Three-dimensional spatiotemporal focusing of holographic patterns

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.

Multicolor two-photon light-patterning microscope exploiting the spatio-temporal properties of a fiber bundle

The development of efficient genetically encoded indicators and actuators has opened up the possibility of reading and manipulating neuronal activity in living tissues with light. To achieve precise and reconfigurable targeting of large numbers of neurons with single-cell resolution within arbitrary volumes, different groups have recently developed all-optical strategies based on two-photon excitation and spatio-temporal shaping of ultrashort laser pulses. However, such techniques are often complex to set up and typically operate at a single wavelength only. To address these issues, we have developed a novel optical approach that uses a fiber bundle and a spatial light modulator to achieve simple and dual-color two-photon light patterning in three dimensions. By leveraging the core-to-core temporal delay and the wavelength-independent divergence characteristics of fiber bundles, we have demonstrated the capacity to generate high-resolution excitation spots in a 3D region with two distinct laser wavelengths simultaneously, offering a suitable and simple alternative for precise multicolor cell targeting.

Holographic Optogenetic Activation of Neurons Eliciting Locomotion in Head-Embedded Larval Zebrafish

Understanding how motor circuits are organized and recruited in order to perform complex behavior is an essential question of neuroscience. Here we present an optogenetic protocol on larval zebrafish that allows spatial selective control of neuronal activity within a genetically defined population. We combine holographic illumination with the use of effective opsin transgenic lines, alongside high-speed behavioral monitoring to dissect the motor circuits of the larval zebrafish.

Wavefront shaping improves the transparency of the scattering media: a review

Significance

Wavefront shaping (WFS) can compensate for distortions by optimizing the wavefront of the input light or reversing the transmission matrix of the media. It is a promising field of research. A thorough understanding of principles and developments of WFS is important for optical research.

Aim

To provide insight into WFS for researchers who deal with scattering in biomedicine, imaging, and optical communication, our study summarizes the basic principles and methods of WFS and reviews recent progress.

Approach

The basic principles, methods of WFS, and the latest applications of WFS in focusing, imaging, and multimode fiber (MMF) endoscopy are described. The practical challenges and prospects of future development are also discussed.

Results

Data-driven learning-based methods are opening up new possibilities for WFS. High-resolution imaging through MMFs can support small-diameter endoscopy in the future.

Conclusion

The rapid development of WFS over the past decade has shown that the best solution is not to avoid scattering but to find ways to correct it or even use it. WFS with faster speed, more optical modes, and more modulation degrees of freedom will continue to drive exciting developments in various fields.

Descanned fast light targeting (deFLiT) two-photon optogenetics

Two-photon light-targeting optogenetics allows controlling selected subsets of neurons with near single-cell resolution and high temporal precision. To push forward this approach, we recently proposed a fast light-targeting strategy (FLiT) to rapidly scan multiple holograms tiled on a spatial light modulator (SLM). This allowed generating sub-ms timely-controlled switch of light patterns enabling to reduce the power budget for multi-target excitation and increase the temporal precision for relative spike tuning in a circuit. Here, we modified the optical design of FLiT by including a de-scan unit (deFLiT) to keep the holographic illumination centered at the middle of the objective pupil independently of the position of the tiled hologram on the SLM. This enables enlarging the number of usable holograms and reaching extended on-axis excitation volumes, and therefore increasing even further the power gain and temporal precision of conventional FLiT.

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.

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.

Scanless two-photon voltage imaging

Parallel light-sculpting methods have been used to perform scanless two-photon photostimulation of multiple neurons simultaneously during all-optical neurophysiology experiments. We demonstrate that scanless two-photon excitation also enables high-resolution, high-contrast, voltage imaging by efficiently exciting fluorescence in a large fraction of the cellular soma. We present a thorough characterisation of scanless two-photon voltage imaging using existing parallel approaches and lasers with different repetition rates. We demonstrate voltage recordings of high frequency spike trains and sub-threshold depolarizations in intact brain tissue from neurons expressing the soma-targeted genetically encoded voltage indicator JEDI-2P-kv. Using a low repetition-rate laser, we perform recordings from up to ten neurons simultaneously. Finally, by co-expressing JEDI-2P-kv and the channelrhodopsin ChroME-ST in neurons of hippocampal organotypic slices, we perform single-beam, simultaneous, two-photon voltage imaging and photostimulation. This enables in-situ validation of the precise number and timing of light evoked action potentials and will pave the way for rapid and scalable identification of functional brain connections in intact neural circuits.

A flexible two-photon fiberscope for fast activity imaging and precise optogenetic photostimulation of neurons in freely moving mice

We developed a flexible two-photon microendoscope (2P-FENDO) capable of all-optical brain investigation at near cellular resolution in freely moving mice. The system performs fast two-photon (2P) functional imaging and 2P holographic photostimulation of single and multiple cells using axially confined extended spots. Proof-of-principle experiments were performed in freely moving mice co-expressing jGCaMP7s and the opsin ChRmine in the visual or barrel cortex. On a field of view of 250 μm in diameter, we demonstrated functional imaging at a frame rate of up to 50 Hz and precise photostimulation of selected groups of cells. With the capability to simultaneously image and control defined neuronal networks in freely moving animals, 2P-FENDO will enable a precise investigation of neuronal functions in the brain during naturalistic behaviors.

WiChR, a highly potassium-selective channelrhodopsin for low-light one- and two-photon inhibition of excitable cells

The electric excitability of muscle, heart, and brain tissue relies on the precise interplay of Na+- and K+-selective ion channels. The involved ion fluxes are controlled in optogenetic studies using light-gated channelrhodopsins (ChRs). While non-selective cation-conducting ChRs are well established for excitation, K+-selective ChRs (KCRs) for efficient inhibition have only recently come into reach. Here, we report the molecular analysis of recently discovered KCRs from the stramenopile Hyphochytrium catenoides and identification of a novel type of hydrophobic K+ selectivity filter. Next, we demonstrate that the KCR signature motif is conserved in related stramenopile ChRs. Among them, WiChR from Wobblia lunata features a so far unmatched preference for K+ over Na+, stable photocurrents under continuous illumination, and a prolonged open-state lifetime. Showing high expression levels in cardiac myocytes and neurons, WiChR allows single- and two-photon inhibition at low irradiance and reduced tissue heating. Therefore, we recommend WiChR as the long-awaited efficient and versatile optogenetic inhibitor.

Light-field microscopy with temporal focusing multiphoton illumination for scanless volumetric bioimaging

A temporal focusing multiphoton illumination (TFMI) method is proposed for achieving selective volume illumination (SVI) (i.e., illuminating only the volume of interest) in light-field microscopy (LFM). The proposed method minimizes the background noise of the LFM images and enhances the contrast, and thus improves the imaging quality. Three-dimensional (3D) volumetric imaging is achieved by reconstructing the LFM images using a phase-space deconvolution algorithm. The experimental results obtained using 100-nm fluorescent beads show that the proposed TFMI-LFM system achieves lateral and axial resolutions of 1.2 µm and 1.1 µm, respectively, at the focal plane. Furthermore, the TFMI-LFM system enables 3D images of the single lobe of the drosophila mushroom body with GFP biomarker (OK-107) to be reconstructed in a one-snapshot record.

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.

Optogenetic manipulation of cell migration with high spatiotemporal resolution using lattice lightsheet microscopy

Lattice lightsheet microscopy (LLSM) featuring three-dimensional recording is improved to manipulate cellular behavior with subcellular resolution through optogenetic activation (optoLLSM). A position-controllable Bessel beam as a stimulation source is integrated into the LLSM to achieve spatiotemporal photoactivation by changing the spatial light modulator (SLM) patterns. Unlike the point-scanning in a confocal microscope, the lattice beams are capable of wide-field optical sectioning for optogenetic activation along the Bessel beam path.We show that the energy power required for optogenetic activations is lower than 1 nW (or 24 mWcm^-2) for time-lapses of CRY2olig clustering proteins, and membrane ruffling can be induced at different locations within a cell with subcellular resolution through light-triggered recruitment of phosphoinositide 3-kinase. Moreover, with the epidermal growth factor receptor (EGFR) fused with CRY2olig, we are able to demonstrate guided cell migration using optogenetic stimulation for up to 6 h, where 463 imaging volumes are collected, without noticeable cellular damages.

Using a Bessel beam as a simulation source allows the use of lattice lightsheet microscopy for spatiotemporal control of photoactivation, illustrated by the control of cellular migration behavior.

An optical approach for mapping functional connectivity at single-cell resolution in brain circuits

In the current issue of Cell Reports Methods, Spampinato et al. demonstrate a multiplexed system combining holographic photo-stimulation and functional imaging that may offer a generalizable approach for revealing how signals interact in complex neural circuits.

Optogenetics for light control of biological systems

Optogenetic techniques have been developed to allow control over the activity of selected cells within a highly heterogeneous tissue, using a combination of genetic engineering and light. Optogenetics employs natural and engineered photoreceptors, mostly of microbial origin, to be genetically introduced into the cells of interest. As a result, cells that are naturally light-insensitive can be made photosensitive and addressable by illumination and precisely controllable in time and space. The selectivity of expression and subcellular targeting in the host is enabled by applying control elements such as promoters, enhancers and specific targeting sequences to the employed photoreceptor-encoding DNA. This powerful approach allows precise characterization and manipulation of cellular functions and has motivated the development of advanced optical methods for patterned photostimulation. Optogenetics has revolutionized neuroscience during the past 15 years and is primed to have a similar impact in other fields, including cardiology, cell biology and plant sciences. In this Primer, we describe the principles of optogenetics, review the most commonly used optogenetic tools, illumination approaches and scientific applications and discuss the possibilities and limitations associated with optogenetic manipulations across a wide variety of optical techniques, cells, circuits and organisms.

Automotive Holographic Head-Up Displays

Driver's access to information about navigation and vehicle data through in-car displays and personal devices distract the driver from safe vehicle management. The discrepancy between road safety and infotainment must be addressed to develop safely operated modern vehicles. Head-up displays (HUDs) aim to introduce a seamless uptake of visual information for the driver while securely operating a vehicle. HUDs projected on the windshield provide the driver with visual navigation and vehicle data within the comfort of the driver's personal eye box through a customizable extended display space. Windshield HUDs do not require the driver to shift the gaze away from the road to attain road information. This article presents a review of technological advances and future perspectives in holographic HUDs by analyzing the optoelectronics devices and the user experience of the driver. The review elucidates holographic displays and full augmented reality in 3D with depth perception when projecting the visual information on the road within the driver's gaze. Design factors, functionality, and the integration of personalized machine learning technologies into holographic HUDs are discussed. Application examples of the display technologies regarding road safety and security are presented. An outlook is provided to reflect on display trends and autonomous driving.

Enhanced Single-Beam Multiple-Intensity Phase Retrieval Using Holographic Illumination

Single-beam multiple-intensity iterative phase retrieval is a high-precision and lens-free computational imaging method, which reconstructs the complex-valued distribution of the object from a volume of axially captured diffraction intensities using the post-processing algorithm. However, for the object with slowly-varying waves, the method may encounter the problem of convergence stagnation since the lack of diversity between the captured intensity patterns. In this paper, a novel technique to enhance phase retrieval using holographic illumination is proposed. One special computer-generated hologram is designed, which can generate multiple significantly different images at the required distances. The incident plane wave is firstly modulated by the hologram, and then the exit wave is used to illuminate the object. Benefitting from this holographic illumination, remarkable intensity changes in the given detector planes can be produced, which is conducive to fast and high-accuracy reconstruction. Simulation and optical experiments are performed to verify the feasibility of the proposed method.

KHz-rate volumetric voltage imaging of the whole Zebrafish heart

Fast volumetric imaging is essential for understanding the function of excitable tissues such as those found in the brain and heart. Measuring cardiac voltage transients in tissue volumes is challenging, especially at the high spatial and temporal resolutions needed to give insight to cardiac function. We introduce a new imaging modality based on simultaneous illumination of multiple planes in the tissue and parallel detection with multiple cameras, avoiding compromises inherent in any scanning approach. The system enables imaging of voltage transients in situ, allowing us, for the first time to our knowledge, to map voltage activity in the whole heart volume at KHz rates. The high spatiotemporal resolution of our method enabled the observation of novel dynamics of electrical propagation through the zebrafish atrioventricular canal.

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.

Neurophotonic tools for microscopic measurements and manipulation: status report

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

Single-Cell Resolution Optogenetics Via Expression of Soma-Targeted Rhodopsins

Optogenetics allows control of neural activity in genetically targeted neuron populations by light. Optogenetic control of individual neurons in neural circuits would enable powerful, causal investigations of neural connectivity and function at single-cell level and provide insights into how neural circuits operate. Such single-cell resolution optogenetics in neuron populations requires precise sculpting of light and subcellular targeting of optogenetic molecules. Here we describe a group of methods for single-cell resolution optogenetics in neuron cultures, in mouse brain slices, and in mouse cortex in-vivo, via patterned light and soma-targeted optogenetic molecules.

Extracting temporal relationships between weakly coupled peptidergic and motoneuronal signaling: Application to Drosophila ecdysis behavior

Neuromodulators, such as neuropeptides, can regulate and reconfigure neural circuits to alter their output, affecting in this way animal physiology and behavior. The interplay between the activity of neuronal circuits, their modulation by neuropeptides, and the resulting behavior, is still poorly understood. Here, we present a quantitative framework to study the relationships between the temporal pattern of activity of peptidergic neurons and of motoneurons during Drosophila ecdysis behavior, a highly stereotyped motor sequence that is critical for insect growth. We analyzed, in the time and frequency domains, simultaneous intracellular calcium recordings of peptidergic CCAP (crustacean cardioactive peptide) neurons and motoneurons obtained from isolated central nervous systems throughout fictive ecdysis behavior induced ex vivo by Ecdysis triggering hormone. We found that the activity of both neuronal populations is tightly coupled in a cross-frequency manner, suggesting that CCAP neurons modulate the frequency of motoneuron firing. To explore this idea further, we used a probabilistic logistic model to show that calcium dynamics in CCAP neurons can predict the oscillation of motoneurons, both in a simple model and in a conductance-based model capable of simulating many features of the observed neural dynamics. Finally, we developed an algorithm to quantify the motor behavior observed in videos of pupal ecdysis, and compared their features to the patterns of neuronal calcium activity recorded ex vivo. We found that the motor activity of the intact animal is more regular than the motoneuronal activity recorded from ex vivo preparations during fictive ecdysis behavior; the analysis of the patterns of movement also allowed us to identify a new post-ecdysis phase.

Remote Focusing in a Temporal Focusing Microscope

In a temporal focusing microscope, dispersion can remotely shift the temporal focal plane axially, but only a single depth can be in focus at a time on a fixed camera. In this paper, we demonstrate remote focusing in a temporal focusing microscope. Dispersion tuning with an electrically tunable lens (ETL) in a 4 f pulse shaper scans the excitation plane axially, and another ETL in the detection path keeps the shifted excitation plane in focus on the camera. Image stacks formed using two ETLs versus a traditional stage scan are equivalent.

Excitatory-inhibitory balance modulates the formation and dynamics of neuronal assemblies in cortical networks

Repetitive activation of subpopulations of neurons leads to the formation of neuronal assemblies, which can guide learning and behavior. Recent technological advances have made the artificial induction of these assemblies feasible, yet how various parameters of induction can be optimized is not clear. Here, we studied this question in large-scale cortical network models with excitatory-inhibitory balance. We found that the background network in which assemblies are embedded can strongly modulate their dynamics and formation. Networks with dominant excitatory interactions enabled a fast formation of assemblies, but this was accompanied by recruitment of other non-perturbed neurons, leading to some degree of nonspecific induction. On the other hand, networks with strong excitatory-inhibitory interactions ensured that the formation of assemblies remained constrained to the perturbed neurons, but slowed down the induction. Our results suggest that these two regimes can be suitable for computational and cognitive tasks with different trade-offs between speed and specificity.

Holographic microscope and its biological application

Holographic structured illumination combined with optogenetics enables patterned stimulation of neurons and glial cells in an intact living brain. Moreover, in vivo functional imaging of cellular activity with recent advanced microscope technologies allows for visualization of the cellular responses during learning, emotion and cognition. Integrating these techniques can be used to verify the link between cell function and behavior output. However, there are technical limitations to stimulate multiple cells with high spatial and temporal resolution with available techniques of optogenetic stimulation. Here, we summarized a two-photon microscope combined with holographic system to stimulate multiple cells with high spatial and temporal resolution for living mice and their biological application.

Probing neural codes with two-photon holographic optogenetics

Optogenetics ushered in a revolution in how neuroscientists interrogate brain function. Because of technical limitations, the majority of optogenetic studies have used low spatial resolution activation schemes that limit the types of perturbations that can be made. However, neural activity manipulations at finer spatial scales are likely to be important to more fully understand neural computation. Spatially precise multiphoton holographic optogenetics promises to address this challenge and opens up many new classes of experiments that were not previously possible. More specifically, by offering the ability to recreate extremely specific neural activity patterns in both space and time in functionally defined ensembles of neurons, multiphoton holographic optogenetics could allow neuroscientists to reveal fundamental aspects of the neural codes for sensation, cognition and behavior that have been beyond reach. This Review summarizes recent advances in multiphoton holographic optogenetics that substantially expand its capabilities, highlights outstanding technical challenges and provides an overview of the classes of experiments it can execute to test and validate key theoretical models of brain function. Multiphoton holographic optogenetics could substantially accelerate the pace of neuroscience discovery by helping to close the loop between experimental and theoretical neuroscience, leading to fundamental new insights into nervous system function and disorder.

Adaptive optics with spatio-temporal lock-in detection for temporal focusing microscopy

Wavefront distortion in temporal focusing microscopy (TFM) results in a distorted temporal profile of the excitation pulses owing to spatio-temporal coupling. Since the pulse duration is dramatically changed in the excitation volume, it is difficult to correct the temporal profile for a thick sample. Here, we demonstrate adaptive optics (AO) correction in a thick sample. We apply structured illumination microscopy (SIM) to an AO correction in wide-field TFM to decrease the change in the pulse duration in the signal detection volume. The AO correction with SIM was very successful in a thick sample for which AO correction with TFM failed.

Precise 3D computer-generated holography based on non-convex optimization with spherical aberration compensation (SAC-NOVO) for two-photon optogenetics

Computer-generated holography (CGH) has been adopted in two-photon optogenetics as a promising technique for selective excitation of neural ensembles. However, 3D CGH by nonconvex optimization, the state of art method, is susceptible to imprecise axial positioning, due to the quadratic phase approximation in 3D target generation. Even though the misplacement of targets in conventional CGH can be solved by pre-calibration, it still suffers from low efficiency and poor axial resolution of two-photon excitation. Here, we propose a novel CGH method based on non-convex optimization with spherical aberration compensation (SAC-NOVO). Through numerical simulations and two-photon excitation experiments, we verify that SAC-NOVO could achieve precise axial positioning for single and multiple expanded disk patterns, while ensuring high two-photon excitation efficiency. Besides, we experimentally show that SAC-NOVO enables the suppression of dark target areas. This work shows the superiority of SAC-NOVO for two-photon optogenetics.

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.

Optogenetic therapy: high spatiotemporal resolution and pattern discrimination compatible with vision restoration in non-human primates

Vision restoration is an ideal medical application for optogenetics, because the eye provides direct optical access to the retina for stimulation. Optogenetic therapy could be used for diseases involving photoreceptor degeneration, such as retinitis pigmentosa or age-related macular degeneration. We describe here the selection, in non-human primates, of a specific optogenetic construct currently tested in a clinical trial. We used the microbial opsin ChrimsonR, and showed that the AAV2.7m8 vector had a higher transfection efficiency than AAV2 in retinal ganglion cells (RGCs) and that ChrimsonR fused to tdTomato (ChR-tdT) was expressed more efficiently than ChrimsonR. Light at 600 nm activated RGCs transfected with AAV2.7m8 ChR-tdT, from an irradiance of 10¹⁵ photons.cm⁻².s⁻¹. Vector doses of 5 × 10¹⁰ and 5 × 10¹¹ vg/eye transfected up to 7000 RGCs/mm² in the perifovea, with no significant immune reaction. We recorded RGC responses from a stimulus duration of 1 ms upwards. When using the recorded activity to decode stimulus information, we obtained an estimated visual acuity of 20/249, above the level of legal blindness (20/400). These results lay the groundwork for the ongoing clinical trial with the AAV2.7m8 - ChR-tdT vector for vision restoration in patients with retinitis pigmentosa.

Gauvain et al demonstrate that optogenetic therapy using the AAV2.7m8- ChR-tdT construct can partially restore vision in non-human primates to levels above those considered legally-blind. This study enables the identification of the most suitable construct for ongoing clinical trials attempting vision restoration in patients with retinitis pigmentosa.

Two-Photon Optogenetic Stimulation of Drosophila Neurons

Optogenetics enables experimental control over neural activity using light. Channelrhodopsin and its variants are typically activated using visible light excitation but can also be activated using infrared two-photon excitation. Two-photon excitation can improve the spatial precision of stimulation in scattering tissue but has several practical limitations that need to be considered before use. Here we describe the methodology and best practices for using two-photon optogenetic stimulation of neurons within the brain of the fruit fly, Drosophila melanogaster, with an emphasis on projection neurons of the antennal lobe.

Time reversed optical waves by arbitrary vector spatiotemporal field generation

Lossless linear wave propagation is symmetric in time, a principle which can be used to create time reversed waves. Such waves are special “pre-scattered” spatiotemporal fields, which propagate through a complex medium as if observing a scattering process in reverse, entering the medium as a complicated spatiotemporal field and arriving after propagation as a desired target field, such as a spatiotemporal focus. Time reversed waves have previously been demonstrated for relatively low frequency phenomena such as acoustics, water waves and microwaves. Many attempts have been made to extend these techniques into optics. However, the much higher frequencies of optics make for very different requirements. A fully time reversed wave is a volumetric field with arbitrary amplitude, phase and polarisation at every point in space and time. The creation of such fields has not previously been possible in optics. We demonstrate time reversed optical waves with a device capable of independently controlling all of light’s classical degrees of freedom simultaneously. Such a class of ultrafast wavefront shaper is capable of generating a sequence of arbitrary 2D spatial/polarisation wavefronts at a bandwidth limited rate of 4.4 THz. This ability to manipulate the full field of an optical beam could be used to control both linear and nonlinear optical phenomena.

Truly arbitrary spatiotemporal wavefront shaping has many potential applications in optics. Here the authors develop a system capable of arbitrary waveshaping to the extent of full time reversal of spatiotemporal optical beams.

Functional interrogation of neural circuits with virally transmitted optogenetic tools

The vertebrate brain comprises a plethora of cell types connected by intertwined pathways. Optogenetics enriches the neuroscientific tool set for disentangling these neuronal circuits in a manner which exceeds the spatio-temporal precision of previously existing techniques. Technically, optogenetics can be divided in three types of optical and genetic combinations: (1) it is primarily understood as the manipulation of the activity of genetically modified cells (typically neurons) with light, i.e. optical actuators. (2) A second combination refers to visualizing the activity of genetically modified cells (again typically neurons), i.e. optical sensors. (3) A completely different interpretation of optogenetics refers to the light activated expression of a genetically induced construct. Here, we focus on the first two types of optogenetics, i.e. the optical actuators and sensors in an attempt to give an overview into the topic. We first cover methods to express opsins into neurons and introduce strategies of targeting specific neuronal populations in different animal species. We then summarize combinations of optogenetics with behavioral read out and neuronal imaging. Finally, we give an overview of the current state-of-the-art and an outlook on future perspectives.

Real-time 3D movement correction for two-photon imaging in behaving animals

Two-photon microscopy is widely used to investigate brain function across multiple spatial scales. However, measurements of neural activity are compromised by brain movement in behaving animals. Brain motion-induced artifacts are typically corrected using post hoc processing of two-dimensional images, but this approach is slow and does not correct for axial movements. Moreover, the deleterious effects of brain movement on high-speed imaging of small regions of interest and photostimulation cannot be corrected post hoc. To address this problem, we combined random-access three-dimensional (3D) laser scanning using an acousto-optic lens and rapid closed-loop field programmable gate array processing to track 3D brain movement and correct motion artifacts in real time at up to 1 kHz. Our recordings from synapses, dendrites and large neuronal populations in behaving mice and zebrafish demonstrate real-time movement-corrected 3D two-photon imaging with submicrometer precision.

Three-Dimensional Single-Molecule Localization Microscopy in Whole-Cell and Tissue Specimens

Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. We focus on three-dimensional single-molecule localization microscopy and review some of the major roadblocks and developing solutions to resolving thick volumes of cells and tissues at the nanoscale in three dimensions. These challenges include background fluorescence, system- and sample-induced aberrations, and information carried by photons, as well as drift correction, volume reconstruction, and photobleaching mitigation. We also highlight examples of innovations that have demonstrated significant breakthroughs in addressing the abovementioned challenges together with their core concepts as well as their trade-offs.

Azimuthal multiplexing 3D diffractive optics

Diffractive optics have increasingly caught the attention of the scientific community. Classical diffractive optics are 2D diffractive optical elements (DOEs) and computer-generated holograms (CGHs), which modulate optical waves on a solitary transverse plane. However, potential capabilities are missed by the inherent two-dimensional nature of these devices. Previous work has demonstrated that extending the modulation from planar (2D) to volumetric (3D) enables new functionalities, such as generating space-variant functions, multiplexing in the spatial or spectral domain, or enhancing information capacity. Unfortunately, despite significant progress fueled by recent interest in metasurface diffraction, 3D diffractive optics still remains relatively unexplored. Here, we introduce the concept of azimuthal multiplexing. We propose, design, and demonstrate 3D diffractive optics showing this multiplexing effect. According to this new phenomenon, multiple pages of information are encoded and can be read out across independent channels by rotating one or more diffractive layers with respect to the others. We implement the concept with multilayer diffractive optical elements. An iterative projection optimization algorithm helps solve the inverse design problem. The experimental realization using photolithographically fabricated multilevel phase layers demonstrates the predicted performance. We discuss the limitations and potential of azimuthal multiplexing 3D diffractive optics.

Scanless two-photon excitation with temporal focusing

Temporal focusing, with its ability to focus light in time, enables scanless illumination of large surface areas at the sample with micrometer axial confinement and robust propagation through scattering tissue. In conventional two-photon microscopy, widely used for the investigation of intact tissue in live animals, images are formed by point scanning of a spatially focused pulsed laser beam, resulting in limited temporal resolution of the excitation. Replacing point scanning with temporally focused widefield illumination removes this limitation and represents an important milestone in two-photon microscopy. Temporal focusing uses a diffusive or dispersive optical element placed in a plane conjugate to the objective focal plane to generate position-dependent temporal pulse broadening that enables axially confined multiphoton absorption, without the need for tight spatial focusing. Many techniques have benefitted from temporal focusing, including scanless imaging, super-resolution imaging, photolithography, uncaging of caged neurotransmitters and control of neuronal activity via optogenetics.

New Vision for Visual Prostheses

Developments of new strategies to restore vision and improving on current strategies by harnessing new advancements in material and electrical sciences, and biological and genetic-based technologies are of upmost health priorities around the world. Federal and private entities are spending billions of dollars on visual prosthetics technologies. This review describes the most current and state-of-the-art bioengineering technologies to restore vision. This includes a thorough description of traditional electrode-based visual prosthetics that have improved substantially since early prototypes. Recent advances in molecular and synthetic biology have transformed vision-assisted technologies; For example, optogenetic technologies that introduce light-responsive proteins offer excellent resolution but cortical applications are restricted by fiber implantation and tissue damage. Other stimulation modalities, such as magnetic fields, have been explored to achieve non-invasive neuromodulation. Miniature magnetic coils are currently being developed to activate select groups of neurons. Magnetically-responsive nanoparticles or exogenous proteins can significantly enhance the coupling between external electromagnetic devices and any neurons affiliated with these modifications. The need to minimize cytotoxic effects for nanoparticle-based therapies will likely restrict the number of usable materials. Nevertheless, advances in identifying and utilizing proteins that respond to magnetic fields may lead to non-invasive, cell-specific stimulation and may overcome many of the limitations that currently exist with other methods. Finally, sensory substitution systems also serve as viable visual prostheses by converting visual input to auditory and somatosensory stimuli. This review also discusses major challenges in the field and offers bioengineering strategies to overcome those.

Temperature Rise under Two-Photon Optogenetic Brain Stimulation

In recent decades, optogenetics has been transforming neuroscience research, enabling neuroscientists to drive and read neural circuits. The recent development in illumination approaches combined with two-photon (2P) excitation, either sequential or parallel, has opened the route for brain circuit manipulation with single-cell resolution and millisecond temporal precision. Yet, the high excitation power required for multi-target photostimulation, especially under 2P illumination, raises questions about the induced local heating inside samples. Here, we present and experimentally validate a theoretical model that makes it possible to simulate 3D light propagation and heat diffusion in optically scattering samples at high spatial and temporal resolution under the illumination configurations most commonly used to perform 2P optogenetics: single- and multi-spot holographic illumination and spiral laser scanning. By investigating the effects of photostimulation repetition rate, spot spacing, and illumination dependence of heat diffusion, we found conditions that make it possible to design a multi-target 2P optogenetics experiment with minimal sample heating.

All-Optical Volumetric Physiology for Connectomics in Dense Neuronal Structures

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

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

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Precise single-photon point stimulation among genetically defined neurons

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

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Observation of 3D functional connectivity in Drosophila anterior visual pathway

Large-scale femtosecond holography for near simultaneous optogenetic neural modulation

For better understanding of brain functions, optogenetic neural modulation has been widely employed in neural science research. For deep tissue in vivo applications, large-scale two-photon based near simultaneous 3D laser excitation is needed. Although 3D holographic laser excitation is nowadays common practice, the inherent short coherence length of the commonly used femtosecond pulses fundamentally restricts the achievable field-of-view. Here we report a technique for near simultaneous large-scale femtosecond holographic 3D excitation. Specifically, we achieved two-photon excitation over 1.3 mm field-of-view within 1.3 milliseconds, which is sufficiently fast even for spike timing recording. The method is scalable and compatible with the commonly used two-photon sources and imaging systems in neuroscience research.

Cracking the Function of Layers in the Sensory Cortex

Understanding how cortical activity generates sensory perceptions requires a detailed dissection of the function of cortical layers. Despite our relatively extensive knowledge of their anatomy and wiring, we have a limited grasp of what each layer contributes to cortical computation. We need to develop a theory of cortical function that is rooted solidly in each layer's component cell types and fine circuit architecture and produces predictions that can be validated by specific perturbations. Here we briefly review the progress toward such a theory and suggest an experimental road map toward this goal. We discuss new methods for the all-optical interrogation of cortical layers, for correlating in vivo function with precise identification of transcriptional cell type, and for mapping local and long-range activity in vivo with synaptic resolution. The new technologies that can crack the function of cortical layers are finally on the immediate horizon.

Multiplexed temporally focused light shaping through a gradient index lens for precise in-depth optogenetic photostimulation

In the past 10 years, the use of light has become irreplaceable for the optogenetic study and control of neurons and neural circuits. Optical techniques are however limited by scattering and can only see through a depth of few hundreds µm in living tissues. GRIN lens based micro-endoscopes represent a powerful solution to reach deeper regions. In this work we demonstrate that cutting edge optical methods for the precise photostimulation of multiple neurons in three dimensions can be performed through a GRIN lens. By spatio-temporally shaping a laser beam in the two-photon regime we project several tens of spatially confined targets in a volume of at least 100 × 150 × 300 µm³. We then apply such approach to the optogenetic stimulation of multiple neurons simultaneously in vivo in mice. Our work paves the way for an all-optical investigation of neural circuits in previously inaccessible brain areas.

Volumetric Ca2+ Imaging in the Mouse Brain Using Hybrid Multiplexed Sculpted Light Microscopy

Calcium imaging using two-photon scanning microscopy has become an essential tool in neuroscience. However, in its typical implementation, the tradeoffs between fields of view, acquisition speeds, and depth restrictions in scattering brain tissue pose severe limitations. Here, using an integrated systems-wide optimization approach combined with multiple technical innovations, we introduce a new design paradigm for optical microscopy based on maximizing biological information while maintaining the fidelity of obtained neuron signals. Our modular design utilizes hybrid multi-photon acquisition and allows volumetric recording of neuroactivity at single-cell resolution within up to 1 × 1 × 1.22 mm volumes at up to 17 Hz in awake behaving mice. We establish the capabilities and potential of the different configurations of our imaging system at depth and across brain regions by applying it to in vivo recording of up to 12,000 neurons in mouse auditory cortex, posterior parietal cortex, and hippocampus.

Breaking crosstalk limits to dynamic holography using orthogonality of high-dimensional random vectors

Holography is the most promising route to true-to-life 3D projections, but the incorporation of complex images with full depth control remains elusive. Digitally synthesised holograms1-7, which do not require real objects to create a hologram, offer the possibility of dynamic projection of 3D video8,9. Extensive efforts aimed 3D holographic projection10-17, however available methods remain limited to creating images on a few planes10-12, over a narrow depth-of-field13,14 or with low resolution15-17. Truly 3D holography also requires full depth control and dynamic projection capabilities, which are hampered by high crosstalk9,18. The fundamental difficulty is in storing all the information necessary to depict a complex 3D image in the 2D form of a hologram without letting projections at different depths contaminate each other. Here, we solve this problem by preshaping the wavefronts to locally reduce Fresnel diffraction to Fourier holography, which allows inclusion of random phase for each depth without altering image projection at that particular depth, but eliminates crosstalk due to near-orthogonality of large-dimensional random vectors. We demonstrate Fresnel holograms that form on-axis with full depth control without any crosstalk, producing large-volume, high-density, dynamic 3D projections with 1000 image planes simultaneously, improving the state-of-the-art12,17 for number of simultaneously created planes by two orders of magnitude. While our proof-of-principle experiments use spatial light modulators, our solution is applicable to all types of holographic media.

All-optical crosstalk-free manipulation and readout of Chronos-expressing neurons

All optical neurophysiology allows manipulation and readout of neural network activity with single-cell spatial resolution and millisecond temporal resolution. Neurons can be made to express proteins that actuate transmembrane currents upon light absorption, enabling optical control of membrane potential and action potential signalling. In addition, neurons can be genetically or synthetically labelled with fluorescent reporters of changes in intracellular calcium concentration or membrane potential. Thus, to optically manipulate and readout neural activity in parallel, two spectra are involved: the action spectrum of the actuator, and the absorption spectrum of the fluorescent reporter. Due to overlap in these spectra, previous all-optical neurophysiology paradigms have been hindered by spurious activation of neuronal activity caused by the readout light. Here, we pair the blue-green absorbing optogenetic actuator, Chronos, with a deep red-emitting fluorescent calcium reporter CaSiR-1. We show that cultured Chinese hamster ovary cells transfected with Chronos do not exhibit transmembrane currents when illuminated with wavelengths and intensities suitable for exciting one-photon CaSiR-1 fluorescence. We then demonstrate crosstalk-free, high signal-to-noise ratio CaSiR-1 red fluorescence imaging at 100 frames s^-1 of Chronos-mediated calcium transients evoked in neurons with blue light pulses at rates up to 20 Hz. These results indicate that the spectral separation between red light excited fluorophores, excited efficiently at or above 640 nm, with blue-green absorbing opsins such as Chronos, is sufficient to avoid spurious opsin actuation by the imaging wavelengths and therefore enable crosstalk-free all-optical neuronal manipulation and readout.

In Vivo Submillisecond Two-Photon Optogenetics with Temporally Focused Patterned Light

To better examine circuit mechanisms underlying perception and behavior, researchers need tools to enable temporally precise control of action-potential generation of individual cells from neuronal ensembles. Here we demonstrate that such precision can be achieved with two-photon (2P) temporally focused computer-generated holography to control neuronal excitability at the supragranular layers of anesthetized and awake visual cortex in both male and female mice. Using 2P-guided whole-cell or cell-attached recordings in positive neurons expressing any of the three opsins ReaChR, CoChR, or ChrimsonR, we investigated the dependence of spiking activity on the opsin's channel kinetics. We found that in all cases the use of brief illumination (≤10 ms) induces spikes of millisecond temporal resolution and submillisecond precision, which were preserved upon repetitive illuminations up to tens of hertz. To reach high temporal precision, we used a large illumination spot covering the entire cell body and an amplified laser at high peak power and low excitation intensity (on average ≤0.2 mW/μm²), thus minimizing the risk for nonlinear photodamage effects. Finally, by combining 2P holographic excitation with electrophysiological recordings and calcium imaging using GCaMP6s, we investigated the factors, including illumination shape and intensity, opsin distribution in the target cell, and cell morphology, which affect the spatial selectivity of single-cell and multicell holographic activation. Parallel optical control of neuronal activity with cellular resolution and millisecond temporal precision should make it easier to investigate neuronal connections and find further links between connectivity, microcircuit dynamics, and brain functions.SIGNIFICANCE STATEMENT Recent developments in the field of optogenetics has enabled researchers to probe the neuronal microcircuit with light by optically actuating genetically encoded light-sensitive opsins expressed in the target cells. Here, we applied holographic light shaping and temporal focusing to simultaneously deliver axially confined holographic patterns to opsin-positive cells in the living mouse cortex. Parallel illumination efficiently induced action potentials with high temporal resolution and precision for three opsins of different kinetics. We extended the parallel optogenetic activation at low intensity to multiple neurons and concurrently monitored their calcium dynamics. These results demonstrate fast and temporally precise in vivo control of a neuronal subpopulation, opening new opportunities for revealing circuit mechanisms underlying brain functions.

Holographic two-photon activation for synthetic optogenetics

Optogenetic tools provide users the ability to photocontrol the activity of cells. Commonly, activation is achieved by expression of proteins from photosynthetic organisms, for example, microbial opsins (e.g., ChR2). Alternatively, a sister approach, synthetic optogenetics, enables photocontrol over proteins of mammalian origin by use of photoswitches, visible light (typically), and genetic modification. Thus, synthetic optogenetics facilitates interrogation of native neuronal signaling mechanisms. However, the poor tissue penetration of visible wavelengths impedes the use of the technique in tissue, as two-photon excitation (2PE) is typically required to access the near-infrared window. Here, we describe an alternative technique that uses 2PE-compatible photoswitches (section 1) for photoactivation of genetically modified glutamate receptors (section 2). Furthermore, for fast, multi-region photoactivation, we describe the use of 2P-digital holography (2P-DH) (section 3). We detail how to combine 2P-DH and synthetic optogenetics with electrophysiology, or with red fluorescence Ca²⁺ recordings, for all-optical neural interrogation. The time required to complete the methods, aside from obtaining the necessary reagents and illumination equipment, is ~3 weeks.