Wide-field and two-photon imaging of brain activity with voltage- and calcium-sensitive dyes

From connectome to effectome: learning the causal interaction map of the fly brain

A long-standing goal of neuroscience is to obtain a causal model of the nervous system. This would allow neuroscientists to explain animal behavior in terms of the dynamic interactions between neurons. The recently reported whole-brain fly connectome [1-7] specifies the synaptic paths by which neurons can affect each other but not whether, or how, they do affect each other in vivo. To overcome this limitation, we introduce a novel combined experimental and statistical strategy for efficiently learning a causal model of the fly brain, which we refer to as the "effectome". Specifically, we propose an estimator for a dynamical systems model of the fly brain that uses stochastic optogenetic perturbation data to accurately estimate causal effects and the connectome as a prior to drastically improve estimation efficiency. We then analyze the connectome to propose circuits that have the greatest total effect on the dynamics of the fly nervous system. We discover that, fortunately, the dominant circuits significantly involve only relatively small populations of neurons-thus imaging, stimulation, and neuronal identification are feasible. Intriguingly, we find that this approach also re-discovers known circuits and generates testable hypotheses about their dynamics. Overall, our analyses of the connectome provide evidence that global dynamics of the fly brain are generated by a large collection of small and often anatomically localized circuits operating, largely, independently of each other. This in turn implies that a causal model of a brain, a principal goal of systems neuroscience, can be feasibly obtained in the fly.

Functional Dissection of Ipsilateral and Contralateral Neural Activity Propagation Using Voltage-Sensitive Dye Imaging in Mouse Prefrontal Cortex

Prefrontal cortex (PFC) intrahemispheric activity and the interhemispheric connection have a significant impact on neuropsychiatric disorder pathology. This study aimed to generate a functional map of FC intrahemispheric and interhemispheric connections. Functional dissection of mouse PFCs was performed using the voltage-sensitive dye (VSD) imaging method with high speed (1 ms/frame), high resolution (256 × 256 pixels), and a large field of view (∼10 mm). Acute serial 350 μm slices were prepared from the bregma covering the PFC and numbered 1-5 based on their distance from the bregma (i.e., 1.70, 1.34, 0.98, 0.62, and 0.26 mm) with reference to the Mouse Brain Atlas (Paxinos and Franklin, 2008). The neural response to electrical stimulation was measured at nine sites and then averaged, and a functional map of the propagation patterns was created. Intracortical propagation was observed in slices 3-5, encompassing the anterior cingulate cortex (ACC) and corpus callosum (CC). The activity reached area 33 of the ACC. Direct white matter stimulation activated area 33 in both hemispheres. Similar findings were obtained via DiI staining of the CC. Imaging analysis revealed directional biases in neural signals traveling within the ACC, whereby the signal transmission speed and probability varied based on the signal direction. Specifically, the spread of neural signals from cg2 to cg1 was stronger than that from cingulate cortex area 1(cg1) to cingulate cortex area 2(cg2), which has implications for interhemispheric functional connections. These findings highlight the importance of understanding the PFC functional anatomy in evaluating neuromodulators like serotonin and dopamine, as well as other factors related to neuropsychiatric diseases.

Wide-Field Calcium Imaging of Neuronal Network Dynamics In Vivo

A central tenet of neuroscience is that sensory, motor, and cognitive behaviors are generated by the communications and interactions among neurons, distributed within and across anatomically and functionally distinct brain regions. Therefore, to decipher how the brain plans, learns, and executes behaviors requires characterizing neuronal activity at multiple spatial and temporal scales. This includes simultaneously recording neuronal dynamics at the mesoscale level to understand the interactions among brain regions during different behavioral and brain states. Wide-field Ca²⁺ imaging, which uses single photon excitation and improved genetically encoded Ca²⁺ indicators, allows for simultaneous recordings of large brain areas and is proving to be a powerful tool to study neuronal activity at the mesoscopic scale in behaving animals. This review details the techniques used for wide-field Ca²⁺ imaging and the various approaches employed for the analyses of the rich neuronal-behavioral data sets obtained. Also discussed is how wide-field Ca²⁺ imaging is providing novel insights into both normal and altered neural processing in disease. Finally, we examine the limitations of the approach and new developments in wide-field Ca²⁺ imaging that are bringing new capabilities to this important technique for investigating large-scale neuronal dynamics.

Cranial and Spinal Window Preparation for in vivo Optical Neuroimaging in Rodents and Related Experimental Techniques

Optical neuroimaging provides an effective neuroscience tool for multi-scale investigation of the neural structures and functions, ranging from molecular, cellular activities to the inter-regional connectivity assessment. Amongst experimental preparations, the implementation of an artificial window to the central nervous system (CNS) is primarily required for optical visualization of the CNS and associated brain activities through the opaque skin and bone. Either thinning down or removing portions of the skull or spine is necessary for unobstructed long-term in vivo observations, for which types of the cranial and spinal window and applied materials vary depending on the study objectives. As diversely useful, a window can be designed to accommodate other experimental methods such as electrophysiology or optogenetics. Moreover, auxiliary apparatuses would allow the recording in synchrony with behavior of large-scale brain connectivity signals across the CNS, such as olfactory bulb, cerebral cortex, cerebellum, and spinal cord. Such advancements in the cranial and spinal window have resulted in a paradigm shift in neuroscience, enabling in vivo investigation of the brain function and dysfunction at the microscopic, cellular level. This Review addresses the types and classifications of windows used in optical neuroimaging while describing how to perform in vivo studies using rodent models in combination with other experimental modalities during behavioral tests. The cranial and spinal window has enabled longitudinal examination of evolving neural mechanisms via in situ visualization of the brain. We expect transformable and multi-functional cranial and spinal windows to become commonplace in neuroscience laboratories, further facilitating advances in optical neuroimaging systems.

GraFT: Graph Filtered Temporal Dictionary Learning for Functional Neural Imaging

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

In-vitro Recordings of Neural Magnetic Activity From the Auditory Brainstem Using Color Centers in Diamond: A Simulation Study

Magnetometry based on nitrogen-vacancy (NV) centers in diamond is a novel technique capable of measuring magnetic fields with high sensitivity and high spatial resolution. With the further advancements of these sensors, they may open up novel approaches for the 2D imaging of neural signals in vitro. In the present study, we investigate the feasibility of NV-based imaging by numerically simulating the magnetic signal from the auditory pathway of a rodent brainstem slice (ventral cochlear nucleus, VCN, to the medial trapezoid body, MNTB) as stimulated by both electric and optic stimulation. The resulting signal from these two stimulation methods are evaluated and compared. A realistic pathway model was created based on published data of the neural morphologies and channel dynamics of the globular bushy cells in the VCN and their axonal projections to the principal cells in the MNTB. The pathway dynamics in response to optic and electric stimulation and the emitted magnetic fields were estimated using the cable equation. For simulating the optic stimulation, the light distribution in brain tissue was numerically estimated and used to model the optogenetic neural excitation based on a four state channelrhodopsin-2 (ChR2) model. The corresponding heating was also estimated, using the bio-heat equation and was found to be low (<2°C) even at excessively strong optic signals. A peak magnetic field strength of ∼0.5 and ∼0.1 nT was calculated from the auditory brainstem pathway after electrical and optical stimulation, respectively. By increasing the stimulating light intensity four-fold (far exceeding commonly used intensities) the peak magnetic signal strength only increased to 0.2 nT. Thus, while optogenetic stimulation would be favorable to avoid artefacts in the recordings, electric stimulation achieves higher peak fields. The present simulation study predicts that high-resolution magnetic imaging of the action potentials traveling along the auditory brainstem pathway will only be possible for next generation NV sensors. However, the existing sensors already have sufficient sensitivity to support the magnetic sensing of cumulated neural signals sampled from larger parts of the pathway, which might be a promising intermediate step toward further maturing this novel technology.

Optimizing Calcium Detection Methods in Animal Systems: A Sandbox for Synthetic Biology

Since the 1970s, the emergence and expansion of novel methods for calcium ion (Ca2+) detection have found diverse applications in vitro and in vivo across a series of model animal systems. Matched with advances in fluorescence imaging techniques, the improvements in the functional range and stability of various calcium indicators have significantly enhanced more accurate study of intracellular Ca2+ dynamics and its effects on cell signaling, growth, differentiation, and regulation. Nonetheless, the current limitations broadly presented by organic calcium dyes, genetically encoded calcium indicators, and calcium-responsive nanoparticles suggest a potential path toward more rapid optimization by taking advantage of a synthetic biology approach. This engineering-oriented discipline applies principles of modularity and standardization to redesign and interrogate endogenous biological systems. This review will elucidate how novel synthetic biology technologies constructed for eukaryotic systems can offer a promising toolkit for interfacing with calcium signaling and overcoming barriers in order to accelerate the process of Ca2+ detection optimization.

Optimization and validation of diffusion MRI-based fiber tracking with neural tracer data as a reference

Diffusion-weighted magnetic resonance imaging (dMRI) allows non-invasive investigation of whole-brain connectivity, which can reveal the brain’s global network architecture and also abnormalities involved in neurological and mental disorders. However, the reliability of connection inferences from dMRI-based fiber tracking is still debated, due to low sensitivity, dominance of false positives, and inaccurate and incomplete reconstruction of long-range connections. Furthermore, parameters of tracking algorithms are typically tuned in a heuristic way, which leaves room for manipulation of an intended result. Here we propose a general data-driven framework to optimize and validate parameters of dMRI-based fiber tracking algorithms using neural tracer data as a reference. Japan’s Brain/MINDS Project provides invaluable datasets containing both dMRI and neural tracer data from the same primates. A fundamental difference when comparing dMRI-based tractography and neural tracer data is that the former cannot specify the direction of connectivity; therefore, evaluating the fitting of dMRI-based tractography becomes challenging. The framework implements multi-objective optimization based on the non-dominated sorting genetic algorithm II. Its performance is examined in two experiments using data from ten subjects for optimization and six for testing generalization. The first uses a seed-based tracking algorithm, iFOD2, and objectives for sensitivity and specificity of region-level connectivity. The second uses a global tracking algorithm and a more refined set of objectives: distance-weighted coverage, true/false positive ratio, projection coincidence, and commissural passage. In both experiments, with optimized parameters compared to default parameters, fiber tracking performance was significantly improved in coverage and fiber length. Improvements were more prominent using global tracking with refined objectives, achieving an average fiber length from 10 to 17 mm, voxel-wise coverage of axonal tracts from 0.9 to 15%, and the correlation of target areas from 40 to 68%, while minimizing false positives and impossible cross-hemisphere connections. Optimized parameters showed good generalization capability for test brain samples in both experiments, demonstrating the flexible applicability of our framework to different tracking algorithms and objectives. These results indicate the importance of data-driven adjustment of fiber tracking algorithms and support the validity of dMRI-based tractography, if appropriate adjustments are employed.

Optogenetic Manipulation of Postsynaptic cAMP Using a Novel Transgenic Mouse Line Enables Synaptic Plasticity and Enhances Depolarization Following Tetanic Stimulation in the Hippocampal Dentate Gyrus

cAMP is a positive regulator tightly involved in certain types of synaptic plasticity and related memory functions. However, its spatiotemporal roles at the synaptic and neural circuit levels remain elusive. Using a combination of a cAMP optogenetics approach and voltage-sensitive dye (VSD) imaging with electrophysiological recording, we define a novel capacity of postsynaptic cAMP in enabling dentate gyrus long-term potentiation (LTP) and depolarization in acutely prepared murine hippocampal slices. To manipulate cAMP levels at medial perforant path to granule neuron (MPP-DG) synapses by light, we generated transgenic (Tg) mice expressing photoactivatable adenylyl cyclase (PAC) in DG granule neurons. Using these Tg(CMV-Camk2a-RFP/bPAC)3Koka mice, we recorded field excitatory postsynaptic potentials (fEPSPs) from MPP-DG synapses and found that photoactivation of PAC during tetanic stimulation enabled synaptic potentiation that persisted for at least 30 min. This form of LTP was induced without the need for GABA receptor blockade that is typically required for inducing DG plasticity. The paired-pulse ratio (PPR) remained unchanged, indicating the cAMP-dependent LTP was likely postsynaptic. By employing fast fluorescent voltage-sensitive dye (VSD: di-4-ANEPPS) and fluorescence imaging, we found that photoactivation of the PAC actuator enhanced the intensity and extent of dentate gyrus depolarization triggered following tetanic stimulation. These results demonstrate that the elevation of cAMP in granule neurons is capable of rapidly enhancing synaptic strength and neuronal depolarization. The powerful actions of cAMP are consistent with this second messenger having a critical role in the regulation of synaptic function.

All-Optical Detection of Neuronal Membrane Depolarization in Live Cells Using Colloidal Quantum Dots

Luminescent semiconductor quantum dots (QDs) have recently been suggested as novel probes for imaging and sensing cell membrane voltages. However, a key bottleneck for their development is a lack of techniques to assess QD responses to voltages generated in the aqueous electrolytic environments typical of biological systems. Even more generally, there have been relatively few efforts to assess the response of QDs to voltage changes in live cells. Here, we develop a platform for monitoring the photoluminescence (PL) response of QDs under AC and DC voltage changes within aqueous ionic environments. We evaluate both traditional CdSe/CdS and more biologically compatible InP/ZnS QDs at a range of ion concentrations to establish their PL/voltage characteristics on chip. Wide-field, few-particle PL measurements with neuronal cells show the QDs can be used to track local voltage changes with greater sensitivity (ΔPL up to twice as large) than state-of-the-art calcium imaging dyes, making them particularly appealing for tracking subthreshold events. Additional physiological observation studies showed that while CdSe/CdS dots have greater PL responses on membrane depolarization, their lower cytotoxicity makes InP/ZnS far more suitable for voltage sensing in living systems. Our results provide a methodology for the rational development of QD voltage sensors and highlight their potential for imaging changes in cell membrane voltage.

High frequency, real-time neurochemical and neuropharmacological measurements in situ in the living body

The beautiful and complex brain machinery is perfectly synchronized, and our bodies have evolved to protect it against a myriad of potential threats. Shielded physically by the skull and chemically by the blood brain barrier, the brain processes internal and external information so that we can efficiently relate to the world that surrounds us while simultaneously and unconsciously controlling our vital functions. When coupled with the brittle nature of its internal chemical and electric signals, the brain's "armor" render accessing it a challenging and delicate endeavor that has historically limited our understanding of its structural and neurochemical intricacies. In this review, we briefly summarize the advancements made over the past 10 years to decode the brain's neurochemistry and neuropharmacology in situ, at the site of interest in the brain, with special focus on what we consider game-changing emerging technologies (eg, genetically encoded indicators and electrochemical aptamer-based sensors) and the challenges these must overcome before chronic, in situ chemosensing measurements become routine.

Ultrasonic sculpting of virtual optical waveguides in tissue

Optical imaging and stimulation are widely used to study biological events. However, scattering processes limit the depth to which externally focused light can penetrate tissue. Optical fibers and waveguides are commonly inserted into tissue when delivering light deeper than a few millimeters. This approach, however, introduces complications arising from tissue damage. In addition, it makes it difficult to steer light. Here, we demonstrate that ultrasound can be used to define and steer the trajectory of light within scattering media by exploiting local pressure differences created by acoustic waves that result in refractive index contrasts. We show that virtual light pipes can be created deep into the tissue (>18 scattering mean free paths). We demonstrate the application of this technology in confining light through mouse brain tissue. This technology is likely extendable to form arbitrary light patterns within tissue, extending both the reach and the flexibility of light-based methods.

Neuronal Response Latencies Encode First Odor Identity Information across Subjects

Odorants are coded in the primary olfactory processing centers by spatially and temporally distributed patterns of glomerular activity. Whereas the spatial distribution of odorant-induced responses is known to be conserved across individuals, the universality of its temporal structure is still debated. Via fast two-photon calcium imaging, we analyzed the early phase of neuronal responses in the form of the activity onset latencies in the antennal lobe projection neurons of honeybee foragers. We show that each odorant evokes a stimulus-specific response latency pattern across the glomerular coding space. Moreover, we investigate these early response features for the first time across animals, revealing that the order of glomerular firing onsets is conserved across individuals and allows them to reliably predict odorant identity, but not concentration. These results suggest that the neuronal response latencies provide the first available code for fast odor identification.SIGNIFICANCE STATEMENT Here, we studied early temporal coding in the primary olfactory processing centers of the honeybee brain by fast imaging of glomerular responses to different odorants across glomeruli and across individuals. Regarding the elusive role of rapid response dynamics in olfactory coding, we were able to clarify the following aspects: (1) the rank of glomerular activation is conserved across individuals, (2) its stimulus prediction accuracy is equal to that of the response amplitude code, and (3) it contains complementary information. Our findings suggest a substantial role of response latencies in odor identification, anticipating the static response amplitude code.

Mild Blast Injury Produces Acute Changes in Basal Intracellular Calcium Levels and Activity Patterns in Mouse Hippocampal Neurons

Mild traumatic brain injury (mTBI) represents a serious public health concern. Although much is understood about long-term changes in cell signaling and anatomical pathologies associated with mTBI, little is known about acute changes in neuronal function. Using large scale Ca2+ imaging in vivo, we characterized the intracellular Ca2+ dynamics in thousands of individual hippocampal neurons using a repetitive mild blast injury model in which blasts were directed onto the cranium of unanesthetized mice on two consecutive days. Immediately following each blast event, neurons exhibited two types of changes in Ca2+ dynamics at different time scales. One was a reduction in slow Ca2+ dynamics that corresponded to shifts in basal intracellular Ca2+ levels at a time scale of minutes, suggesting a disruption of biochemical signaling. The second was a reduction in the rates of fast transient Ca2+ fluctuations at the sub-second time scale, which are known to be closely linked to neural activity. Interestingly, the blast-induced changes in basal Ca2+ levels were independent of the changes in the rates of fast Ca2+ transients, suggesting that blasts had heterogeneous effects on different cell populations. Both types of changes recovered after ∼1 h. Together, our results demonstrate that mTBI induced acute, heterogeneous changes in neuronal function, altering intracellular Ca2+ dynamics across different time scales, which may contribute to the initiation of longer-term pathologies.

Modeling psychiatric disorders: from genomic findings to cellular phenotypes

Major programs in psychiatric genetics have identified >150 risk loci for psychiatric disorders. These loci converge on a small number of functional pathways, which span conventional diagnostic criteria, suggesting a partly common biology underlying schizophrenia, autism and other psychiatric disorders. Nevertheless, the cellular phenotypes that capture the fundamental features of psychiatric disorders have not yet been determined. Recent advances in genetics and stem cell biology offer new prospects for cell-based modeling of psychiatric disorders. The advent of cell reprogramming and induced pluripotent stem cells (iPSC) provides an opportunity to translate genetic findings into patient-specific in vitro models. iPSC technology is less than a decade old but holds great promise for bridging the gaps between patients, genetics and biology. Despite many obvious advantages, iPSC studies still present multiple challenges. In this expert review, we critically review the challenges for modeling of psychiatric disorders, potential solutions and how iPSC technology can be used to develop an analytical framework for the evaluation and therapeutic manipulation of fundamental disease processes.

Fine and distributed subcellular retinotopy of excitatory inputs to the dendritic tree of a collision-detecting neuron

Individual neurons in several sensory systems receive synaptic inputs organized according to subcellular topographic maps, yet the fine structure of this topographic organization and its relation to dendritic morphology have not been studied in detail. Subcellular topography is expected to play a role in dendritic integration, particularly when dendrites are extended and active. The lobula giant movement detector (LGMD) neuron in the locust visual system is known to receive topographic excitatory inputs on part of its dendritic tree. The LGMD responds preferentially to objects approaching on a collision course and is thought to implement several interesting dendritic computations. To study the fine retinotopic mapping of visual inputs onto the excitatory dendrites of the LGMD, we designed a custom microscope allowing visual stimulation at the native sampling resolution of the locust compound eye while simultaneously performing two-photon calcium imaging on excitatory dendrites. We show that the LGMD receives a distributed, fine retinotopic projection from the eye facets and that adjacent facets activate overlapping portions of the same dendritic branches. We also demonstrate that adjacent retinal inputs most likely make independent synapses on the excitatory dendrites of the LGMD. Finally, we show that the fine topographic mapping can be studied using dynamic visual stimuli. Our results reveal the detailed structure of the dendritic input originating from individual facets on the eye and their relation to that of adjacent facets. The mapping of visual space onto the LGMD's dendrites is expected to have implications for dendritic computation.

Optical detection of neuron connectivity by random access two-photon microscopy

BACKGROUND

Knowledge about the distribution, strength, and direction of synaptic connections within neuronal networks are crucial for understanding brain function. Electrophysiology using multiple electrodes provides a very high temporal resolution, but does not yield sufficient spatial information for resolving neuronal connection topology. Optical recording techniques using single-cell resolution have provided promise for providing spatial information. Although calcium imaging from hundreds of neurons has provided a novel view of the neural connections within the network, the kinetics of calcium responses are not fast enough to resolve each action potential event with high fidelity. Therefore, it is not possible to detect the direction of neuronal connections.

NEW METHOD

We took advantage of the fast kinetics and large dynamic range of the DiO/DPA combination of voltage sensitive dye and the fast scan speed of a custom-made random-access two-photon microscope to resolve each action potential event from multiple neurons in culture.

RESULTS

Long-duration recording up to 100min from cultured hippocampal neurons yielded sufficient numbers of spike events for analyzing synaptic connections. Cross-correlation analysis of neuron pairs clearly distinguished synaptically connected neuron pairs with the connection direction.

COMPARISON WITH EXISTING METHOD

The long duration recording of action potentials with voltage-sensitive dye utilized in the present study is much longer than in previous studies. Simultaneous optical voltage and calcium measurements revealed that voltage-sensitive dye is able to detect firing events more reliably than calcium indicators.

CONCLUSIONS

This novel method reveals a new view of the functional structure of neuronal networks.

Strategies for optical control and simultaneous electrical readout of extended cortical circuits

BACKGROUND

To dissect the intricate workings of neural circuits, it is essential to gain precise control over subsets of neurons while retaining the ability to monitor larger-scale circuit dynamics. This requires the ability to both evoke and record neural activity simultaneously with high spatial and temporal resolution.

NEW METHOD

In this paper we present approaches that address this need by combining micro-electrocorticography (μECoG) with optogenetics in ways that avoid photovoltaic artifacts.

RESULTS

We demonstrate that variations of this approach are broadly applicable across three commonly studied mammalian species - mouse, rat, and macaque monkey - and that the recorded μECoG signal shows complex spectral and spatio-temporal patterns in response to optical stimulation.

COMPARISON WITH EXISTING METHODS

While optogenetics provides the ability to excite or inhibit neural subpopulations in a targeted fashion, large-scale recording of resulting neural activity remains challenging. Recent advances in optical physiology, such as genetically encoded Ca(2+) indicators, are promising but currently do not allow simultaneous recordings from extended cortical areas due to limitations in optical imaging hardware.

CONCLUSIONS

We demonstrate techniques for the large-scale simultaneous interrogation of cortical circuits in three commonly used mammalian species.

Measurement science in the circulatory system

The dynamics of the cellular and molecular constituents of the circulatory system are regulated by the biophysical properties of the heart, vasculature and blood cells and proteins. In this review, we discuss measurement techniques that have been developed to characterize the physical and mechanical parameters of the circulatory system across length scales ranging from the tissue scale (centimeter) to the molecular scale (nanometer) and time scales of years to milliseconds. We compare the utility of measurement techniques as a function of spatial resolution and penetration depth from both a diagnostic and research perspective. Together, this review provides an overview of the utility of measurement science techniques to study the spatial systems of the circulatory system in health and disease.

Quantifying network properties in multi-electrode recordings: spatiotemporal characterization and inter-trial variation of evoked gamma oscillations in mouse somatosensory cortex in vitro

Linking the structural connectivity of brain circuits to their cooperative dynamics and emergent functions is a central aim of neuroscience research. Graph theory has recently been applied to study the structure-function relationship of networks, where dynamical similarity of different nodes has been turned into a “static” functional connection. However, the capability of the brain to adapt, learn and process external stimuli requires a constant dynamical functional rewiring between circuitries and cell assemblies. Hence, we must capture the changes of network functional connectivity over time. Multi-electrode array data present a unique challenge within this framework. We study the dynamics of gamma oscillations in acute slices of the somatosensory cortex from juvenile mice recorded by planar multi-electrode arrays. Bursts of gamma oscillatory activity lasting a few hundred milliseconds could be initiated only by brief trains of electrical stimulations applied at the deepest cortical layers and simultaneously delivered at multiple locations. Local field potentials were used to study the spatio-temporal properties and the instantaneous synchronization profile of the gamma oscillatory activity, combined with current source density (CSD) analysis. Pair-wise differences in the oscillation phase were used to determine the presence of instantaneous synchronization between the different sites of the circuitry during the oscillatory period. Despite variation in the duration of the oscillatory response over successive trials, they showed a constant average power, suggesting that the rate of expenditure of energy during the gamma bursts is consistent across repeated stimulations. Within each gamma burst, the functional connectivity map reflected the columnar organization of the neocortex. Over successive trials, an apparently random rearrangement of the functional connectivity was observed, with a more stable columnar than horizontal organization. This work reveals new features of evoked gamma oscillations in developing cortex.

Measuring membrane voltage with fluorescent proteins

Measuring signal transduction in large numbers of cells with high spatial and temporal resolution is fundamental to studying information processing in the nervous system. DNA-encoded sensors have an advantage in that they can be introduced into an organism noninvasively and targeted to specific brain regions, cell types, or subcellular compartments. A variety of chimeric proteins that report transmembrane voltage have been developed. The prototype sensor, FlaSh, is a green fluorescent protein fused to a voltage-sensitive K(+) channel, where voltage-dependent rearrangements in the channel induce changes in the protein's fluorescence. Subsequent sensors have refined this basic design using a monomeric voltage-sensing phosphatase domain from Ciona intestinalis and pairs of fluorescent proteins to produce a larger fluorescent signal. These sensors and their uses are discussed here.

Light sources and cameras for standard in vitro membrane potential and high-speed ion imaging

Membrane potential and fast ion imaging are now standard optical techniques routinely used to record dynamic physiological signals in several preparations in vitro. Although detailed resolution of optical signals can be improved by confocal or two-photon microscopy, high spatial and temporal resolution can be obtained using conventional microscopy and affordable light sources and cameras. Thus, standard wide-field imaging methods are still the most common in research laboratories and can often produce measurements with a signal-to-noise ratio that is superior to other optical approaches. This paper seeks to review the most important instrumentation used in these experiments, with particular reference to recent technological advances. We analyse in detail the optical constraints dictating the type of signals that are obtained with voltage and ion imaging and we discuss how to use this information to choose the optimal apparatus. Then, we discuss the available light sources with specific attention to light emitting diodes and solid state lasers. We then address the current state-of-the-art of available charge coupled device, electron multiplying charge coupled device and complementary metal oxide semiconductor cameras and we analyse the characteristics that need to be taken into account for the choice of optimal detector. Finally, we conclude by discussing prospective future developments that are likely to further improve the quality of the signals expanding the capability of the techniques and opening the gate to novel applications.

Imaging calcium signals in vivo: a powerful tool in physiology and pharmacology

The design and engineering of organic fluorescent Ca(2+) indicators approximately 30 years ago opened the door for imaging cellular Ca(2+) signals with a high degree of temporal and spatial resolution. Over this time, Ca(2+) imaging has revolutionized our approaches for tissue-level spatiotemporal analysis of functional organization and has matured into a powerful tool for in situ imaging of cellular activity in the living animal. In vivo Ca(2+) imaging with temporal resolution at the millisecond range and spatial resolution at micrometer range has been achieved through novel designs of Ca(2+) sensors, development of modern microscopes and powerful imaging techniques such as two-photon microscopy. Imaging Ca(2+) signals in ensembles of cells within tissue in 3D allows for analysis of integrated cellular function, which, in the case of the brain, enables recording activity patterns in local circuits. The recent development of miniaturized compact, fibre-optic-based, mechanically flexible microendoscopes capable of two-photon microscopy opens the door for imaging activity in awake, behaving animals. This development is poised to open a new chapter in physiological experiments and for pharmacological approaches in the development of novel therapies.

An old hypothesis and new tools: Alfred Fessard's approach to the problem of consciousness

In 1954, a symposium was held in Canada on "Brain Mechanisms and Consciousness." It was a time for the promotion of international and interdisciplinary scientific cooperation, of new technological expectation, and of speculating about complex human behavior. Alfred Fessard's lecture on "Mechanisms of Nervous Integration and Conscious Experience" was one of the outstanding presentations, rich in critical analysis of the then available experimental data and in working hypothesis proposals. Reading the concept expressed by Fessard, it was found that several of his ideas had anticipated data obtained in modern research with new technologies.

Optimal experimental design for sampling voltage on dendritic trees in the low-SNR regime

Due to the limitations of current voltage sensing techniques, optimal filtering of noisy, undersampled voltage signals on dendritic trees is a key problem in computational cellular neuroscience. These limitations lead to voltage data that is incomplete (in the sense of only capturing a small portion of the full spatiotemporal signal) and often highly noisy. In this paper we use a Kalman filtering framework to develop optimal experimental design methods for voltage sampling. Our approach is to use a simple greedy algorithm with lazy evaluation to minimize the expected square error of the estimated spatiotemporal voltage signal. We take advantage of some particular features of the dendritic filtering problem to efficiently calculate the Kalman estimator's covariance. We test our framework with simulations of real dendritic branching structures and compare the quality of both time-invariant and time-varying sampling schemes. While the benefit of using the experimental design methods was modest in the time-invariant case, improvements of 25-100% over more naïve methods were found when the observation locations were allowed to change with time. We also present a heuristic approximation to the greedy algorithm that is an order of magnitude faster while still providing comparable results.

Denoising two-photon calcium imaging data

Two-photon calcium imaging is now an important tool for in vivo imaging of biological systems. By enabling neuronal population imaging with subcellular resolution, this modality offers an approach for gaining a fundamental understanding of brain anatomy and physiology. Proper analysis of calcium imaging data requires denoising, that is separating the signal from complex physiological noise. To analyze two-photon brain imaging data, we present a signal plus colored noise model in which the signal is represented as harmonic regression and the correlated noise is represented as an order autoregressive process. We provide an efficient cyclic descent algorithm to compute approximate maximum likelihood parameter estimates by combing a weighted least-squares procedure with the Burg algorithm. We use Akaike information criterion to guide selection of the harmonic regression and the autoregressive model orders. Our flexible yet parsimonious modeling approach reliably separates stimulus-evoked fluorescence response from background activity and noise, assesses goodness of fit, and estimates confidence intervals and signal-to-noise ratio. This refined separation leads to appreciably enhanced image contrast for individual cells including clear delineation of subcellular details and network activity. The application of our approach to in vivo imaging data recorded in the ferret primary visual cortex demonstrates that our method yields substantially denoised signal estimates. We also provide a general Volterra series framework for deriving this and other signal plus correlated noise models for imaging. This approach to analyzing two-photon calcium imaging data may be readily adapted to other computational biology problems which apply correlated noise models.

In vivo visualization of olfactory pathophysiology induced by intranasal cadmium instillation in mice

Intranasal exposure to cadmium has been related to olfactory dysfunction in humans and to nasal epithelial damage and altered odorant-guided behavior in rodent models. The pathophysiology underlying these deficits has not been fully elucidated. Here we use optical imaging techniques to visualize odorant-evoked neurotransmitter release from the olfactory nerve into the brain's olfactory bulbs in vivo in mice. Intranasal cadmium chloride instillations reduced this sensory activity by up to 91% in a dose-dependent manner. In the olfactory bulbs, afferents from the olfactory epithelium could be quantified by their expression of a genetically encoded fluorescent marker for olfactory marker protein. At the highest dose tested, cadmium exposure reduced the density of these projections by 20%. In a behavioral psychophysical task, mice were trained to sample from an odor port and make a response when they detected an odorant against a background of room air. After intranasal cadmium exposure, mice were unable to detect the target odor. These experiments serve as proof of concept for a new approach to the study of the neural effects of inhaled toxicants. The use of in vivo functional imaging of the neuronal populations exposed to the toxicant permits the direct observation of primary pathophysiology. In this study optical imaging revealed significant reductions in odorant-evoked release from the olfactory nerve at a cadmium chloride dose two orders of magnitude less than that required to induce morphological changes in the nerve in the same animals, demonstrating that it is a more sensitive technique for assessing the consequences of intranasal neurotoxicant exposure. This approach is potentially useful in exploring the effects of any putative neurotoxicant that can be delivered intranasally.

Shining light into the black box of spinal locomotor networks

Rhythmic activity is responsible for numerous essential motor functions including locomotion, breathing and chewing. In the case of locomotion, it has been realized for some time that the spinal cord contains sufficient circuitry to produce a sophisticated stepping pattern. However, the central pattern generator for locomotion in mammals has remained a 'black box' where inputs to the network were manipulated and the outputs interpreted. Over the last decade, new genetic approaches and techniques have been developed that provide ways to identify and manipulate the activity of classes of interneurons. The use of these techniques will be critically discussed and related to current models of network function.

A framework for simulating and estimating the state and functional topology of complex dynamic geometric networks

We introduce a framework for simulating signal propagation in geometric networks (networks that can be mapped to geometric graphs in some space) and developing algorithms that estimate (i.e., map) the state and functional topology of complex dynamic geometric networks. Within the framework, we define the key features typically present in such networks and of particular relevance to biological cellular neural networks: dynamics, signaling, observation, and control. The framework is particularly well suited for estimating functional connectivity in cellular neural networks from experimentally observable data and has been implemented using graphics processing unit high-performance computing. Computationally, the framework can simulate cellular network signaling close to or faster than real time. We further propose a standard test set of networks to measure performance and compare different mapping algorithms.

Wide-field and two-photon imaging of brain activity with voltage- and calcium-sensitive dyes

This review presents three examples of using voltage- or calcium-sensitive dyes to image the activity of the brain. Our aim is to discuss the advantages and disadvantages of each method with particular reference to its application to the study of the brainstem. Two of the examples use wide-field (one-photon) imaging; the third uses two-photon scanning microscopy. Because the measurements have limited signal-to-noise ratio, the paper also discusses the methodological aspects that are critical for optimizing the signal. The three examples are the following. (i) An intracellularly injected voltage-sensitive dye was used to monitor membrane potential in the dendrites of neurons in in vitro preparations. These experiments were directed at understanding how individual neurons convert complex synaptic inputs into the output spike train. (ii) An extracellular, bath application of a voltage-sensitive dye was used to monitor population signals from different parts of the dorsal brainstem. We describe recordings made during respiratory activity. The population signals indicated four different regions with distinct activity correlated with inspiration. (iii) Calcium-sensitive dyes can be used to label many individual cells in the mammalian brain. This approach, combined with two-photon microscopy, made it possible to follow the spike activity in an in vitro brainstem preparation during fictive respiratory rhythms. The organic voltage- and ion-sensitive dyes used today indiscriminatively stain all of the cell types in the preparation. A major effort is underway to develop fluorescent protein sensors of activity for selectively staining individual cell types.

Structure-function analysis of rhythmogenic inspiratory pre-Bötzinger complex networks in "calibrated" newborn rat brainstem slices

Inspiratory pre-Bötzinger complex (preBötC) networks remain active in perinatal rodent brainstem slices. Our analysis of (crescendo-like) inspiratory-related population and cellular bursting in novel histologically identified transversal preBötC slices in physiological (3 mM) superfusate [K(+)] revealed: (i) the preBötC extent sufficient for rhythm in thin slices is at most 175 microm. (ii) In 700 microm thick slices with unilaterally exposed preBötC, a <100 microm kernel generates a eupnea-like inspiratory pattern under predominant influence of caudally adjacent structures or thyrotropin-releasing hormone-like transmitters, but a mixed eupnea-sigh-like pattern when influence of rostral structures or substance-P-like transmitters dominates. (iii) Primarily presynaptic processes may underlie inhibition of rhythm by opioids or raising superfusate [Ca(2+)] from lower to upper physiological limits (1-1.5 mM). (iv) High K(+) reverses depression of rhythm by raised Ca(2+), opioids and anoxia. In summary, distinct activity patterns of spatiochemically organized isolated inspiratory networks depend on both an extracellular "Ca(2+)-K(+) antagonism" and slice dimensions. This explains some discrepant findings between studies and suggests use of "calibrated" slices and more uniform experimental conditions.

Rapid neocortical dynamics: cellular and network mechanisms

The highly interconnected local and large-scale networks of the neocortical sheet rapidly and dynamically modulate their functional connectivity according to behavioral demands. This basic operating principle of the neocortex is mediated by the continuously changing flow of excitatory and inhibitory synaptic barrages that not only control participation of neurons in networks but also define the networks themselves. The rapid control of neuronal responsiveness via synaptic bombardment is a fundamental property of cortical dynamics that may provide the basis of diverse behaviors, including sensory perception, motor integration, working memory, and attention.

Imaging activity of neuronal populations with new long-wavelength voltage-sensitive dyes

We have assessed the utility of five new long-wavelength fluorescent voltage-sensitive dyes (VSD) for imaging the activity of populations of neurons in mouse brain slices. Although all the five were capable of detecting activity resulting from activation of the Schaffer collateral-CA1 pyramidal cell synapse, they differed significantly in their properties, most notably in the signal-to-noise ratio of the changes in dye fluorescence associated with neuronal activity. Two of these dyes, Di-2-ANBDQPQ and Di-1-APEFEQPQ, should prove particularly useful for imaging activity in brain tissue and for combining VSD imaging with the control of neuronal activity via light-activated proteins such as channelrhodopsin-2 and halorhodopsin.