution. A microprism underneath the sample enhances the axial resolution and optical sectioning through total internal reflection of the light-sheet. Through rapid refocusing of the light-sheet, the imaging depth is extended up to threefold while keeping the axial resolution constant. Using low magnification objectives with a large field of view, we realize mesoscopic imaging over a volume of 3.7×1.5×1 mm3 with ~2.3 microns lateral and ~9.2 microns axial resolution. Applying the mesoscopic OPM, we demonstrate in vivo and in toto whole organism imaging of the zebrafish vasculature and its endothelial nuclei, and blood flow dynamics at 12 Hz acquisition rate, resulting in a quantitative map of blood flow across the entire organism.

A weak-labelling and deep learning approach for in-focus object segmentation in 3D widefield microscopy

Three-dimensional information is crucial to our understanding of biological phenomena. The vast majority of biological microscopy specimens are inherently three-dimensional. However, conventional light microscopy is largely geared towards 2D images, while 3D microscopy and image reconstruction remain feasible only with specialised equipment and techniques. Inspired by the working principles of one such technique-confocal microscopy, we propose a novel approach to 3D widefield microscopy reconstruction through semantic segmentation of in-focus and out-of-focus pixels. For this, we explore a number of rule-based algorithms commonly used for software-based autofocusing and apply them to a dataset of widefield focal stacks. We propose a computation scheme allowing the calculation of lateral focus score maps of the slices of each stack using these algorithms. Furthermore, we identify algorithms preferable for obtaining such maps. Finally, to ensure the practicality of our approach, we propose a surrogate model based on a deep neural network, capable of segmenting in-focus pixels from the out-of-focus background in a fast and reliable fashion. The deep-neural-network-based approach allows a major speedup for data processing making it usable for online data processing.

From the beginnings to multidimensional light and electron microscopy of virus morphogenesis

Individual functional viral morphogenesis events are often dynamic, short, and infrequent and might be obscured by other pathways and dead-end products. Volumetric live cell imaging has become an essential tool for studying viral morphogenesis events. It allows following entire dynamic processes while providing functional evidence that the imaged process is involved in viral production. Moreover, it allows to capture many individual events and allows quantitative analysis. Finally, the correlation of volumetric live-cell data with volumetric electron microscopy (EM) can provide crucial insights into the ultrastructure and mechanisms of viral morphogenesis events. Here, we provide an overview and discussion of suitable imaging methods for volumetric correlative imaging of viral morphogenesis and frame them in a historical summary of their development.

Advanced fluorescence microscopy in respiratory virus cell biology

Respiratory viruses are a major public health burden across all age groups around the globe, and are associated with high morbidity and mortality rates. They can be transmitted by multiple routes, including physical contact or droplets and aerosols, resulting in efficient spreading within the human population. Investigations of the cell biology of virus replication are thus of utmost importance to gain a better understanding of virus-induced pathogenicity and the development of antiviral countermeasures. Light and fluorescence microscopy techniques have revolutionized investigations of the cell biology of virus infection by allowing the study of the localization and dynamics of viral or cellular components directly in infected cells. Advanced microscopy including high- and super-resolution microscopy techniques available today can visualize biological processes at the single-virus and even single-molecule level, thus opening a unique view on virus infection. We will highlight how fluorescence microscopy has supported investigations on virus cell biology by focusing on three major respiratory viruses: respiratory syncytial virus (RSV), Influenza A virus (IAV) and SARS-CoV-2. We will review our current knowledge of virus replication and highlight how fluorescence microscopy has helped to improve our state of understanding. We will start by introducing major imaging and labeling modalities and conclude the chapter with a perspective discussion on remaining challenges and potential opportunities.

Tissue optical clearing and 3D imaging of virus infections

Imaging pathogens within 3D environment of biological tissues provides spatial information about their localization and interactions with the host. Technological advances in fluorescence microscopy and 3D image analysis now permit visualization and quantification of pathogens directly in large tissue volumes and in great detail. In recent years large volume imaging became an important tool in virology research helping to understand the properties of viruses and the host response to infection. In this chapter we give a review of fluorescence microscopy modalities and tissue optical clearing methods used for large volume tissue imaging. A summary of recent applications for virus research is provided with particular emphasis on studies using light sheet fluorescence microscopy. We describe the challenges and approaches for volumetric image analysis. Practical examples of volumetric imaging implemented in virology laboratories and addressing specialized research questions, such as virus tropism and immune host response are described. We conclude with an overview of the emerging technologies and their potential for virus research.

Enhancer trap lines with GFP driven by smad6b and frizzled1 regulatory sequences for the study of epithelial morphogenesis in the developing zebrafish inner ear

Live imaging in the zebrafish embryo using tissue-specific expression of fluorescent proteins can yield important insights into the mechanisms that drive sensory organ morphogenesis and cell differentiation. Morphogenesis of the semicircular canal ducts of the vertebrate inner ear requires a complex rearrangement of epithelial cells, including outgrowth, adhesion, fusion and perforation of epithelial projections to generate pillars of tissue that form the hubs of each canal. We report the insertion sites and expression patterns of two enhancer trap lines in the developing zebrafish embryo, each of which highlight different aspects of epithelial cell morphogenesis in the inner ear. A membrane-linked EGFP driven by smad6b regulatory sequences is expressed throughout the otic epithelium, most strongly on the lateral side of the ear and in the sensory cristae. A second enhancer trap line, with cytoplasmic EGFP driven by frizzled1 (fzd1) regulatory sequences, specifically marks cells of the ventral projection and pillar in the developing ear, and marginal cells in the sensory cristae, together with variable expression in the retina and epiphysis, and neurons elsewhere in the developing central nervous system. We have used a combination of methods to identify the insertion sites of these two transgenes, which were generated through random insertion, and show that Targeted Locus Amplification is a rapid and reliable method for the identification of insertion sites of randomly inserted transgenes.

In vitro models to study natural killer cell dynamics in the tumor microenvironment

Immunotherapy is revolutionizing cancer therapy. The rapid development of new immunotherapeutic strategies to treat solid tumors is posing new challenges for preclinical research, demanding novel in vitro methods to test treatments. Such methods should meet specific requirements, such as enabling the evaluation of immune cell responses like cytotoxicity or cytokine release, and infiltration into the tumor microenvironment using cancer models representative of the original disease. They should allow high-throughput and high-content analysis, to evaluate the efficacy of treatments and understand immune-evasion processes to facilitate development of new therapeutic targets. Ideally, they should be suitable for personalized immunotherapy testing, providing information for patient stratification. Consequently, the application of in vitro 3-dimensional (3D) cell culture models, such as tumor spheroids and organoids, is rapidly expanding in the immunotherapeutic field, coupled with the development of novel imaging-based techniques and -omic analysis. In this paper, we review the recent advances in the development of in vitro 3D platforms applied to natural killer (NK) cell-based cancer immunotherapy studies, highlighting the benefits and limitations of the current methods, and discuss new concepts and future directions of the field.

3D Chemical Imaging by Fluorescence-detected Mid-Infrared Photothermal Fourier Light Field Microscopy

Three-dimensional molecular imaging of living organisms and cells plays a significant role in modern biology. Yet, current volumetric imaging modalities are largely fluorescence-based and thus lack chemical content information. Mid-infrared photothermal microscopy as a chemical imaging technology provides infrared spectroscopic information at submicrometer spatial resolution. Here, by harnessing thermosensitive fluorescent dyes to sense the mid-infrared photothermal effect, we demonstrate 3D fluorescence-detected mid-infrared photothermal Fourier light field (FMIP-FLF) microscopy at the speed of 8 volumes per second and submicron spatial resolution. Protein contents in bacteria and lipid droplets in living pancreatic cancer cells are visualized. Altered lipid metabolism in drug-resistant pancreatic cancer cells is observed with the FMIP-FLF microscope.

Dynamic Volumetric Imaging of Mouse Cerebral Blood Vessels In Vivo with an Ultralong Anti-Diffracting Beam

Volumetric imaging of a mouse brain in vivo with one-photon and two-photon ultralong anti-diffracting (UAD) beam illumination was performed. The three-dimensional (3D) structure of blood vessels in the mouse brain were mapped to a two-dimensional (2D) image. The speed of volumetric imaging was significantly improved due to the long focal length of the UAD beam. Comparing one-photon and two-photon UAD beam volumetric imaging, we found that the imaging depth of two-photon volumetric imaging (80 μm) is better than that of one-photon volumetric imaging (60 μm), and the signal-to-background ratio (SBR) of two-photon volumetric imaging is two times that of one-photon volumetric imaging. Therefore, we used two-photon UAD volumetric imaging to perform dynamic volumetric imaging of mouse brain blood vessels in vivo, and obtained the blood flow velocity.

Live Cell Light Sheet Imaging with Low- and High-Spatial-Coherence Detection Approaches Reveals Spatiotemporal Aspects of Neuronal Signaling

Light sheet microscopy in live cells requires minimal excitation intensity and resolves three-dimensional (3D) information rapidly. Lattice light sheet microscopy (LLSM) works similarly but uses a lattice configuration of Bessel beams to generate a flatter, diffraction-limited z-axis sheet suitable for investigating subcellular compartments, with better tissue penetration. We developed a LLSM method for investigating cellular properties of tissue in situ. Neural structures provide an important target. Neurons are complex 3D structures, and signaling between cells and subcellular structures requires high resolution imaging. We developed an LLSM configuration based on the Janelia Research Campus design or in situ recording that allows simultaneous electrophysiological recording. We give examples of using LLSM to assess synaptic function in situ. In presynapses, evoked Ca²⁺ entry causes vesicle fusion and neurotransmitter release. We demonstrate the use of LLSM to measure stimulus-evoked localized presynaptic Ca²⁺ entry and track synaptic vesicle recycling. We also demonstrate the resolution of postsynaptic Ca²⁺ signaling in single synapses. A challenge in 3D imaging is the need to move the emission objective to maintain focus. We have developed an incoherent holographic lattice light-sheet (IHLLS) technique to replace the LLS tube lens with a dual diffractive lens to obtain 3D images of spatially incoherent light diffracted from an object as incoherent holograms. The 3D structure is reproduced within the scanned volume without moving the emission objective. This eliminates mechanical artifacts and improves temporal resolution. We focus on LLS and IHLLS applications and data obtained in neuroscience and emphasize increases in temporal and spatial resolution using these approaches.

Extended Depth of Focus Two-Photon Light-Sheet Microscopy for In Vivo Fluorescence Imaging of Large Multicellular Organisms at Cellular Resolution

Two-photon excitation in light-sheet microscopy advances applications to live imaging of multicellular organisms. In a previous study, we developed a two-photon Bessel beam light-sheet microscope with a nearly 1-mm field of view and less than 4-μm axial resolution, using a low magnification (10×), middle numerical aperture (NA 0.5) detection objective. In this study, we aimed to construct a light-sheet microscope with higher resolution imaging while maintaining the large field of view, using low magnification (16×) with a high NA 0.8 objective. To address potential illumination and detection mismatch, we investigated the use of a depth of focus (DOF) extension method. Specifically, we used a stair-step device composed of five-layer annular zones that extended DOF two-fold, enough to cover the light-sheet thickness. Resolution measurements using fluorescent beads showed that the reduction in resolutions was small. We then applied this system to in vivo imaging of medaka fish and found that image quality degradation at the distal site of the beam injection could be compensated. This demonstrates that the extended DOF system combined with wide-field two-photon light-sheet microscopy offers a simple and easy setup for live imaging application of large multicellular organism specimens with sub-cellular resolution.

Recent Advances in Single-Molecule Tracking and Imaging Techniques

Since the early 1990s, single-molecule detection in solution at room temperature has enabled direct observation of single biomolecules at work in real time and under physiological conditions, providing insights into complex biological systems that the traditional ensemble methods cannot offer. In particular, recent advances in single-molecule tracking techniques allow researchers to follow individual biomolecules in their native environments for a timescale of seconds to minutes, revealing not only the distinct pathways these biomolecules take for downstream signaling but also their roles in supporting life. In this review, we discuss various single-molecule tracking and imaging techniques developed to date, with an emphasis on advanced three-dimensional (3D) tracking systems that not only achieve ultrahigh spatiotemporal resolution but also provide sufficient working depths suitable for tracking single molecules in 3D tissue models. We then summarize the observables that can be extracted from the trajectory data. Methods to perform single-molecule clustering analysis and future directions are also discussed.

Nondestructive 3D Pathology with Light-Sheet Fluorescence Microscopy for Translational Research and Clinical Assays

In recent years, there has been a revived appreciation for the importance of spatial context and morphological phenotypes for both understanding disease progression and guiding treatment decisions. Compared with conventional 2D histopathology, which is the current gold standard of medical diagnostics, nondestructive 3D pathology offers researchers and clinicians the ability to visualize orders of magnitude more tissue within their natural volumetric context. This has been enabled by rapid advances in tissue-preparation methods, high-throughput 3D microscopy instrumentation, and computational tools for processing these massive feature-rich data sets. Here, we provide a brief overview of many of these technical advances along with remaining challenges to be overcome. We also speculate on the future of 3D pathology as applied in translational investigations, preclinical drug development, and clinical decision-support assays.

Imaging Approaches to Investigate Pathophysiological Mechanisms of Brain Disease in Zebrafish

Zebrafish has become an essential model organism in modern biomedical research. Owing to its distinctive features and high grade of genomic homology with humans, it is increasingly employed to model diverse neurological disorders, both through genetic and pharmacological intervention. The use of this vertebrate model has recently enhanced research efforts, both in the optical technology and in the bioengineering fields, aiming at developing novel tools for high spatiotemporal resolution imaging. Indeed, the ever-increasing use of imaging methods, often combined with fluorescent reporters or tags, enable a unique chance for translational neuroscience research at different levels, ranging from behavior (whole-organism) to functional aspects (whole-brain) and down to structural features (cellular and subcellular). In this work, we present a review of the imaging approaches employed to investigate pathophysiological mechanisms underlying functional, structural, and behavioral alterations of human neurological diseases modeled in zebrafish.

High-throughput confocal airy beam oblique light-sheet tomography of brain-wide imaging at single-cell resolution

Brain research is an area of research characterized by its cutting-edge nature, with brain mapping constituting a crucial aspect of this field. As sequencing tools have played a crucial role in gene sequencing, brain mapping largely depends on automated, high-throughput and high-resolution imaging techniques. Over the years, the demand for high-throughput imaging has scaled exponentially with the rapid development of microscopic brain mapping. In this paper, we introduce the novel concept of confocal Airy beam into oblique light-sheet tomography named CAB-OLST. We demonstrate that this technique enables the high throughput of brain-wide imaging of long-distance axon projection for the entire mouse brain at a resolution of 0.26 μm × 0.26 μm × 1.06 μm in 58 hours. This technique represents an innovative contribution to the field of brain research by setting a new standard for high-throughput imaging techniques.

Recent advances in oblique plane microscopy

Oblique plane microscopy (OPM) directly captures object information in a plane tilted from the focal plane of the objective lens without the need for slow z-stack acquisition. This unconventional widefield imaging approach is made possible by using a remote focusing principle that eliminates optical aberrations for object points beyond the focal plane. Together with oblique lightsheet illumination, OPM can make conventional lightsheet imaging fully compatible with standard biological specimens prepared on microscope slides. OPM is not only an excellent high-speed volumetric imaging platform by sweeping oblique lightsheet illumination without mechanically moving either the sample or objective lens in sample space, but also provides a solution for direct oblique plane imaging along any orientation of interest on the sample in a single shot. Since its first demonstration in 2008, OPM has continued to evolve into an advanced microscope platform for biological, medical, and materials science applications. In recent years, many technological advances have been made in OPM with the goal of super-resolution, fast volumetric imaging, and a large imaging field of view, etc. This review gives an overview of OPM's working principle and imaging performance and introduces recent technical developments in OPM methods and applications. OPM has strong potential in a variety of research fields, including cellular and developmental biology, clinical diagnostics in histology and ophthalmology, flow cytometry, microfluidic devices, and soft materials.

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

Volume imaging to interrogate cancer cell-tumor microenvironment interactions in space and time

Volume imaging visualizes the three-dimensional (3D) complexity of tumors to unravel the dynamic crosstalk between cancer cells and the heterogeneous landscape of the tumor microenvironment (TME). Tissue clearing and intravital microscopy (IVM) constitute rapidly progressing technologies to study the architectural context of such interactions. Tissue clearing enables high-resolution imaging of large samples, allowing for the characterization of entire tumors and even organs and organisms with tumors. With IVM, the dynamic engagement between cancer cells and the TME can be visualized in 3D over time, allowing for acquisition of 4D data. Together, tissue clearing and IVM have been critical in the examination of cancer-TME interactions and have drastically advanced our knowledge in fundamental cancer research and clinical oncology. This review provides an overview of the current technical repertoire of fluorescence volume imaging technologies to study cancer and the TME, and discusses how their recent applications have been utilized to advance our fundamental understanding of tumor architecture, stromal and immune infiltration, vascularization and innervation, and to explore avenues for immunotherapy and optimized chemotherapy delivery.

Light-sheets and smart microscopy, an exciting future is dawning

Light-sheet fluorescence microscopy has transformed our ability to visualize and quantitatively measure biological processes rapidly and over long time periods. In this review, we discuss current and future developments in light-sheet fluorescence microscopy that we expect to further expand its capabilities. This includes smart and adaptive imaging schemes to overcome traditional imaging trade-offs, i.e., spatiotemporal resolution, field of view and sample health. In smart microscopy, a microscope will autonomously decide where, when, what and how to image. We further assess how image restoration techniques provide avenues to overcome these tradeoffs and how "open top" light-sheet microscopes may enable multi-modal imaging with high throughput. As such, we predict that light-sheet microscopy will fulfill an important role in biomedical and clinical imaging in the future.

Differential synthetic illumination based on multi-line detection for resolution and contrast enhancement of line confocal microscopy

Line confocal (LC) microscopy is a fast 3D imaging technique, but its asymmetric detection slit limits resolution and optical sectioning. To address this, we propose the differential synthetic illumination (DSI) method based on multi-line detection to enhance the spatial resolution and optical sectioning capability of the LC system. The DSI method allows the imaging process to simultaneously accomplish on a single camera, which ensures the rapidity and stability of the imaging process. DSI-LC improves X- and Z-axis resolution by 1.28 and 1.26 times, respectively, and optical sectioning by 2.6 times compared to LC. Furthermore, the spatially resolved power and contrast are also demonstrated by imaging pollen, microtubule, and the fiber of the GFP fluorescence-labeled mouse brain. Finally, Video-rate imaging of zebrafish larval heart beating in a 665.6 × 332.8 µm² field-of-view is achieved. DSI-LC provides a promising approach for 3D large-scale and functional imaging in vivo with improved resolution, contrast, and robustness.

Chemical-imaging-guided optical manipulation of biomolecules

Chemical imaging via advanced optical microscopy technologies has revealed remarkable details of biomolecules in living specimens. However, the ways to control chemical processes in biological samples remain preliminary. The lack of appropriate methods to spatially regulate chemical reactions in live cells in real-time prevents investigation of site-specific molecular behaviors and biological functions. Chemical- and site-specific control of biomolecules requires the detection of chemicals with high specificity and spatially precise modulation of chemical reactions. Laser-scanning optical microscopes offer great platforms for high-speed chemical detection. A closed-loop feedback control system, when paired with a laser scanning microscope, allows real-time precision opto-control (RPOC) of chemical processes for dynamic molecular targets in live cells. In this perspective, we briefly review recent advancements in chemical imaging based on laser scanning microscopy, summarize methods developed for precise optical manipulation, and highlight a recently developed RPOC technology. Furthermore, we discuss future directions of precision opto-control of biomolecules.

Active mesh and neural network pipeline for cell aggregate segmentation

Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology due to improvements in capacity and accuracy of microscopy techniques. Here, we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary gland organoids imaged over 24 h with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin that implements active mesh deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction.

Rapid biomechanical imaging at low irradiation level via dual line-scanning Brillouin microscopy

Brillouin microscopy is a technique for mechanical characterization of biological material without contact at high three-dimensional resolution. Here, we introduce dual line-scanning Brillouin microscopy (dLSBM), which improves acquisition speed and reduces irradiation dose by more than one order of magnitude with selective illumination and single-shot analysis of hundreds of points along the incident beam axis. Using tumor spheroids, we demonstrate the ability to capture the sample response to rapid mechanical perturbations as well as the spatially resolved evolution of the mechanical properties in growing spheroids.

OptoRheo: Simultaneous in situ micro-mechanical sensing and imaging of live 3D biological systems

Biomechanical cues from the extracellular matrix (ECM) are essential for directing many cellular processes, from normal development and repair, to disease progression. To better understand cell-matrix interactions, we have developed a new instrument named 'OptoRheo' that combines light sheet fluorescence microscopy with particle tracking microrheology. OptoRheo lets us image cells in 3D as they proliferate over several days while simultaneously sensing the mechanical properties of the surrounding extracellular and pericellular matrix at a sub-cellular length scale. OptoRheo can be used in two operational modalities (with and without an optical trap) to extend the dynamic range of microrheology measurements. We corroborated this by characterising the ECM surrounding live breast cancer cells in two distinct culture systems, cell clusters in 3D hydrogels and spheroids in suspension culture. This cutting-edge instrument will transform the exploration of drug transport through complex cell culture matrices and optimise the design of the next-generation of disease models.

Large-scale interrogation of retinal cell functions by 1-photon light-sheet microscopy

Visual processing in the retina depends on the collective activity of large ensembles of neurons organized in different layers. Current techniques for measuring activity of layer-specific neural ensembles rely on expensive pulsed infrared lasers to drive 2-photon activation of calcium-dependent fluorescent reporters. We present a 1-photon light-sheet imaging system that can measure the activity in hundreds of neurons in the ex vivo retina over a large field of view while presenting visual stimuli. This allows for a reliable functional classification of different retinal cell types. We also demonstrate that the system has sufficient resolution to image calcium entry at individual synaptic release sites across the axon terminals of dozens of simultaneously imaged bipolar cells. The simple design, large field of view, and fast image acquisition make this a powerful system for high-throughput and high-resolution measurements of retinal processing at a fraction of the cost of alternative approaches.

A single-shot hyperspectral phasor camera for fast, multi-color fluorescence microscopy

Hyperspectral fluorescence imaging improves multiplexed observations of biological samples by utilizing multiple color channels across the spectral range to compensate for spectral overlap between labels. Typically, spectral resolution comes at a cost of decreased detection efficiency, which both hampers imaging speed and increases photo-toxicity to the samples. Here, we present a high-speed, high-efficiency snapshot spectral acquisition method, based on optical compression of the fluorescence spectra via Fourier transform, that overcomes the challenges of discrete spectral sampling: single-shot hyperspectral phasor camera (SHy-Cam). SHy-Cam captures fluorescence spatial and spectral information in a single exposure with a standard scientific CMOS camera, with photon efficiency of over 80%, easily and with acquisition rates exceeding 30 datasets per second, making it a powerful tool for multi-color in vivo imaging. Its simple design, using readily available optical components, and its easy integration provide a low-cost solution for multi-color fluorescence imaging with increased efficiency and speed.

Dual-slit confocal light-sheet microscopy using birefringent crystals

We present a method to use a birefringent crystal for generating two illumination beams in a digital scanned laser light-sheet microscopy (DSLM) system. Upon this, a conventional confocal DSLM can be easily upgraded to a dual-slit confocal DSLM with two-fold imaging speed. We have implemented this method to our bidirectional DSLM system, locating two identical calcite crystals on both illumination paths from both sides of the sample. The neurons of in vivo larval zebrafish have been fast imaged with sterling image quality, especially ~2.5 times higher contrast, compared to the conventional DSLM.

Applications and Advances of Multicellular Tumor Spheroids: Challenges in Their Development and Analysis

Biomedical research requires both in vitro and in vivo studies in order to explore disease processes or drug interactions. Foundational investigations have been performed at the cellular level using two-dimensional cultures as the gold-standard method since the early 20th century. However, three-dimensional (3D) cultures have emerged as a new tool for tissue modeling over the last few years, bridging the gap between in vitro and animal model studies. Cancer has been a worldwide challenge for the biomedical community due to its high morbidity and mortality rates. Various methods have been developed to produce multicellular tumor spheroids (MCTSs), including scaffold-free and scaffold-based structures, which usually depend on the demands of the cells used and the related biological question. MCTSs are increasingly utilized in studies involving cancer cell metabolism and cell cycle defects. These studies produce massive amounts of data, which demand elaborate and complex tools for thorough analysis. In this review, we discuss the advantages and disadvantages of several up-to-date methods used to construct MCTSs. In addition, we also present advanced methods for analyzing MCTS features. As MCTSs more closely mimic the in vivo tumor environment, compared to 2D monolayers, they can evolve to be an appealing model for in vitro tumor biology studies.

Volumetric light sheet imaging with adaptive optics correction

Light sheet microscopy has developed quickly over the past decades and become a popular method for imaging live model organisms and other thick biological tissues. For rapid volumetric imaging, an electrically tunable lens can be used to rapidly change the imaging plane in the sample. For larger fields of view and higher NA objectives, the electrically tunable lens introduces aberrations in the system, particularly away from the nominal focus and off-axis. Here, we describe a system that employs an electrically tunable lens and adaptive optics to image over a volume of 499 × 499 × 192 μm3 with close to diffraction-limited resolution. Compared to the system without adaptive optics, the performance shows an increase in signal to background ratio by a factor of 3.5. While the system currently requires 7s/volume, it should be straightforward to increase the imaging speed to under 1s per volume.

Large-scale high-throughput 3D culture, imaging, and analysis of cell spheroids using microchip-enhanced light-sheet microscopy

Light sheet microscopy combined with a microchip is an emerging tool in biomedical research that notably improves efficiency. However, microchip-enhanced light-sheet microscopy is limited by noticeable aberrations induced by the complex refractive indices in the chip. Herein, we report a droplet microchip that is specifically engineered to be capable of large-scale culture of 3D spheroids (over 600 samples per chip) and has a polymer index matched to water (difference <1%). When combined with a lab-built open-top light-sheet microscope, this microchip-enhanced microscopy technique allows 3D time-lapse imaging of the cultivated spheroids with ∼2.5-µm single-cell resolution and a high throughput of ∼120 spheroids per minute. This technique was validated by a comparative study on the proliferation and apoptosis rates of hundreds of spheroids with or without treatment with the apoptosis-inducing drug Staurosporine.

Single-molecule localization microscopy goes quantitative

In the last few years, single-molecule localization (SMLM) techniques have been used to address biological questions in different research fields. More recently, super-resolution has also been proposed as a quantitative tool for quantifying protein copy numbers at the nanoscale level. In this scenario, quantitative approaches, mainly based on stepwise photobleaching and quantitative SMLM assisted by calibration standards, offer an exquisite tool for investigating protein complexes. This primer focuses on the basic concepts behind quantitative super-resolution microscopy, also providing strategies to overcome the technical hurdles that could limit their application.

Adaptive optics for optical microscopy [Invited]

Optical microscopy is widely used to visualize fine structures. When applied to bioimaging, its performance is often degraded by sample-induced aberrations. In recent years, adaptive optics (AO), originally developed to correct for atmosphere-associated aberrations, has been applied to a wide range of microscopy modalities, enabling high- or super-resolution imaging of biological structure and function in complex tissues. Here, we review classic and recently developed AO techniques and their applications in optical microscopy.

Compact, high-speed multi-directional selective plane illumination microscopy

We present an elegant scheme for providing multi-directional illumination in selective plane illumination microscopy (SPIM). Light sheets can be delivered from one of two opposed directions at a time and pivoted about their center for efficient stripe artifact suppression using only a single galvanometric scanning mirror to perform both functions. The scheme results in a much smaller instrument footprint and allows multi-directional illumination with reduced expense compared with comparable schemes. Switching between the illumination paths is near instantaneous and the whole-plane illumination scheme of SPIM maintains the lowest rates of photodamage, which is often sacrificed by other recently reported destriping strategies. The ease of synchronization allows this scheme to be used at higher speeds than resonant mirrors typically used in this regard. We provide validation of this approach in the dynamic environment of the zebrafish beating heart, where imaging at up to 800 frames per second is demonstrated alongside efficient suppression of artifacts.

Imaging Approaches and the Quantitative Analysis of Heart Development

Heart morphogenesis is a complex and dynamic process that has captivated researchers for almost a century. This process involves three main stages, during which the heart undergoes growth and folding on itself to form its common chambered shape. However, imaging heart development presents significant challenges due to the rapid and dynamic changes in heart morphology. Researchers have used different model organisms and developed various imaging techniques to obtain high-resolution images of heart development. Advanced imaging techniques have allowed the integration of multiscale live imaging approaches with genetic labeling, enabling the quantitative analysis of cardiac morphogenesis. Here, we discuss the various imaging techniques used to obtain high-resolution images of whole-heart development. We also review the mathematical approaches used to quantify cardiac morphogenesis from 3D and 3D+time images and to model its dynamics at the tissue and cellular levels.

Time-lapse and cleared imaging of mouse embryonic lung explants to study three-dimensional cell morphology and topology dynamics

Here, we present a protocol for collecting high-spatiotemporal-resolution datasets of undisturbed mouse embryonic epithelial rudiments using light-sheet fluorescence microscopy. We describe steps for rudiment dissection, clearing, and embedding for cleared and live imaging. We then detail procedures for light-sheet imaging followed by image processing and morphometric analysis. We provide protocol variations for imaging both growing and optically cleared lung explants to encourage the quantitative exploration of three-dimensional cell shapes, cell organization, and complex cell-cell dynamics. For complete details on the use and execution of this protocol, please refer to Gómez et al. (2021).¹.

Airy beam light sheet microscopy boosted by deep learning deconvolution

Common light sheet microscopy comes with a trade-off between light sheet width defining the optical sectioning and the usable field of view arising from the divergence of the illuminating Gaussian beam. To overcome this, low-diverging Airy beams have been introduced. Airy beams, however, exhibit side lobes degrading image contrast. Here, we constructed an Airy beam light sheet microscope, and developed a deep learning image deconvolution to remove the effects of the side lobes without knowledge of the point spread function. Using a generative adversarial network and high-quality training data, we significantly enhanced image contrast and improved the performance of a bicubic upscaling. We evaluated the performance with fluorescently labeled neurons in mouse brain tissue samples. We found that deep learning-based deconvolution was about 20-fold faster than the standard approach. The combination of Airy beam light sheet microscopy and deep learning deconvolution allows imaging large volumes rapidly and with high quality.

Smart Lattice Light Sheet Microscopy for imaging rare and complex cellular events

Light sheet microscopes enable rapid, high-resolution imaging of biological specimens; however, biological processes span a variety of spatiotemporal scales. Moreover, long-term phenotypes are often instigated by rare or fleeting biological events that are difficult to capture with a single imaging modality and constant imaging parameters. To overcome this limitation, we present smartLLSM, a microscope that incorporates AI-based instrument control to autonomously switch between epifluorescent inverted imaging and lattice light sheet microscopy. We apply this technology to two major scenarios. First, we demonstrate that the instrument provides population-level statistics of cell cycle states across thousands of cells on a coverslip. Second, we show that by using real-time image feedback to switch between imaging modes, the instrument autonomously captures multicolor 3D datasets or 4D time-lapse movies of dividing cells at rates that dramatically exceed human capabilities. Quantitative image analysis on high-content + high-throughput datasets reveal kinetochore and chromosome dynamics in dividing cells and determine the effects of drug perturbation on cells in specific mitotic stages. This new methodology enables efficient detection of rare events within a heterogeneous cell population and records these processes with high spatiotemporal 4D imaging over statistically significant replicates.

Sidelobe suppression in structured light sheet fluorescence microscopy by the superposition of two light sheets

Light sheet microscopy has emerged as a powerful technique for three-dimensional and long-term vivo imaging within neuroscience and developmental biology. A light sheet illumination with structured light fields allows a better tradeoff between the field of view and axial resolution but suffers from strong side lobes. Here, we propose a method of producing structured light sheet illumination with suppressed side lobes by applying the superposition of two light sheets. The side lobe suppression results from the destructive interference between the side lobes and constructive interference between the main lobe of the two light sheets. In the proposed method, the incident light pattern in the rear pupil plane of the illumination objective is a combination of the incident light line beams required for the generation of the two interfering light sheets. We present a fast and simple calculation method to determine the incident light pattern in the rear pupil plane. Simulation results demonstrate the effectiveness of the proposed sidelobe suppression method for double-line light sheet, four-line light sheet, as well as line Bessel sheet. In particular, an 81% decrease in the relative side lobe energy can be achieved in case of double-line light sheet with an almost nonchanging propagation length. We show a way of using combined incident light patterns to generate structured light sheets with interference-resulted side lobe suppression, which is straightforward in design and with advantages of improved imaging performance.

Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture

Improving cardiac function through stem-cell regenerative therapy requires functional and structural integration of the transplanted cells with the host tissue. Visualizing the electromechanical interaction between native and graft cells necessitates 3D imaging with high spatio-temporal resolution and low photo-toxicity. A custom light-sheet fluorescence microscope was used for volumetric imaging of calcium dynamics in co-cultures of adult rat left ventricle cardiomyocytes and human induced pluripotent stem cell-derived cardiomyocytes. Aberration-free remote refocus of the detection plane synchronously to the scanning of the light sheet along the detection axis enabled fast dual-channel 3D imaging at subcellular resolution without mechanical sample disturbance at up to 8 Hz over a ∼300 µm × 40 µm × 50 µm volume. The two cell types were found to undergo electrically stimulated and spontaneous synchronized calcium transients and contraction. Electromechanical coupling improved with co-culture duration, with 50% of adult-CM coupled after 24 h of co-culture, compared to 19% after 4 h (p = 0.0305). Immobilization with para-nitroblebbistatin did not prevent calcium transient synchronization, with 35% and 36% adult-CM coupled in control and treated samples respectively (p = 0.91), indicating that electrical coupling can be maintained independently of mechanotransduction.

Light-sheet microscopy reveals dorsoventral asymmetric membrane dynamics of Amoeba proteus during pressure-driven locomotion

Amoebae are found all around the world and play an essential role in the carbon cycle in the environment. Therefore, the behavior of amoebae is a crucial factor when considering the global environment. Amoebae change their distribution through amoeboid locomotion, which are classified into several modes. In the pressure-driven mode, intracellular hydrostatic pressure generated by the contraction of cellular cortex actomyosin causes the pseudopod to extend. During amoeboid locomotion, the cellular surface exhibits dynamic deformation. Therefore, to understand the mechanism of amoeboid locomotion, it is important to characterize cellular membrane dynamics. Here, to clarify membrane dynamics during pressure-driven amoeboid locomotion, we developed a polkadot membrane staining method and performed light-sheet microscopy in Amoeba proteus, which exhibits typical pressure-driven amoeboid locomotion. It was observed that the whole cell membrane moved in the direction of movement, and the dorsal cell membrane in the posterior part of the cell moved more slowly than the other membrane. In addition, membrane complexity varied depending on the focused characteristic size of the membrane structure, and in general, the dorsal side was more complex than the ventral side. In summary, the membrane dynamics of Amoeba proteus during pressure-driven locomotion are asymmetric between the dorsal and ventral sides. This article has an associated interview with the co-first authors of the paper.

High-speed 2D light-sheet fluorescence microscopy enables quantification of spatially varying calcium dynamics in ventricular cardiomyocytes

Introduction: Reduced synchrony of calcium release and t-tubule structure organization in individual cardiomyocytes has been linked to loss of contractile strength and arrhythmia. Compared to confocal scanning techniques widely used for imaging calcium dynamics in cardiac muscle cells, light-sheet fluorescence microscopy enables fast acquisition of a 2D plane in the sample with low phototoxicity. Methods: A custom light-sheet fluorescence microscope was used to achieve dual-channel 2D timelapse imaging of calcium and the sarcolemma, enabling calcium sparks and transients in left and right ventricle cardiomyocytes to be correlated with the cell microstructure. Imaging electrically stimulated dual-labelled cardiomyocytes immobilized with para-nitroblebbistatin, a non-phototoxic, low fluorescence contraction uncoupler, with sub-micron resolution at 395 fps over a 38 μm × 170 µm FOV allowed characterization of calcium spark morphology and 2D mapping of the calcium transient time-to-half-maximum across the cell. Results: Blinded analysis of the data revealed sparks with greater amplitude in left ventricle myocytes. The time for the calcium transient to reach half-maximum amplitude in the central part of the cell was found to be, on average, 2 ms shorter than at the cell ends. Sparks co-localized with t-tubules were found to have significantly longer duration, larger area and spark mass than those further away from t-tubules. Conclusion: The high spatiotemporal resolution of the microscope and automated image-analysis enabled detailed 2D mapping and quantification of calcium dynamics of n = 60 myocytes, with the findings demonstrating multi-level spatial variation of calcium dynamics across the cell, supporting the dependence of synchrony and characteristics of calcium release on the underlying t-tubule structure.

Label-free, fast, 2-photon volume imaging of the organization of neurons and glia in the enteric nervous system

The enteric nervous system (ENS), sometimes referred to as a "second brain" is a quasi-autonomous nervous system, made up of interconnected plexuses organized in a mesh-like network lining the gastrointestinal tract. Originally described as an actor in the regulation of digestion, bowel contraction, and intestinal secretion, the implications of the ENS in various central neuropathologies has recently been demonstrated. However, with a few exceptions, the morphology and pathologic alterations of the ENS have mostly been studied on thin sections of the intestinal wall or, alternatively, in dissected explants. Precious information on the three-dimensional (3-D) architecture and connectivity is hence lost. Here, we propose the fast, label-free 3-D imaging of the ENS, based on intrinsic signals. We used a custom, fast tissue-clearing protocol based on a high refractive-index aqueous solution to increase the imaging depth and allow us the detection of faint signals and we characterized the autofluorescence (AF) from the various cellular and sub-cellular components of the ENS. Validation by immunofluorescence and spectral recordings complete this groundwork. Then, we demonstrate the rapid acquisition of detailed 3-D image stacks from unlabeled mouse ileum and colon, across the whole intestinal wall and including both the myenteric and submucosal enteric nervous plexuses using a new spinning-disk two-photon (2P) microscope. The combination of fast clearing (less than 15 min for 73% transparency), AF detection and rapid volume imaging [less than 1 min for the acquisition of a z-stack of 100 planes (150*150 μm) at sub-300-nm spatial resolution] opens up the possibility for new applications in fundamental and clinical research.

Single-shot optical projection tomography for high-speed volumetric imaging of dynamic biological samples

A single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic biological samples is presented. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio, but the sequential acquisition of projection images typically requires samples to be immobilized during the acquisition. A proof-of-principle system capable of single-shot tomography of a ~1 mm3 volume is presented, demonstrating camera-limited rates of up to 62.5 volumes/s, which has been applied to 3D imaging of a freely swimming zebrafish embryo. This is achieved by recording eight projection views simultaneously on four low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under £5000. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including high throughput flow cytometry applied to model organisms and fluid dynamics studies.