Live imaging of nervous system development and function using light-sheet microscopy

Airy-like beam-based light-sheet microscopy with improved FOV for zebrafish intracerebral hemorrhage

Airy light-sheet microscopy is rapidly gaining importance for imaging intact biological specimens because of the rapid speed, high resolution, and wide field nature of the imaging method. However, the depth of field (DOF) of the detection objective imposes limitations on the modulation transfer function (MTF) of the light sheet, which in turn affects the size of the field of view (FOV). Here we present an optimized phase modulation model, based on 'Airy-like' beam family, to stretch the curved lobes, which brings a wider FOV while maintaining high resolution. In addition, we further develop a planar 'Airy-like' light-sheet by two-photon excitation which can avoid the deconvolution process. We validated the new imaging method by performing a real-time monitoring of the dynamic process of cerebral hemorrhage in zebrafish larva. The proposed Airy-like beam-based light-sheet microscopy has great potential to be applied to the precise screening of cerebral hemorrhage-related drugs to help precision medicine in the future.

Optogenetic and thermogenetic manipulation of defined neural circuits and behaviors in Drosophila

Neural network dynamics underlying flexible animal behaviors remain elusive. The fruit fly Drosophila melanogaster is considered an excellent model in behavioral neuroscience because of its simple neuroanatomical architecture and the availability of various genetic methods. Moreover, Drosophila larvae's transparent body allows investigators to use optical methods on freely moving animals, broadening research directions. Activating or inhibiting well-defined events in excitable cells with a fine temporal resolution using optogenetics and thermogenetics led to the association of functions of defined neural populations with specific behavioral outputs such as the induction of associative memory. Furthermore, combining optogenetics and thermogenetics with state-of-the-art approaches, including connectome mapping and machine learning-based behavioral quantification, might provide a complete view of the experience- and time-dependent variations of behavioral responses. These methodologies allow further understanding of the functional connections between neural circuits and behaviors such as chemosensory, motivational, courtship, and feeding behaviors and sleep, learning, and memory.

From whole organism to ultrastructure: progress in axonal imaging for decoding circuit development

Since the pioneering work of Ramón y Cajal, scientists have sought to unravel the complexities of axon development underlying neural circuit formation. Micrometer-scale axonal growth cones navigate to targets that are often centimeters away. To reach their targets, growth cones react to dynamic environmental cues that change in the order of seconds to days. Proper axon growth and guidance are essential to circuit formation, and progress in imaging has been integral to studying these processes. In particular, advances in high- and super-resolution microscopy provide the spatial and temporal resolution required for studying developing axons. In this Review, we describe how improved microscopy has revolutionized our understanding of axonal development. We discuss how novel technologies, specifically light-sheet and super-resolution microscopy, led to new discoveries at the cellular scale by imaging axon outgrowth and circuit wiring with extreme precision. We next examine how advanced microscopy broadened our understanding of the subcellular dynamics driving axon growth and guidance. We finally assess the current challenges that the field of axonal biology still faces for imaging axons, and examine how future technology could meet these needs.

Zebrafish Models of Neurodevelopmental Disorders: Limitations and Benefits of Current Tools and Techniques

For the past few years there has been an exponential increase in the use of animal models to confirm the pathogenicity of candidate disease-causing genetic variants found in patients. One such animal model is the zebrafish. Despite being a non-mammalian animal, the zebrafish model has proven its potential in recapitulating the phenotypes of many different human genetic disorders. This review will focus on recent advances in the modeling of neurodevelopmental disorders in zebrafish, covering aspects from early brain development to techniques used for modulating gene expression, as well as how to best characterize the resulting phenotypes. We also review other existing models of neurodevelopmental disorders, and the current efforts in developing and testing compounds with potential therapeutic value.

Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited]

The development of imaging techniques beyond the diffraction limit has paved the way for detailed studies of nanostructures and molecular mechanisms in biological systems. Imaging thicker samples, such as mammalian cells and tissue, in all three dimensions, is challenging due to increased background and volumes to image. Light sheet illumination is a method that allows for selective irradiation of the image plane, and its inherent optical sectioning capability allows for imaging of biological samples with reduced background, photobleaching, and photodamage. In this review, we discuss the advantage of combining single-molecule imaging with light sheet illumination. We begin by describing the principles of single-molecule localization microscopy and of light sheet illumination. Finally, we present examples of designs that successfully have married single-molecule super-resolution imaging with light sheet illumination for improved precision in mammalian cells.

Technical implementations of light sheet microscopy

Fluorescence-based microscopy is among the most successful methods in biological studies. It played a critical role in the visualization of subcellular structures and in the analysis of complex cellular processes, and it is nowadays commonly employed in genetic and drug screenings. Among the fluorescence-based microscopy techniques, light sheet fluorescence microscopy (LSFM) has shown a quite interesting set of benefits. The technique combines the speed of epi-fluorescence acquisition with the optical sectioning capability typical of confocal microscopes. Its unique configuration allows the excitation of only a thin plane of the sample, thus fast, high resolution imaging deep inside tissues is nowadays achievable. The low peak intensity with which the sample is illuminated diminishes phototoxic effects and decreases photobleaching of fluorophores, ensuring data collection for days with minimal adverse consequences on the sample. It is no surprise that LSFM applications have raised in just few years and the technique has been applied to study a wide variety of samples, from whole organism, to tissues, to cell clusters, and single cells. As a consequence, in recent years numerous set-ups have been developed, each one optimized for the type of sample in use and the requirements of the question at hand. Hereby, we aim to review the most advanced LSFM implementations to assist new LSFM users in the choice of the LSFM set-up that suits their needs best. We also focus on new commercial microscopes and "do-it-yourself" strategies; likewise we review recent designs that allow a swift integration of LSFM on existing microscopes.

Deciphering tissue morphodynamics using bioimage informatics

In recent years developmental biology has greatly benefited from the latest advances in fluorescence microscopy techniques. Consequently, quantitative and automated analysis of this data is becoming a vital first step in the quest for novel insights into the various aspects of development. Here we present an introductory overview of the various image analysis methods proposed for developmental biology images, with particular attention to openly available software packages. These tools, as well as others to come, are rapidly paving the way towards standardized and reproducible bioimaging studies at the whole-tissue level. Reflecting on these achievements, we discuss the remaining challenges and the future endeavours lying ahead in the post-image analysis era.This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'.

Efficient processing and analysis of large-scale light-sheet microscopy data

Light-sheet microscopy is a powerful method for imaging the development and function of complex biological systems at high spatiotemporal resolution and over long time scales. Such experiments typically generate terabytes of multidimensional image data, and thus they demand efficient computational solutions for data management, processing and analysis. We present protocols and software to tackle these steps, focusing on the imaging-based study of animal development. Our protocols facilitate (i) high-speed lossless data compression and content-based multiview image fusion optimized for multicore CPU architectures, reducing image data size 30-500-fold; (ii) automated large-scale cell tracking and segmentation; and (iii) visualization, editing and annotation of multiterabyte image data and cell-lineage reconstructions with tens of millions of data points. These software modules are open source. They provide high data throughput using a single computer workstation and are readily applicable to a wide spectrum of biological model systems.

Quantitative imaging of cell dynamics in mouse embryos using light-sheet microscopy

Single/selective-plane illumination, or light-sheet, systems offer several advantages over other fluorescence microscopy methods for live, 3D microscopy. These systems are valuable for studying embryonic development in several animal systems, such as Drosophila, C. elegans and zebrafish. The geometry of the light path in this form of microscopy requires the sample to be accessible from multiple sides and fixed in place so that it can be rotated around a single axis. Popular methods for mounting include hanging the specimen from a pin or embedding it in 1-2% agarose. These methods can be particularly problematic for certain samples, such as post-implantation mouse embryos, that expand significantly in size and are very delicate and sensitive to mounting. To overcome the current limitations and to establish a robust strategy for long-term (24 h) time-lapse imaging of E6.5-8.5 mouse embryos with light-sheet microscopy, we developed and tested a method using hollow agarose cylinders designed to accommodate for embryonic growth, yet provide boundaries to minimize tissue drift and enable imaging in multiple orientations. Here, we report the first 24-h time-lapse sequences of post-implantation mouse embryo development with light-sheet microscopy. We demonstrate that light-sheet imaging can provide both quantitative data for tracking changes in morphogenesis and reveal new insights into mouse embryogenesis. Although we have used this approach for imaging mouse embryos, it can be extended to imaging other types of embryos as well as tissue explants.

Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data

The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for the segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (i) generality by reconstructing cell lineages in four-dimensional, terabyte-sized image data sets of fruit fly, zebrafish and mouse embryos acquired with three types of fluorescence microscopes, (ii) scalability by analyzing advanced stages of development with up to 20,000 cells per time point at 26,000 cells min(-1) on a single computer workstation and (iii) ease of use by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities. Using our system, we performed the first cell lineage reconstruction of early Drosophila melanogaster nervous system development, revealing neuroblast dynamics throughout an entire embryo.