Two-photon photostimulation and imaging of neural circuits

Pathogenesis, diagnosis, and treatment of epilepsy: electromagnetic stimulation-mediated neuromodulation therapy and new technologies

Epilepsy is a severe, relapsing, and multifactorial neurological disorder. Studies regarding the accurate diagnosis, prognosis, and in-depth pathogenesis are crucial for the precise and effective treatment of epilepsy. The pathogenesis of epilepsy is complex and involves alterations in variables such as gene expression, protein expression, ion channel activity, energy metabolites, and gut microbiota composition. Satisfactory results are lacking for conventional treatments for epilepsy. Surgical resection of lesions, drug therapy, and non-drug interventions are mainly used in clinical practice to treat pain associated with epilepsy. Non-pharmacological treatments, such as a ketogenic diet, gene therapy for nerve regeneration, and neural regulation, are currently areas of research focus. This review provides a comprehensive overview of the pathogenesis, diagnostic methods, and treatments of epilepsy. It also elaborates on the theoretical basis, treatment modes, and effects of invasive nerve stimulation in neurotherapy, including percutaneous vagus nerve stimulation, deep brain electrical stimulation, repetitive nerve electrical stimulation, in addition to non-invasive transcranial magnetic stimulation and transcranial direct current stimulation. Numerous studies have shown that electromagnetic stimulation-mediated neuromodulation therapy can markedly improve neurological function and reduce the frequency of epileptic seizures. Additionally, many new technologies for the diagnosis and treatment of epilepsy are being explored. However, current research is mainly focused on analyzing patients' clinical manifestations and exploring relevant diagnostic and treatment methods to study the pathogenesis at a molecular level, which has led to a lack of consensus regarding the mechanisms related to the disease.

Energy transfer booster: how a leaving group controls the excited state pathway within a caging BASHY-BODIPY dyad

Photocages are powerful tools for spatiotemporal control of molecule release or biological activity. However, many photocages are unsuitable for biological experiments since they are mostly activated by harmful ultraviolet (UV) light and often lack a sufficient optical readout. Thus, there is a high demand for near infrared (NIR) and/or two-photon activatable photocages with a characteristic readout. In this report, we will study a supramolecular, covalently linked energy-transfer dyad based on a BASHY fluorophore serving as a two-photon antenna for a poorly two-photon absorbing BODIPY photocage. The herein investigated systems, with and without a leaving group (LG), show different excitation energy transfer (EET) efficiencies and therefore differ in their fluorescence properties. To understand the molecular basis for these significant differences, detailed spectroscopic and theoretical analyses were employed from ultrafast transient absorption spectroscopy to excited-state electronic structure calculations and quantum dynamical modelling. The result of our comprehensive study reveals the pivotal role of the LG as an EET booster through specific pathway guidance. In contrast, without the LG, the EET efficiency is reduced and the excitation energy predominantly dissipates within the BASHY chromophore. The present study highlights that LGs can actively contribute to optimizing the properties of dyad based systems and offers new design principles for monitoring uncaging via an intrinsic fluorescence readout.

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.

Neuronal ensembles: Building blocks of neural circuits

Neuronal ensembles, defined as groups of neurons displaying recurring patterns of coordinated activity, represent an intermediate functional level between individual neurons and brain areas. Novel methods to measure and optically manipulate the activity of neuronal populations have provided evidence of ensembles in the neocortex and hippocampus. Ensembles can be activated intrinsically or in response to sensory stimuli and play a causal role in perception and behavior. Here we review ensemble phenomenology, developmental origin, biophysical and synaptic mechanisms, and potential functional roles across different brain areas and species, including humans. As modular units of neural circuits, ensembles could provide a mechanistic underpinning of fundamental brain processes, including neural coding, motor planning, decision-making, learning, and adaptability.

Numerical study of a convective cooling strategy for increasing safe power levels in two-photon brain imaging

Two-photon excitation fluorescence microscopy has become an effective tool for tracking neural activity in the brain at high resolutions thanks to its intrinsic optical sectioning and deep penetration capabilities. However, advanced two-photon microscopy modalities enabling high-speed and/or deep-tissue imaging necessitate high average laser powers, thus increasing the susceptibility of tissue heating due to out-of-focus absorption. Despite cooling the cranial window by maintaining the objective at a fixed temperature, average laser powers exceeding 100-200 mW have been shown to exhibit the potential for altering physiological responses of the brain. This paper proposes an enhanced cooling technique for inducing a laminar flow to the objective immersion layer while implementing duty cycles. Through a numerical study, we analyze the efficacy of heat dissipation of the proposed method and compare it with that of the conventional, fixed-temperature objective cooling technique. The results show that improved cooling could be achieved by choosing appropriate flow rates and physiologically relevant immersion cooling temperatures, potentially increasing safe laser power levels by up to three times (3×). The proposed active cooling method can provide an opportunity for faster scan speeds and enhanced signals in nonlinear deep brain imaging.

A Photoactivatable Norepinephrine for Probing Adrenergic Neural Circuits

Norepinephrine (NE) is a critical neuromodulator that mediates a wide range of behavior and neurophysiology, including attention, arousal, plasticity, and memory consolidation. A major source of NE is the brainstem nucleus the locus coeruleus (LC), which sends widespread projections throughout the central nervous system (CNS). Efforts to dissect this complex noradrenergic circuitry have driven the development of many tools that detect endogenous NE or modulate widespread NE release via LC activation and inhibition. While these tools have enabled research that elucidates physiological roles of NE, additional tools to probe these circuits with a higher degree of spatial precision could enable a finer delineation of function. Here, we describe the synthesis and chemical properties of a photo-activatable NE, [Ru(bpy) 2 (PMe 3 )(NE)]PF 6 (RuBi-NE). We validate the one-photon (1P) release of NE using whole-cell patch clamp electrophysiology in acute mouse brain slices containing the LC. We show that a 10 ms pulse of blue light, in the presence of RuBi-NE, briefly modulates the firing rate of LC neurons via α-2 adrenergic receptors. The development of a photo-activatable NE that can be released with light in the visible spectrum provides a new tool for fine-grained mapping of complex noradrenergic circuits, as well as the ability to probe how NE acts on non-neuronal cells in the CNS.

Inferring causal connectivity from pairwise recordings and optogenetics

To understand the neural mechanisms underlying brain function, neuroscientists aim to quantify causal interactions between neurons, for instance by perturbing the activity of neuron A and measuring the effect on neuron B. Recently, manipulating neuron activity using light-sensitive opsins, optogenetics, has increased the specificity of neural perturbation. However, using widefield optogenetic interventions, multiple neurons are usually perturbed, producing a confound-any of the stimulated neurons can have affected the postsynaptic neuron making it challenging to discern which neurons produced the causal effect. Here, we show how such confounds produce large biases in interpretations. We explain how confounding can be reduced by combining instrumental variables (IV) and difference in differences (DiD) techniques from econometrics. Combined, these methods can estimate (causal) effective connectivity by exploiting the weak, approximately random signal resulting from the interaction between stimulation and the absolute refractory period of the neuron. In simulated neural networks, we find that estimates using ideas from IV and DiD outperform naïve techniques suggesting that methods from causal inference can be useful to disentangle neural interactions in the brain.

Aberration-free holographic microscope for simultaneous imaging and stimulation of neuronal populations

A technical challenge in neuroscience is to record and specifically manipulate the activity of neurons in living animals. This can be achieved in some preparations with two-photon calcium imaging and photostimulation. These methods can be extended to three dimensions by holographic light sculpting with spatial light modulators (SLMs). At the same time, performing simultaneous holographic imaging and photostimulation is still cumbersome, requiring two light paths with separate SLMs. Here we present an integrated optical design using a single SLM for simultaneous imaging and photostimulation. Furthermore, we applied axially dependent adaptive optics to make the system aberration-free, and developed software for calibrations and closed-loop neuroscience experiments. Finally, we demonstrate the performance of the system with simultaneous calcium imaging and optogenetics in mouse primary auditory cortex in vivo. Our integrated holographic system could facilitate the systematic investigation of neural circuit function in awake behaving animals.

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.

Neural Circuit Changes in Neurological Disorders: Evidence from in vivo Two-photon Imaging

Neural circuits, such as synaptic plasticity and neural activity, are critical components of healthy brain function. The consequent dynamic remodeling of neural circuits is an ongoing procedure affecting neuronal activities. Disruption of this essential process results in diseases. Advanced microscopic applications such as two-photon laser scanning microscopy have recently been applied to understand neural circuit changes during disease since it can visualize fine structural and functional cellular activation in living animals. In this review, we have summarized the latest work assessing the dynamic rewiring of postsynaptic dendritic spines and modulation of calcium transients in neurons of the intact living brain, focusing on their potential roles in neurological disorders (e.g. Alzheimer's disease, stroke, and epilepsy). Understanding the fine changes that occurred in the brain during disease is crucial for future clinical intervention developments.

Photoactive Nanomaterials for Wireless Neural Biomimetics, Stimulation, and Regeneration

Nanomaterials at the neural interface can provide the bridge between bioelectronic devices and native neural tissues and achieve bidirectional transmission of signals with our brain. Photoactive nanomaterials, such as inorganic and polymeric nanoparticles, nanotubes, nanowires, nanorods, nanosheets or related, are being explored to mimic, modulate, control, or even substitute the functions of neural cells or tissues. They show great promise in next generation technologies for the neural interface with excellent spatial and temporal accuracy. In this review, we highlight the discovery and understanding of these nanomaterials in precise control of an individual neuron, biomimetic retinal prosthetics for vision restoration, repair or regeneration of central or peripheral neural tissues, and wireless deep brain stimulation for treatment of movement or mental disorders. The most intriguing feature is that the photoactive materials fit within a minimally invasive and wireless strategy to trigger the flux of neurologically active molecules and thus influences the cell membrane potential or key signaling molecule related to gene expression. In particular, we focus on worthy pathways of photosignal transduction at the nanomaterial-neural interface and the behavior of the biological system. Finally, we describe the challenges on how to design photoactive nanomaterials specific to neurological disorders. There are also some open issues such as long-term interface stability and signal transduction efficiency to further explore for clinical practice.

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.

A Platform for Spatiotemporal "Matrix" Stimulation in Brain Networks Reveals Novel Forms of Circuit Plasticity

Here we demonstrate a facile method by which to deliver complex spatiotemporal stimulation to neural networks in fast patterns, to trigger interesting forms of circuit-level plasticity in cortical areas. We present a complete platform by which patterns of electricity can be arbitrarily defined and distributed across a brain circuit, either simultaneously, asynchronously, or in complex patterns that can be easily designed and orchestrated with precise timing. Interfacing with acute slices of mouse cortex, we show that our system can be used to activate neurons at many locations and drive synaptic transmission in distributed patterns, and that this elicits new forms of plasticity that may not be observable via traditional methods, including interesting measurements of associational and sequence plasticity. Finally, we introduce an automated "network assay" for imaging activation and plasticity across a circuit. Spatiotemporal stimulation opens the door for high-throughput explorations of plasticity at the circuit level, and may provide a basis for new types of adaptive neural prosthetics.

Efficient Simulation of 3D Reaction-Diffusion in Models of Neurons and Networks

Neuronal activity is the result of both the electrophysiology and chemophysiology. A neuron can be well-represented for the purposes of electrophysiological simulation as a tree composed of connected cylinders. This representation is also apt for 1D simulations of their chemophysiology, provided the spatial scale is larger than the diameter of the cylinders and there is radial symmetry. Higher dimensional simulation is necessary to accurately capture the dynamics when these criteria are not met, such as with wave curvature, spines, or diffusion near the soma. We have developed a solution to enable efficient finite volume method simulation of reaction-diffusion kinetics in intracellular 3D regions in neuron and network models and provide an implementation within the NEURON simulator. An accelerated version of the CTNG 3D reconstruction algorithm transforms morphologies suitable for ion-channel based simulations into consistent 3D voxelized regions. Kinetics are then solved using a parallel algorithm based on Douglas-Gunn that handles the irregular 3D geometry of a neuron; these kinetics are coupled to NEURON's 1D mechanisms for ion channels, synapses, pumps, and so forth. The 3D domain may cover the entire cell or selected regions of interest. Simulations with dendritic spines and of the soma reveal details of dynamics that would be missed in a pure 1D simulation. We describe and validate the methods and discuss their performance.

All-optical approaches to studying psychiatric disease

Improvements in all-optical means of monitoring and manipulating neural activity have generated new ways of studying psychiatric disease. The combination of calcium imaging techniques with optogenetics to concurrently record and manipulate neural activity has been used to create new disease models that link distinct circuit abnormalities to specific disease dimensions. These approaches represent a new path towards the development of more effective treatments, as they allow researchers to identify circuit manipulations that normalize pathological network activity. In this review we highlight the utility of all-optical approaches to generate new psychiatric disease models where the specific circuit abnormalities associated with disease symptomology can be assessed in vivo and in response to manipulations designed to normalize disease states. We then outline the principles underlying all-optical interrogations of neural circuits and discuss practical considerations for experimental design.

Engineered Illumination Devices for Optogenetic Control of Cellular Signaling Dynamics

Spatially and temporally varying patterns of morphogen signals during development drive cell fate specification at the proper location and time. However, current in vitro methods typically do not allow for precise, dynamic spatiotemporal control of morphogen signaling and are thus insufficient to readily study how morphogen dynamics affect cell behavior. Here, we show that optogenetic Wnt/β-catenin pathway activation can be controlled at user-defined intensities, temporal sequences, and spatial patterns using engineered illumination devices for optogenetic photostimulation and light activation at variable amplitudes (LAVA). By patterning human embryonic stem cell (hESC) cultures with varying light intensities, LAVA devices enabled dose-responsive control of optoWnt activation and Brachyury expression. Furthermore, time-varying and spatially localized patterns of light revealed tissue patterning that models the embryonic presentation of Wnt signals in vitro. LAVA devices thus provide a low-cost, user-friendly method for high-throughput and spatiotemporal optogenetic control of cell signaling for applications in developmental and cell biology.

Holographic Imaging and Stimulation of Neural Circuits

A critical neuroscience challenge is the need to optically image and manipulate neural activity with high spatiotemporal resolution over large brain volumes. The last three decades have seen the development of calcium imaging to record activity from neuronal populations, as well as optochemistry and optogenetics to optically manipulate neural activity. These methods are typically implemented with wide-field or laser-scanning microscopes. While the former approach has a good temporal resolution, it generally lacks spatial resolution or specificity, particularly in scattering tissues such as the nervous system; meanwhile, the latter approach, particularly when combined with two-photon excitation, has high spatial resolution and specificity but poor temporal resolution. As a new technique, holographic microscopy combines the advantages of both approaches. By projecting a holographic pattern on the brain through a spatial light modulator, the activity of specific groups of neurons in 3D brain volumes can be imaged or stimulated with high spatiotemporal resolution. In a combination of other techniques such as fast scanning or temporal focusing, this high spatiotemporal resolution can be further improved. Holographic microscopy enables all-optical interrogating of neural activity in 3D, a critical tool to dissect the function of neural circuits.

Axon hillock currents enable single-neuron-resolved 3D reconstruction using diamond nitrogen-vacancy magnetometry

Sensing neuronal action potential associated magnetic fields (APMFs) is an emerging viable alternative of functional brain mapping. Measurement of APMFs of large axons of worms have been possible due to their size. In the mammalian brain, axon sizes, their numbers and routes, restricts using such functional imaging methods. With a segmented model of mammalian pyramidal neurons, we show that the APMF of intra-axonal currents in the axon hillock are two orders of magnitude larger than other neuronal locations. Expected 2D magnetic field maps of naturalistic spiking activity of a volume of neurons via widefield diamond-nitrogen-vacancy-center-magnetometry were simulated. A dictionary-based matching pursuit type algorithm applied to the data using the axon-hillock's APMF signature allowed spatiotemporal reconstruction of action potentials in the volume of brain tissue at single cell resolution. Enhancement of APMF signals coupled with magnetometry advances thus can potentially replace current functional brain mapping techniques.

Playing the piano with the cortex: role of neuronal ensembles and pattern completion in perception and behavior

Neuronal ensembles, i.e. coactive groups of neurons, have been long postulated to be functional building blocks of cortical circuits and units of the neural code. Calcium imaging of neuronal populations has demonstrated the widespread existence of spontaneous and sensory-evoked ensembles in cortical circuits in vivo. The development of two-photon optical techniques to simultaneously record and activate neurons with single cell resolution ("piano" experiments) has revealed the existence of pattern completion neurons, which can trigger an entire ensemble, and demonstrated a causal relation between ensembles and behavior. We review recent results controlling visual perception with targeted holographic manipulation of cortical ensembles by stimulating pattern completion neurons. Analyzing population activity as neuronal ensembles and exploiting pattern completion could enable control of brain states in health and disease.

NeuroPath2Path: Classification and elastic morphing between neuronal arbors using path-wise similarity

Neuron shape and connectivity affect function. Modern imaging methods have proven successful at extracting morphological information. One potential path to achieve analysis of this morphology is through graph theory. Encoding by graphs enables the use of high throughput informatic methods to extract and infer brain function. However, the application of graph-theoretic methods to neuronal morphology comes with certain challenges in term of complex subgraph matching and the difficulty in computing intermediate shapes in between two imaged temporal samples. Here we report a novel, efficacious graph-theoretic method that rises to the challenges. The morphology of a neuron, which consists of its overall size, global shape, local branch patterns, and cell-specific biophysical properties, can vary significantly with the cell's identity, location, as well as developmental and physiological state. Various algorithms have been developed to customize shape based statistical and graph related features for quantitative analysis of neuromorphology, followed by the classification of neuron cell types using the features. Unlike the classical feature extraction based methods from imaged or 3D reconstructed neurons, we propose a model based on the rooted path decomposition from the soma to the dendrites of a neuron and extract morphological features from each constituent path. We hypothesize that measuring the distance between two neurons can be realized by minimizing the cost of continuously morphing the set of all rooted paths of one neuron to another. To validate this claim, we first establish the correspondence of paths between two neurons using a modified Munkres algorithm. Next, an elastic deformation framework that employs the square root velocity function is established to perform the continuous morphing, which, as an added benefit, provides an effective visualization tool. We experimentally show the efficacy of NeuroPath2Path, NeuroP2P, over the state of the art.

Fast, 3D Isotropic Imaging of Whole Mouse Brain Using Multiangle-Resolved Subvoxel SPIM

The recent integration of light-sheet microscopy and tissue-clearing has facilitated an important alternative to conventional histological imaging approaches. However, the in toto cellular mapping of neural circuits throughout an intact mouse brain remains highly challenging, requiring complicated mechanical stitching, and suffering from anisotropic resolution insufficient for high-quality reconstruction in 3D. Here, the use of a multiangle-resolved subvoxel selective plane illumination microscope (Mars-SPIM) is proposed to achieve high-throughput imaging of whole mouse brain at isotropic cellular resolution. This light-sheet imaging technique can computationally improve the spatial resolution over six times under a large field of view, eliminating the use of slow tile stitching. Furthermore, it can recover complete structural information of the sample from images subject to thick-tissue scattering/attenuation. With Mars-SPIM, a digital atlas of a cleared whole mouse brain (≈7 mm × 9.5 mm × 5 mm) can readily be obtained with an isotropic resolution of ≈2 µm (1 µm voxel) and a short acquisition time of 30 min. It provides an efficient way to implement system-level cellular analysis, such as the mapping of different neuron populations and tracing of long-distance neural projections over the entire brain. Mars-SPIM is thus well suited for high-throughput cell-profiling phenotyping of brain and other mammalian organs.

Probing Single Synapses via the Photolytic Release of Neurotransmitters

The development of two-photon microscopy has revolutionized our understanding of how synapses are formed and how they transform synaptic inputs in dendritic spines-tiny protrusions that cover the dendrites of pyramidal neurons that receive most excitatory synaptic information in the brain. These discoveries have led us to better comprehend the neuronal computations that take place at the level of dendritic spines as well as within neuronal circuits with unprecedented resolution. Here, we describe a method that uses a two-photon (2P) microscope and 2P uncaging of caged neurotransmitters for the activation of single and multiple spines in the dendrites of cortical pyramidal neurons. In addition, we propose a cost-effective description of the components necessary for the construction of a one laser source-2P microscope capable of nearly simultaneous 2P uncaging of neurotransmitters and 2P calcium imaging of the activated spines and nearby dendrites. We provide a brief overview on how the use of these techniques have helped researchers in the last 15 years unravel the function of spines in: (a) information processing; (b) storage; and (c) integration of excitatory synaptic inputs.

Searching basic units in memory traces: associative memory cells

The acquisition of associated signals is commonly seen in life. The integrative storage of these exogenous and endogenous signals is essential for cognition, emotion and behaviors. In terms of basic units of memory traces or engrams, associative memory cells are recruited in the brain during learning, cognition and emotional reactions. The recruitment and refinement of associative memory cells facilitate the retrieval of memory-relevant events and the learning of reorganized unitary signals that have been acquired. The recruitment of associative memory cells is fulfilled by generating mutual synapse innervations among them in coactivated brain regions. Their axons innervate downstream neurons convergently and divergently to recruit secondary associative memory cells. Mutual synapse innervations among associative memory cells confer the integrative storage and reciprocal retrieval of associated signals. Their convergent synapse innervations to secondary associative memory cells endorse integrative cognition. Their divergent innervations to secondary associative memory cells grant multiple applications of associated signals. Associative memory cells in memory traces are defined to be nerve cells that are able to encode multiple learned signals and receive synapse innervations carrying these signals. An impairment in the recruitment and refinement of associative memory cells will lead to the memory deficit associated with neurological diseases and psychological disorders. This review presents a comprehensive diagram for the recruitment and refinement of associative memory cells for memory-relevant events in a lifetime.

A compact holographic projector module for high-resolution 3D multi-site two-photon photostimulation

Patterned two-photon (2P) photolysis via holographic illumination is a powerful method to investigate neuronal function because of its capability to emulate multiple synaptic inputs in three dimensions (3D) simultaneously. However, like any optical system, holographic projectors have a finite space-bandwidth product that restricts the spatial range of patterned illumination or field-of-view (FOV) for a desired resolution. Such trade-off between holographic FOV and resolution restricts the coverage within a limited domain of the neuron's dendritic tree to perform highly resolved patterned 2P photolysis on individual spines. Here, we integrate a holographic projector into a commercial 2P galvanometer-based 2D scanning microscope with an uncaging unit and extend the accessible holographic FOV by using the galvanometer scanning mirrors to reposition the holographic FOV arbitrarily across the imaging FOV. The projector system utilizes the microscope's built-in imaging functions. Stimulation positions can be selected from within an acquired 3D image stack (the volume-of-interest, VOI) and the holographic projector then generates 3D illumination patterns with multiple uncaging foci. The imaging FOV of our system is 800×800 μm2 within which a holographic VOI of 70×70×70 μm3 can be chosen at arbitrary positions and also moved during experiments without moving the sample. We describe the design and alignment protocol as well as the custom software plugin that controls the 3D positioning of stimulation sites. We demonstrate the neurobiological application of the system by simultaneously uncaging glutamate at multiple spines within dendritic domains and consequently observing summation of postsynaptic potentials at the soma, eventually resulting in action potentials. At the same time, it is possible to perform two-photon Ca2+ imaging in 2D in the dendrite and thus to monitor synaptic Ca2+ entry in selected spines and also local regenerative events such as dendritic action potentials.

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.

Closed-loop all-optical interrogation of neural circuits in vivo

Understanding the causal relationship between neural activity and behavior requires the ability to perform rapid and targeted interventions in ongoing activity. Here we describe a closed-loop all-optical strategy for dynamically controlling neuronal activity patterns in awake mice. We rapidly tailored and delivered two-photon optogenetic stimulation based on online readout of activity using simultaneous two-photon imaging, thus enabling the manipulation of neural circuit activity 'on the fly' during behavior.

Two-Photon Optogenetic Mapping of Excitatory Synaptic Connectivity and Strength

The development of optical methods to activate neurons with single-cell resolution has enabled systematic mapping of inhibitory connections. In contrast, optical mapping of excitatory connections between pyramidal neurons (PCs) has been a major challenge due to their high densities in cortical tissue and their weak and stochastic connectivity. Here we present an optogenetic two-photon mapping method in mouse neocortical slices by activating PCs with the red-shifted opsin C1V1 while recording postsynaptic responses in whole-cell configuration. Comparison of delays from triggered action potentials (APs) with those from synaptic inputs allowed us to predict connected PCs in three dimensions. We confirmed these predictions with paired recordings, and used this method to map strong connections among large populations of layer 2/3 PCs. Our method can be used for fast, systematic mapping of synaptic connectivity and weights.

•

Two-photon optogenetic mapping of excitatory connectivity and strength in neocortex

•

Identification of connected neurons in acute slices through numerical optimization

•

Synaptic delays align with location of connected presynaptic cell

•

Confirmation of predicted connections by dual patch-clamp recordings

Porphyrin Dyes for Nonlinear Optical Imaging of Live Cells

Second harmonic generation (SHG)-based probes are useful for nonlinear optical imaging of biological structures, such as the plasma membrane. Several amphiphilic porphyrin-based dyes with high SHG coefficients have been synthesized with different hydrophilic head groups, and their cellular targeting has been studied. The probes with cationic head groups localize better at the plasma membrane than the neutral probes with zwitterionic or non-charged ethylene glycol-based head groups. Porphyrin dyes with only dications as hydrophilic head groups localize inside HEK293T cells to give SHG, whereas tricationic dyes localize robustly at the plasma membrane of cells, including neurons, in vitro and ex vivo. The copper(II) complex of the tricationic dye with negligible fluorescence quantum yield works as an SHG-only dye. The free-base tricationic dye has been demonstrated for two-photon fluorescence and SHG-based multimodal imaging. This study demonstrates the importance of a balance between the hydrophobicity and hydrophilicity of amphiphilic dyes for effective plasma membrane localization.

Stretchable Transparent Electrode Arrays for Simultaneous Electrical and Optical Interrogation of Neural Circuits in Vivo

Recent developments of transparent electrode arrays provide a unique capability for simultaneous optical and electrical interrogation of neural circuits in the brain. However, none of these electrode arrays possess the stretchability highly desired for interfacing with mechanically active neural systems, such as the brain under injury, the spinal cord, and the peripheral nervous system (PNS). Here, we report a stretchable transparent electrode array from carbon nanotube (CNT) web-like thin films that retains excellent electrochemical performance and broad-band optical transparency under stretching and is highly durable under cyclic stretching deformation. We show that the CNT electrodes record well-defined neuronal response signals with negligible light-induced artifacts from cortical surfaces under optogenetic stimulation. Simultaneous two-photon calcium imaging through the transparent CNT electrodes from cortical surfaces of GCaMP-expressing mice with epilepsy shows individual activated neurons in brain regions from which the concurrent electrical recording is taken, thus providing complementary cellular information in addition to the high-temporal-resolution electrical recording. Notably, the studies on rats show that the CNT electrodes remain operational during and after brain contusion that involves the rapid deformation of both the electrode array and brain tissue. This enables real-time, continuous electrophysiological monitoring of cortical activity under traumatic brain injury. These results highlight the potential application of the stretchable transparent CNT electrode arrays in combining electrical and optical modalities to study neural circuits, especially under mechanically active conditions, which could potentially provide important new insights into the local circuit dynamics of the spinal cord and PNS as well as the mechanism underlying traumatic injuries of the nervous system.

Holographic imaging and photostimulation of neural activity

Optical imaging methods are powerful tools in neuroscience as they can systematically monitor the activity of neuronal populations with high spatiotemporal resolution using calcium or voltage indicators. Moreover, caged compounds and optogenetic actuators enable to optically manipulate neural activity. Among optical methods, computer-generated holography offers an enormous flexibility to sculpt the excitation light in three-dimensions (3D), particularly when combined with two-photon light sources. By projecting holographic light patterns on the sample, the activity of multiple neurons across a 3D brain volume can be simultaneously imaged or optically manipulated with single-cell precision. This flexibility makes two-photon holographic microscopy an ideal all-optical platform to simultaneously read and write activity in neuronal populations in vivo in 3D, a critical ability to dissect the function of neural circuits.

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

The simultaneous imaging and manipulating of neural activity could enable the functional dissection of neural circuits. Here we have combined two-photon optogenetics with simultaneous volumetric two-photon calcium imaging to measure and manipulate neural activity in mouse neocortex in vivo in three-dimensions (3D) with cellular resolution. Using a hybrid holographic approach, we simultaneously photostimulate more than 80 neurons over 150 μm in depth in layer 2/3 of the mouse visual cortex, while simultaneously imaging the activity of the surrounding neurons. We validate the usefulness of the method by photoactivating in 3D selected groups of interneurons, suppressing the response of nearby pyramidal neurons to visual stimuli in awake animals. Our all-optical approach could be used as a general platform to read and write neuronal activity.

Modern microscopy provides a window into the brain. The first light microscopes were able to magnify cells only in thin slices of tissue. By contrast, today’s light microscopes can image cells below the surface of the brain of a living animal. Even so, this remains challenging for several reasons. One is that the brain is three-dimensional. Another is that brain tissue scatters light. Trying to view neurons deep within the brain is a little like trying to view them through a glass of milk. Most of the light scatters on its way through the tissue with the result that little of the light reaches the target neurons.

Yang et al. have now tackled these challenges using a technique called holography. Holography produces 3D images of objects by splitting a beam of light and then recombining the beams in a specific way. Yang et al. applied this technique to an infrared laser beam, opting for infrared because it scatters much less in brain tissue than visible light. Directing each of the infrared beams to a different neuron can produce 3D images of multiple cells within the brain’s outer layer, the cortex, all at the same time.

The holographic infrared microscope can be used alongside two techniques called optogenetics and calcium imaging, in which light-sensitive proteins are inserted into neurons. Depending on the proteins introduced, shining light onto the neurons will either change their activity, or cause them to fluoresce whenever they are active. Just as a computer can both “read” and “write” data, the holographic microscope can thus read out existing neuronal activity or write new patterns of activity. By combining these techniques, Yang et al. were able to stimulate more than 80 neurons at the same time – and meanwhile visualize the activity of the surrounding neurons – at multiple depths within the mouse cortex.

This new microscopy technique, while a clear advance over existing methods, still cannot image and control neurons throughout the entire cortex. The next goal is to further extend this method across multiple brain areas and manipulate the activity of any subset of neurons at will. Neuroscientists will greatly benefit from the ability to image and alter the activity of living neural circuits in 3D. In the future, clinicians may be able to use this technique to treat brain disorders by adjusting the activity of abnormal neural circuits.

Studies of cortical connectivity using optical circuit mapping methods

An important consideration when probing the function of any neuron is to uncover the source of synaptic input onto the cell, its intrinsic physiology and efferent targets. Over the years, electrophysiological approaches have generated considerable insight into these properties in a variety of cortical neuronal subtypes and circuits. However, as researchers explore neuronal function in greater detail, they are increasingly turning to optical techniques to bridge the gap between local network interactions and behaviour. The application of optical methods has increased dramatically over the past decade, spurred on by the optogenetic revolution. In this review, we provide an account of recent innovations, providing researchers with a primer detailing circuit mapping strategies in the cerebral cortex. We will focus on technical aspects of performing neurotransmitter uncaging and channelrhodopsin-assisted circuit mapping, with the aim of identifying common pitfalls that can negatively influence the collection of reliable data.

Intrinsic optical sectioning with upconverting nanoparticles

Scanning laser upconversion microscopy yields true multiphoton sectioning power at very low excitation densities.

Three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT)

Optical methods capable of manipulating neural activity with cellular resolution and millisecond precision in three dimensions will accelerate the pace of neuroscience research. Existing approaches for targeting individual neurons, however, fall short of these requirements. Here we present a new multiphoton photo-excitation method, termed three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT), which allows precise, simultaneous photo-activation of arbitrary sets of neurons anywhere within the addressable volume of a microscope. This technique uses point-cloud holography to place multiple copies of a temporally focused disc matching the dimensions of a neuron's cell body. Experiments in cultured cells, brain slices, and in living mice demonstrate single-neuron spatial resolution even when optically targeting randomly distributed groups of neurons in 3D. This approach opens new avenues for mapping and manipulating neural circuits, allowing a real-time, cellular resolution interface to the brain.

Plasmonic Enhancement of Selective Photonic Virus Inactivation

Femtosecond (fs) pulsed laser irradiation techniques have attracted interest as a photonic approach for the selective inactivation of virus contaminations in biological samples. Conventional pulsed laser approaches require, however, relatively long irradiation times to achieve a significant inactivation of virus. In this study, we investigate the enhancement of the photonic inactivation of Murine Leukemia Virus (MLV) via 805 nm femtosecond pulses through gold nanorods whose localized surface plasmon resonance overlaps with the excitation laser. We report a plasmonically enhanced virus inactivation, with greater than 3.7-log reduction measured by virus infectivity assays. Reliable virus inactivation was obtained for 10 s laser exposure with incident laser powers ≥0.3 W. Importantly, the fs-pulse induced inactivation was selective to the virus and did not induce any measurable damage to co-incubated antibodies. The loss in viral infection was associated with reduced viral fusion, linking the loss in infectivity with a perturbation of the viral envelope. Based on the observations that physical contact between nanorods and virus particles was not required for viral inactivation and that reactive oxygen species (ROS) did not participate in the detected viral inactivation, a model of virus inactivation based on plasmon enhanced shockwave generation is proposed.

Toward Whole-Body Connectomics

Recent advances in neuro-technologies have revolutionized knowledge of brain structure and functions. Governments and private organizations worldwide have initiated several large-scale brain connectome projects, to further understand how the brain works at the systems levels. Most recent projects focus on only brain neurons, with the exception of an early effort to reconstruct the 302 neurons that comprise the whole body of the small worm, Caenorhabditis elegans However, to fully elucidate the neural circuitry of complex behavior, it is crucial to understand brain interactions with the whole body, which can be achieved only by mapping the whole-body connectome. In this article, we discuss the current state of connectomics study, focusing on novel optical approaches and related imaging technologies. We also discuss the challenges encountered by scientists who endeavor to map these whole-body connectomes in large animals.

Technologies for imaging neural activity in large volumes

Neural circuitry has evolved to form distributed networks that act dynamically across large volumes. Conventional microscopy collects data from individual planes and cannot sample circuitry across large volumes at the temporal resolution relevant to neural circuit function and behaviors. Here we review emerging technologies for rapid volume imaging of neural circuitry. We focus on two critical challenges: the inertia of optical systems, which limits image speed, and aberrations, which restrict the image volume. Optical sampling time must be long enough to ensure high-fidelity measurements, but optimized sampling strategies and point-spread function engineering can facilitate rapid volume imaging of neural activity within this constraint. We also discuss new computational strategies for processing and analyzing volume imaging data of increasing size and complexity. Together, optical and computational advances are providing a broader view of neural circuit dynamics and helping elucidate how brain regions work in concert to support behavior.

Enriched Endogenous Omega-3 Fatty Acids in Mice Ameliorate Parenchymal Cell Death After Traumatic Brain Injury

Currently no effective therapies are available for the treatment of traumatic brain injury (TBI). Early intervention that specifically provides neuroprotection is of most importance which profoundly influences the outcome of TBI. In the present study, we adopted a closed-skull mild TBI model to investigate potential roles of omega-3 polyunsaturated fatty acids (ω-3 PUFAs) in protecting against TBI. Using two-photon laser scanning microscopy (2PLSM), parenchymal cell death and reactive oxidative species (ROS) expression were directly observed and recorded after TBI through a thinned skull bone window. Fat-1 mice with high endogenous ω-3 PUFAs significantly inhibited ROS expression and attenuated parenchymal cell death after compression injury during the early injury phase. Elevated generation of glutathione (GSH) and neuroprotectin D1 (NPD1) in the parenchyma of fat-1 mice could be the contributor to the beneficial role of ω-3 PUFAs in TBI. The results of the study suggest that ω-3 PUFAs is an effective neuroprotectant as an early pharmacological intervention for TBI and the information derived from this study may help guide dietary advice for those who are susceptible to repetitive mild TBI.

Brain-Machine Interfaces: From Basic Science to Neuroprostheses and Neurorehabilitation

Brain-machine interfaces (BMIs) combine methods, approaches, and concepts derived from neurophysiology, computer science, and engineering in an effort to establish real-time bidirectional links between living brains and artificial actuators. Although theoretical propositions and some proof of concept experiments on directly linking the brains with machines date back to the early 1960s, BMI research only took off in earnest at the end of the 1990s, when this approach became intimately linked to new neurophysiological methods for sampling large-scale brain activity. The classic goals of BMIs are 1) to unveil and utilize principles of operation and plastic properties of the distributed and dynamic circuits of the brain and 2) to create new therapies to restore mobility and sensations to severely disabled patients. Over the past decade, a wide range of BMI applications have emerged, which considerably expanded these original goals. BMI studies have shown neural control over the movements of robotic and virtual actuators that enact both upper and lower limb functions. Furthermore, BMIs have also incorporated ways to deliver sensory feedback, generated from external actuators, back to the brain. BMI research has been at the forefront of many neurophysiological discoveries, including the demonstration that, through continuous use, artificial tools can be assimilated by the primate brain's body schema. Work on BMIs has also led to the introduction of novel neurorehabilitation strategies. As a result of these efforts, long-term continuous BMI use has been recently implicated with the induction of partial neurological recovery in spinal cord injury patients.

Combination of High-density Microelectrode Array and Patch Clamp Recordings to Enable Studies of Multisynaptic Integration

We present a novel, all-electric approach to record and to precisely control the activity of tens of individual presynaptic neurons. The method allows for parallel mapping of the efficacy of multiple synapses and of the resulting dynamics of postsynaptic neurons in a cortical culture. For the measurements, we combine an extracellular high-density microelectrode array, featuring 11’000 electrodes for extracellular recording and stimulation, with intracellular patch-clamp recording. We are able to identify the contributions of individual presynaptic neurons - including inhibitory and excitatory synaptic inputs - to postsynaptic potentials, which enables us to study dendritic integration. Since the electrical stimuli can be controlled at microsecond resolution, our method enables to evoke action potentials at tens of presynaptic cells in precisely orchestrated sequences of high reliability and minimum jitter. We demonstrate the potential of this method by evoking short- and long-term synaptic plasticity through manipulation of multiple synaptic inputs to a specific neuron.

Imaging and Optically Manipulating Neuronal Ensembles

The neural code that relates the firing of neurons to the generation of behavior and mental states must be implemented by spatiotemporal patterns of activity across neuronal populations. These patterns engage selective groups of neurons, called neuronal ensembles, which are emergent building blocks of neural circuits. We review optical and computational methods, based on two-photon calcium imaging and two-photon optogenetics, to detect, characterize, and manipulate neuronal ensembles in three dimensions. We review data using these methods in the mammalian cortex that demonstrate the existence of neuronal ensembles in the spontaneous and evoked cortical activity in vitro and in vivo. Moreover, two-photon optogenetics enable the possibility of artificially imprinting neuronal ensembles into awake, behaving animals and of later recalling those ensembles selectively by stimulating individual cells. These methods could enable deciphering the neural code and also be used to understand the pathophysiology of and design novel therapies for neurological and mental diseases.

Induction of neuronal activation by femtosecond-pulsed laser irradiation and its potential application for amyloid-β-induced toxicity assessment

Manipulating neural activity is crucial for studying the neural connectivity and the pathophysiology of neurodegenerative disease. Among various techniques for neural activation, direct optical stimulation method with femtosecond-pulsed laser is simple and can be specifically applied on a single neuron. Brief irradiation of femtosecond laser pulses on a neuron elevates intracellular calcium, and it propagates to adjacent neurons. However, the mechanisms of laser-induced neural activation are still unclear. In this report, we have elucidated the mechanism of laser-induced neural activation which could be mediated by superoxide, specifically blocked by diphenyleneiodonium chloride, and depletion in intracellular calcium storage. Furthermore, we also showed that the propagation of calcium initiated by laser stimulation is dependent on the presence of extracellular calcium as well as electrical and chemical synapses. We verified the applicability of such mechanism for the assessment of neuronal functionality, by measuring calcium elevation, intracellular calcium propagation, ROS increase, and performing cell death assay in vehicle and Aβ-treated neurons. This work suggests promising applications of the potential for implementing such laser-induced neural activation for rapid and reliable drug screening.

Cellular resolution circuit mapping with temporal-focused excitation of soma-targeted channelrhodopsin

We describe refinements in optogenetic methods for circuit mapping that enable measurements of functional synaptic connectivity with single-neuron resolution. By expanding a two-photon beam in the imaging plane using the temporal focusing method and restricting channelrhodopsin to the soma and proximal dendrites, we are able to reliably evoke action potentials in individual neurons, verify spike generation with GCaMP6s, and determine the presence or absence of synaptic connections with patch-clamp electrophysiological recording.

Cell Type-Specific Circuit Mapping Reveals the Presynaptic Connectivity of Developing Cortical Circuits

The mammalian cerebral cortex is a dense network composed of local, subcortical, and intercortical synaptic connections. As a result, mapping cell type-specific neuronal connectivity in the cerebral cortex in vivo has long been a challenge for neurobiologists. In particular, the development of excitatory and inhibitory interneuron presynaptic input has been hard to capture. We set out to analyze the development of this connectivity in the first postnatal month using a murine model. First, we surveyed the connectivity of one of the earliest populations of neurons in the brain, the Cajal-Retzius (CR) cells in the neocortex, which are known to be critical for cortical layer formation and are hypothesized to be important in the establishment of early cortical networks. We found that CR cells receive inputs from deeper-layer excitatory neurons and inhibitory interneurons in the first postnatal week. We also found that both excitatory pyramidal neurons and inhibitory interneurons received broad inputs in the first postnatal week, including inputs from CR cells. Expanding our analysis into the more mature brain, we assessed the inputs onto inhibitory interneurons and excitatory projection neurons, labeling neuronal progenitors with Cre drivers to study discrete populations of neurons in older cortex, and found that excitatory cortical and subcortical inputs are refined by the fourth week of development, whereas local inhibitory inputs increase during this postnatal period. Cell type-specific circuit mapping is specific, reliable, and effective, and can be used on molecularly defined subtypes to determine connectivity in the cortex.

SIGNIFICANCE STATEMENT

Mapping cortical connectivity in the developing mammalian brain has been an intractable problem, in part because it has not been possible to analyze connectivity with cell subtype precision. Our study systematically targets the presynaptic connections of discrete neuronal subtypes in both the mature and developing cerebral cortex. We analyzed the connections that Cajal-Retzius cells make and receive, and found that these cells receive inputs from deeper-layer excitatory neurons and inhibitory interneurons in the first postnatal week. We assessed the inputs onto inhibitory interneurons and excitatory projection neurons, the major two types of neurons in the cortex, and found that excitatory inputs are refined by the fourth week of development, whereas local inhibitory inputs increase during this postnatal period.

Astrocytes regulate cortical state switching in vivo

The role of astrocytes in neuronal function has received increasing recognition, but disagreement remains about their function at the circuit level. Here we use in vivo two-photon calcium imaging of neocortical astrocytes while monitoring the activity state of the local neuronal circuit electrophysiologically and optically. We find that astrocytic calcium activity precedes spontaneous circuit shifts to the slow-oscillation-dominated state, a neocortical rhythm characterized by synchronized neuronal firing and important for sleep and memory. Further, we show that optogenetic activation of astrocytes switches the local neuronal circuit to this slow-oscillation state. Finally, using two-photon imaging of extracellular glutamate, we find that astrocytic transients in glutamate co-occur with shifts to the synchronized state and that optogenetically activated astrocytes can generate these glutamate transients. We conclude that astrocytes can indeed trigger the low-frequency state of a cortical circuit by altering extracellular glutamate, and therefore play a causal role in the control of cortical synchronizations.

Optogenetic Manipulation of Selective Neural Activity in Free-Moving Drosophila Adults

Activating selected neurons elicits specific behaviors in Drosophila adults. By combining optogenetics and laser-tracking techniques, we have recently developed an automated laser-tracking and optogenetic manipulation system (ALTOMS) for studying how brain circuits orchestrate complex behaviors. The established ALTOMS can independently target three lasers (473-nm blue laser, 593.5-nm yellow laser, and 1064-nm infrared laser) on any specified body part of two freely moving flies. Triggering light-sensitive proteins in real time, the blue laser and yellow laser can respectively activate and inhibit target neurons in artificial transgenic flies. Since infrared light is invisible to flies, we use the 1064-nm laser as an aversive stimulus in operant learning without perturbing visual inputs. Herein, we provide a detailed protocol for the construction of ALTOMS and optogenetic manipulation of target neurons in Drosophila adults during social interactions.

Pathway-Specific Striatal Substrates for Habitual Behavior

The dorsolateral striatum (DLS) is implicated in habit formation. However, the DLS circuit mechanisms underlying habit remain unclear. A key role for DLS is to transform sensorimotor cortical input into firing of output neurons that project to the mutually antagonistic direct and indirect basal ganglia pathways. Here we examine whether habit alters this input-output function. By imaging cortically evoked firing in large populations of pathway-defined striatal projection neurons (SPNs), we identify features that strongly correlate with habitual behavior on a subject-by-subject basis. Habitual behavior correlated with strengthened DLS output to both pathways as well as a tendency for action-promoting direct pathway SPNs to fire before indirect pathway SPNs. In contrast, habit suppression correlated solely with a weakened direct pathway output. Surprisingly, all effects were broadly distributed in space. Together, these findings indicate that the striatum imposes broad, pathway-specific modulations of incoming activity to render learned motor behaviors habitual.