A focusing image probe for assessing neural activity in vivo

Emerging imaging methods to study whole-brain function in rodent models

In the past decade, the idea that single populations of neurons support cognition and behavior has gradually given way to the realization that connectivity matters and that complex behavior results from interactions between remote yet anatomically connected areas that form specialized networks. In parallel, innovation in brain imaging techniques has led to the availability of a broad set of imaging tools to characterize the functional organization of complex networks. However, each of these tools poses significant technical challenges and faces limitations, which require careful consideration of their underlying anatomical, physiological, and physical specificity. In this review, we focus on emerging methods for measuring spontaneous or evoked activity in the brain. We discuss methods that can measure large-scale brain activity (directly or indirectly) with a relatively high temporal resolution, from milliseconds to seconds. We further focus on methods designed for studying the mammalian brain in preclinical models, specifically in mice and rats. This field has seen a great deal of innovation in recent years, facilitated by concomitant innovation in gene-editing techniques and the possibility of more invasive recordings. This review aims to give an overview of currently available preclinical imaging methods and an outlook on future developments. This information is suitable for educational purposes and for assisting scientists in choosing the appropriate method for their own research question.

Imaging the Dynamics of Mammalian Neocortical Population Activity In-Vivo

Neural computations underlying sensory perception, cognition and motor control are performed by populations of neurons at different anatomical and temporal scales. Few techniques are currently available for exploring dynamics of local and large range populations. Voltage-sensitive dye imaging (VSDI) reveals neural population activity in areas ranging from a few tens of microns to a couple of centimeters, or two areas up to ~10 cm apart. VSDI provides a sub-millisecond temporal resolution, and a spatial resolution of about 50 μm. The dye signal emphasizes subthreshold synaptic potentials. VSDI has been applied in the mouse, rat, gerbil, ferret, tree shrew, cat and monkey cortices, in order to explore lateral spread of retinotopic or somatotopic activation, the dynamic spatiotemporal pattern resulting from sensory activation, including the somatosensory, olfactory, auditory, and visual modalities, as well as motor preparation and the properties of spontaneously-occurring population activity. In this chapter we focus on VSDI in-vivo and review results obtained mostly in the visual system in our laboratory.

Long-term optical imaging of intrinsic signals in anesthetized and awake monkeys

Some exciting new efforts to use intrinsic signal optical imaging methods for long-term studies in anesthetized and awake monkeys are reviewed. The development of such methodologies opens the door for studying behavioral states such as attention, motivation, memory, emotion, and other higher-order cognitive functions. Long-term imaging is also ideal for studying changes in the brain that accompany development, plasticity, and learning. Although intrinsic imaging lacks the temporal resolution offered by dyes, it is a high spatial resolution imaging method that does not require application of any external agents to the brain. The bulk of procedures described here have been developed in the monkey but can be applied to the study of surface structures in any in vivo preparation.

Independent component analysis of high-resolution imaging data identifies distinct functional domains

In the vertebrate brain external stimuli are often represented in distinct functional domains distributed across the cortical surface. Fast imaging techniques used to measure patterns of population activity record movies with many pixels and many frames, i.e., data sets with high dimensionality. Here we demonstrate that principal component analysis (PCA) followed by spatial independent component analysis (sICA), can be exploited to reduce the dimensionality of data sets recorded in the olfactory bulb and the somatosensory cortex of mice as well as the visual cortex of monkeys, without loosing the stimulus-specific responses. Different neuronal populations are separated based on their stimulus-specific spatiotemporal activation. Both, spatial and temporal response characteristics can be objectively obtained, simultaneously. In the olfactory bulb, groups of glomeruli with different response latencies can be identified. This is shown for recordings of olfactory receptor neuron input measured with a calcium-sensitive axon tracer and for network dynamics measured with the voltage-sensitive dye RH 1838. In the somatosensory cortex, barrels responding to the stimulation of single whiskers can be automatically detected. In the visual cortex orientation columns can be extracted. In all cases artifacts due to movement, heartbeat or respiration were separated from the functional signal by sICA and could be removed from the data set. sICA following PCA is therefore a powerful technique for data compression, unbiased analysis and dissection of imaging data of population activity, collected with high spatial and temporal resolution.

Spatiotemporal Activity Patterns During Respiratory Rhythmogenesis in the Rat Ventrolateral Medulla

One of the most important brain rhythms is that which generates involuntary breathing movements. The lower brain stem contains neural circuitry for respiratory rhythm generation in mammals. To date, microsectioning and selective lesioning studies have revealed anatomical regions necessary for respiratory rhythmogenesis. Although respiratory neurons distributed within these regions can be identified by their firing patterns in different phases of the respiratory cycle, conventional electrophysiology techniques have limited the study of spatial organization within this network. Optical imaging techniques offer the potential for monitoring the spatiotemporal activity of large groups of neurons simultaneously. Using high-speed voltage-sensitive dye imaging and spatial correlation analysis in an arterially perfused in situ preparation of the juvenile rat, we determined the spatial distribution of respiratory neuronal activity in a region of the ventrolateral respiratory group containing the pre-Bötzinger complex (pBC) during spontaneous eupneic breathing. While distinctly pre- and postinspiratory-related responses were spatially localizable on length scales less than 100 μm, we found the studied area on whole exhibited a spatial mixture of phase-spanning and postinspiratory-related activity. Additionally, optical recordings revealed significant widespread hyperpolarization, suggesting inhibition in the same region during expiration. This finding is consistent with the hypothesis that inhibitory neurons play a crucial role in the inspiration-expiration phase transition in the pBC. To our knowledge this is the first optical imaging of a near fully intact in situ preparation that exhibits both eupneic respiratory activity and functional reflexes.

Fiber-optic fluorescence imaging

Optical fibers guide light between separate locations and enable new types of fluorescence imaging. Fiber-optic fluorescence imaging systems include portable handheld microscopes, flexible endoscopes well suited for imaging within hollow tissue cavities and microendoscopes that allow minimally invasive high-resolution imaging deep within tissue. A challenge in the creation of such devices is the design and integration of miniaturized optical and mechanical components. Until recently, fiber-based fluorescence imaging was mainly limited to epifluorescence and scanning confocal modalities. Two new classes of photonic crystal fiber facilitate ultrashort pulse delivery for fiber-optic two-photon fluorescence imaging. An upcoming generation of fluorescence imaging devices will be based on microfabricated device components.

Rapid optical coherence tomography and recording functional scattering changes from activated frog retina

Optical coherence tomography (OCT) has important potential advantages for fast functional neuroimaging. However, dynamic neuroimaging poses demanding requirements for fast and stable acquisition of optical scans. Optical phase modulators based on the electro-optic effect allow rapid phase modulation; however, applications to low-coherence tomography are limited by the optical dispersion of a broadband light source by the electro-optic crystal. We show that the optical dispersion can be theoretically estimated and experimentally compensated. With an electro-optic phase modulator-based, no-moving-parts OCT system, near-infrared scattering changes associated with neural activation were recorded from isolated frog retinas activated by visible light.

Cross-polarized reflected light measurement of fast optical responses associated with neural activation

We developed an optical probe for cross-polarized reflected light measurements and investigated optical signals associated with electrophysiological activation in isolated lobster nerves. The cross-polarized baseline light intensity (structural signal) and the amplitude of the transient response to stimulation (functional signal) measured in reflected mode were dependent on the orientation of the nerve axis relative to the polarization plane of incident light. The maximum structural signal and functional response amplitude were observed at 45 degrees , and the ratio of functional to structural signals was approximately constant across orientations. Functional responses were measured in single trials in both transmitted and reflected geometries and responses had similar waveforms. Both structural and functional signals were an order of magnitude smaller in reflected than in transmitted light measurements, but functional responses had similar signal/noise ratios. We propose a theoretical model based on geometrical optics that is consistent with experimental results. In the model, the cross-polarized structural signal results from light reflection from axonal fibers and the transient functional response arises from axonal swelling associated with neural activation. Polarization-sensitive reflected light measurements could greatly enhance in vivo imaging of neural activation since cross-polarized responses are much larger than scattering signals now employed for dynamic functional neuroimaging.

VSDI: a new era in functional imaging of cortical dynamics

During the last few decades, neuroscientists have benefited from the emergence of many powerful functional imaging techniques that cover broad spatial and temporal scales. We can now image single molecules controlling cell differentiation, growth and death; single cells and their neurites processing electrical inputs and sending outputs; neuronal circuits performing neural computations in vitro; and the intact brain. At present, imaging based on voltage-sensitive dyes (VSDI) offers the highest spatial and temporal resolution for imaging neocortical functions in the living brain, and has paved the way for a new era in the functional imaging of cortical dynamics. It has facilitated the exploration of fundamental mechanisms that underlie neocortical development, function and plasticity at the fundamental level of the cortical column.

Simultaneous birefringence and scattered light measurements reveal anatomical features in isolated crustacean nerve

Simultaneous fast birefringence and scattered light changes associated with crustacean nerve activation have different time courses and are produced by separate biophysical mechanisms. Technological advances in illumination, photodiodes and amplification circuitry achieved better signal-to-noise than earlier studies revealing optical signals in axonal nerve bundles as small as crayfish ventral cord and claw. The birefringence measurements yielded signals that could be observed in single trials, with temporally separated peaks associated with axonal populations of different diameters. A slit aperture placed perpendicular to the nerve reduced the spatial-temporal integration and enhanced the temporal structure of the separate peaks in the birefringence signal. Moving the slit aperture farther from the stimulation point delayed the signal in time, and also enhanced the separation between peaks. Different propagation velocities of the separate peaks provided evidence for at least three neuronal populations in the bundle. These studies underscore the advantages of birefringence over scattering measurements. Application of birefringence methods can optimize non-invasive imaging techniques being developed to detect fast optical responses associated with electrical neural activity in humans.

Optical tomographic mapping of cerebral haemodynamics by means of time-domain detection: methodology and phantom validation

One of the primary applications of diffuse optical imaging is to localize and quantify the changes in the cerebral oxygenation during functional brain activation. Up to now, data from an optical imager are simply presented as a two-dimensional (2D) topographic map using the modified Beer-Lambert law that assumes homogeneous optical properties beneath each optode. Due to the highly heterogeneous nature of the optical properties in the brain, the assumption is evidently invalid, leading to both low spatial resolution and inaccurate quantification in the assessment of haemodynamic changes. To cope with these difficulties, we propose a nonlinear tomographic image reconstruction algorithm for a two-layered slab geometry that uses time-resolved reflected light. The algorithm is based on the previously developed generalized pulse spectrum technique, and implemented within a semi-three-dimensional (3D) framework to conform to the topographic visualization and to reduce computational load. We demonstrate the advantages of the algorithm in quantifying simulated changes in haemoglobin concentrations and investigate its robustness to the uncertainties in the cortical structure and optical properties, as well as the effects of random noises on image quality. The methodology is also validated by experiments using a solid layered phantom.

In vivo fluorescence microscopy of neuronal activity in three dimensions by use of voltage-sensitive dyes

We report in vivo imaging of neuronal electrical activity from superficial layers of the mouse barrel cortex. The measurements have approximately 16-microm spatial and 3-ms temporal resolution and reach depths of 150 microm below the cortical surface. The depth-dependent differential-fluorescence optical sections of activity are consistent with known cortical architecture and represent an important step toward in vivo measurement of functioning complex neural networks. Our observations employ a custom gradient-index lens probe and voltage-sensitive dye fluorescence; the use of epi-illumination rather than dark-field illumination provides the dramatic signal-to-noise improvement necessary for fast three-dimensional imaging.

Optical lever recording of displacements from activated lobster nerve bundles and Nitella internodes

An optical lever was designed for studying physical displacements associated with electrophysiological activation of lobster nerve bundles. Stimulation current pulses generated a compound action potential volley, and upward physical displacements of <1 nm were recorded. The swelling displacement propagated in the same direction as the action potential volley, occurred simultaneously with the action potentials, and required 10 ms to relax after the electrical potential was restored. For comparison with previous reports, we also recorded the displacement of Nitella internodes associated with electrical stimulation. We found that a rapid swelling displacement (approximately 10 nm) was followed by a larger, slow-shrinking displacement (approximately 100 nm).

Ultrafast-laser-radiation transfer in heterogeneous tissues with the discrete-ordinates method

Here light propagation and radiation transfer of ultrafast laser pulses in heterogeneous biological tissues are simulated by use of the discrete-ordinates method (DOM). Formulations for solving the time-dependent radiation-transfer equation are deduced for three-dimensional geometries incorporating the Fresnel specularly reflecting boundary condition and characteristics of ultrafast laser pulses. The present method can treat both the incident laser intensity and the scattered radiation intensity from the walls of the targeted tissue as two components, i.e., a diffuse part and a specular part. Reflectivity at the tissue-air interface is calculated by use of Snell's law and the Fresnel equation. The high-order S10 DOM method is found to be adequate for describing the propagation and transfer of ultrafast laser radiation in heterogeneous tissues. The time-dependent radiation field in the tissue as well as the temporal radiation intensity profiles at the boundaries can be obtained simultaneously. The absolute values of the logarithmic slope of the temporal reflectance and transmittance at various detector positions are found to converge to a constant value in a homogeneous tissue model. With the inclusion of a small inhomogeneity, such a value will change in line with the property of the embedded inhomogeneity. The orientation of heterogeneity of the tissues also substantially affects the radiation intensity at the boundaries. The effect of the Fresnel boundary in the modeling is pronounced. The simulated transmitted signals are broadened and amplified under specularly reflecting boundary condition as compared with those under diffusely reflecting boundary conditions.

High-performance confocal system for microscopic or endoscopic applications

We designed a high-performance confocal system that can be easily adapted to an existing light microscope or coupled with an endoscope for remote imaging. The system employs spatially and temporally patterned illumination produced by one of several mechanisms, including a micromirror array video projection device driven by a computer video source or a microlens array scanned by a piezo actuator in the microscope illumination path. A series of subsampled "component" video images are acquired from a solid-state video camera. Confocal images are digitally reconstructed using "virtual pinhole" synthetic aperture techniques applied to the collection of component images. Unlike conventional confocal techniques that raster scan a single detector and illumination point, our system samples multiple locations in parallel, with particular advantages for monitoring fast dynamic processes. We compared methods of patterned illumination and confocal image reconstruction by characterizing the point spread function, contrast, and intensity of imaged objects. Sample 3D reconstructions include a diatom and a Golgi-stained nerve cell collected in transmission.

A chamber and artificial dura method for long-term optical imaging in the monkey

Optical imaging over extended periods of time in non-human primates presents serious challenges because the dura mater must be removed to expose the cortical surface. We present a novel nylon imaging chamber with a transparent artificial dura implant, which allows repeated, long-term optical recordings from the cortex. The cylinder of the chamber is inserted into a cranial trephination and held in place with a minimum of screws and acrylic cement. A round patch of artificial dura with a perpendicular wall protects the cortical surface and slows re-growth of dural tissue within the chamber. A cap, manufactured from the same material as the cylinder, is screwed into the chamber and seals it completely. Over a period of 1-4 months, the chamber required a minimum of maintenance and stayed infection-free without local antibiotic application. We repeatedly performed optical imaging in the same animal with the advantages of shortened preparation time. To permit precise alignment and comparison of maps obtained from different imaging sessions, we developed a program that calculated a 2-dimensional spatial transformation between maps of different magnifications, translations, and distortions. We suggest that these methods provide a practical solution to long-term optical imaging in the anesthetized or alert monkey. The exclusive use of non-metallic materials offers the benefit of a lighter and more compact implant, and the possibility to perform MRI scans after chamber implantation.

Scattered-light imaging in vivo tracks fast and slow processes of neurophysiological activation

We imaged fast optical changes associated with evoked neural activation in the dorsal brainstem of anesthetized rats, using a novel imaging device. The imager consisted of a gradient-index (GRIN) lens, a microscope objective, and a miniature charged-coupled device (CCD) video camera. We placed the probe in contact with tissue above cardiorespiratory areas of the nucleus of the solitary tract and illuminated the tissue with 780-nm light through flexible fibers around the probe perimeter. The focus depth was adjusted by moving the camera and microscope objective relative to the fixed GRIN lens. Back-scattered light images were relayed through the GRIN lens to the CCD camera. Video frames were digitized at 100 frames per second, along with tracheal pressure, arterial blood pressure, and electrocardiogram signals recorded at 1 kHz per channel. A macroelectrode placed under the GRIN lens recorded field potentials from the imaged area. Aortic, vagal, and superior laryngeal nerves were dissected free of surrounding tissue within the neck. Separate shocks to each dissected nerve elicited evoked electrical responses and caused localized optical activity patterns. The optical response was modeled by four distinct temporal components corresponding to putative physical mechanisms underlying scattered light changes. Region-of-interest analysis revealed image areas which were dominated by one or more of the different time-course components, some of which were also optimally recorded at different tissue depths. Two slow optical components appear to correspond to hemodynamic responses to metabolic demand associated with activation. Two fast optical components paralleled electrical evoked responses.

Continuous image and electrophysiological recording with real-time processing and control

Collecting continuous video together with multichannel electrophysiological data and other experimental modalities requires high bandwidth and storage capacities, as well as accurate synchronization to detect correlations between different recorded events. Often, experiments are highly complex, with many variables requiring immediate analysis and feedback during the course of the experiment. In addition, output channels require real-time control with high time resolution. We have explored several approaches to a system that can perform the above functions. The design of our system considered a number of issues, including time intervals between control and acquisition events, longest continuous recording period, data transfer bottleneck considerations, file archiving and format, and real-time display and processing. To demonstrate the system, we describe an experiment for characterizing rapid evoked scattered light changes in neural tissue, in vivo, using simultaneous electronic image acquisition and electrophysiological recording.