Simultaneous two-photon imaging and two-photon optogenetics of cortical circuits in three dimensions

Optogenetic estimation of synaptic connections in brain slices

BACKGROUND

Detection of synaptic connections is essential for understanding neural circuits. By using optogenetics, current injection, and glutamate uncaging to activate presynaptic cells and simultaneously recording the subsequent response of postsynaptic cells, the presence of synaptic connections can be confirmed. However, these methods present throughput challenges, such as the need for simultaneous multicellular patch-clamp recording and two-photon microscopy. These challenges lead to a trade-off between sacrificing resolution and experimental throughput.

NEW METHOD

We adopted the laser, typically used for local field ablation, and combined this with post hoc analysis. We successfully approximated the synaptic connection probabilities using only an epi-fluorescence microscope and single-cell recordings.

RESULTS

We sequentially stimulated the channelrhodopsin 2-expressing cells surrounding the recorded cell and approximated the synaptic connection probabilities. This probability value was comparable to that obtained from simultaneous multi-cell patch-clamp recordings, which included more than 600 pairs.

COMPARISON WITH EXISTING METHODS

Our setup allows us to estimate connection probabilities within 100 s, outperforming existing methods. We successfully estimated synaptic connection probabilities using only the optical path typically used by an epi-fluorescence microscope and single-cell recordings. It may also be suitable for dendritic ablation experiments.

CONCLUSIONS

The proposed method simplifies the estimation of connection probabilities, which is expected to advance the study of neural circuits in conditions such as autism and schizophrenia where connection probabilities vary. Furthermore, this approach is applicable not only to local circuits but also to long-range connections, thus increasing experimental throughput.

Neural stimulation and modulation with sub-cellular precision by optomechanical bio-dart

Neural stimulation and modulation at high spatial resolution are crucial for mediating neuronal signaling and plasticity, aiding in a better understanding of neuronal dysfunction and neurodegenerative diseases. However, developing a biocompatible and precisely controllable technique for accurate and effective stimulation and modulation of neurons at the subcellular level is highly challenging. Here, we report an optomechanical method for neural stimulation and modulation with subcellular precision using optically controlled bio-darts. The bio-dart is obtained from the tip of sunflower pollen grain and can generate transient pressure on the cell membrane with submicrometer spatial resolution when propelled by optical scattering force controlled with an optical fiber probe, which results in precision neural stimulation via precisely activation of membrane mechanosensitive ion channel. Importantly, controllable modulation of a single neuronal cell, even down to subcellular neuronal structures such as dendrites, axons, and soma, can be achieved. This bio-dart can also serve as a drug delivery tool for multifunctional neural stimulation and modulation. Remarkably, our optomechanical bio-darts can also be used for in vivo neural stimulation in larval zebrafish. This strategy provides a novel approach for neural stimulation and modulation with sub-cellular precision, paving the way for high-precision neuronal plasticity and neuromodulation.

Identifying dysfunctional cell types and circuits in animal models for psychiatric disorders with calcium imaging

A central goal of neuroscience is to understand how the brain transforms external stimuli and internal bodily signals into patterns of activity that underlie cognition, emotional states, and behavior. Understanding how these patterns of activity may be disrupted in mental illness is crucial for developing novel therapeutics. It is well appreciated that psychiatric disorders are complex, circuit-based disorders that arise from dysfunctional activity patterns generated in discrete cell types and their connections. Recent advances in large-scale, cell-type specific calcium imaging approaches have shed new light on the cellular, circuit, and network-level dysfunction in animal models for psychiatric disorders. Here, we highlight a series of recent findings over the last ~10 years from in vivo calcium imaging studies that show how aberrant patterns of activity in discrete cell types and circuits may underlie behavioral deficits in animal models for several psychiatric disorders, including depression, anxiety, autism spectrum disorders, and schizophrenia. These advances in calcium imaging in pre-clinical models demonstrate the power of cell-type-specific imaging tools in understanding the underlying dysfunction in cell types, activity patterns, and neural circuits that may contribute to disease and provide new blueprints for developing more targeted therapeutics and treatment strategies.

Large field-of-view metabolic profiling of murine brain tissue following morphine incubation using label-free multiphoton microscopy

BACKGROUND

Although the effects on neural activation and glucose consumption caused by opiates such as morphine are known, the metabolic machinery underlying opioid use and misuse is not fully explored. Multiphoton microscopy (MPM) techniques have been developed for optical imaging at high spatial resolution. Despite the increased use of MPM for neural imaging, the use of intrinsic optical contrast has seen minimal use in neuroscience.

NEW METHOD

We present a label-free, multimodal microscopy technique for metabolic profiling of murine brain tissue following incubation with morphine sulfate (MSO4). We evaluate two- and three-photon excited autofluorescence, and second and third harmonic generation to determine meaningful intrinsic contrast mechanisms in brain tissue using simultaneous label-free, autofluorescence multi-harmonic (SLAM) microscopy.

RESULTS

Regional differences quantified in the cortex, caudate, and thalamus of the brain demonstrate region-specific changes to metabolic profiles measured from FAD intensity, along with brain-wide quantification. While the overall intensity of FAD signal significantly decreased after morphine incubation, this metabolic molecule accumulated near the nucleus accumbens.

COMPARISON WITH EXISTING METHODS

Histopathology requires tissue fixation and staining to determine cell type and morphology, lacking information about cellular metabolism. Tools such as fMRI or PET imaging have been widely used, but lack cellular resolution. SLAM microscopy obviates the need for tissue preparation, permitting immediate use and imaging of tissue with subcellular resolution in its native environment.

CONCLUSIONS

This study demonstrates the utility of SLAM microscopy for label-free investigations of neural metabolism, especially the intensity changes in FAD autofluorescence and structural morphology from third-harmonic generation.

Two-photon optogenetics-based assessment of neuronal connectivity in healthy and chronic hypoperfusion mice

Significance

Two-photon optogenetics and simultaneous calcium imaging can be used to visualize the response of surrounding neurons with respect to the activity of an optically stimulated target neuron, providing a direct method to assess neuronal connectivity.

Aim

We aim to develop a two-photon optogenetics-based method for evaluating neuronal connectivity, compare it to the existing indirect resting-state synchrony method, and investigate the application of the method to brain pathophysiology.

Approach

C1V1-mScarlet was introduced into GCaMP6s-expressing transgenic mice with an adeno-associated virus. Optical stimulation of a single target neuron and simultaneous calcium imaging of the target and surrounding cells were performed. Neuronal connectivity was evaluated from the correlation between the fluorescence intensity of the target and surrounding cells.

Results

The neuronal connectivity in the living brain was evaluated using two-photon optogenetics. However, resting-state synchrony was not always consistent with two-photon optogenetics-based connectivity. Comparison with neuronal synchrony measured during sensory stimulation suggested that the disagreement was due to external sensory input. Two-photon optogenetics-based connectivity significantly decreased in the common carotid artery occlusion model, whereas there was no significant change in the control group.

Conclusions

We successfully developed a direct method to evaluate neuronal connectivity in the living brain using two-photon optogenetics. The technique was successful in detecting connectivity impairment in hypoperfusion model mice.

Closed-loop experiments and brain machine interfaces with multiphoton microscopy

In the field of neuroscience, the importance of constructing closed-loop experimental systems has increased in conjunction with technological advances in measuring and controlling neural activity in live animals. We provide an overview of recent technological advances in the field, focusing on closed-loop experimental systems where multiphoton microscopy-the only method capable of recording and controlling targeted population activity of neurons at a single-cell resolution in vivo-works through real-time feedback. Specifically, we present some examples of brain machine interfaces (BMIs) using in vivo two-photon calcium imaging and discuss applications of two-photon optogenetic stimulation and adaptive optics to real-time BMIs. We also consider conditions for realizing future optical BMIs at the synaptic level, and their possible roles in understanding the computational principles of the brain.

Spatiotemporally Precise Optical Manipulation of Intracellular Molecular Activities

Controlling chemical processes in live cells is a challenging task. The spatial heterogeneity of biochemical reactions in cells is often overlooked by conventional means of incubating cells with desired chemicals. A comprehensive understanding of spatially diverse biochemical processes requires precise control over molecular activities at the subcellular level. Herein, a closed-loop optoelectronic control system is developed that allows the manipulation of biomolecular activities in live cells at high spatiotemporal precision. Chemical-selective fluorescence signals are utilized to command lasers that trigger specific chemical processes or control the activation of photoswitchable inhibitors at desired targets. This technology is fully compatible with laser scanning confocal fluorescence microscopes. The authors demonstrate selective interactions of a 405 nm laser with targeted organelles and simultaneous monitoring of cell responses by fluorescent protein signals. Notably, blue laser interaction with the endoplasmic reticulum leads to a more pronounced reduction in cytosolic green fluorescent protein signals in comparison to that with nuclei and lipid droplets. Moreover, when combined with a photoswitchable inhibitor, microtubule polymerization is selectively inhibited within the subcellular compartments. This technology enables subcellular spatiotemporal optical manipulation over chemical processes and drug activities, exclusively at desired targets, while minimizing undesired effects on non-targeted locations.

Removing crosstalk signals in neuron activity by time multiplexed excitations in a two-photon all-optical physiology system

The two-photon all-optical physiology system has attracted great interest in deciphering neuronal circuits in vivo, benefiting from its advantages in recording and modulating neuronal activities at single neuron resolutions. However, the interference, or crosstalk, between the imaging and photostimulation beams introduces a significant challenge and may impede the future application of voltage indicators in two-photon all-optical physiology system. Here, we propose the time multiplexed excitation method to distinguish signals from neuronal activities and crosstalks from photostimulation. In our system, the laser pulses of the imaging beam and photostimulation beam are synchronized, and a time delay is introduced into these pulses to separate the fluorescence signal generated by these two beams. We demonstrate the efficacy of our system in eliminating crosstalk signals from photostimulation and evaluate its influence on both genetically encoded calcium indicators (GECIs) and genetically encoded voltage indicators (GEVIs) through in vivo experiments.

More than double the fun with two-photon excitation microscopy

For generations researchers have been observing the dynamic processes of life through the lens of a microscope. This has offered tremendous insights into biological phenomena that span multiple orders of time- and length-scales ranging from the pure magic of molecular reorganization at the membrane of immune cells, to cell migration and differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses at such processes in vitro, however, when applied in intact systems, they are challenged by reduced signal strengths and signal-to-noise ratios that result from deeper imaging. As a remedy, two-photon excitation (TPE) microscopy takes a special place, because it allows us to investigate processes in vivo, in their natural environment, even in a living animal. Here, we review the fundamental principles underlying TPE aimed at basic and advanced microscopy users interested in adopting TPE for intravital imaging. We focus on applications in neurobiology, present current trends towards faster, wider and deeper imaging, discuss the combination with photon counting technologies for metabolic imaging and spectroscopy, as well as highlight outstanding issues and drawbacks in development and application of these methodologies.

The influence of cortical activity on perception depends on behavioral state and sensory context

The mechanistic link between neural circuit activity and behavior remains unclear. While manipulating cortical activity can bias certain behaviors and elicit artificial percepts, some tasks can still be solved when cortex is silenced or removed. Here, mice were trained to perform a visual detection task during which we selectively targeted groups of visually responsive and co-tuned neurons in L2/3 of primary visual cortex (V1) for two-photon photostimulation. The influence of photostimulation was conditional on two key factors: the behavioral state of the animal and the contrast of the visual stimulus. The detection of low-contrast stimuli was enhanced by photostimulation, while the detection of high-contrast stimuli was suppressed, but crucially, only when mice were highly engaged in the task. When mice were less engaged, our manipulations of cortical activity had no effect on behavior. The behavioral changes were linked to specific changes in neuronal activity. The responses of non-photostimulated neurons in the local network were also conditional on two factors: their functional similarity to the photostimulated neurons and the contrast of the visual stimulus. Functionally similar neurons were increasingly suppressed by photostimulation with increasing visual stimulus contrast, correlating with the change in behavior. Our results show that the influence of cortical activity on perception is not fixed, but dynamically and contextually modulated by behavioral state, ongoing activity and the routing of information through specific circuits.

Holographic stimulation of opposing amygdala ensembles bidirectionally modulates valence-specific behavior via mutual inhibition

The basolateral amygdala (BLA) is an evolutionarily conserved brain region, well known for valence processing. Despite this central role, the relationship between activity of BLA neuronal ensembles in response to appetitive and aversive stimuli and the subsequent expression of valence-specific behavior has remained elusive. Here, we leverage two-photon calcium imaging combined with single-cell holographic photostimulation through an endoscopic lens to demonstrate a direct causal role for opposing ensembles of BLA neurons in the control of oppositely valenced behavior in mice. We report that targeted photostimulation of either appetitive or aversive BLA ensembles results in mutual inhibition and shifts behavioral responses to promote consumption of an aversive tastant or reduce consumption of an appetitive tastant, respectively. Here, we identify that neuronal encoding of valence in the BLA is graded and relies on the relative proportion of individual BLA neurons recruited in a stable appetitive or quinine ensemble.

Unleashing Precision and Freedom in Optical Manipulation: Software-Assisted Real-Time Precision Opto-Control of Intracellular Molecular Activities and Cell Functions

The traditional method in biological science to regulate cell functions often employs chemical interventions, which commonly lack precision in space and time. While optical manipulation offers superior spatial precision, existing technologies are constrained by limitations in flexibility, accuracy, and response time. Here, we present an adaptable and interactive optical manipulation platform that integrates laser scanning, chemical sensing, synchronized multi-laser control, adaptable target selection, flexible decision-making, and real-time monitoring of sample responses. This software-assisted real-time precision opto-control (S-RPOC) platform facilitates automatic target selection driven by optical signals while permitting user-defined manual delineation. It allows the treatment of mobile or stationary targets with varying laser dosages and wavelengths simultaneously at diffraction-limited spatial precision and optimal accuracy. Significantly, S-RPOC showcases versatile capabilities including adaptive photobleaching, comprehensive quantification of protein dynamics, selective organelle perturbation, control of cell division, and manipulation of individual cell behaviors within a population. With its unprecedented spatiotemporal precision and adaptable decision-making, S-RPOC holds the potential for extensive applications in biological science.

Dynamic Multiplex Tissue Imaging in Inflammation Research

Inflammation is a highly dynamic process with immune cells that continuously interact with each other and parenchymal components as they migrate through tissue. The dynamic cellular responses and interaction patterns are a function of the complex tissue environment that cannot be fully reconstructed ex vivo, making it necessary to assess cell dynamics and changing spatial patterning in vivo. These dynamics often play out deep within tissues, requiring the optical focus to be placed far below the surface of an opaque organ. With the emergence of commercially available two-photon excitation lasers that can be combined with existing imaging systems, new avenues for imaging deep tissues over long periods of time have become available. We discuss a selected subset of studies illustrating how two-photon microscopy (2PM) has helped to relate the dynamics of immune cells to their in situ function and to understand the molecular patterns that govern their behavior in vivo. We also review some key practical aspects of 2PM methods and point out issues that can confound the results, so that readers can better evaluate the reliability of conclusions drawn using this technology.

Contribution of optical resolution to the spatial precision of two-photon optogenetic photostimulation in vivo

Significance

Two-photon optogenetics combines nonlinear excitation with noninvasive activation of neurons to enable the manipulation of neural circuits with a high degree of spatial precision. Combined with two-photon population calcium imaging, these approaches comprise a flexible platform for all-optical interrogation of neural circuits. However, a multitude of optical and biological factors dictate the exact precision of this approach in vivo, where it is most usefully applied.

Aim

We aimed to assess how the optical point spread function (OPSF) contributes to the spatial precision of two-photon photostimulation in neurobiology.

Approach

We altered the axial spread of the OPSF of the photostimulation beam using a spatial light modulator. Subsequently, calcium imaging was used to monitor the axial spatial precision of two-photon photostimulation of layer 2 neurons in the mouse neocortex.

Results

We found that optical resolution is not always the limiting factor of the spatial precision of two-photon optogenetic photostimulation and, by doing so, reveal the key factors that must be improved to achieve maximal precision.

Conclusions

Our results enable future work to focus on the optimal factors by providing key insight from controlled experiments in a manner not previously reported. This research can be applied to advance the state-of-the-art of all-optical interrogation, extending the toolkit for neuroscience research to achieve spatiotemporal precision at the crucial levels in which neural circuits operate.

Deep-brain optical recording of neural dynamics during behavior

In vivo fluorescence recording techniques have produced landmark discoveries in neuroscience, providing insight into how single cell and circuit-level computations mediate sensory processing and generate complex behaviors. While much attention has been given to recording from cortical brain regions, deep-brain fluorescence recording is more complex because it requires additional measures to gain optical access to harder to reach brain nuclei. Here we discuss detailed considerations and tradeoffs regarding deep-brain fluorescence recording techniques and provide a comprehensive guide for all major steps involved, from project planning to data analysis. The goal is to impart guidance for new and experienced investigators seeking to use in vivo deep fluorescence optical recordings in awake, behaving rodent models.

Fast 2-photon stimulation using holographic patterns

Two decades after its introduction, optogenetics - a biological technique to control the activity of neurons or other cell types with light - remains a cutting edge and promising tool to study biological processes. Its increasing usage in research varies widely from causally exploring biological mechanisms and neural computations, to neurostimulation and sensory restauration. To stimulate neurons in the brain, a variety of approaches have been developed to generate precise spatiotemporal light patterns. Yet certain constrains still exists in the current optical techniques to activate a neuronal population with both cellular resolution and millisecond precision. Here, we describe an experimental setup allowing to stimulate a few tens of neurons in a plane at sub-millisecond rates using 2-photon activation. A liquid crystal on silicon spatial light modulator (LCoS-SLM) was used to generate spatial patterns in 2 dimensions. The image of the patterns was formed on the plane of a digital micromirror device (DMD) that was used as a fast temporal modulator of each region of interest. Using fluorescent microscopy and patch-clamp recording of neurons in culture expressing the light-gated ion channels, we characterized the temporal and spatial resolution of the microscope. We described the advantages of combining the LCoS-SLM with the DMD to maximize the temporal precision, modulate the illumination amplitude, and reduce background activation. Finally, we showed that this approach can be extended to patterns in 3 dimensions. We concluded that the methodology is well suited to address important questions about the role of temporal information in neuronal coding.

Single cell in vivo optogenetic stimulation by two-photon excitation fluorescence transfer

Optogenetic manipulation with single-cell resolution can be achieved by two-photon excitation. However, this frequently requires relatively high laser powers. Here, we developed a novel strategy that can improve the efficiency of current two-photon stimulation technologies by positioning fluorescent proteins or small fluorescent molecules with high two-photon cross-sections in the vicinity of opsins. This generates a highly localized source of endogenous single-photon illumination that can be tailored to match the optimal opsin absorbance. Through neuronal and vascular stimulation in the live mouse brain, we demonstrate the utility of this technique to achieve efficient opsin stimulation, without loss of cellular resolution. We also provide a theoretical framework for understanding the potential advantages and constrains of this methodology, with directions for future improvements. Altogether, this fluorescence transfer illumination method opens new possibilities for experiments difficult to implement in the live brain such as all-optical neural interrogation and control of regional cerebral blood flow.

From static to dynamic: live observation of the support system after ischemic stroke by two photon-excited fluorescence laser-scanning microscopy

Ischemic stroke is one of the most common causes of mortality and disability worldwide. However, treatment efficacy and the progress of research remain unsatisfactory. As the critical support system and essential components in neurovascular units, glial cells and blood vessels (including the blood-brain barrier) together maintain an optimal microenvironment for neuronal function. They provide nutrients, regulate neuronal excitability, and prevent harmful substances from entering brain tissue. The highly dynamic networks of this support system play an essential role in ischemic stroke through processes including brain homeostasis, supporting neuronal function, and reacting to injuries. However, most studies have focused on postmortem animals, which inevitably lack critical information about the dynamic changes that occur after ischemic stroke. Therefore, a high-precision technique for research in living animals is urgently needed. Two-photon fluorescence laser-scanning microscopy is a powerful imaging technique that can facilitate live imaging at high spatiotemporal resolutions. Two-photon fluorescence laser-scanning microscopy can provide images of the whole-cortex vascular 3D structure, information on multicellular component interactions, and provide images of structure and function in the cranial window. This technique shifts the existing research paradigm from static to dynamic, from flat to stereoscopic, and from single-cell function to multicellular intercommunication, thus providing direct and reliable evidence to identify the pathophysiological mechanisms following ischemic stroke in an intact brain. In this review, we discuss exciting findings from research on the support system after ischemic stroke using two-photon fluorescence laser-scanning microscopy, highlighting the importance of dynamic observations of cellular behavior and interactions in the networks of the brain's support systems. We show the excellent application prospects and advantages of two-photon fluorescence laser-scanning microscopy and predict future research developments and directions in the study of ischemic stroke.

Two-photon manipulation of neuronal activity and behavior in Hydra vulgaris

The introduction of calcium imaging has rendered cnidarians, such as Hydra vulgaris, valuable model organisms for investigating neuronal activity and behavior. Here, we present a comprehensive protocol to image and manipulate neuronal activity and behavior of Hydra. We describe steps for wide-field imaging and two-photon simulation and ablation of neurons. We then detail imaging behavior and post-ablation analysis. We address challenges that may arise during the preparation and execution of the experiments.

FIOLA: an accelerated pipeline for fluorescence imaging online analysis

Optical microscopy methods such as calcium and voltage imaging enable fast activity readout of large neuronal populations using light. However, the lack of corresponding advances in online algorithms has slowed progress in retrieving information about neural activity during or shortly after an experiment. This gap not only prevents the execution of real-time closed-loop experiments, but also hampers fast experiment-analysis-theory turnover for high-throughput imaging modalities. Reliable extraction of neural activity from fluorescence imaging frames at speeds compatible with indicator dynamics and imaging modalities poses a challenge. We therefore developed FIOLA, a framework for fluorescence imaging online analysis that extracts neuronal activity from calcium and voltage imaging movies at speeds one order of magnitude faster than state-of-the-art methods. FIOLA exploits algorithms optimized for parallel processing on GPUs and CPUs. We demonstrate reliable and scalable performance of FIOLA on both simulated and real calcium and voltage imaging datasets. Finally, we present an online experimental scenario to provide guidance in setting FIOLA parameters and to highlight the trade-offs of our approach.

All-optical recreation of naturalistic neural activity with a multifunctional transgenic reporter mouse

Determining which features of the neural code drive behavior requires the ability to simultaneously read out and write in neural activity patterns with high precision across many neurons. All-optical systems that combine two-photon calcium imaging and targeted photostimulation enable the activation of specific, functionally defined groups of neurons. However, these techniques are unable to test how patterns of activity across a population contribute to computation because of an inability to both read and write cell-specific firing rates. To overcome this challenge, we make two advances: first, we introduce a genetic line of mice for Cre-dependent co-expression of a calcium indicator and a potent soma-targeted microbial opsin. Second, using this line, we develop a method for read-out and write-in of precise population vectors of neural activity by calibrating the photostimulation to each cell. These advances offer a powerful and convenient platform for investigating the neural codes of computation and behavior.

Practical considerations in an era of multicolor optogenetics

The ability to control synaptic communication is indispensable to modern neuroscience. Until recently, only single-pathway manipulations were possible due to limited availability of opsins activated by distinct wavelengths. However, extensive protein engineering and screening efforts have drastically expanded the optogenetic toolkit, ushering in an era of multicolor approaches for studying neural circuits. Nonetheless, opsins with truly discrete spectra are scarce. Experimenters must therefore take care to avoid unintended cross-activation of optogenetic tools (crosstalk). Here, we demonstrate the multidimensional nature of crosstalk in a single model synaptic pathway, testing stimulus wavelength, irradiance, duration, and opsin choice. We then propose a "lookup table" method for maximizing the dynamic range of opsin responses on an experiment-by-experiment basis.

Ultrafast light targeting for high-throughput precise control of neuronal networks

Two-photon, single-cell resolution optogenetics based on holographic light-targeting approaches enables the generation of precise spatiotemporal neuronal activity patterns and thus a broad range of experimental applications, such as high throughput connectivity mapping and probing neural codes for perception. Yet, current holographic approaches limit the resolution for tuning the relative spiking time of distinct cells to a few milliseconds, and the achievable number of targets to 100-200, depending on the working depth. To overcome these limitations and expand the capabilities of single-cell optogenetics, we introduce an ultra-fast sequential light targeting (FLiT) optical configuration based on the rapid switching of a temporally focused beam between holograms at kHz rates. We used FLiT to demonstrate two illumination protocols, termed hybrid- and cyclic-illumination, and achieve sub-millisecond control of sequential neuronal activation and high throughput multicell illumination in vitro (mouse organotypic and acute brain slices) and in vivo (zebrafish larvae and mice), while minimizing light-induced thermal rise. These approaches will be important for experiments that require rapid and precise cell stimulation with defined spatio-temporal activity patterns and optical control of large neuronal ensembles.

Neuromorphic-Based Neuroprostheses for Brain Rewiring: State-of-the-Art and Perspectives in Neuroengineering

Neuroprostheses are neuroengineering devices that have an interface with the nervous system and supplement or substitute functionality in people with disabilities. In the collective imagination, neuroprostheses are mostly used to restore sensory or motor capabilities, but in recent years, new devices directly acting at the brain level have been proposed. In order to design the next-generation of neuroprosthetic devices for brain repair, we foresee the increasing exploitation of closed-loop systems enabled with neuromorphic elements due to their intrinsic energy efficiency, their capability to perform real-time data processing, and of mimicking neurobiological computation for an improved synergy between the technological and biological counterparts. In this manuscript, after providing definitions of key concepts, we reviewed the first exploitation of a real-time hardware neuromorphic prosthesis to restore the bidirectional communication between two neuronal populations in vitro. Starting from that 'case-study', we provide perspectives on the technological improvements for real-time interfacing and processing of neural signals and their potential usage for novel in vitro and in vivo experimental designs. The development of innovative neuroprosthetics for translational purposes is also presented and discussed. In our understanding, the pursuit of neuromorphic-based closed-loop neuroprostheses may spur the development of novel powerful technologies, such as 'brain-prostheses', capable of rewiring and/or substituting the injured nervous system.

A kinetic-optimized CoChR variant with enhanced high-frequency spiking fidelity

Channelrhodopsins are a promising toolset for noninvasive optical manipulation of genetically identifiable neuron populations. Existing channelrhodopsins have generally suffered from a trade-off between two desired properties: fast channel kinetics and large photocurrent. Such a trade-off hinders spatiotemporally precise optogenetic activation during both one-photon and two-photon photostimulation. Furthermore, the simultaneous use of spectrally separated genetically encoded indicators and channelrhodopsins has generally suffered from non-negligible crosstalk in photocurrent or fluorescence. These limitations have hindered crosstalk-free dual-channel experiments needed to establish relationships between multiple neural populations. Recent large-scale transcriptome sequencing revealed one potent optogenetic actuator, the channelrhodopsin from species Chloromonas oogama (CoChR), which possessed high cyan light-driven photocurrent but slow channel kinetics. We rationally designed and engineered a kinetic-optimized CoChR variant that was faster than native CoChR while maintaining large photocurrent amplitude. When expressed in cultured hippocampal pyramidal neurons, our CoChR variant improved high-frequency spiking fidelity under one-photon illumination. Our CoChR variant's blue-shifted excitation spectrum enabled simultaneous cyan photostimulation and red calcium imaging with negligible photocurrent crosstalk.

Computational models of neurotransmission at cerebellar synapses unveil the impact on network computation

The neuroscientific field benefits from the conjoint evolution of experimental and computational techniques, allowing for the reconstruction and simulation of complex models of neurons and synapses. Chemical synapses are characterized by presynaptic vesicle cycling, neurotransmitter diffusion, and postsynaptic receptor activation, which eventually lead to postsynaptic currents and subsequent membrane potential changes. These mechanisms have been accurately modeled for different synapses and receptor types (AMPA, NMDA, and GABA) of the cerebellar cortical network, allowing simulation of their impact on computation. Of special relevance is short-term synaptic plasticity, which generates spatiotemporal filtering in local microcircuits and controls burst transmission and information flow through the network. Here, we present how data-driven computational models recapitulate the properties of neurotransmission at cerebellar synapses. The simulation of microcircuit models is starting to reveal how diverse synaptic mechanisms shape the spatiotemporal profiles of circuit activity and computation.

Dynamic processing of hunger and thirst by common mesolimbic neural ensembles

The nucleus accumbens (NAc) is a canonical reward center that regulates feeding and drinking but it is not known whether these behaviors are mediated by same or different neurons. We employed two-photon calcium imaging in awake, behaving mice and found that during the appetitive phase, both hunger and thirst are sensed by a nearly identical population of individual D1 and D2 neurons in the NAc that respond monophasically to food cues in fasted animals and water cues in dehydrated animals. During the consummatory phase, we identified three distinct neuronal clusters that are temporally correlated with action initiation, consumption, and cessation shared by feeding and drinking. These dynamic clusters also show a nearly complete overlap of individual D1 neurons and extensive overlap among D2 neurons. Modulating D1 and D2 neural activities revealed analogous effects on feeding versus drinking behaviors. In aggregate, these data show that a highly overlapping set of D1 and D2 neurons in NAc detect food and water reward and elicit concordant responses to hunger and thirst. These studies establish a general role of this mesolimbic pathway in mediating instinctive behaviors by controlling motivation-associated variables rather than conferring behavioral specificity.

Conceptual framework for neuronal ensemble identification and manipulation related to behavior using calcium imaging

Significance: The identification and manipulation of spatially identified neuronal ensembles with optical methods have been recently used to prove the causal link between neuronal ensemble activity and learned behaviors. However, the standardization of a conceptual framework to identify and manipulate neuronal ensembles from calcium imaging recordings is still lacking. Aim: We propose a conceptual framework for the identification and manipulation of neuronal ensembles using simultaneous calcium imaging and two-photon optogenetics in behaving mice. Approach: We review the computational approaches that have been used to identify and manipulate neuronal ensembles with single cell resolution during behavior in different brain regions using all-optical methods. Results: We proposed three steps as a conceptual framework that could be applied to calcium imaging recordings to identify and manipulate neuronal ensembles in behaving mice: (1) transformation of calcium transients into binary arrays; (2) identification of neuronal ensembles as similar population vectors; and (3) targeting of neuronal ensemble members that significantly impact behavioral performance. Conclusions: The use of simultaneous two-photon calcium imaging and two-photon optogenetics allowed for the experimental demonstration of the causal relation of population activity and learned behaviors. The standardization of analytical tools to identify and manipulate neuronal ensembles could accelerate interventional experiments aiming to reprogram the brain in normal and pathological conditions.

Computational optics for high-throughput imaging of neural activity

Optical microscopy offers a noninvasive way to image neural activity in the mouse brain. To simultaneously record neural activity across a large population of neurons, optical systems that have high spatiotemporal resolution and can access a large volume are necessary. The throughput of a system, that is, the number of resolvable spots acquired by the system at a given time, is usually limited by optical hardware. To overcome this limitation, computation optics that designs optical hardware and computer software jointly becomes a new approach that achieves micronscale resolution, millimeter-scale field-of-view, and hundreds of hertz imaging speed at the same time. This review article summarizes recent advances in computational optics for high-throughput imaging of neural activity, highlighting technologies for three-dimensional parallelized excitation and detection. Computational optics can substantially accelerate the study of neural circuits with previously unattainable precision and speed.

Advances in computer-generated holography for targeted neuronal modulation

Genetically encoded calcium indicators and optogenetics have revolutionized neuroscience by enabling the detection and modulation of neural activity with single-cell precision using light. To fully leverage the immense potential of these techniques, advanced optical instruments that can place a light on custom ensembles of neurons with a high level of spatial and temporal precision are required. Modern light sculpting techniques that have the capacity to shape a beam of light are preferred because they can precisely target multiple neurons simultaneously and modulate the activity of large ensembles of individual neurons at rates that match natural neuronal dynamics. The most versatile approach, computer-generated holography (CGH), relies on a computer-controlled light modulator placed in the path of a coherent laser beam to synthesize custom three-dimensional (3D) illumination patterns and illuminate neural ensembles on demand. Here, we review recent progress in the development and implementation of fast and spatiotemporally precise CGH techniques that sculpt light in 3D to optically interrogate neural circuit functions.

A one-photon endoscope for simultaneous patterned optogenetic stimulation and calcium imaging in freely behaving mice

Optogenetics and calcium imaging can be combined to simultaneously stimulate and record neural activity in vivo. However, this usually requires two-photon microscopes, which are not portable nor affordable. Here we report the design and implementation of a miniaturized one-photon endoscope for performing simultaneous optogenetic stimulation and calcium imaging. By integrating digital micromirrors, the endoscope makes it possible to activate any neuron of choice within the field of view, and to apply arbitrary spatiotemporal patterns of photostimulation while imaging calcium activity. We used the endoscope to image striatal neurons from either the direct pathway or the indirect pathway in freely moving mice while activating any chosen neuron in the field of view. The endoscope also allows for the selection of neurons based on their relationship with specific animal behaviour, and to recreate the behaviour by mimicking the natural neural activity with photostimulation. The miniaturized endoscope may facilitate the study of how neural activity gives rise to behaviour in freely moving animals.

Looking to the stars for answers: Strategies for determining how astrocytes influence neuronal activity

Astrocytes are critical components of neural circuits positioned in close proximity to the synapse, allowing them to rapidly sense and respond to neuronal activity. One repeatedly observed biomarker of astroglial activation is an increase in intracellular Ca²⁺ levels. These astroglial Ca²⁺ signals are often observed spreading throughout various cellular compartments from perisynaptic astroglial processes, to major astrocytic branches and on to the soma or cell body. Here we review recent evidence demonstrating that astrocytic Ca²⁺ events are remarkably heterogeneous in both form and function, propagate through the astroglial syncytia, and are directly linked to the ability of astroglia to influence local neuronal activity. As many of the cellular functions of astroglia can be linked to intracellular Ca²⁺ signaling, and the diversity and heterogeneity of these events becomes more apparent, there is an increasing need for novel experimental strategies designed to better understand the how these signals evolve in parallel with neuronal activity. Here we review the recent advances that enable the characterization of both subcellular and population-wide astrocytic Ca²⁺ dynamics. Additionally, we also outline the experimental design required for simultaneous in vivo Ca²⁺ imaging in the context of neuronal or astroglial manipulation, highlighting new experimental strategies made possible by recent advances in viral vector, imaging, and quantification technologies. Through combined usage of these reagents and methodologies, we provide a conceptual framework to study how astrocytes functionally integrate into neural circuits and to what extent they influence and direct the synaptic activity underlying behavioral responses.

All-optical interrogation of neural circuits in behaving mice

Recent advances combining two-photon calcium imaging and two-photon optogenetics with computer-generated holography now allow us to read and write the activity of large populations of neurons in vivo at cellular resolution and with high temporal resolution. Such 'all-optical' techniques enable experimenters to probe the effects of functionally defined neurons on neural circuit function and behavioral output with new levels of precision. This greatly increases flexibility, resolution, targeting specificity and throughput compared with alternative approaches based on electrophysiology and/or one-photon optogenetics and can interrogate larger and more densely labeled populations of neurons than current voltage imaging-based implementations. This protocol describes the experimental workflow for all-optical interrogation experiments in awake, behaving head-fixed mice. We describe modular procedures for the setup and calibration of an all-optical system (~3 h), the preparation of an indicator and opsin-expressing and task-performing animal (~3-6 weeks), the characterization of functional and photostimulation responses (~2 h per field of view) and the design and implementation of an all-optical experiment (achievable within the timescale of a normal behavioral experiment; ~3-5 h per field of view). We discuss optimizations for efficiently selecting and targeting neuronal ensembles for photostimulation sequences, as well as generating photostimulation response maps from the imaging data that can be used to examine the impact of photostimulation on the local circuit. We demonstrate the utility of this strategy in three brain areas by using different experimental setups. This approach can in principle be adapted to any brain area to probe functional connectivity in neural circuits and investigate the relationship between neural circuit activity and behavior.

Versatile software and hardware combo enabling photon counting acquisition and real-time display for multiplexing, 2D and continuous 3D two-photon imaging applications

Significance: rPySight brings a flexible and highly customizable open-software platform built around a powerful multichannel digitizer; combined, it enables performing complex photon counting-based experiments. We exploited advanced programming technology to share the photon counting stream with the graphical processing unit (GPU), making possible real-time display of two-dimensional (2D) and three-dimensional (3D) experiments and paving the road for other real-time applications. Aim: Photon counting improves multiphoton imaging by providing better signal-to-noise ratio in photon-deprived applications and is becoming more widely implemented, as indicated by its increasing presence in many microscopy vendor portfolios. Despite the relatively easy access to this technology offered in commercial systems, these remain limited to one or two channels of data and might not enable highly tailored experiments, forcing most researchers to develop their own electronics and code. We set to develop a flexible and open-source interface to a cutting-edge multichannel fast digitizer that can be easily integrated into existing imaging systems. Approach: We selected an advanced multichannel digitizer capable of generating 70M tags/s and wrote an open software application, based on Rust and Python languages, to share the stream of detected events with the GPU, enabling real-time data processing. Results: rPySight functionality was showcased in real-time monitoring of 2D imaging, improved calcium imaging, multiplexing, and 3D imaging through a varifocal lens. We provide a detailed protocol for implementing out-of-the-box rPySight and its related hardware. Conclusions: Applying photon-counting approaches is becoming a fundamental component in recent technical developments that push well beyond existing acquisition speed limitations of classical multiphoton approaches. Given the performance of rPySight, we foresee its use to capture, among others, the joint dynamics of hundreds (if not thousands) of neuronal and vascular elements across volumes, as is likely required to uncover in a much broader sense the hemodynamic transform function.

Advantages, Pitfalls, and Developments of All Optical Interrogation Strategies of Microcircuits in vivo

The holy grail for every neurophysiologist is to conclude a causal relationship between an elementary behaviour and the function of a specific brain area or circuit. Our effort to map elementary behaviours to specific brain loci and to further manipulate neural activity while observing the alterations in behaviour is in essence the goal for neuroscientists. Recent advancements in the area of experimental brain imaging in the form of longer wavelength near infrared (NIR) pulsed lasers with the development of highly efficient optogenetic actuators and reporters of neural activity, has endowed us with unprecedented resolution in spatiotemporal precision both in imaging neural activity as well as manipulating it with multiphoton microscopy. This readily available toolbox has introduced a so called all-optical physiology and interrogation of circuits and has opened new horizons when it comes to precisely, fast and non-invasively map and manipulate anatomically, molecularly or functionally identified mesoscopic brain circuits. The purpose of this review is to describe the advantages and possible pitfalls of all-optical approaches in system neuroscience, where by all-optical we mean use of multiphoton microscopy to image the functional response of neuron(s) in the network so to attain flexible choice of the cells to be also optogenetically photostimulated by holography, in absence of electrophysiology. Spatio-temporal constraints will be compared toward the classical reference of electrophysiology methods. When appropriate, in relation to current limitations of current optical approaches, we will make reference to latest works aimed to overcome these limitations, in order to highlight the most recent developments. We will also provide examples of types of experiments uniquely approachable all-optically. Finally, although mechanically non-invasive, all-optical electrophysiology exhibits potential off-target effects which can ambiguate and complicate the interpretation of the results. In summary, this review is an effort to exemplify how an all-optical experiment can be designed, conducted and interpreted from the point of view of the integrative neurophysiologist.

Advancements in the Quest to Map, Monitor, and Manipulate Neural Circuitry

Neural circuits and the cells that comprise them represent the functional units of the brain. Circuits relay and process sensory information, maintain homeostasis, drive behaviors, and facilitate cognitive functions such as learning and memory. Creating a functionally-precise map of the mammalian brain requires anatomically tracing neural circuits, monitoring their activity patterns, and manipulating their activity to infer function. Advancements in cell-type-specific genetic tools allow interrogation of neural circuits with increased precision. This review provides a broad overview of recombination-based and activity-driven genetic targeting approaches, contemporary viral tracing strategies, electrophysiological recording methods, newly developed calcium, and voltage indicators, and neurotransmitter/neuropeptide biosensors currently being used to investigate circuit architecture and function. Finally, it discusses methods for acute or chronic manipulation of neural activity, including genetically-targeted cellular ablation, optogenetics, chemogenetics, and over-expression of ion channels. With this ever-evolving genetic toolbox, scientists are continuing to probe neural circuits with increasing resolution, elucidating the structure and function of the incredibly complex mammalian brain.

In Utero Electroporation for Manipulation of Specific Neuronal Populations

The complexity of brain functions is supported by the heterogeneity of brain tissue and millisecond-scale information processing. Understanding how complex neural circuits control animal behavior requires the precise manipulation of specific neuronal subtypes at high spatiotemporal resolution. In utero electroporation, when combined with optogenetics, is a powerful method for precisely controlling the activity of specific neurons. Optogenetics allows for the control of cellular membrane potentials through light-sensitive ion channels artificially expressed in the plasma membrane of neurons. Here, we first review the basic mechanisms and characteristics of in utero electroporation. Then, we discuss recent applications of in utero electroporation combined with optogenetics to investigate the functions and characteristics of specific regions, layers, and cell types. These techniques will pave the way for further advances in understanding the complex neuronal and circuit mechanisms that underlie behavioral outputs.

Engineering rhodopsins' activation spectra using a FRET-based approach

In the past decade, optogenetics has become a nearly ubiquitous tool in neuroscience because it enables researchers to manipulate neural activity with high temporal resolution and genetic specificity. Rational engineering of optogenetic tools has produced channelrhodopsins with a wide range of kinetics and photocurrent magnitude. Genome mining for previously unidentified species of rhodopsin has uncovered optogenetic tools with diverse spectral sensitivities. However, rational engineering of a rhodopsin has thus far been unable to re-engineer spectral sensitivity while preserving full photocurrent. Here, we developed and characterized ChroME-mTFP, a rhodopsin-fluorescent protein fusion that drives photocurrent through Förster resonance energy transfer (FRET). This FRET-opsin mechanism artificially broadened the activation spectrum of the blue-green-light-activated rhodopsin ChroME by approximately 50 nm, driving higher photocurrent at blue-shifted excitation wavelengths without sacrificing kinetics. The excitation spectra's increase at short wavelengths enabled us to optogenetically excite neurons at lower excitation powers with shorter wavelengths of light. Increasing this rhodopsin's sensitivity to shorter, bluer wavelengths pushes it toward dual-channel, crosstalk-free optogenetic stimulation and imaging with green-light-activated sensors. However, this iteration of FRET-opsin suffers from some imaging-light-induced photocurrent crosstalk from green or yellow light due to maintained, low-efficiency excitation at longer wavelengths.

An increase in spontaneous activity mediates visual habituation

The cerebral cortex is spontaneously active, but the function of this ongoing activity remains unclear. To test whether spontaneous activity encodes learned experiences, we measured the response of neuronal populations in mouse primary visual cortex with chronic two-photon calcium imaging during visual habituation to a specific oriented stimulus. We find that, during habituation, spontaneous activity increases in neurons across the full range of orientation selectivity, eventually matching that of evoked levels. This increase in spontaneous activity robustly correlates with the degree of habituation. Moreover, boosting spontaneous activity with two-photon optogenetic stimulation to the levels of visually evoked activity accelerates habituation. Our study shows that cortical spontaneous activity is linked to habituation, and we propose that habituation unfolds by minimizing the difference between spontaneous and stimulus-evoked activity levels. We conclude that baseline spontaneous activity could gate incoming sensory information to the cortex based on the learned experience of the animal.

Complex-Amplitude-Modulation Vectorial Excitation Beam for High-Resolution Observation of Deep Regions in Two-Photon Microscopy

In two-photon microscopy, aberration correction is an essential technique for realizing high resolution in deep regions. A spatial light modulator (SLM) incorporated into an optical system for two-photon microscopy performs pre-compensation on the wavefront of the excitation beam, restoring the resolution close to the diffraction limit even in the deep region of a biological sample. If a spatial resolution smaller than the diffraction limit can be achieved along with aberration correction, the importance of two-photon microscopy for deep region observation will increase further. In this study, we realize higher resolution observations in the deep region by combining two resolution-enhancement methods and an aberration correction method. Therefore, a z-polarizer is added to the aberration-correction optical system, and the SLM modulates the amplitude and phase of the excitation beam; in other words, complex-amplitude modulation is performed. The lateral resolution is found to be approximately 20% higher than the diffraction limit obtained using a circularly polarized beam. Verification was conducted by simulation and experimentation using model samples and ex vivo biological samples. The proposed method has the potential to be effective for live imaging and photostimulation of the deep region of the sample, although it requires only minor changes to the conventional optical system that performs aberration correction.

Tracking connectivity maps in human stem cell-derived neuronal networks by holographic optogenetics

Holographic optogenetic stimulation of human iPSC–derived neuronal networks was exploited to map precise functional connectivity motifs and their long-term dynamics during network development.

Neuronal networks derived from human induced pluripotent stem cells have been exploited widely for modeling neuronal circuits, neurological diseases, and drug screening. As these networks require extended culturing periods to functionally mature in vitro, most studies are based on immature networks. To obtain insights on long-term functional features, we improved a glia–neuron co-culture protocol within multi-electrode arrays, facilitating continuous assessment of electrical features in weekly intervals. By full-field optogenetic stimulation, we detected an earlier onset of neuronal firing and burst activity compared with spontaneous activity. Full-field stimulation enhanced the number of active neurons and their firing rates. Compared with full-field stimulation, which evoked synchronized activity across all neurons, holographic stimulation of individual neurons resulted in local activity. Single-cell holographic stimulation facilitated to trace propagating evoked activities of 400 individually stimulated neurons per multi-electrode array. Thereby, we revealed precise functional neuronal connectivity motifs. Holographic stimulation data over time showed increasing connection numbers and strength with culture age. This holographic stimulation setup has the potential to establish a profound functional testbed for in-depth analysis of human-induced pluripotent stem cell-derived neuronal networks.

High-performance microbial opsins for spatially and temporally precise perturbations of large neuronal networks

The biophysical properties of existing optogenetic tools constrain the scale, speed, and fidelity of precise optogenetic control. Here, we use structure-guided mutagenesis to engineer opsins that exhibit very high potency while retaining fast kinetics. These new opsins enable large-scale, temporally and spatially precise control of population neural activity. We extensively benchmark these new opsins against existing optogenetic tools and provide a detailed biophysical characterization of a diverse family of opsins under two-photon illumination. This establishes a resource for matching the optimal opsin to the goals and constraints of patterned optogenetics experiments. Finally, by combining these new opsins with optimized procedures for holographic photostimulation, we demonstrate the simultaneous coactivation of several hundred spatially defined neurons with a single hologram and nearly double that number by temporally interleaving holograms at fast rates. These newly engineered opsins substantially extend the capabilities of patterned illumination optogenetic paradigms for addressing neural circuits and behavior.

Discovering Microcircuit Secrets With Multi-Spot Imaging and Electrophysiological Recordings: The Example of Cerebellar Network Dynamics

The cerebellar cortex microcircuit is characterized by a highly ordered neuronal architecture having a relatively simple and stereotyped connectivity pattern. For a long time, this structural simplicity has incorrectly led to the idea that anatomical considerations would be sufficient to understand the dynamics of the underlying circuitry. However, recent experimental evidence indicates that cerebellar operations are much more complex than solely predicted by anatomy, due to the crucial role played by neuronal and synaptic properties. To be able to explore neuronal and microcircuit dynamics, advanced imaging, electrophysiological techniques and computational models have been combined, allowing us to investigate neuronal ensembles activity and to connect microscale to mesoscale phenomena. Here, we review what is known about cerebellar network organization, neural dynamics and synaptic plasticity and point out what is still missing and would require experimental assessments. We consider the available experimental techniques that allow a comprehensive assessment of circuit dynamics, including voltage and calcium imaging and extracellular electrophysiological recordings with multi-electrode arrays (MEAs). These techniques are proving essential to investigate the spatiotemporal pattern of activity and plasticity in the cerebellar network, providing new clues on how circuit dynamics contribute to motor control and higher cognitive functions.

Local feedback inhibition tightly controls rapid formation of hippocampal place fields

Hippocampal place cells underlie spatial navigation and memory. Remarkably, CA1 pyramidal neurons can form new place fields within a single trial by undergoing rapid plasticity. However, local feedback circuits likely restrict the rapid recruitment of individual neurons into ensemble representations. This interaction between circuit dynamics and rapid feature coding remains unexplored. Here, we developed "all-optical" approaches combining novel optogenetic induction of rapidly forming place fields with 2-photon activity imaging during spatial navigation in mice. We find that induction efficacy depends strongly on the density of co-activated neurons. Place fields can be reliably induced in single cells, but induction fails during co-activation of larger subpopulations due to local circuit constraints imposed by recurrent inhibition. Temporary relief of local inhibition permits the simultaneous induction of place fields in larger ensembles. We demonstrate the behavioral implications of these dynamics, showing that our ensemble place field induction protocol can enhance subsequent spatial association learning.

Orchestration of Ion Channels and Transporters in Neocortical Development and Neurological Disorders

Electrical activity plays crucial roles in neural circuit formation and remodeling. During neocortical development, neurons are generated in the ventricular zone, migrate to their correct position, elongate dendrites and axons, and form synapses. In this review, we summarize the functions of ion channels and transporters in neocortical development. Next, we discuss links between neurological disorders caused by dysfunction of ion channels (channelopathies) and neocortical development. Finally, we introduce emerging optical techniques with potential applications in physiological studies of neocortical development and the pathophysiology of channelopathies.

Three-dimensional multi-site random access photostimulation (3D-MAP)

Optical control of neural ensemble activity is crucial for understanding brain function and disease, yet no technology can achieve optogenetic control of very large numbers of neurons at an extremely fast rate over a large volume. State-of-the-art multiphoton holographic optogenetics requires high-power illumination that only addresses relatively small populations of neurons in parallel. Conversely, one-photon holographic techniques can stimulate more neurons with two to three orders lower power, but with limited resolution or addressable volume. Perhaps most problematically, two-photon holographic optogenetic systems are extremely expensive and sophisticated which has precluded their broader adoption in the neuroscience community. To address this technical gap, we introduce a new one-photon light sculpting technique, three-dimensional multi-site random access photostimulation (3D-MAP), that overcomes these limitations by modulating light dynamically, both in the spatial and in the angular domain at multi-kHz rates. We use 3D-MAP to interrogate neural circuits in 3D and demonstrate simultaneous photostimulation and imaging of dozens of user-selected neurons in the intact mouse brain in vivo with high spatio-temporal resolution. 3D-MAP can be broadly adopted for high-throughput all-optical interrogation of brain circuits owing to its powerful combination of scale, speed, simplicity, and cost.

Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm

Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.

Non-telecentric two-photon microscopy for 3D random access mesoscale imaging

Diffraction-limited two-photon microscopy permits minimally invasive optical monitoring of neuronal activity. However, most conventional two-photon microscopes impose significant constraints on the size of the imaging field-of-view and the specific shape of the effective excitation volume, thus limiting the scope of biological questions that can be addressed and the information obtainable. Here, employing a non-telecentric optical design, we present a low-cost, easily implemented and flexible solution to address these limitations, offering a several-fold expanded three-dimensional field of view. Moreover, rapid laser-focus control via an electrically tunable lens allows near-simultaneous imaging of remote regions separated in three dimensions and permits the bending of imaging planes to follow natural curvatures in biological structures. Crucially, our core design is readily implemented (and reversed) within a matter of hours, making it highly suitable as a base platform for further development. We demonstrate the application of our system for imaging neuronal activity in a variety of examples in zebrafish, mice and fruit flies.

Synaptic connectivity to L2/3 of primary visual cortex measured by two-photon optogenetic stimulation

Understanding cortical microcircuits requires thorough measurement of physiological properties of synaptic connections formed within and between diverse subclasses of neurons. Towards this goal, we combined spatially precise optogenetic stimulation with multicellular recording to deeply characterize intralaminar and translaminar monosynaptic connections to supragranular (L2/3) neurons in the mouse visual cortex. The reliability and specificity of multiphoton optogenetic stimulation were measured across multiple Cre lines, and measurements of connectivity were verified by comparison to paired recordings and targeted patching of optically identified presynaptic cells. With a focus on translaminar pathways, excitatory and inhibitory synaptic connections from genetically defined presynaptic populations were characterized by their relative abundance, spatial profiles, strength, and short-term dynamics. Consistent with the canonical cortical microcircuit, layer 4 excitatory neurons and interneurons within L2/3 represented the most common sources of input to L2/3 pyramidal cells. More surprisingly, we also observed strong excitatory connections from layer 5 intratelencephalic neurons and potent translaminar inhibition from multiple interneuron subclasses. The hybrid approach revealed convergence to and divergence from excitatory and inhibitory neurons within and across cortical layers. Divergent excitatory connections often spanned hundreds of microns of horizontal space. In contrast, divergent inhibitory connections were more frequently measured from postsynaptic targets near each other.

Fluorescence imaging of large-scale neural ensemble dynamics

Recent progress in fluorescence imaging allows neuroscientists to observe the dynamics of thousands of individual neurons, identified genetically or by their connectivity, across multiple brain areas and for extended durations in awake behaving mammals. We discuss advances in fluorescent indicators of neural activity, viral and genetic methods to express these indicators, chronic animal preparations for long-term imaging studies, and microscopes to monitor and manipulate the activity of large neural ensembles. Ca2+ imaging studies of neural activity can track brain area interactions and distributed information processing at cellular resolution. Across smaller spatial scales, high-speed voltage imaging reveals the distinctive spiking patterns and coding properties of targeted neuron types. Collectively, these innovations will propel studies of brain function and dovetail with ongoing neuroscience initiatives to identify new neuron types and develop widely applicable, non-human primate models. The optical toolkit's growing sophistication also suggests that "brain observatory" facilities would be useful open resources for future brain-imaging studies.