Imaging cellular network dynamics in three dimensions using fast 3D laser scanning

Optical projection tomography implemented for accessibility and low cost (OPTImAL)

Optical projection tomography (OPT) is a three-dimensional mesoscopic imaging modality that can use absorption or fluorescence contrast, and is widely applied to fixed and live samples in the mm-cm scale. For fluorescence OPT, we present OPT implemented for accessibility and low cost, an open-source research-grade implementation of modular OPT hardware and software that has been designed to be widely accessible by using low-cost components, including light-emitting diode (LED) excitation and cooled complementary metal-oxide-semiconductor (CMOS) cameras. Both the hardware and software are modular and flexible in their implementation, enabling rapid switching between sample size scales and supporting compressive sensing to reconstruct images from undersampled sparse OPT data, e.g. to facilitate rapid imaging with low photobleaching/phototoxicity. We also explore a simple implementation of focal scanning OPT to achieve higher resolution, which entails the use of a fan-beam geometry reconstruction method to account for variation in magnification. This article is part of the Theo Murphy meeting issue 'Open, reproducible hardware for microscopy'.

Large-volume focus control at 10 MHz refresh rate via fast line-scanning amplitude-encoded scattering-assisted holography

The capability of focus control has been central to optical technologies that require both high temporal and spatial resolutions. However, existing varifocal lens schemes are commonly limited to the response time on the microsecond timescale and share the fundamental trade-off between the response time and the tuning power. Here, we propose an ultrafast holographic focusing method enabled by translating the speed of a fast 1D beam scanner into the speed of the complex wavefront modulation of a relatively slow 2D spatial light modulator. Using a pair of a digital micromirror device and a resonant scanner, we demonstrate an unprecedented refresh rate of focus control of 31 MHz, which is more than 1,000 times faster than the switching rate of a digital micromirror device. We also show that multiple micrometer-sized focal spots can be independently addressed in a range of over 1 MHz within a large volume of 5 mm × 5 mm × 5.5 mm, validating the superior spatiotemporal characteristics of the proposed technique - high temporal and spatial precision, high tuning power, and random accessibility in a three-dimensional space. The demonstrated scheme offers a new route towards three-dimensional light manipulation in the 100 MHz regime.

A Comprehensive Review of Vision-Based 3D Reconstruction Methods

With the rapid development of 3D reconstruction, especially the emergence of algorithms such as NeRF and 3DGS, 3D reconstruction has become a popular research topic in recent years. 3D reconstruction technology provides crucial support for training extensive computer vision models and advancing the development of general artificial intelligence. With the development of deep learning and GPU technology, the demand for high-precision and high-efficiency 3D reconstruction information is increasing, especially in the fields of unmanned systems, human-computer interaction, virtual reality, and medicine. The rapid development of 3D reconstruction is becoming inevitable. This survey categorizes the various methods and technologies used in 3D reconstruction. It explores and classifies them based on three aspects: traditional static, dynamic, and machine learning. Furthermore, it compares and discusses these methods. At the end of the survey, which includes a detailed analysis of the trends and challenges in 3D reconstruction development, we aim to provide a comprehensive introduction for individuals who are currently engaged in or planning to conduct research on 3D reconstruction. Our goal is to help them gain a comprehensive understanding of the relevant knowledge related to 3D reconstruction.

Multibeam continuous axial scanning two-photon microscopy for in vivo volumetric imaging in mouse brain

This study presents an alternative approach for two-photon volumetric imaging that combines multibeam lateral scanning with continuous axial scanning using a confocal spinning-disk scanner and an electrically focus tunable lens. Using this proposed system, the brain of a living mouse could be imaged at a penetration depth of over 450 μm from the surface. In vivo volumetric Ca2+ imaging at a volume rate of 1.5 Hz within a depth range of 130-200 μm, was segmented with an axial pitch of approximately 5-µm and revealed spontaneous activity of neurons with their 3D positions. This study offers a practical microscope design equipped with compact scanners, a simple control system, and readily adjustable imaging parameters, which is crucial for the widespread adoption of two-photon volumetric imaging.

High-speed multiplane confocal microscopy for voltage imaging in densely labeled neuronal populations

Genetically encoded voltage indicators (GEVIs) hold immense potential for monitoring neuronal population activity. To date, best-in-class GEVIs rely on one-photon excitation. However, GEVI imaging of dense neuronal populations remains difficult because out-of-focus background fluorescence produces low contrast and excess noise when paired with conventional one-photon widefield imaging methods. To address this challenge, we developed an imaging system capable of efficient, high-contrast GEVI imaging at near-kHz rates and demonstrate it for in vivo and ex vivo imaging applications in the mouse neocortex. Our approach uses simultaneous multiplane imaging to monitor activity within contiguous tissue volumes with no penalty in speed or requirement for high excitation power. This approach, multi-Z imaging with confocal detection (MuZIC), permits high signal-to-noise ratio voltage imaging in densely labeled neuronal populations and is compatible with imaging through micro-optics. Moreover, it minimizes artifacts associated with concurrent imaging and optogenetic photostimulation for all-optical electrophysiology.

Review of data processing of functional optical microscopy for neuroscience

Functional optical imaging in neuroscience is rapidly growing with the development of optical systems and fluorescence indicators. To realize the potential of these massive spatiotemporal datasets for relating neuronal activity to behavior and stimuli and uncovering local circuits in the brain, accurate automated processing is increasingly essential. We cover recent computational developments in the full data processing pipeline of functional optical microscopy for neuroscience data and discuss ongoing and emerging challenges.

Two-photon calcium imaging of neuronal activity

In vivo two-photon calcium imaging (2PCI) is a technique used for recording neuronal activity in the intact brain. It is based on the principle that, when neurons fire action potentials, intracellular calcium levels rise, which can be detected using fluorescent molecules that bind to calcium. This Primer is designed for scientists who are considering embarking on experiments with 2PCI. We provide the reader with a background on the basic concepts behind calcium imaging and on the reasons why 2PCI is an increasingly powerful and versatile technique in neuroscience. The Primer explains the different steps involved in experiments with 2PCI, provides examples of what ideal preparations should look like and explains how data are analysed. We also discuss some of the current limitations of the technique, and the types of solutions to circumvent them. Finally, we conclude by anticipating what the future of 2PCI might look like, emphasizing some of the analysis pipelines that are being developed and international efforts for data sharing.

A review on structural development and recognition–localization methods for end-effector of fruit–vegetable picking robots

The excellent performance of fruit and vegetable picking robots is usually contributed by the reasonable structure of end-effector and recognition–localization methods with high accuracy. As a result, efforts are focused on two aspects, and diverse structures of end-effector, target recognition methods as well as their combinations are yielded continuously. A good understanding for the working principle, advantages, limitations, and the adaptability in respective fields is helpful to design picking robots. Therefore, depending on different grasping ways, separating methods, structures, materials, and driving modes, main characteristics existing in traditional schemes will be depicted firstly. According to technical routes, advantages, potential applications, and challenges, underactuated manipulators and soft manipulators representing future development are then summarized systematically. Secondly, partial recognition and localization methods are also demonstrated. Specifically, current recognition manners adopting the single-feature, multi-feature fusion and deep learning are explained in view of their advantages, limitations, and successful instances. In the field of 3D localization, active vision based on the structured light, laser scanning, time of flight, and radar is reflected through the respective applications. Also, another 3D localization method called passive vision is also evaluated by advantages, limitations, the degree of automation, reconstruction effects, and the application scenario, such as monocular vision, binocular vision, and multiocular vision. Finally portrayed from structural development, recognition, and localization methods, it is possible to develop future end-effectors for fruit and vegetable picking robots with superior characteristics containing the less driving element, rigid–flexible–bionic coupling soft manipulators, simple control program, high efficiency, low damage, low cost, high versatility, and high recognition accuracy in all-season picking tasks.

Breaking trade-offs: development of fast, high-resolution, wide-field two-photon microscopes to reveal the computational principles of the brain

Information in the brain is represented by the collective and coordinated activity of single neurons. Activity is determined by a large amount of dynamic synaptic inputs from neurons in the same and/or distant brain regions. Therefore, the simultaneous recording of single neurons across several brain regions is critical for revealing the interactions among neurons that reflect the computational principles of the brain. Recently, several wide-field two-photon (2P) microscopes equipped with sizeable objective lenses have been reported. These microscopes enable large-scale in vivo calcium imaging and have the potential to make a significant contribution to the elucidation of information-processing mechanisms in the cerebral cortex. This review discusses recent reports on wide-field 2P microscopes and describes the trade-offs encountered in developing wide-field 2P microscopes. Large-scale imaging of neural activity allows us to test hypotheses proposed in theoretical neuroscience, and to identify rare but influential neurons that have potentially significant impacts on the whole-brain system.

Emerging Roles of Microfluidics in Brain Research: From Cerebral Fluids Manipulation to Brain-on-a-Chip and Neuroelectronic Devices Engineering

Remarkable progress made in the past few decades in brain research enables the manipulation of neuronal activity in single neurons and neural circuits and thus allows the decipherment of relations between nervous systems and behavior. The discovery of glymphatic and lymphatic systems in the brain and the recently unveiled tight relations between the gastrointestinal (GI) tract and the central nervous system (CNS) further revolutionize our understanding of brain structures and functions. Fundamental questions about how neurons conduct two-way communications with the gut to establish the gut-brain axis (GBA) and interact with essential brain components such as glial cells and blood vessels to regulate cerebral blood flow (CBF) and cerebrospinal fluid (CSF) in health and disease, however, remain. Microfluidics with unparalleled advantages in the control of fluids at microscale has emerged recently as an effective approach to address these critical questions in brain research. The dynamics of cerebral fluids (i.e., blood and CSF) and novel in vitro brain-on-a-chip models and microfluidic-integrated multifunctional neuroelectronic devices, for example, have been investigated. This review starts with a critical discussion of the current understanding of several key topics in brain research such as neurovascular coupling (NVC), glymphatic pathway, and GBA and then interrogates a wide range of microfluidic-based approaches that have been developed or can be improved to advance our fundamental understanding of brain functions. Last, emerging technologies for structuring microfluidic devices and their implications and future directions in brain research are discussed.

3D Scanning/Printing: A Technological Stride in Sculpture

The creation of innovative tools, objects and artifacts that introduce abstract ideas in the real world is a necessary step for the evolution process and characterize the creative capacity of civilization. Sculpture is based on the available technology for its creation process and is strongly related to the level of technological sophistication of each era. This paper analyzes the evolution of basic sculpture techniques (carving, lost-wax casting and 3D scanning/printing), and their importance as a culture footprint. It also presents and evaluates the added creative capacities of each technological step and the different methods of 3D scanning/printing concerning sculpture. It is also an attempt to define the term “material poetics”, which is connected to sculpture artifacts. We conclude that 3D scanning/printing is an important sign of civilization, although artifacts lose a part of material poetics with additive manufacturing. Subsequently, there are various causes of the destruction of sculptures, leaving a hole in the history of art. Finally, this paper showcases the importance of 3D scanning/printing in salvaging cultural heritage, as it has radically altered the way we “backup” objects.

Fast optical recording of neuronal activity by three-dimensional custom-access serial holography

Optical recording of neuronal activity in three-dimensional (3D) brain circuits at cellular and millisecond resolution in vivo is essential for probing information flow in the brain. While random-access multiphoton microscopy permits fast optical access to neuronal targets in three dimensions, the method is challenged by motion artifacts when recording from behaving animals. Therefore, we developed three-dimensional custom-access serial holography (3D-CASH). Built on a fast acousto-optic light modulator, 3D-CASH performs serial sampling at 40 kHz from neurons at freely selectable 3D locations. Motion artifacts are eliminated by targeting each neuron with a size-optimized pattern of excitation light covering the cell body and its anticipated displacement field. Spike rates inferred from GCaMP6f recordings in visual cortex of awake mice tracked the phase of a moving bar stimulus with higher spike correlation between intra compared to interlaminar neuron pairs. 3D-CASH offers access to the millisecond correlation structure of in vivo neuronal activity in 3D microcircuits.

Neurophotonic tools for microscopic measurements and manipulation: status report

Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.

GraFT: Graph Filtered Temporal Dictionary Learning for Functional Neural Imaging

Optical imaging of calcium signals in the brain has enabled researchers to observe the activity of hundreds-to-thousands of individual neurons simultaneously. Current methods predominantly use morphological information, typically focusing on expected shapes of cell bodies, to better identify neurons in the field-of-view. The explicit shape constraints limit the applicability of automated cell identification to other important imaging scales with more complex morphologies, e.g., dendritic or widefield imaging. Specifically, fluorescing components may be broken up, incompletely found, or merged in ways that do not accurately describe the underlying neural activity. Here we present Graph Filtered Temporal Dictionary (GraFT), a new approach that frames the problem of isolating independent fluorescing components as a dictionary learning problem. Specifically, we focus on the time-traces-the main quantity used in scientific discovery-and learn a time trace dictionary with the spatial maps acting as the presence coefficients encoding which pixels the time-traces are active in. Furthermore, we present a novel graph filtering model which redefines connectivity between pixels in terms of their shared temporal activity, rather than spatial proximity. This model greatly eases the ability of our method to handle data with complex non-local spatial structure. We demonstrate important properties of our method, such as robustness to morphology, simultaneously detecting different neuronal types, and implicitly inferring number of neurons, on both synthetic data and real data examples. Specifically, we demonstrate applications of our method to calcium imaging both at the dendritic, somatic, and widefield scales.

Video-rate remote refocusing through continuous oscillation of a membrane deformable mirror

This paper presents the use of a deformable mirror (DM) configured to rapidly refocus a microscope employing a high numerical aperture (NA) objective lens. An Alpao DM97-15 membrane DM was used to refocus a 40×/0.80 NA water-immersion objective through a defocus range of -50-50 μm at 26.3 sweeps s^-1. We achieved imaging with a mean Strehl metric of >0.6 over a field of view in the sample of 200 × 200 μm² over a defocus range of 77 μm. We describe an optimisation procedure where the mirror is swept continuously in order to avoid known problems of hysteresis associated with the membrane DM employed. This work demonstrates that a DM-based refocusing system could in the future be used in light-sheet fluorescence microscopes to achieve video-rate volumetric imaging.

Eavesdropping wires: Recording activity in axons using genetically encoded calcium indicators

Neurons broadcast electrical signals to distal brain regions through extensive axonal arbors. Genetically encoded calcium sensors permit the direct observation of action potential activity at axonal terminals, providing unique insights on the organization and function of neural projections. Here, we consider what information can be gleaned from axonal recordings made at scales ranging from the summed activity extracted from multi-cell axon projections to single boutons. In particular, we discuss the application of different recently developed multi photon and fiber photometry methods for recording neural activity in axons of rodents. We define experimental difficulties associated with imaging approaches in the axonal compartment and highlight the latest methodological advances for addressing these issues. Finally, we reflect on ways in which new technologies can be used in conjunction with axon calcium imaging to address current questions in neurobiology.

Temporally multiplexed dual-plane imaging of neural activity with four-dimensional precision

Spatiotemporal patterns of neural activity generate brain functions, such as perception, memory, and behavior. Four-dimensional (4-D: x, y, z, t) analyses of such neural activity will facilitate understanding of brain functions. However, conventional two-photon microscope systems observe single-plane brain tissue alone at a time with cellular resolution. It faces a trade-off between the spatial resolution in the x-, y-, and z-axes and the temporal resolution by a limited point-by-point scan speed. To overcome this trade-off in 4-D imaging, we developed a holographic two-photon microscope for dual-plane imaging. A spatial light modulator (SLM) provided an additional focal plane at a different depth. Temporal multiplexing of split lasers with an optical chopper allowed fast imaging of two different focal planes. We simultaneously recorded the activities of neurons on layers 2/3 and 5 of the cerebral cortex in awake mice in vivo. The present study demonstrated the proof-of-concept of dual-plane two-photon imaging of neural circuits by using the temporally multiplexed SLM-based microscope. The temporally multiplexed holographic microscope, combined with in vivo labeling with genetically encoded probes, enabled 4-D imaging and analysis of neural activities at cellular resolution and physiological timescales. Large-scale 4-D imaging and analysis will facilitate studies of not only the nervous system but also of various biological systems.

Smart nano-micro platforms for ophthalmological applications: The state-of-the-art and future perspectives

Smart nano-micro platforms have been extensively applied for diverse biomedical applications, mostly focusing on cancer therapy. In comparison with conventional nanotechnology, the smart nano-micro matrix can exhibit specific response to exogenous or endogenous triggers, and thus can achieve multiple functions e.g. site-specific drug delivery, bio-imaging and detection of bio-molecules. These intriguing techniques have expanded into ophthalmology in recent years, yet few works have been summarized in this field. In this work, we provide the state-of-the-art of diverse nano-micro platforms based on both the conventional materials (e.g. natural or synthetic polymers, lipid nanomaterials, metal and metal oxide nanoparticles) and emerging nanomaterials (e.g. up-conversion nanoparticles, quantum dots and carbon materials) in ophthalmology, with some smart nano/micro platformers highlighted. The common ocular diseases studied in the field of nano-micro systems are firstly introduced, and their therapeutic method and the related drawback in clinic treatment are presented. The recent progress of different materials for diverse ocular applications is then demonstrated, with the representative nano- and micro-systems highlighted in detail. At last, an in-depth discussion on the clinical translation challenges faced in this field and the future direction are provided. This review would allow the researchers to design more smart nanomedicines in a more rational manner for specific ophthalmology applications.

High-speed volumetric two-photon fluorescence imaging of neurovascular dynamics

Understanding the structure and function of vasculature in the brain requires us to monitor distributed hemodynamics at high spatial and temporal resolution in three-dimensional (3D) volumes in vivo. Currently, a volumetric vasculature imaging method with sub-capillary spatial resolution and blood flow-resolving speed is lacking. Here, using two-photon laser scanning microscopy (TPLSM) with an axially extended Bessel focus, we capture volumetric hemodynamics in the awake mouse brain at a spatiotemporal resolution sufficient for measuring capillary size and blood flow. With Bessel TPLSM, the fluorescence signal of a vessel becomes proportional to its size, which enables convenient intensity-based analysis of vessel dilation and constriction dynamics in large volumes. We observe entrainment of vasodilation and vasoconstriction with pupil diameter and measure 3D blood flow at 99 volumes/second. Demonstrating high-throughput monitoring of hemodynamics in the awake brain, we expect Bessel TPLSM to make broad impacts on neurovasculature research.

Long-range remote focusing by image-plane aberration correction

Laser scanning plays an important role in a broad range of applications. Toward 3D aberration-free scanning, a remote focusing technique has been developed for high-speed imaging applications. However, the implementation of remote focusing often suffers from a limited axial scan range as a result of unknown aberration. Through simple analysis, we show that the sample-to-image path length conservation is crucially important to the remote focusing performance. To enhance the axial scan range, we propose and demonstrate an image-plane aberration correction method. Using a static correction, we can effectively improve the focus quality over a large defocusing range. Experimentally, we achieved ∼three times greater defocusing range than that of conventional methods. This technique can broadly benefit the implementations of high-speed large-volume 3D imaging.

Volumetric Lissajous confocal microscopy with tunable spatiotemporal resolution

Dynamic biological systems present challenges to existing three-dimensional (3D) optical microscopes because of their continuous temporal and spatial changes. Most techniques are rigid in adapting the acquisition parameters over time, as in confocal microscopy, where a laser beam is sequentially scanned at a predefined spatial sampling rate and pixel dwell time. Such lack of tunability forces a user to provide scan parameters, which may not be optimal, based on the best assumption before an acquisition starts. Here, we developed volumetric Lissajous confocal microscopy to achieve unsurpassed 3D scanning speed with a tunable sampling rate. The system combines an acoustic liquid lens for continuous axial focus translation with a resonant scanning mirror. Accordingly, the excitation beam follows a dynamic Lissajous trajectory enabling sub-millisecond acquisitions of image series containing 3D information at a sub-Nyquist sampling rate. By temporal accumulation and/or advanced interpolation algorithms, the volumetric imaging rate is selectable using a post-processing step at the desired spatiotemporal resolution for events of interest. We demonstrate multicolor and calcium imaging over volumes of tens of cubic microns with 3D acquisition speeds of 30 Hz and frame rates up to 5 kHz.

Volumetric chemical imaging in vivo by a remote-focusing stimulated Raman scattering microscope

Operable under ambient light and providing chemical selectivity, stimulated Raman scattering (SRS) microscopy opens a new window for imaging molecular events on a human subject, such as filtration of topical drugs through the skin. A typical approach for volumetric SRS imaging is through piezo scanning of an objective lens, which often disturbs the sample and offers a low axial scan rate. To address these challenges, we have developed a deformable mirror-based remote-focusing SRS microscope, which not only enables high-quality volumetric chemical imaging without mechanical scanning of the objective but also corrects the system aberrations simultaneously. Using the remote-focusing SRS microscope, we performed volumetric chemical imaging of living cells and captured in real time the dynamic diffusion of topical chemicals into human sweat pores.

Design of a multi-modality DMD-based two-photon microscope system

We present the modular design and characterization of a multi-modality video-rate two-photon excitation (TPE) microscope based on integrating a digital micromirror device (DMD), which functions as an ultrafast beam shaper and random-access scanner, with a pair of galvanometric scanners. The TPE microscope system realizes a suite of new imaging functionalities, including (1) multi-layer imaging with 3D programmable imaging planes, (2) DMD-based wavefront correction, and (3) multi-focus optical stimulation (up to 22.7 kHz) with simultaneous TPE imaging, all in real-time. We also report the detailed optomechanical design and software development that achieves high level system automation. To verify the performance of different microscope functions, we have devised and performed imaging experiments on Drosophila brain, mouse kidney and human stem cells. The results not only show improved imaging resolution and depths via the DMD-based adaptive optics, but also demonstrate fast multi-focus stimulation for the first time. With the new imaging capabilities, e.g., tools for optogenetics, the multi-modality TPE microscope may play a critical role in the applications pertinent to neuroscience and biophotonics.

Pupil plane actuated remote focusing for rapid focal depth control

Laser scanning is widely employed in imaging and material processing. Common laser scanners are often fast for 2D transverse scanning. Rapid focal depth control is highly desired in many applications. Although remote focusing has been developed to achieve fast focal depth control, the implementation is limited by the laser damage to the actuator near laser focus. Here, we present a new method named pupil plane actuated remote focusing, which enables sub-millisecond response time while avoiding laser damage. We demonstrate its application by implementing a dual-plane two-photon laser scanning fluorescence microscope for in vivo recording of calcium transient of neurons in mouse neocortex.

Comprehensive Imaging of Sensory-Evoked Activity of Entire Neurons Within the Awake Developing Brain Using Ultrafast AOD-Based Random-Access Two-Photon Microscopy

Determining how neurons transform synaptic input and encode information in action potential (AP) firing output is required for understanding dendritic integration, neural transforms and encoding. Limitations in the speed of imaging 3D volumes of brain encompassing complex dendritic arbors in vivo using conventional galvanometer mirror-based laser-scanning microscopy has hampered fully capturing fluorescent sensors of activity throughout an individual neuron's entire complement of synaptic inputs and somatic APs. To address this problem, we have developed a two-photon microscope that achieves high-speed scanning by employing inertia-free acousto-optic deflectors (AODs) for laser beam positioning, enabling random-access sampling of hundreds to thousands of points-of-interest restricted to a predetermined neuronal structure, avoiding wasted scanning of surrounding extracellular tissue. This system is capable of comprehensive imaging of the activity of single neurons within the intact and awake vertebrate brain. Here, we demonstrate imaging of tectal neurons within the brains of albino Xenopus laevis tadpoles labeled using single-cell electroporation for expression of a red space-filling fluorophore to determine dendritic arbor morphology, and either the calcium sensor jGCaMP7s or the glutamate sensor iGluSnFR as indicators of neural activity. Using discrete, point-of-interest scanning we achieve sampling rates of 3 Hz for saturation sampling of entire arbors at 2 μm resolution, 6 Hz for sequentially sampling 3 volumes encompassing the dendritic arbor and soma, and 200–250 Hz for scanning individual planes through the dendritic arbor. This system allows investigations of sensory-evoked information input-output relationships of neurons within the intact and awake brain.

Spinning disk-remote focusing microscopy

Fast confocal imaging was achieved by combining remote focusing with differential spinning disk optical sectioning to rapidly acquire images of live samples at cellular resolution. Axial and lateral full width half maxima less than 5 µm and 490 nm respectively are demonstrated over 130 µm axial range with a 256 × 128 µm field of view. A water-index calibration slide was used to achieve an alignment that minimises image volume distortion. Application to live biological samples was demonstrated by acquiring image volumes over a 24 µm axial range at 1 volume/s, allowing for the detection of calcium-based neuronal activity in Platynereis dumerilii larvae.

The temporal structure of the inner retina at a single glance

The retina decomposes visual stimuli into parallel channels that encode different features of the visual environment. Central to this computation is the synaptic processing in a dense layer of neuropil, the so-called inner plexiform layer (IPL). Here, different types of bipolar cells stratifying at distinct depths relay the excitatory feedforward drive from photoreceptors to amacrine and ganglion cells. Current experimental techniques for studying processing in the IPL do not allow imaging the entire IPL simultaneously in the intact tissue. Here, we extend a two-photon microscope with an electrically tunable lens allowing us to obtain optical vertical slices of the IPL, which provide a complete picture of the response diversity of bipolar cells at a "single glance". The nature of these axial recordings additionally allowed us to isolate and investigate batch effects, i.e. inter-experimental variations resulting in systematic differences in response speed. As a proof of principle, we developed a simple model that disentangles biological from experimental causes of variability and allowed us to recover the characteristic gradient of response speeds across the IPL with higher precision than before. Our new framework will make it possible to study the computations performed in the central synaptic layer of the retina more efficiently.

Design rules for dense and rapid Lissajous scanning

Lissajous microscanners are very popular in compact laser-scanning applications, such as solid-state light detection and ranging (LIDAR), owing to their high-quality factor and low power consumption. In the Lissajous scanner driven by a two-axis micro-electro-mechanical system scanning mirror (MEMS-SM), the design theory is insufficient to meet the temporal and spatial resolution at the same time. In this paper, the greatest common divisor of the two-axis driving frequency is used as the temporal resolution, the concept of the fill factor (FF) is used to describe the spatial resolution of the scanner, and a general algorithm for calculating the FF is presented. Combined with the characteristics of the Lissajous trajectory, three design rules of the general Lissajous scanner are proposed, and the design theory of the Lissajous scanner enabling MEMS LIDAR is perfected. Experimental results show that the proposed design rules can effectively meet the LIDAR design requirements.

Wide. Fast. Deep: Recent Advances in Multiphoton Microscopy of In Vivo Neuronal Activity

Multiphoton microscopy (MPM) has emerged as one of the most powerful and widespread technologies to monitor the activity of neuronal networks in awake, behaving animals over long periods of time. MPM development spanned across decades and crucially depended on the concurrent improvement of calcium indicators that report neuronal activity as well as surgical protocols, head fixation approaches, and innovations in optics and microscopy technology. Here we review the last decade of MPM development and highlight how in vivo imaging has matured and diversified, making it now possible to concurrently monitor thousands of neurons across connected brain areas or, alternatively, small local networks with sampling rates in the kilohertz range. This review includes different laser scanning approaches, such as multibeam technologies as well as recent developments to image deeper into neuronal tissues using new, long-wavelength laser sources. As future development will critically depend on our ability to resolve and discriminate individual neuronal spikes, we will also describe a simple framework that allows performing quantitative comparisons between the reviewed MPM instruments. Finally, we provide our own opinion on how the most recent MPM developments can be leveraged at scale to enable the next generation of discoveries in brain function.

All-Optical Volumetric Physiology for Connectomics in Dense Neuronal Structures

All-optical physiology (AOP) manipulates and reports neuronal activities with light, allowing for interrogation of neuronal functional connections with high spatiotemporal resolution. However, contemporary high-speed AOP platforms are limited to single-depth or discrete multi-plane recordings that are not suitable for studying functional connections among densely packed small neurons, such as neurons in Drosophila brains. Here, we constructed a 3D AOP platform by incorporating single-photon point stimulation and two-photon high-speed volumetric recordings with a tunable acoustic gradient-index (TAG) lens. We demonstrated the platform effectiveness by studying the anterior visual pathway (AVP) of Drosophila. We achieved functional observation of spatiotemporal coding and the strengths of calcium-sensitive connections between anterior optic tubercle (AOTU) sub-compartments and >70 tightly assembled 2-μm bulb (BU) microglomeruli in 3D coordinates with a single trial. Our work aids the establishment of in vivo 3D functional connectomes in neuron-dense brain areas.

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All-optical volumetric physiology = precise stimulation + fast volumetric recording

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Precise single-photon point stimulation among genetically defined neurons

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3D two-photon imaging by an acoustic gradient-index lens for dense neural structures

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Observation of 3D functional connectivity in Drosophila anterior visual pathway

Multi-plane remote refocusing epifluorescence microscopy to image dynamic Ca 2 + events

Rapid imaging of multiple focal planes without sample movement may be achieved through remote refocusing, where imaging is carried out in a plane conjugate to the sample plane. The technique is ideally suited to studying the endothelial and smooth muscle cell layers of blood vessels. These are intrinsically linked through rapid communication and must be separately imaged at a sufficiently high frame rate in order to understand this biologically crucial interaction. We have designed and implemented an epifluoresence-based remote refocussing imaging system that can image each layer at up to 20fps using different dyes and excitation light for each layer, without the requirement for optically sectioning microscopy. A novel triggering system is used to activate the appropriate laser and image acquisition at each plane of interest. Using this method, we are able to achieve axial plane separations down to 15  μ m, with a mean lateral stability of ≤ 0.32  μ m displacement using a 60x, 1.4NA imaging objective and a 60x, 0.7NA reimaging objective. The system allows us to image and quantify endothelial cell activity and smooth muscle cell activity at a high framerate with excellent lateral and good axial resolution without requiring complex beam scanning confocal microscopes, delivering a cost effective solution for imaging two planes rapidly. We have successfully imaged and analysed Ca 2 + activity of the endothelial cell layer independently of the smooth muscle layer for several minutes.

Quantum Dots in Ophthalmology: A Literature Review

Purpose: The aim of the current review was to summarize the current applications, the latest advances and importantly, highlight research gaps in the use of quantum dots in the eye. Quantum dots are nanoscale semiconductor crystals with characteristic size and tunable optical properties, which deliver bright and stable fluorescence suitable for bioimaging and labelling. Methods: A systematic search was conducted following the PRISMA guidelines. This review systematically searched published data to summarize the characteristics and applications of quantum dots in ophthalmology. Two hundred and eighty published articles were initially selected for this review following searches using the criteria quantum dots AND nanoparticles AND ophthalmology in the databases PubMed, MEDLINE, Scopus, Embase and Web of Science. Results: After duplicates were removed, a total of 22 eligible articles were included for the review. Quantum dots potentially provide a range of diagnostic and therapeutic applications in ophthalmology. Quantum dots offer visible and near-infrared emission, which is highly desirable for bioimaging, due to reduced light scattering and low tissue absorption. Their applications include in vivo bioimaging, labelling of cells and tissues, delivery of genes or drugs and as antimicrobial composites. Conclusion: Quantum dots have been used in ophthalmology for bioimaging, electrical stimulation and tracking of gene/stems cells, and ocular lymphatics. However, there is no detailed description of their desirable characteristics for use in ophthalmology, and there is limited information about their cytotoxicity to ocular cells and tissues.

Millisecond two-photon optical ribbon imaging for small-animal functional connectome study

We developed a high-speed two-photon optical ribbon imaging system, which combines galvo-mirrors for an arbitrary curve scan on a lateral plane and a tunable acoustic gradient-index lens for a 100 kHz-1 MHz axial scan. The system provides micrometer/millisecond spatiotemporal resolutions, which enable continuous readout of functional dynamics from small and densely packed neurons in a living adult Drosophila brain. Compared to sparse sampling techniques, the ribbon imaging modality avoids motion artifacts. Combined with a Drosophila anatomical connectome database, which is the most complete among all model animals, this technique paves the way toward establishing whole-brain functional connectome.

Narrowly Confined and Glomerulus-Specific Onset Latencies of Odor-Evoked Calcium Transients in the Juxtaglomerular Cells of the Mouse Main Olfactory Bulb

Odor information is transmitted from olfactory sensory neurons to principal neurons at the glomeruli of the olfactory bulb. The intraglomerular neuronal circuit also includes hundreds of interneurons referred to as juxtaglomerular (JG) cells. Stimulus selectivity is well correlated among many JG cells that are associated with the same glomerulus, consistent with their highly homogeneous sensory inputs. However, much less is known about the temporal aspects of their activity, including the temporal coordination of their odor-evoked responses. As many JG cells within a glomerular module respond to the same stimulus, the extent to which their activity is temporally aligned will affect the temporal profile of their population inhibitory inputs. Using random-access high-speed two-photon microscopy, we recorded the odor-evoked calcium transients of mouse JG cells and compared the onset latency and rise time among neurons putatively associated with the same and different glomeruli. Whereas the overall onset latencies of odor-evoked transients were distributed across a ∼150 ms time window, those from cells putatively associated with the same glomerulus were confined to a much narrower window of several tens of milliseconds. This result suggests that onset latency primarily depends on the associated glomerulus. We also observed glomerular specificity in the rise time. The glomerulus-specific temporal pattern of odor-evoked activity implies that the temporal patterns of inputs from the intraglomerular circuit are unique to individual glomerulus–odor pairs, which may contribute to efficient shaping of the temporal pattern of activity in the principal neurons.

Methods for Three-Dimensional All-Optical Manipulation of Neural Circuits

Optical means for modulating and monitoring neuronal activity, have provided substantial insights to neurophysiology and toward our understanding of how the brain works. Optogenetic actuators, calcium or voltage imaging probes and other molecular tools, combined with advanced microscopies have allowed an "all-optical" readout and modulation of neural circuits. Completion of this remarkable work is evolving toward a three-dimensional (3D) manipulation of neural ensembles at a high spatiotemporal resolution. Recently, original optical methods have been proposed for both activating and monitoring neurons in a 3D space, mainly through optogenetic compounds. Here, we review these methods and anticipate possible combinations among them.

Fidelity test for through-focus or volumetric type of optical imaging methods

Rapid increase in interest and applications of through-focus (TF) or volumetric type of optical imaging in biology and other areas has resulted in the development of several TF image collection methods. Achieving quantitative results from images requires standardization and optimization of image acquisition protocols. Several standardization protocols are available for conventional optical microscopy where a best-focus image is used, but to date, rigorous testing protocols do not exist for TF optical imaging. In this paper, we present a method to determine the fidelity of the TF optical data using the TF scanning optical microscopy images.

Through-focus or volumetric type of optical imaging methods: a review

In recent years, the use of through-focus (TF) or volumetric type of optical imaging has gained momentum in several areas such as biological imaging, microscopy, adaptive optics, material processing, optical data storage, and optical inspection. We provide a review of basic TF optical methods highlighting their design, major unique characteristics, and application space.

Remote focusing in confocal microscopy by means of a modified Alvarez lens

Alvarez lenses are actuated lens-pairs which allow one to tune the optical power by mechanical displacement of subelements. Here, we show that a recently realized modified Alvarez lens design which does not require mechanical actuation can be integrated into a confocal microscope. Instead of mechanically moving them, the sublenses are imaged onto each other in a 4f-configuration, where the lateral image shift leading to a change in optical power is created by a galvo-mirror. The avoidance of mechanical lens shifts leads to a large speed gain for axial (and hence also 3D) image scans compared to classical Alvarez lenses. We demonstrate that the suggested operation principle is compatible with confocal microscopy. In order to optimize the system, we have drawn advantage of the flexibility a liquid-crystal spatial light modulator offers for the implementation. For given specifications, dedicated diffractive optical elements or freeform elements can be used in combination with resonant galvo-scanners or acousto-optic beam deflectors, to achieve even faster z-scans than reported here, reaching video rate.

High-speed 3D imaging of cellular activity in the brain using axially-extended beams and light sheets

As optical reporters and modulators of cellular activity have become increasingly sophisticated, the amount that can be learned about the brain via high-speed cellular imaging has increased dramatically. However, despite fervent innovation, point-scanning microscopy is facing a fundamental limit in achievable 3D imaging speeds and fields of view. A range of alternative approaches are emerging, some of which are moving away from point-scanning to use axially-extended beams or sheets of light, for example swept confocally aligned planar excitation (SCAPE) microscopy. These methods are proving effective for high-speed volumetric imaging of the nervous system of small organisms such as Drosophila (fruit fly) and D. Rerio (Zebrafish), and are showing promise for imaging activity in the living mammalian brain using both single and two-photon excitation. This article describes these approaches and presents a simple model that demonstrates key advantages of axially-extended illumination over point-scanning strategies for high-speed volumetric imaging, including longer integration times per voxel, improved photon efficiency and reduced photodamage.

Three dimensional two-photon brain imaging in freely moving mice using a miniature fiber coupled microscope with active axial-scanning

We present a miniature head mounted two-photon fiber-coupled microscope (2P-FCM) for neuronal imaging with active axial focusing enabled using a miniature electrowetting lens. We show three-dimensional two-photon imaging of neuronal structure and record neuronal activity from GCaMP6s fluorescence from multiple focal planes in a freely-moving mouse. Two-color simultaneous imaging of GFP and tdTomato fluorescence is also demonstrated. Additionally, dynamic control of the axial scanning of the electrowetting lens allows tilting of the focal plane enabling neurons in multiple depths to be imaged in a single plane. Two-photon imaging allows increased penetration depth in tissue yielding a working distance of 450 μm with an additional 180 μm of active axial focusing. The objective NA is 0.45 with a lateral resolution of 1.8 μm, an axial resolution of 10 μm, and a field-of-view of 240 μm diameter. The 2P-FCM has a weight of only ~2.5 g and is capable of repeatable and stable head-attachment. The 2P-FCM with dynamic axial scanning provides a new capability to record from functionally distinct neuronal layers, opening new opportunities in neuroscience research.

Studying Axon-Astrocyte Functional Interactions by 3D Two-Photon Ca2+ Imaging: A Practical Guide to Experiments and "Big Data" Analysis

Recent advances in fast volumetric imaging have enabled rapid generation of large amounts of multi-dimensional functional data. While many computer frameworks exist for data storage and analysis of the multi-gigabyte Ca²⁺ imaging experiments in neurons, they are less useful for analyzing Ca²⁺ dynamics in astrocytes, where transients do not follow a predictable spatio-temporal distribution pattern. In this manuscript, we provide a detailed protocol and commentary for recording and analyzing three-dimensional (3D) Ca²⁺ transients through time in GCaMP6f-expressing astrocytes of adult brain slices in response to axonal stimulation, using our recently developed tools to perform interactive exploration, filtering, and time-correlation analysis of the transients. In addition to the protocol, we release our in-house software tools and discuss parameters pertinent to conducting axonal stimulation/response experiments across various brain regions and conditions. Our software tools are available from the Volterra Lab webpage at https://wwwfbm.unil.ch/dnf/group/glia-an-active-synaptic-partner/member/volterra-andrea-volterra in the form of software plugins for Image J (NIH)—a de facto standard in scientific image analysis. Three programs are available: MultiROI_TZ_profiler for interactive graphing of several movable ROIs simultaneously, Gaussian_Filter5D for Gaussian filtering in several dimensions, and Correlation_Calculator for computing various cross-correlation parameters on voxel collections through time.

Rapid three dimensional two photon neural population scanning

Recording the activity of neural populations at high sampling rates is a fundamental requirement for understanding computation in neural circuits. Two photon microscopy provides one promising approach towards this. However, neural circuits are three dimensional, and functional imaging in two dimensions fails to capture the 3D nature of neural dynamics. Electrically tunable lenses (ETLs) provide a simple and cheap method to extend laser scanning microscopy into the relatively unexploited third dimension. We have therefore incorporated them into our Adaptive Spiral Scanning (SSA) algorithm, which calculates kinematically efficient scanning strategies using radially modulated spiral paths. We characterised the response of the ETL, incorporated its dynamics using MATLAB models of the SSA algorithm and tested the models on populations of Izhikevich neurons of varying size and density. From this, we show that our algorithms can theoretically at least achieve sampling rates of 36.2Hz compared to 21.6Hz previously reported for 3D scanning techniques.

Large Scale In Vivo Recording of Sensory Neuron Activity with GCaMP6

Greater emphasis on the study of intact cellular networks in their physiological environment has led to rapid advances in intravital imaging of the central nervous system (CNS), while the peripheral system remains largely unexplored. To assess large networks of sensory neurons, we selectively label primary afferents with GCaMP6s in male and female C57bl/6 mice and visualize their functional responses to peripheral stimulation in vivo. We show that we are able to monitor the activity of hundreds of sensory neurons simultaneously, with sufficient sensitivity to detect, in most cases, single action potentials with a typical rise time of around 200 ms, and an exponential decay with a time constant of approximately 700 ms. With this technique we are able to characterize the responses of large populations of sensory neurons to innocuous and noxious mechanical and thermal stimuli under normal and inflammatory conditions. We demonstrate that the majority of primary afferents are polymodal with between 50-80% of thermally sensitive DRG neurons responding also to noxious mechanical stimulation. We also specifically assess the small population of peripheral cold neurons and demonstrate significant sensitization to cooling after a model of sterile and persistent inflammation, with significantly increased sensitivity already at decreases of 5°C when compared to uninflamed responses. This not only reveals interesting new insights into the (patho)physiology of the peripheral nervous system but also demonstrates the sensitivity of this imaging technique to physiological changes in primary afferents.

Single-cell analysis of diversity in human stem cell-derived neurons

Neural stem and progenitor cells produce one of the most remarkable organs in nature, the human brain. Among neural stem cell progeny, post-mitotic neurons are likewise remarkably diverse. Single-cell transcriptomic approaches are now cataloging a long-sought-after molecular taxonomy of neuronal diversity in the brain. Contemporary single-cell omic classifications of neuronal diversity build from electrophysiological approaches that for decades have measured and cataloged diverse biophysical properties of single neurons. With the widespread application of human pluripotent stem cell-based models of neurogenesis to investigate disease pathology and to develop new drugs, a high-resolution understanding of neuronal diversity in vivo is essential to benchmark the state of in vitro models of human neurological disease.

Microglia and astrocyte activation in the spinal cord of lame horses

OBJECTIVE

To determine the microglial and astrocyte response to painful lameness in horses.

STUDY DESIGN

Ionized calcium binding adaptor molecule 1 (Iba-1) and glial fibrillary acidic protein (GFAP) expression, cell density and morphology were determined through immunofluorescence within the dorsal horn of equine spinal cord.

ANIMALS

A total of five adult horses with acute or chronic unilateral lameness, previously scheduled for euthanasia.

METHODS

Musculoskeletal lameness was evaluated in five horses through visual evaluation according to clinical guidelines. Spinal cord samples were obtained immediately after euthanasia, and distal limb lesions were confirmed through dissection and radiography. Iba-1 immunostaining was used for detection and characterization of dorsal horn microglia. GFAP was used for immunostaining of dorsal horn astrocytes. Iba-1 and GFAP labeled cells were quantified in the dorsal horn, and intensity of fluorescence was compared between the ipsi- and contralateral dorsal horn to the affected limb, and between dorsal horn segments of all horses.

RESULTS

Iba-1 expression was higher in the ipsilateral dorsal horn of the affected limb in contrast to the contralateral side dorsal horn. GFAP markers did not demonstrate increased astrocytic activity on the dorsal horn ipsilateral side to the distal limb lesion of affected horses. Horses with acute lameness predominantly had a spherical shape microglial phenotype, while cells from chronic lameness cases had variable morphology. Astrocytes evidenced small somas and large processes in both acute and chronic lameness, with higher GFAP localization in the main branches. As in the case of rodents, the localization of microglia and astrocytes in horses was mainly situated within laminae I, II and III.

CONCLUSIONS AND CLINICAL RELEVANCE

Iba-1 and GFAP are functional and morphological markers of spinal microglial cells and astrocytes in horses with lameness.

Anticipating, measuring, and minimizing MEMS mirror scan error to improve laser scanning microscopy's speed and accuracy

We describe a method to speed up microelectromechanical system (MEMS) mirror scanning by > 20x, while also improving scan accuracy. We use Landweber deconvolution to determine an input voltage which would produce a desired output, based on the measured MEMS impulse response. Since the MEMS is weakly nonlinear, the observed behavior deviates from expectations, and we iteratively improve our input to minimize this deviation. This allows customizable MEMS angle vs. time with <1% deviation from the desired scan pattern. We demonstrate our technique by optimizing a point scanning microscope's raster patterns to image mammal submandibular gland and pollen at ~10 frames/s.

Automated Functional Analysis of Astrocytes from Chronic Time-Lapse Calcium Imaging Data

Recent discoveries that astrocytes exert proactive regulatory effects on neural information processing and that they are deeply involved in normal brain development and disease pathology have stimulated broad interest in understanding astrocyte functional roles in brain circuit. Measuring astrocyte functional status is now technically feasible, due to recent advances in modern microscopy and ultrasensitive cell-type specific genetically encoded Ca²⁺ indicators for chronic imaging. However, there is a big gap between the capability of generating large dataset via calcium imaging and the availability of sophisticated analytical tools for decoding the astrocyte function. Current practice is essentially manual, which not only limits analysis throughput but also risks introducing bias and missing important information latent in complex, dynamic big data. Here, we report a suite of computational tools, called Functional AStrocyte Phenotyping (FASP), for automatically quantifying the functional status of astrocytes. Considering the complex nature of Ca²⁺ signaling in astrocytes and low signal to noise ratio, FASP is designed with data-driven and probabilistic principles, to flexibly account for various patterns and to perform robustly with noisy data. In particular, FASP explicitly models signal propagation, which rules out the applicability of tools designed for other types of data. We demonstrate the effectiveness of FASP using extensive synthetic and real data sets. The findings by FASP were verified by manual inspection. FASP also detected signals that were missed by purely manual analysis but could be confirmed by more careful manual examination under the guidance of automatic analysis. All algorithms and the analysis pipeline are packaged into a plugin for Fiji (ImageJ), with the source code freely available online at https://github.com/VTcbil/FASP.

Optimizing depth-of-field extension in optical sectioning microscopy techniques using a fast focus-tunable lens

Volume imaging based on a fast focus-tunable lens (FTL) allows three-dimensional (3D) observation within milliseconds by extending the depth-of-field (DOF) with sub-micrometer transverse resolution on optical sectioning microscopes. However, the previously published DOF extensions were neither axially uniform nor fit with theoretical prediction. In this work, complete theoretical treatments of focus extension with confocal and various multiphoton microscopes are established to correctly explain the previous results. Moreover, by correctly placing the FTL and properly adjusting incident beam diameter, a uniform DOF is achieved in which the actual extension nicely agrees with the theory. Our work not only provides a theoretical platform for volumetric imaging with FTL but also demonstrates the optimized imaging condition.