Simultaneous cellular-resolution optical perturbation and imaging of place cell firing fields

Three-dimensional spatiotemporal focusing of holographic patterns

Two-photon excitation with temporally focused pulses can be combined with phase-modulation approaches, such as computer-generated holography and generalized phase contrast, to efficiently distribute light into two-dimensional, axially confined, user-defined shapes. Adding lens-phase modulations to 2D-phase holograms enables remote axial pattern displacement as well as simultaneous pattern generation in multiple distinct planes. However, the axial confinement linearly degrades with lateral shape area in previous reports where axially shifted holographic shapes were not temporally focused. Here we report an optical system using two spatial light modulators to independently control transverse- and axial-target light distribution. This approach enables simultaneous axial translation of single or multiple spatiotemporally focused patterns across the sample volume while achieving the axial confinement of temporal focusing. We use the system's capability to photoconvert tens of Kaede-expressing neurons with single-cell resolution in live zebrafish larvae.

Three-dimensional computer-generated holography cannot be implemented with temporal focusing. Here, Hernandez et al. use two spatial light modulators to control transverse- and axial-target light distribution, generating spatiotemporally focused patterns with uniform light distribution throughout the entire volume.

Two-Photon Lifetime Imaging of Voltage Indicating Proteins as a Probe of Absolute Membrane Voltage

Genetically encoded voltage indicators (GEVIs) can report cellular electrophysiology with high resolution in space and time. Two-photon (2P) fluorescence has been explored as a means to image voltage in tissue. Here, we used the 2P electronic excited-state lifetime to probe absolute membrane voltage in a manner that is insensitive to the protein expression level, illumination intensity, or photon detection efficiency. First, we tested several GEVIs for 2P brightness, response speed, and voltage sensitivity. ASAP1 and a previously described citrine-Arch electrochromic Förster resonance energy transfer sensor (dubbed CAESR) showed the best characteristics. We then characterized the voltage-dependent lifetime of ASAP1, CAESR, and ArcLight under voltage-clamp conditions. ASAP1 and CAESR showed voltage-dependent lifetimes, whereas ArcLight did not. These results establish 2P fluorescence lifetime imaging as a viable means of measuring absolute membrane voltage. We discuss the prospects and improvements necessary for applications in tissue.

Optical electrophysiology for probing function and pharmacology of voltage-gated ion channels

Voltage-gated ion channels mediate electrical dynamics in excitable tissues and are an important class of drug targets. Channels can gate in sub-millisecond timescales, show complex manifolds of conformational states, and often show state-dependent pharmacology. Mechanistic studies of ion channels typically involve sophisticated voltage-clamp protocols applied through manual or automated electrophysiology. Here, we develop all-optical electrophysiology techniques to study activity-dependent modulation of ion channels, in a format compatible with high-throughput screening. Using optical electrophysiology, we recapitulate many voltage-clamp protocols and apply to Na_v1.7, a channel implicated in pain. Optical measurements reveal that a sustained depolarization strongly potentiates the inhibitory effect of PF-04856264, a Na_v1.7-specific blocker. In a pilot screen, we stratify a library of 320 FDA-approved compounds by binding mechanism and kinetics, and find close concordance with patch clamp measurements. Optical electrophysiology provides a favorable tradeoff between throughput and information content for studies of Na_V channels, and possibly other voltage-gated channels.

DOI:http://dx.doi.org/10.7554/eLife.15202.001

Ion channels are specialized proteins that span the cell membrane. When activated, these channels allow ions to pass through them, which can produce electrical spikes that carry information in nerve cells and regulate the beating of the heart. Researchers interested in understanding how ion channels behave often use a technique called patch clamp electrophysiology to measure the electrical current across the cell membrane. The technique can be used to probe if a specific drug can block an ion channel, but it is not well suited to screening lots of potential drugs because it is slow and expensive.

A group of ion channels known as voltage-gated sodium channels play an important role in generating the electrical spikes in nerve cells. One subtype called Na_V1.7 is involved in sensing pain and drugs that block Na_V1.7 might be useable as painkillers, but only if they are specific to this channel. This is because there are many similar sodium channels that are important in other processes in the body.

Zhang et al. have now developed a new light-based technique to measure how ion channels behave. The technique uses light to activate the channel and a fluorescent protein to report on the membrane’s voltage. Zhang et al. used the new technique to probe how sodium channels, in particular Na_V1.7, interact with drugs. Mammalian cells grown in the lab were engineered to produce Na_V1.7, a light-activated ion channel (called CheRiff), and a fluorescent reporter protein. A flash of blue light delivered to the cells activated CheRiff, which in turn activated Na_V1.7. At the same time, the fluorescence of the reporter protein was used as a read-out of Na_V1.7’s activity.

Zhang et al. showed that they could reproduce many conventional electrophysiology measurements using their new light-based approach. Optical measurements were then used to screen 320 drugs to see whether they could block Na_V1.7. The results of the screen corresponded closely with measurements made using conventional electrophysiology. These results demonstrate that the new optical technique is both fast and precise enough to be used in drug discovery. Further studies could now ask if this optical technique can also be used to study other ion channels, such as potassium channels and calcium channels.

DOI:http://dx.doi.org/10.7554/eLife.15202.002

Large-Scale Fluorescence Calcium-Imaging Methods for Studies of Long-Term Memory in Behaving Mammals

During long-term memory formation, cellular and molecular processes reshape how individual neurons respond to specific patterns of synaptic input. It remains poorly understood how such changes impact information processing across networks of mammalian neurons. To observe how networks encode, store, and retrieve information, neuroscientists must track the dynamics of large ensembles of individual cells in behaving animals, over timescales commensurate with long-term memory. Fluorescence Ca(2+)-imaging techniques can monitor hundreds of neurons in behaving mice, opening exciting avenues for studies of learning and memory at the network level. Genetically encoded Ca(2+) indicators allow neurons to be targeted by genetic type or connectivity. Chronic animal preparations permit repeated imaging of neural Ca(2+) dynamics over multiple weeks. Together, these capabilities should enable unprecedented analyses of how ensemble neural codes evolve throughout memory processing and provide new insights into how memories are organized in the brain.

In vivo whole brain, cellular and molecular imaging in nonhuman primate models of neuropathology

Rodents have been the principal model to study brain anatomy and function due to their well-mapped brain architecture, rapid reproduction and amenability to genetic modification. However, there are clear limitations, for example their simpler neocortex, necessitating the need to adopt a model that is closer to humans in order to understand human cognition and brain conditions. Nonhuman primates (NHPs) are ideally suited as they are our closest relatives in the animal kingdom but in vivo imaging technologies to study brain structure and function in these species can be challenging. With the surge in NHP research in recent years, scientists have begun adapting imaging technologies, such as two-photon microscopy, for these species. Here we review the various NHP models that exist as well as their use in advanced microscopic and mesoscopic studies. We discuss the challenges in the field and investigate the opportunities that lie ahead.

Targeting Neural Circuits

Optogenetic methodology enables direct targeting of specific neural circuit elements for inhibition or excitation while spanning timescales from the acute (milliseconds) to the chronic (many days or more). Although the impact of this temporal versatility and cellular specificity has been greater for basic science than clinical research, it is natural to ask whether the dynamic patterns of neural circuit activity discovered to be causal in adaptive or maladaptive behaviors could become targets for treatment of neuropsychiatric diseases. Here, we consider the landscape of ideas related to therapeutic targeting of circuit dynamics. Specifically, we highlight optical, ultrasonic, and magnetic concepts for the targeted control of neural activity, preclinical/clinical discovery opportunities, and recently reported optogenetically guided clinical outcomes.

Sensitive red protein calcium indicators for imaging neural activity

Genetically encoded calcium indicators (GECIs) allow measurement of activity in large populations of neurons and in small neuronal compartments, over times of milliseconds to months. Although GFP-based GECIs are widely used for in vivo neurophysiology, GECIs with red-shifted excitation and emission spectra have advantages for in vivo imaging because of reduced scattering and absorption in tissue, and a consequent reduction in phototoxicity. However, current red GECIs are inferior to the state-of-the-art GFP-based GCaMP6 indicators for detecting and quantifying neural activity. Here we present improved red GECIs based on mRuby (jRCaMP1a, b) and mApple (jRGECO1a), with sensitivity comparable to GCaMP6. We characterized the performance of the new red GECIs in cultured neurons and in mouse, Drosophila, zebrafish and C. elegans in vivo. Red GECIs facilitate deep-tissue imaging, dual-color imaging together with GFP-based reporters, and the use of optogenetics in combination with calcium imaging.

Sensitive red protein calcium indicators for imaging neural activity

Genetically encoded calcium indicators (GECIs) allow measurement of activity in large populations of neurons and in small neuronal compartments, over times of milliseconds to months. Although GFP-based GECIs are widely used for in vivo neurophysiology, GECIs with red-shifted excitation and emission spectra have advantages for in vivo imaging because of reduced scattering and absorption in tissue, and a consequent reduction in phototoxicity. However, current red GECIs are inferior to the state-of-the-art GFP-based GCaMP6 indicators for detecting and quantifying neural activity. Here we present improved red GECIs based on mRuby (jRCaMP1a, b) and mApple (jRGECO1a), with sensitivity comparable to GCaMP6. We characterized the performance of the new red GECIs in cultured neurons and in mouse, Drosophila, zebrafish and C. elegans in vivo. Red GECIs facilitate deep-tissue imaging, dual-color imaging together with GFP-based reporters, and the use of optogenetics in combination with calcium imaging.

Sensitive red protein calcium indicators for imaging neural activity

Genetically encoded calcium indicators (GECIs) allow measurement of activity in large populations of neurons and in small neuronal compartments, over times of milliseconds to months. Although GFP-based GECIs are widely used for in vivo neurophysiology, GECIs with red-shifted excitation and emission spectra have advantages for in vivo imaging because of reduced scattering and absorption in tissue, and a consequent reduction in phototoxicity. However, current red GECIs are inferior to the state-of-the-art GFP-based GCaMP6 indicators for detecting and quantifying neural activity. Here we present improved red GECIs based on mRuby (jRCaMP1a, b) and mApple (jRGECO1a), with sensitivity comparable to GCaMP6. We characterized the performance of the new red GECIs in cultured neurons and in mouse, Drosophila, zebrafish and C. elegans in vivo. Red GECIs facilitate deep-tissue imaging, dual-color imaging together with GFP-based reporters, and the use of optogenetics in combination with calcium imaging.

Communication in Neural Circuits: Tools, Opportunities, and Challenges

Communication, the effective delivery of information, is fundamental to life across all scales and species. Nervous systems (by necessity) may be most specifically adapted among biological tissues for high rate and complexity of information transmitted, and thus, the properties of neural tissue and principles of its organization into circuits may illuminate capabilities and limitations of biological communication. Here, we consider recent developments in tools for studying neural circuits with particular attention to defining neuronal cell types by input and output information streams--i.e., by how they communicate. Complementing approaches that define cell types by virtue of genetic promoter/enhancer properties, this communication-based approach to defining cell types operationally by input/output (I/O) relationships links structure and function, resolves difficulties associated with single-genetic-feature definitions, leverages technology for observing and testing significance of precisely these I/O relationships in intact brains, and maps onto processes through which behavior may be adapted during development, experience, and evolution.

Multisite silicon neural probes with integrated silicon nitride waveguides and gratings for optogenetic applications

Optimal optogenetic perturbation of brain circuit activity often requires light delivery in a precise spatial pattern that cannot be achieved with conventional optical fibers. We demonstrate an implantable silicon-based probe with a compact light delivery system, consisting of silicon nitride waveguides and grating couplers for out-of-plane light emission with high spatial resolution. 473 nm light is coupled into and guided in cm-long waveguide and emitted at the output grating coupler. Using the direct cut-back and out-scattering measurement techniques, the propagation optical loss of the waveguide is measured to be below 3 dB/cm. The grating couplers provide collimated light emission with sufficient irradiance for neural stimulation. Finally, a probe with multisite light delivery with three output grating emitters from a single laser input is demonstrated.

The Anatomy of Suffering: Understanding the Relationship between Nociceptive and Empathic Pain

Pain features centrally in numerous illnesses and generates enormous public health costs. Despite its ubiquity, the psychological and neurophysiological nature of pain remains controversial. Here, we survey one controversy in particular: the relation between nociceptive pain, which is somatic in origin, and empathic pain, which arises from observing others in pain. First, we review evidence for neural overlap between nociceptive and empathic pain and what this overlap implies about underlying mental representations. Then, we propose a framework for understanding the nature of the psychological and neurophysiological correspondence across these types of 'pain'. This framework suggests new directions for research that can better identify shared and dissociable representations underlying different types of distress, and can inform theories about the nature of pain.

Nanoscale bio-platforms for living cell interrogation: current status and future perspectives

The living cell is a complex entity that dynamically responds to both intracellular and extracellular environments. Extensive efforts have been devoted to the understanding intracellular functions orchestrated with mRNAs and proteins in investigation of the fate of a single-cell, including proliferation, apoptosis, motility, differentiation and mutations. The rapid development of modern cellular analysis techniques (e.g. PCR, western blotting, immunochemistry, etc.) offers new opportunities in quantitative analysis of RNA/protein expression up to a single cell level. The recent entries of nanoscale platforms that include kinds of methodologies with high spatial and temporal resolution have been widely employed to probe the living cells. In this tutorial review paper, we give insight into background introduction and technical innovation of currently reported nanoscale platforms for living cell interrogation. These highlighted technologies are documented in details within four categories, including nano-biosensors for label-free detection of living cells, nanodevices for living cell probing by intracellular marker delivery, high-throughput platforms towards clinical current, and the progress of microscopic imaging platforms for cell/tissue tracking in vitro and in vivo. Perspectives for system improvement were also discussed to solve the limitations remains in current techniques, for the purpose of clinical use in future.

Restoring Behavior via Inverse Neurocontroller in a Lesioned Cortical Spiking Model Driving a Virtual Arm

Neural stimulation can be used as a tool to elicit natural sensations or behaviors by modulating neural activity. This can be potentially used to mitigate the damage of brain lesions or neural disorders. However, in order to obtain the optimal stimulation sequences, it is necessary to develop neural control methods, for example by constructing an inverse model of the target system. For real brains, this can be very challenging, and often unfeasible, as it requires repeatedly stimulating the neural system to obtain enough probing data, and depends on an unwarranted assumption of stationarity. By contrast, detailed brain simulations may provide an alternative testbed for understanding the interactions between ongoing neural activity and external stimulation. Unlike real brains, the artificial system can be probed extensively and precisely, and detailed output information is readily available. Here we employed a spiking network model of sensorimotor cortex trained to drive a realistic virtual musculoskeletal arm to reach a target. The network was then perturbed, in order to simulate a lesion, by either silencing neurons or removing synaptic connections. All lesions led to significant behvaioral impairments during the reaching task. The remaining cells were then systematically probed with a set of single and multiple-cell stimulations, and results were used to build an inverse model of the neural system. The inverse model was constructed using a kernel adaptive filtering method, and was used to predict the neural stimulation pattern required to recover the pre-lesion neural activity. Applying the derived neurostimulation to the lesioned network improved the reaching behavior performance. This work proposes a novel neurocontrol method, and provides theoretical groundwork on the use biomimetic brain models to develop and evaluate neurocontrollers that restore the function of damaged brain regions and the corresponding motor behaviors.

Priming Spatial Activity by Single-Cell Stimulation in the Dentate Gyrus of Freely Moving Rats

An essential requirement for hippocampal circuits to function in episodic memory is the ability to rapidly disambiguate and store incoming sensory information. This "pattern separation" function has been classically associated to the dentate gyrus, where spatial learning is accompanied by rapid and persistent modifications of place-cell representation. How these rapid modifications are implemented at the cellular level has remained largely unresolved. Here, we tested whether plasticity-inducing stimuli--spike trains--evoked in postsynaptic neurons are sufficient for the rapid induction of place-field activity in the dentate gyrus. We juxtacellularly stimulated 67 silent granule cells while rats explored a maze for the first time. Spike trains with different characteristics (e.g., number of spikes, frequency, and theta-rhythmicity) were evoked at randomly selected spatial locations. We found that, under novelty, ∼30% (10/33) of the stimulated neurons fired selectively at the "primed" spatial location on subsequent laps. Induced place fields were either transient or persisted for multiple laps. The "priming" effect was experience dependent, as it was less frequently observed in habituated animals (3/34 neurons), and it correlated with the number of spikes and theta-rhythmicity of the stimulus trains. These data indicate that, albeit with low efficiency, evoked theta-rhythmic spike trains can be sufficient for priming spatial activity in the dentate gyrus and thus recruiting silent granule cells into the coding population.

All-Optical Interrogation of Neural Circuits

There have been two recent revolutionary advances in neuroscience: First, genetically encoded activity sensors have brought the goal of optical detection of single action potentials in vivo within reach. Second, optogenetic actuators now allow the activity of neurons to be controlled with millisecond precision. These revolutions have now been combined, together with advanced microscopies, to allow "all-optical" readout and manipulation of activity in neural circuits with single-spike and single-neuron precision. This is a transformational advance that will open new frontiers in neuroscience research. Harnessing the power of light in the all-optical approach requires coexpression of genetically encoded activity sensors and optogenetic probes in the same neurons, as well as the ability to simultaneously target and record the light from the selected neurons. It has recently become possible to combine sensors and optical strategies that are sufficiently sensitive and cross talk free to enable single-action-potential sensitivity and precision for both readout and manipulation in the intact brain. The combination of simultaneous readout and manipulation from the same genetically defined cells will enable a wide range of new experiments as well as inspire new technologies for interacting with the brain. The advances described in this review herald a future where the traditional tools used for generations by physiologists to study and interact with the brain-stimulation and recording electrodes-can largely be replaced by light. We outline potential future developments in this field and discuss how the all-optical strategy can be applied to solve fundamental problems in neuroscience.

SIGNIFICANCE STATEMENT

This review describes the nexus of dramatic recent developments in optogenetic probes, genetically encoded activity sensors, and novel microscopies, which together allow the activity of neural circuits to be recorded and manipulated entirely using light. The optical and protein engineering strategies that form the basis of this "all-optical" approach are now sufficiently advanced to enable single-neuron and single-action potential precision for simultaneous readout and manipulation from the same functionally defined neurons in the intact brain. These advances promise to illuminate many fundamental challenges in neuroscience, including transforming our search for the neural code and the links between neural circuit activity and behavior.

Simultaneous Multi-plane Imaging of Neural Circuits

Recording the activity of large populations of neurons is an important step toward understanding the emergent function of neural circuits. Here we present a simple holographic method to simultaneously perform two-photon calcium imaging of neuronal populations across multiple areas and layers of mouse cortex in vivo. We use prior knowledge of neuronal locations, activity sparsity, and a constrained nonnegative matrix factorization algorithm to extract signals from neurons imaged simultaneously and located in different focal planes or fields of view. Our laser multiplexing approach is simple and fast, and could be used as a general method to image the activity of neural circuits in three dimensions across multiple areas in the brain.

Enhancing Channelrhodopsins: An Overview

After the discovery of Channelrhodopsin, a light-gated ion channel, only a few people saw the diverse range of applications for such a protein. Now, more than 10 years later Channelrhodopsins have become widely accepted as the ultimate tool to control the membrane potential of excitable cells via illumination. The demand for more application-specific Channelrhodopsin variants started a race between protein engineers to design improved variants. Even though many engineered variants have undisputable advantages compared to wild-type variants, many users are alienated by the tremendous amount of new variants and their perplexing names. Here, we review new variants whose efficacy has already been proven in neurophysiological experiments, or variants which are likely to extend the optogenetic toolbox. Variants are described based on their mechanistic and operational properties in terms of expression, kinetics, ion selectivity, and wavelength responsivity.

The BRAIN Initiative: developing technology to catalyse neuroscience discovery

The evolution of the field of neuroscience has been propelled by the advent of novel technological capabilities, and the pace at which these capabilities are being developed has accelerated dramatically in the past decade. Capitalizing on this momentum, the United States launched the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative to develop and apply new tools and technologies for revolutionizing our understanding of the brain. In this article, we review the scientific vision for this initiative set forth by the National Institutes of Health and discuss its implications for the future of neuroscience research. Particular emphasis is given to its potential impact on the mapping and study of neural circuits, and how this knowledge will transform our understanding of the complexity of the human brain and its diverse array of behaviours, perceptions, thoughts and emotions.

Sources of noise during accumulation of evidence in unrestrained and voluntarily head-restrained rats

Decision-making behavior is often characterized by substantial variability, but its source remains unclear. We developed a visual accumulation of evidence task designed to quantify sources of noise and to be performed during voluntary head restraint, enabling cellular resolution imaging in future studies. Rats accumulated discrete numbers of flashes presented to the left and right visual hemifields and indicated the side that had the greater number of flashes. Using a signal-detection theory-based model, we found that the standard deviation in their internal estimate of flash number scaled linearly with the number of flashes. This indicates a major source of noise that, surprisingly, is not consistent with the widely used 'drift-diffusion modeling' (DDM) approach but is instead closely related to proposed models of numerical cognition and counting. We speculate that this form of noise could be important in accumulation of evidence tasks generally.

DOI:http://dx.doi.org/10.7554/eLife.11308.001

Perceptual decision-making, i.e. making choices based on observed evidence, is rarely perfect. Humans and other animals tend to respond correctly on some trials and incorrectly on others. For over a century, this variability has been used to study the basis of decision-making. Most behavioral models assume that random fluctuations or 'noise' in the decision-making process is the primary source of variability and errors. However, the nature of this noise is unclear and the subject of intense scrutiny.

To investigate the sources of the behavioral variability during decision-making, Scott, Constantinople et al. trained rats to perform a visual 'accumulation of evidence' task. The animals counted flashes of light that appeared on either their left or their right. Up to 15 flashes occurred on each side, in a random order, and the rats then received a reward if they selected the side that the greatest number of flashes had occurred on. The rats chose correctly on many occasions but not on every single one.

Using a computer-controlled rat training facility or 'rat academy', Scott, Constantinople et al. collected hundreds of thousands of behavioral trials from over a dozen rats. This large dataset provided the statistical power necessary to test the assumptions of leading models of behavioral variability during decision-making, and revealed that noise grew more rapidly with the number of flashes than previously predicted. This finding explained patterns of behavior that previous models struggled with, most notably the fact that individuals make errors even on the easiest trials. The analysis also revealed that animals maintain two separate running totals – one of stimuli on the left and another of stimuli on the right – rather than a single tally of the difference between the two.

Scott, Constantinople et al. further demonstrated that rats could be trained to perform this task using a new system that enables functional brain imaging. The next step is to repeat these experiments while simultaneously recording brain activity to study the neural circuits that underlie decision-making and its variability.

DOI:http://dx.doi.org/10.7554/eLife.11308.002

The utility of rodent models of autism spectrum disorders

PURPOSE OF REVIEW

This review discusses the ways that rodent models of autism spectrum disorders (ASDs) have been used to gain critical information about convergent molecular pathways, the mechanisms underlying altered microcircuit structure and function, and as a screen for potential cutting edge-treatments for ASDs.

RECENT FINDINGS

There is convergent evidence that impaired developmental pruning of connections may be a common finding among several mouse models of ASDs. Recent studies have uncovered impaired autophagy by pathological mTOR activation as a potential contributor to microcircuit dysfunction and behavior. ASD-related disinhibition and exaggerated synaptic plasticity in multiple distinct circuits in cortex and reward circuits in striatum also contribute to social dysfunction and repetitive behaviors. New exciting molecular therapeutic techniques have reversed cognitive deficits in models of ASD, indicating that mouse models could be used for preclinical translational studies of new treatments.

SUMMARY

Rodent models of ASDs coupled to new emerging technologies for genome editing, cell-specific functional and structural imaging, and neuronal activity manipulation will yield critical insights into ASD pathogenesis and fuel the emergence of new treatments.

Optogenetic spatial and temporal control of cortical circuits on a columnar scale

Many circuits in the mammalian brain are organized in a topographic or columnar manner. These circuits could be activated-in ways that reveal circuit function or restore function after disease-by an artificial stimulation system that is capable of independently driving local groups of neurons. Here we present a simple custom microscope called ProjectorScope 1 that incorporates off-the-shelf parts and a liquid crystal display (LCD) projector to stimulate surface brain regions that express channelrhodopsin-2 (ChR2). In principle, local optogenetic stimulation of the brain surface with optical projection systems might not produce local activation of a highly interconnected network like the cortex, because of potential stimulation of axons of passage or extended dendritic trees. However, here we demonstrate that the combination of virally mediated ChR2 expression levels and the light intensity of ProjectorScope 1 is capable of producing local spatial activation with a resolution of ∼200-300 μm. We use the system to examine the role of cortical activity in the experience-dependent emergence of motion selectivity in immature ferret visual cortex. We find that optogenetic cortical activation alone-without visual stimulation-is sufficient to produce increases in motion selectivity, suggesting the presence of a sharpening mechanism that does not require precise spatiotemporal activation of the visual system. These results demonstrate that optogenetic stimulation can sculpt the developing brain.

Monolithically Integrated μLEDs on Silicon Neural Probes for High-Resolution Optogenetic Studies in Behaving Animals

We report a scalable method to monolithically integrate microscopic light emitting diodes (μLEDs) and recording sites onto silicon neural probes for optogenetic applications in neuroscience. Each μLED and recording site has dimensions similar to a pyramidal neuron soma, providing confined emission and electrophysiological recording of action potentials and local field activity. We fabricated and implanted the four-shank probes, each integrated with 12 μLEDs and 32 recording sites, into the CA1 pyramidal layer of anesthetized and freely moving mice. Spikes were robustly induced by 60 nW light power, and fast population oscillations were induced at the microwatt range. To demonstrate the spatiotemporal precision of parallel stimulation and recording, we achieved independent control of distinct cells ∼ 50 μm apart and of differential somato-dendritic compartments of single neurons. The scalability and spatiotemporal resolution of this monolithic optogenetic tool provides versatility and precision for cellular-level circuit analysis in deep structures of intact, freely moving animals.

Synthesis of FMRFaNV, a Photoreleasable Caged Transmitter Designed to Study Neuron-Glia Interactions in the Central Nervous System

Neuroscience studies require technologies able to deliver compounds with both scale and timing compatibility with morphological and physiological synaptic properties. In this light, two-photon flash photolysis has been extensively used to successfully apply glutamate or other neurotransmitters at the synaptic level. However, the set of commercially available caged compounds is restricted and incompatible with studies demanding high cell specificity. The gain in cell specificity is especially relevant and challenging when studying neuron-glia interactions in the central nervous system. Here we develop a system to mimic the metabotropic glutamate receptor-dependent response of astrocytes, a glial cell type, following synaptic glutamate release. For this, we expressed an exogeneous orphan Gq-coupled protein of the Mas-related-gene (Mrg) family in glial cells and generated an MrgR's agonist peptide (FMRFa) that was chemically caged with a nitroveratryl photolabile protecting group (NV). NV has an appropriate quantum yield and a high absorption maximum that makes it very adapted to experiments with very short irradiation time. This novel caged compound allowed the activation of MrgR with both single- and two-photon light sources. Indeed, MrgR activation induced calcium transients and morphological changes in astrocytes as described previously. Thus, FMRFaNV is a very promising tool to study neuron-glia interactions.

Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data

Inferring connectivity in neuronal networks remains a key challenge in statistical neuroscience. The “common input” problem presents a major roadblock: it is difficult to reliably distinguish causal connections between pairs of observed neurons versus correlations induced by common input from unobserved neurons. Available techniques allow us to simultaneously record, with sufficient temporal resolution, only a small fraction of the network. Consequently, naive connectivity estimators that neglect these common input effects are highly biased. This work proposes a “shotgun” experimental design, in which we observe multiple sub-networks briefly, in a serial manner. Thus, while the full network cannot be observed simultaneously at any given time, we may be able to observe much larger subsets of the network over the course of the entire experiment, thus ameliorating the common input problem. Using a generalized linear model for a spiking recurrent neural network, we develop a scalable approximate expected loglikelihood-based Bayesian method to perform network inference given this type of data, in which only a small fraction of the network is observed in each time bin. We demonstrate in simulation that the shotgun experimental design can eliminate the biases induced by common input effects. Networks with thousands of neurons, in which only a small fraction of the neurons is observed in each time bin, can be quickly and accurately estimated, achieving orders of magnitude speed up over previous approaches.

Optical imaging of the activity in a neuronal network is limited by the scanning speed of the imaging device. Therefore, typically, only a small fixed part of the network is observed during the entire experiment. However, in such an experiment, it can be hard to infer from the observed activity patterns whether (1) a neuron A directly affects neuron B, or (2) another, unobserved neuron C affects both A and B. To deal with this issue, we propose a “shotgun” observation scheme, in which, at each time point, we observe a small changing subset of the neurons from the network. Consequently, many fewer neurons remain completely unobserved during the entire experiment, enabling us to eventually distinguish between cases (1) and (2) given sufficiently long experiments. Since previous inference algorithms cannot efficiently handle so many missing observations, we develop a scalable algorithm for data acquired using the shotgun observation scheme, in which only a small fraction of the neurons are observed in each time bin. Using this kind of simulated data, we show the algorithm is able to quickly infer connectivity in spiking recurrent networks with thousands of neurons.

Projections from neocortex mediate top-down control of memory retrieval

Top-down prefrontal cortex inputs to the hippocampus have been hypothesized to be important in memory consolidation, retrieval, and the pathophysiology of major psychiatric diseases; however, no such direct projections have been identified and functionally described. Here we report the discovery of a monosynaptic prefrontal cortex (predominantly anterior cingulate) to hippocampus (CA3 to CA1 region) projection in mice, and find that optogenetic manipulation of this projection (here termed AC-CA) is capable of eliciting contextual memory retrieval. To explore the network mechanisms of this process, we developed and applied tools to observe cellular-resolution neural activity in the hippocampus while stimulating AC-CA projections during memory retrieval in mice behaving in virtual-reality environments. Using this approach, we found that learning drives the emergence of a sparse class of neurons in CA2/CA3 that are highly correlated with the local network and that lead synchronous population activity events; these neurons are then preferentially recruited by the AC-CA projection during memory retrieval. These findings reveal a sparsely implemented memory retrieval mechanism in the hippocampus that operates via direct top-down prefrontal input, with implications for the patterning and storage of salient memory representations.

Network analysis of mesoscale optical recordings to assess regional, functional connectivity

With modern optical imaging methods, it is possible to map structural and functional connectivity. Optical imaging studies that aim to describe large-scale neural connectivity often need to handle large and complex datasets. In order to interpret these datasets, new methods for analyzing structural and functional connectivity are being developed. Recently, network analysis, based on graph theory, has been used to describe and quantify brain connectivity in both experimental and clinical studies. We outline how to apply regional, functional network analysis to mesoscale optical imaging using voltage-sensitive-dye imaging and channelrhodopsin-2 stimulation in a mouse model. We include links to sample datasets and an analysis script. The analyses we employ can be applied to other types of fluorescence wide-field imaging, including genetically encoded calcium indicators, to assess network properties. We discuss the benefits and limitations of using network analysis for interpreting optical imaging data and define network properties that may be used to compare across preparations or other manipulations such as animal models of disease.

The fiber-optic imaging and manipulation of neural activity during animal behavior

Recent progress with optogenetic probes for imaging and manipulating neural activity has further increased the relevance of fiber-optic systems for neural circuitry research. Optical fibers, which bi-directionally transmit light between separate sites (even at a distance of several meters), can be used for either optical imaging or manipulating neural activity relevant to behavioral circuitry mechanisms. The method's flexibility and the specifications of the light structure are well suited for following the behavior of freely moving animals. Furthermore, thin optical fibers allow researchers to monitor neural activity from not only the cortical surface but also deep brain regions, including the hippocampus and amygdala. Such regions are difficult to target with two-photon microscopes. Optogenetic manipulation of neural activity with an optical fiber has the advantage of being selective for both cell-types and projections as compared to conventional electrophysiological brain tissue stimulation. It is difficult to extract any data regarding changes in neural activity solely from a fiber-optic manipulation device; however, the readout of data is made possible by combining manipulation with electrophysiological recording, or the simultaneous application of optical imaging and manipulation using a bundle-fiber. The present review introduces recent progress in fiber-optic imaging and manipulation methods, while also discussing fiber-optic system designs that are suitable for a given experimental protocol.

Optogenetics: 10 years of microbial opsins in neuroscience

Over the past 10 years, the development and convergence of microbial opsin engineering, modular genetic methods for cell-type targeting and optical strategies for guiding light through tissue have enabled versatile optical control of defined cells in living systems, defining modern optogenetics. Despite widespread recognition of the importance of spatiotemporally precise causal control over cellular signaling, for nearly the first half (2005-2009) of this 10-year period, as optogenetics was being created, there were difficulties in implementation, few publications and limited biological findings. In contrast, the ensuing years have witnessed a substantial acceleration in the application domain, with the publication of thousands of discoveries and insights into the function of nervous systems and beyond. This Historical Commentary reflects on the scientific landscape of this decade-long transition.

Making Sense of Optogenetics

This review, one of a series of articles, tries to make sense of optogenetics, a recently developed technology that can be used to control the activity of genetically-defined neurons with light. Cells are first genetically engineered to express a light-sensitive opsin, which is typically an ion channel, pump, or G protein-coupled receptor. When engineered cells are then illuminated with light of the correct frequency, opsin-bound retinal undergoes a conformational change that leads to channel opening or pump activation, cell depolarization or hyperpolarization, and neural activation or silencing. Since the advent of optogenetics, many different opsin variants have been discovered or engineered, and it is now possible to stimulate or inhibit neuronal activity or intracellular signaling pathways on fast or slow timescales with a variety of different wavelengths of light. Optogenetics has been successfully employed to enhance our understanding of the neural circuit dysfunction underlying mood disorders, addiction, and Parkinson's disease, and has enabled us to achieve a better understanding of the neural circuits mediating normal behavior. It has revolutionized the field of neuroscience, and has enabled a new generation of experiments that probe the causal roles of specific neural circuit components.

From the neuron doctrine to neural networks

For over a century, the neuron doctrine--which states that the neuron is the structural and functional unit of the nervous system--has provided a conceptual foundation for neuroscience. This viewpoint reflects its origins in a time when the use of single-neuron anatomical and physiological techniques was prominent. However, newer multineuronal recording methods have revealed that ensembles of neurons, rather than individual cells, can form physiological units and generate emergent functional properties and states. As a new paradigm for neuroscience, neural network models have the potential to incorporate knowledge acquired with single-neuron approaches to help us understand how emergent functional states generate behaviour, cognition and mental disease.

Optogenetic feedback control of neural activity

Optogenetic techniques enable precise excitation and inhibition of firing in specified neuronal populations and artifact-free recording of firing activity. Several studies have suggested that optical stimulation provides the precision and dynamic range requisite for closed-loop neuronal control, but no approach yet permits feedback control of neuronal firing. Here we present the ‘optoclamp’, a feedback control technology that provides continuous, real-time adjustments of bidirectional optical stimulation in order to lock spiking activity at specified targets over timescales ranging from seconds to days. We demonstrate how this system can be used to decouple neuronal firing levels from ongoing changes in network excitability due to multi-hour periods of glutamatergic or GABAergic neurotransmission blockade in vitro as well as impinging vibrissal sensory drive in vivo. This technology enables continuous, precise optical control of firing in neuronal populations in order to disentangle causally related variables of circuit activation in a physiologically and ethologically relevant manner.

DOI:http://dx.doi.org/10.7554/eLife.07192.001

Cells called neurons use electrical signals to rapidly carry information around the body. When a neuron is activated, it generates (or ‘fires’) a short electrical impulse that travels along the cell to relay a message to other neurons, muscles or organs. Optogenetics is a technique that allows scientists to genetically modify neurons to produce proteins that make them light sensitive.

One of the most commonly used light-sensitive proteins is called channelrhodopsin-2. It is activated by blue light and increases the electrical activity of neurons. Another protein is called halorhodopsin, which responds to yellow light and inhibits the firing of neurons. By shining light of particular colors onto neurons that produce these and other light-sensitive proteins, it is possible to manipulate the activity of large populations of neurons.

Most previous optogenetic experiments have involved altering the activity of neurons and then observing the outcome at a later point in time. However, it would be very useful to be able to alter the amount of optical stimulation to achieve particular levels of neuron activity in real time. To achieve this, the level of neuron activity at any point in time would need to be quickly compared to the desired level, so that optogenetics could be used to increase or decrease the firing of neurons as appropriate.

Newman et al. have now developed an optogenetic system called ‘optoclamp’ that can control the activity of neurons in real time. In neurons grown in cell culture, the optoclamp is able to hold the level of neuron activity at particular values for periods of time ranging from 60 seconds to 24 hours. It can be used to restore and maintain the baseline level of neuron activity in the presence of drugs that would otherwise produce large increases or decreases in the firing of neurons. Moreover, in anaesthetized rats, the optoclamp can prevent some neurons from being activated even when the rats' whiskers move, which would normally change their firing level.

Newman et al.'s findings open the door to a new type of neuroscience experiment where it is possible to manipulate activity patterns as they are produced by the brain. This will help researchers to understand how particular patterns of brain activity are linked to learning, memory, and behavior.

DOI:http://dx.doi.org/10.7554/eLife.07192.002

All-optical bidirectional neural interfacing using hybrid multiphoton holographic optogenetic stimulation

Our understanding of neural information processing could potentially be advanced by combining flexible three-dimensional (3-D) neuroimaging and stimulation. Recent developments in optogenetics suggest that neurophotonic approaches are in principle highly suited for noncontact stimulation of network activity patterns. In particular, two-photon holographic optical neural stimulation (2P-HONS) has emerged as a leading approach for multisite 3-D excitation, and combining it with temporal focusing (TF) further enables axially confined yet spatially extended light patterns. Here, we study key steps toward bidirectional cell-targeted 3-D interfacing by introducing and testing a hybrid new 2P-TF-HONS stimulation path for accurate parallel optogenetic excitation into a recently developed hybrid multiphoton 3-D imaging system. The system is shown to allow targeted all-optical probing of in vitro cortical networks expressing channelrhodopsin-2 using a regeneratively amplified femtosecond laser source tuned to 905 nm. These developments further advance a prospective new tool for studying and achieving distributed control over 3-D neuronal circuits both in vitro and in vivo.

Optrodes for combined optogenetics and electrophysiology in live animals

Optical tissue properties limit visible light depth penetration in tissue. Because of this, the recent development of optogenetic tools was quickly followed by the development of light delivery devices for in vivo optogenetics applications. We summarize the efforts made in the last decade to design neural probes that combine conventional electrophysiological recordings and optical channel(s) for optogenetic activation, often referred to as optodes or optrodes. Several aspects including challenges for light delivery in living brain tissue, the combination of light delivery with electrophysiological recordings, probe designs, multimodality, wireless implantable system, and practical considerations guiding the choice of configuration depending on the questions one seeks to address are presented.

Closed-loop and activity-guided optogenetic control

Advances in optical manipulation and observation of neural activity have set the stage for widespread implementation of closed-loop and activity-guided optical control of neural circuit dynamics. Closing the loop optogenetically (i.e., basing optogenetic stimulation on simultaneously observed dynamics in a principled way) is a powerful strategy for causal investigation of neural circuitry. In particular, observing and feeding back the effects of circuit interventions on physiologically relevant timescales is valuable for directly testing whether inferred models of dynamics, connectivity, and causation are accurate in vivo. Here we highlight technical and theoretical foundations as well as recent advances and opportunities in this area, and we review in detail the known caveats and limitations of optogenetic experimentation in the context of addressing these challenges with closed-loop optogenetic control in behaving animals.

Cellular level brain imaging in behaving mammals: an engineering approach

Fluorescence imaging offers expanding capabilities for recording neural dynamics in behaving mammals, including the means to monitor hundreds of cells targeted by genetic type or connectivity, track cells over weeks, densely sample neurons within local microcircuits, study cells too inactive to isolate in extracellular electrical recordings, and visualize activity in dendrites, axons, or dendritic spines. We discuss recent progress and future directions for imaging in behaving mammals from a systems engineering perspective, which seeks holistic consideration of fluorescent indicators, optical instrumentation, and computational analyses. Today, genetically encoded indicators of neural Ca(2+) dynamics are widely used, and those of trans-membrane voltage are rapidly improving. Two complementary imaging paradigms involve conventional microscopes for studying head-restrained animals and head-mounted miniature microscopes for imaging in freely behaving animals. Overall, the field has attained sufficient sophistication that increased cooperation between those designing new indicators, light sources, microscopes, and computational analyses would greatly benefit future progress.

Optogenetic activation of neocortical neurons in vivo with a sapphire-based micro-scale LED probe

Optogenetics has proven to be a revolutionary technology in neuroscience and has advanced continuously over the past decade. However, optical stimulation technologies for in vivo need to be developed to match the advances in genetics and biochemistry that have driven this field. In particular, conventional approaches for in vivo optical illumination have a limitation on the achievable spatio-temporal resolution. Here we utilize a sapphire-based microscale gallium nitride light-emitting diode (μLED) probe to activate neocortical neurons in vivo. The probes were designed to contain independently controllable multiple μLEDs, emitting at 450 nm wavelength with an irradiance of up to 2 W/mm². Monte-Carlo stimulations predicted that optical stimulation using a μLED can modulate neural activity within a localized region. To validate this prediction, we tested this probe in the mouse neocortex that expressed channelrhodopsin-2 (ChR2) and compared the results with optical stimulation through a fiber at the cortical surface. We confirmed that both approaches reliably induced action potentials in cortical neurons and that the μLED probe evoked strong responses in deep neurons. Due to the possibility to integrate many optical stimulation sites onto a single shank, the μLED probe is thus a promising approach to control neurons locally in vivo.

Preparing and selecting actions with neural populations: toward cortical circuit mechanisms

How the brain selects one action among multiple alternatives is a central question of neuroscience. An influential model is that action preparation and selection arise from subthreshold activation of the very neurons encoding the action. Recent work, however, shows a much greater diversity of decision-related and action-related signals coexisting with other signals in populations of motor and parietal cortical neurons. We discuss how such distributed signals might be decoded by biologically plausible mechanisms. We also discuss how neurons within cortical circuits might interact with each other during action selection and preparation and how recurrent network models can help to reveal dynamical principles underlying cortical computation.

Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo

We describe an all-optical strategy for simultaneously manipulating and recording the activity of multiple neurons with cellular resolution in vivo. We performed simultaneous two-photon optogenetic activation and calcium imaging by coexpression of a red-shifted opsin and a genetically encoded calcium indicator. A spatial light modulator allows tens of user-selected neurons to be targeted for spatiotemporally precise concurrent optogenetic activation, while simultaneous fast calcium imaging provides high-resolution network-wide readout of the manipulation with negligible optical cross-talk. Proof-of-principle experiments in mouse barrel cortex demonstrate interrogation of the same neuronal population during different behavioral states and targeting of neuronal ensembles based on their functional signature. This approach extends the optogenetic toolkit beyond the specificity obtained with genetic or viral approaches, enabling high-throughput, flexible and long-term optical interrogation of functionally defined neural circuits with single-cell and single-spike resolution in the mouse brain in vivo.

Cellular resolution optical access to brain regions in fissures: imaging medial prefrontal cortex and grid cells in entorhinal cortex

In vivo two-photon microscopy provides the foundation for an array of powerful techniques for optically measuring and perturbing neural circuits. However, challenging tissue properties and geometry have prevented high-resolution optical access to regions situated within deep fissures. These regions include the medial prefrontal and medial entorhinal cortex (mPFC and MEC), which are of broad scientific and clinical interest. Here, we present a method for in vivo, subcellular resolution optical access to the mPFC and MEC using microprisms inserted into the fissures. We chronically imaged the mPFC and MEC in mice running on a spherical treadmill, using two-photon laser-scanning microscopy and genetically encoded calcium indicators to measure network activity. In the MEC, we imaged grid cells, a widely studied cell type essential to memory and spatial information processing. These cells exhibited spatially modulated activity during navigation in a virtual reality environment. This method should be extendable to other brain regions situated within deep fissures, and opens up these regions for study at cellular resolution in behaving animals using a rapidly expanding palette of optical tools for perturbing and measuring network structure and function.

Optical dissection of brain circuits with patterned illumination through the phase modulation of light

Brain function relies on electrical signaling among ensembles of neurons. These signals are encoded in space - neurons are organized in complex three-dimensional networks - and in time-cells generate electrical signals on a millisecond scale. How the spatial and temporal structure of these signals controls higher brain functions is largely unknown. The recent advent of novel molecules that manipulate and monitor electrical activity in genetically identified cells provides, for the first time, the ability to causally test the contribution of specific cell subpopulations in these complex brain phenomena. However, most of the commonly used approaches are limited in their ability to illuminate brain tissue with high spatial and temporal precision. In this review article, we focus on one technique, patterned illumination through the phase modulation of light using liquid crystal spatial light modulators (LC-SLMs), which has the potential to overcome some of the major limitations of current experimental approaches.