A miniature head-mounted two-photon microscope. high-resolution brain imaging in freely moving animals

Simultaneous CMOS-Based Imaging of Calcium Signaling of the Central Amygdala and the Dorsal Raphe Nucleus During Nociception in Freely Moving Mice

Fluorescence imaging devices have been indispensable in elucidating the workings of the brain in living animals, including unrestrained, active ones. Various devices are available, each with their own strengths and weaknesses in terms of many factors. We have developed CMOS-based needle-type imaging devices that are small and lightweight enough to be doubly implanted in freely moving mice. The design also allowed angled implantations to avoid critical areas. We demonstrated the utility of the devices by using them on GCaMP6 mice in a formalin test experiment. Simultaneous implantations to the capsular-lateral central amygdala (CeLC) and dorsal raphe nucleus (DRN) were proven to be safe and did not hinder the execution of the study. Analysis of the collected calcium signaling data, supported by behavior data, showed increased activity in both regions as a result of pain stimulation. Thus, we have successfully demonstrated the various advantages of the device in its application in the pain experiment.

Monitoring In Vivo Neural Activity to Understand Gut-Brain Signaling

Appropriate food intake requires exquisite coordination between the gut and the brain. Indeed, it has long been known that gastrointestinal signals communicate with the brain to promote or inhibit feeding behavior. Recent advances in the ability to monitor and manipulate neural activity in awake, behaving rodents has facilitated important discoveries about how gut signaling influences neural activity and feeding behavior. This review emphasizes recent studies that have advanced our knowledge of gut-brain signaling and food intake control, with a focus on how gut signaling influences in vivo neural activity in animal models. Moving forward, dissecting the complex pathways and circuits that transmit nutritive signals from the gut to the brain will reveal fundamental principles of energy balance, ultimately enabling new treatment strategies for diseases rooted in body weight control.

Design of a Cell Phone Lens-Based Miniature Microscope with Configurable Magnification Ratio

Application of cell-phone-based microscopes has been hindered by limitations such as inferior image quality, fixed magnification and inconvenient operation. In this paper, we propose a reverse cell phone lens-based miniature microscope with a configurable magnification ratio. By switching the objectives of three camera lens and applying the digital zooming function of the cell phone, a cell phone microscope is built with the continuously configurable magnification ratio between 0.8×–11.5×. At the same time, the miniature microscope can capture high-quality microscopic images with a maximum resolution of up to 575 lp/mm and a maximum field of view (FOV) of up to 7213 × 5443 μm. Furthermore, by moving the tube lens module of the microscope out of the cell phone body, the built miniature microscope is as compact as a <20 mm side length cube, improving operational experience profoundly. The proposed scheme marks a big step forward in terms of the imaging performance and user operational convenience for cell phone microscopes.

Fluorescence microendoscopy for in vivo deep-brain imaging of neuronal circuits

Imaging neuronal activity in awake, behaving animals has become a groundbreaking method in neuroscience that has rapidly enhanced our understanding of how the brain works. In vivo microendoscopic imaging has enabled researchers to see inside the brains of experimental animals and thus has emerged as a technology fit to answer many experimental questions. By combining microendoscopy with cutting edge targeting strategies and sophisticated analysis tools, neuronal activity patterns that underlie changes in behavior and physiology can be identified. However, new users may find it challenging to understand the techniques and to leverage this technology to best suit their needs. Here we present a background and overview of the necessary components for performing in vivo optical calcium imaging and offer some detailed guidance for current recommended approaches.

Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging

We have developed a miniature two-photon microscope equipped with an axial scanning mechanism and a long-working-distance miniature objective to enable multi-plane imaging over a volume of 420 × 420 × 180 μm³ at a lateral resolution of ~1 μm. Together with the detachable design that permits long-term recurring imaging, our miniature two-photon microscope can help decipher neuronal mechanisms in freely behaving animals.

From Neurons to Cognition: Technologies for Precise Recording of Neural Activity Underlying Behavior

Understanding how brain activity encodes information and controls behavior is a long-standing question in neuroscience. This complex problem requires converging efforts from neuroscience and engineering, including technological solutions to perform high-precision and large-scale recordings of neuronal activity in vivo as well as unbiased methods to reliably measure and quantify behavior. Thanks to advances in genetics, molecular biology, engineering, and neuroscience, in recent decades, a variety of optical imaging and electrophysiological approaches for recording neuronal activity in awake animals have been developed and widely applied in the field. Moreover, sophisticated computer vision and machine learning algorithms have been developed to analyze animal behavior. In this review, we provide an overview of the current state of technology for neuronal recordings with a focus on optical and electrophysiological methods in rodents. In addition, we discuss areas that future technological development will need to cover in order to further our understanding of the neural activity underlying behavior.

Identification and quantification of neuronal ensembles in optical imaging experiments

Recent technical advances in molecular biology and optical imaging have made it possible to record from up to thousands of densely packed neurons in superficial and deep brain regions in vivo, with cellular subtype specificity and high spatiotemporal fidelity. Such optical neurotechnologies are enabling increasingly fine-scaled studies of neuronal circuits and reliably co-active groups of neurons, so-called ensembles. Neuronal ensembles are thought to constitute the basic functional building blocks of brain systems, potentially exhibiting collective computational properties. While the technical framework of in vivo optical imaging and quantification of neuronal activity follows certain widely held standards, analytical methods for study of neuronal co-activity and ensembles lack consensus and are highly varied across the field. Here we provide a comprehensive step-by-step overview of theoretical, experimental, and analytical considerations for the identification and quantification of neuronal ensemble dynamics in high-resolution in vivo optical imaging studies.

Perspective of fibre-optical microendoscopy with microlenses

Fibre-optical microendoscopy is based on fibre-optical confocal scanning microscopy, where optical fibres are introduced for delivery of the source and collection of the signal. Fibre-optical microendoscopy has led to innovations in imaging of freely moving animals, long-term imaging, minimally invasive diagnostics, and microsurgery. The lens system in fibre-optical microendoscopy is significant because of the imaging resolution and miniaturisation possibility. State-of-the-art fibre-optical microendoscopy based on various types of lens systems is introduced and compared. The lens system contains an objective lens, a gradient index microlens, and other novel lens systems fabricated by electric arc discharge or two-photon lithography.

GPCR-Based Dopamine Sensors-A Detailed Guide to Inform Sensor Choice for In vivo Imaging

Understanding how dopamine (DA) encodes behavior depends on technologies that can reliably monitor DA release in freely-behaving animals. Recently, red and green genetically encoded sensors for DA (dLight, GRAB-DA) were developed and now provide the ability to track release dynamics at a subsecond resolution, with submicromolar affinity and high molecular specificity. Combined with rapid developments in in vivo imaging, these sensors have the potential to transform the field of DA sensing and DA-based drug discovery. When implementing these tools in the laboratory, it is important to consider there is not a 'one-size-fits-all' sensor. Sensor properties, most importantly their affinity and dynamic range, must be carefully chosen to match local DA levels. Molecular specificity, sensor kinetics, spectral properties, brightness, sensor scaffold and pharmacology can further influence sensor choice depending on the experimental question. In this review, we use DA as an example; we briefly summarize old and new techniques to monitor DA release, including DA biosensors. We then outline a map of DA heterogeneity across the brain and provide a guide for optimal sensor choice and implementation based on local DA levels and other experimental parameters. Altogether this review should act as a tool to guide DA sensor choice for end-users.

Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy

Miniature fluorescence microscopes are a standard tool in systems biology. However, widefield miniature microscopes capture only 2D information, and modifications that enable 3D capabilities increase the size and weight and have poor resolution outside a narrow depth range. Here, we achieve the 3D capability by replacing the tube lens of a conventional 2D Miniscope with an optimized multifocal phase mask at the objective's aperture stop. Placing the phase mask at the aperture stop significantly reduces the size of the device, and varying the focal lengths enables a uniform resolution across a wide depth range. The phase mask encodes the 3D fluorescence intensity into a single 2D measurement, and the 3D volume is recovered by solving a sparsity-constrained inverse problem. We provide methods for designing and fabricating the phase mask and an efficient forward model that accounts for the field-varying aberrations in miniature objectives. We demonstrate a prototype that is 17 mm tall and weighs 2.5 grams, achieving 2.76 μm lateral, and 15 μm axial resolution across most of the 900 × 700 × 390 μm3 volume at 40 volumes per second. The performance is validated experimentally on resolution targets, dynamic biological samples, and mouse brain tissue. Compared with existing miniature single-shot volume-capture implementations, our system is smaller and lighter and achieves a more than 2× better lateral and axial resolution throughout a 10× larger usable depth range. Our microscope design provides single-shot 3D imaging for applications where a compact platform matters, such as volumetric neural imaging in freely moving animals and 3D motion studies of dynamic samples in incubators and lab-on-a-chip devices.

Miniature Fluorescence Microscopy for Imaging Brain Activity in Freely-Behaving Animals

An ultimate goal of neuroscience is to decipher the principles underlying neuronal information processing at the molecular, cellular, circuit, and system levels. The advent of miniature fluorescence microscopy has furthered the quest by visualizing brain activities and structural dynamics in animals engaged in self-determined behaviors. In this brief review, we summarize recent advances in miniature fluorescence microscopy for neuroscience, focusing mostly on two mainstream solutions - miniature single-photon microscopy, and miniature two-photon microscopy. We discuss their technical advantages and limitations as well as unmet challenges for future improvement. Examples of preliminary applications are also presented to reflect on a new trend of brain imaging in experimental paradigms involving body movements, long and complex protocols, and even disease progression and aging.

Deciphering Brain Function by Miniaturized Fluorescence Microscopy in Freely Behaving Animals

Animal behavior is regulated by environmental stimuli and is shaped by the activity of neural networks, underscoring the importance of assessing the morpho-functional properties of different populations of cells in freely behaving animals. In recent years, a number of optical tools have been developed to monitor and modulate neuronal and glial activity at the protein, cellular, or network level and have opened up new avenues for studying brain function in freely behaving animals. Tools such as genetically encoded sensors and actuators are now commonly used for studying brain activity and function through their expression in different neuronal ensembles. In parallel, microscopy has also made major progress over the last decades. The advent of miniature microscopes (mini-microscopes also called mini-endoscopes) has become a method of choice for studying brain activity at the cellular and network levels in different brain regions of freely behaving mice. This technique also allows for longitudinal investigations while animals carrying the microscope on their head are performing behavioral tasks. In this review, we will discuss mini-endoscopic imaging and the advantages that these devices offer to research. We will also discuss current limitations of and potential future improvements in mini-endoscopic imaging.

Functional interrogation of neural circuits with virally transmitted optogenetic tools

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

High-speed fiber-optic scanning nonlinear endomicroscopy for imaging neuron dynamicsin vivo

Fiber-optic-based two-photon fluorescence endomicroscopy is emerging as an enabling technology for in vivo histological imaging of internal organs and functional neuronal imaging on freely-behaving animals. However, high-speed imaging remains challenging due to the expense of miniaturization and lack of suited fast beam scanners. For many applications, a higher imaging speed is highly desired, especially for monitoring functional dynamics such as transient dendritic responses in neuroscience. This Letter reports the development of a fast fiber-optic scanning endo-microscope with an imaging speed higher than 26 frames/s. In vivo neural dynamics imaging with the high-speed endomicroscope was performed on a freely-behaving mouse over the primary motor cortex that expressed GCaMP6m. The results demonstrate its capability of real-time monitoring of transient neuronal dynamics with very fine temporal resolution.

Three-photon head-mounted microscope for imaging deep cortical layers in freely moving rats

We designed a head-mounted three-photon microscope for imaging deep cortical layer neuronal activity in a freely moving rat. Delivery of high-energy excitation pulses at 1,320 nm required both a hollow-core fiber whose transmission properties did not change with fiber movement and dispersion compensation. These developments enabled imaging at >1.1 mm below the cortical surface and stable imaging of layer 5 neuronal activity for >1 h in freely moving rats performing a range of behaviors.

Stereotaxic endoscopy for the ocular imaging of awake, freely moving animal models

Stereotaxic instruments are increasingly used in research animals for the study of disease, but typically require restraints and anesthetic procedures. A stereotaxic head mount that enables imaging of the anterior chamber of the eye in alert and freely mobile mice is presented in this study. The head mount is fitted based on computed tomography scans and manufactured using 3D printing. The system is placed noninvasively using temporal mount bars and a snout mount, without breaking the skin or risking suffocation, while an instrument channel stabilizes the ocular probes. With a flexible micro-endoscopic probe and a confocal scanning laser microscopy system, <20 μm resolution is achieved in vivo with a field of view of nearly 1 mm. Discomfort is minimal, and further adaptations for minimally invasive neuroscience, optogenetics and auditory studies are possible.

The cellular and molecular basis of in vivo synaptic plasticity in rodents

Plasticity within the neuronal networks of the brain underlies the ability to learn and retain new information. The initial discovery of synaptic plasticity occurred by measuring synaptic strength in vivo, applying external stimulation and observing an increase in synaptic strength termed long-term potentiation (LTP). Many of the molecular pathways involved in LTP and other forms of synaptic plasticity were subsequently uncovered in vitro. Over the last few decades, technological advances in recording and imaging in live animals have seen many of these molecular mechanisms confirmed in vivo, including structural changes both pre- and postsynaptically, changes in synaptic strength, and changes in neuronal excitability. A well-studied aspect of neuronal plasticity is the capacity of the brain to adapt to its environment, gained by comparing the brains of deprived and experienced animals in vivo, and in direct response to sensory stimuli. Multiple in vivo studies have also strongly linked plastic changes to memory by interfering with the expression of plasticity and by manipulating memory engrams. Plasticity in vivo also occurs in the absence of any form of external stimulation, i.e., during spontaneous network activity occurring with brain development. However, there is still much to learn about how plasticity is induced during natural learning and how this is altered in neurological disorders.

Miniaturized precalibration-based Lissajous scanning fiber probe for high speed endoscopic optical coherence tomography

We present a miniaturized precalibration-based forward-viewing Lissajous scanning fiber probe for high speed endoscopic optical coherence tomography (OCT). The probe is based on an asymmetric fiber cantilever driven by the piezoelectric bender to realize two-dimensional (2D) Lissajous scanning. The stability and repeatability of the Lissajous scanning trajectory of the probe is tested by a position sensitive detector (PSD)-based position calibration setup. The two orthogonal resonant frequencies of the cantilever are measured to be 167.2 and 121 Hz. A 25 µm focal spot is formed at the working distance of 5 mm by the graded-index (GRIN) lens, and the field of view of the imaging probe is around ${1.5}\;{\rm mm} \times {1.5}\;{\rm mm}$1.5mm×1.5mm. The probe is fully packaged in a hypodermic tube for endoscopic imaging. The total rigid length and outer diameter are 35 mm and 3.5 mm, respectively. The probe is incorporated in a 50 KHz swept source OCT system with the axial resolution of 14 µm, and its imaging performance is validated by the 2D en face and 3D volumetric OCT imaging of the phantom and the biological tissue.

Software-Based Phase Control, Video-Rate Imaging, and Real-Time Mosaicing With a Lissajous-Scanned Confocal Microscope

We present software-based methods for automatic phase control and for mosaicing high-speed, Lissajous-scanned images. To achieve imaging speeds fast enough for mosaicing, we first increase the image update rate tenfold from 3 to 30 Hz, then vertically interpolate each sparse image in real-time to eliminate fixed pattern noise. We validate our methods by imaging fluorescent beads and automatically maintaining phase control over the course of one hour. We then image fixed mouse brain tissues at varying update rates and compare the resulting mosaics. Using reconstructed image data as feedback for phase control eliminates the need for phase sensors and feedback controllers, enabling long-term imaging experiments without additional hardware. Mosaicing subsampled images results in video-rate imaging speeds, nearly fully recovered spatial resolution, and millimeter-scale fields of view.

Probing Cortical Activity During Head-Fixed Behavior

The cortex is crucial for many behaviors, ranging from sensory-based behaviors to working memory and social behaviors. To gain an in-depth understanding of the contribution to these behaviors, cellular and sub-cellular recordings from both individual and populations of cortical neurons are vital. However, techniques allowing such recordings, such as two-photon imaging and whole-cell electrophysiology, require absolute stability of the head, a requirement not often fulfilled in freely moving animals. Here, we review and compare behavioral paradigms that have been developed and adapted for the head-fixed preparation, which together offer the needed stability for live recordings of neural activity in behaving animals. We also review how the head-fixed preparation has been used to explore the function of primary sensory cortices, posterior parietal cortex (PPC) and anterior lateral motor (ALM) cortex in sensory-based behavioral tasks, while also discussing the considerations of performing such recordings. Overall, this review highlights the head-fixed preparation as allowing in-depth investigation into the neural activity underlying behaviors by providing highly controllable settings for precise stimuli presentation which can be combined with behavioral paradigms ranging from simple sensory detection tasks to complex, cross-modal, memory-guided decision-making tasks.

Wide. Fast. Deep: Recent Advances in Multiphoton Microscopy of In Vivo Neuronal Activity

Multiphoton microscopy (MPM) has emerged as one of the most powerful and widespread technologies to monitor the activity of neuronal networks in awake, behaving animals over long periods of time. MPM development spanned across decades and crucially depended on the concurrent improvement of calcium indicators that report neuronal activity as well as surgical protocols, head fixation approaches, and innovations in optics and microscopy technology. Here we review the last decade of MPM development and highlight how in vivo imaging has matured and diversified, making it now possible to concurrently monitor thousands of neurons across connected brain areas or, alternatively, small local networks with sampling rates in the kilohertz range. This review includes different laser scanning approaches, such as multibeam technologies as well as recent developments to image deeper into neuronal tissues using new, long-wavelength laser sources. As future development will critically depend on our ability to resolve and discriminate individual neuronal spikes, we will also describe a simple framework that allows performing quantitative comparisons between the reviewed MPM instruments. Finally, we provide our own opinion on how the most recent MPM developments can be leveraged at scale to enable the next generation of discoveries in brain function.

Circuit Mechanisms of Neurodegenerative Diseases: A New Frontier With Miniature Fluorescence Microscopy

Neurodegenerative diseases (NDDs), such as Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD), are devastating age-associated brain disorders. Significant efforts have been made to uncover the molecular and cellular pathogenic mechanisms that underlie NDDs. However, our understanding of the neural circuit mechanisms that mediate NDDs and associated symptomatic features have been hindered by technological limitations. Our inability to identify and track individual neurons longitudinally in subcortical brain regions that are preferentially targeted in NDDs has left gaping holes in our knowledge of NDDs. Recent development and advancement of the miniature fluorescence microscope (miniscope) has opened up new avenues for examining spatially and temporally coordinated activity from hundreds of cells in deep brain structures in freely moving rodents. In the present mini-review, we examine the capabilities of current and future miniscope tools and discuss the innovative applications of miniscope imaging techniques that can push the boundaries of our understanding of neural circuit mechanisms of NDDs into new territories.

Fluorescent Biosensors for Neurotransmission and Neuromodulation: Engineering and Applications

Understanding how neuronal activity patterns in the brain correlate with complex behavior is one of the primary goals of modern neuroscience. Chemical transmission is the major way of communication between neurons, however, traditional methods of detection of neurotransmitter and neuromodulator transients in mammalian brain lack spatiotemporal precision. Modern fluorescent biosensors for neurotransmitters and neuromodulators allow monitoring chemical transmission in vivo with millisecond precision and single cell resolution. Changes in the fluorescent biosensor brightness occur upon neurotransmitter binding and can be detected using fiber photometry, stationary microscopy and miniaturized head-mounted microscopes. Biosensors can be expressed in the animal brain using adeno-associated viral vectors, and their cell-specific expression can be achieved with Cre-recombinase expressing animals. Although initially fluorescent biosensors for chemical transmission were represented by glutamate biosensors, nowadays biosensors for GABA, acetylcholine, glycine, norepinephrine, and dopamine are available as well. In this review, we overview functioning principles of existing intensiometric and ratiometric biosensors and provide brief insight into the variety of neurotransmitter-binding proteins from bacteria, plants, and eukaryotes including G-protein coupled receptors, which may serve as neurotransmitter-binding scaffolds. We next describe a workflow for development of neurotransmitter and neuromodulator biosensors. We then discuss advanced setups for functional imaging of neurotransmitter transients in the brain of awake freely moving animals. We conclude by providing application examples of biosensors for the studies of complex behavior with the single-neuron precision.

Design and Fabrication of a Push-Pull Electrostatic Actuated Cantilever Waveguide Scanner

The paper presents a novel fully integrated MEMS-based non-resonating operated 2D mechanical scanning system using a 1D push-pull actuator. Details of the design, fabrication and tests performed are presented. The current design utilizes an integrated electrostatic push-pull actuator and a SU-8 rib waveguide with a large core cross section (4 μm in height and 20 μm in width) in broadband single mode operation (λ = 0.4 μm to 0.65 μm). We have successfully demonstrated a 2D scanning motion using non- resonating operation with 201 Hz in vertical direction and 20 Hz in horizontal direction. This non-resonating scanner system has achieved a field of view (FOV) of 0.019 to 0.072 radians in vertical and horizontal directions, with the advantage of overcoming its frequency shift caused by fabrication uncertainties. In addition, we observed two fundamental resonances at 201 and 536 Hz in the vertical and horizontal directions with corresponding displacements of 130 and 19 μm, or 0.072 and 0.0105 radian field of view operating at a +150 V input. A gradient index (GRIN) lens is placed at the end of the waveguide to focus the diverging beam output from the waveguide and a 20 μm beam diameter is observed at the focal plane. The transmission efficiency of the waveguide is slightly low (~10%) and slight tensile residual stress can be observed at the cantilever portion of the waveguide due to inherent imperfections in the fabrication process.

Imaging and analysis of genetically encoded calcium indicators linking neural circuits and behaviors

Confirming the direct link between neural circuit activity and animal behavior has been a principal aim of neuroscience. The genetically encoded calcium indicator (GECI), which binds to calcium ions and emits fluorescence visualizing intracellular calcium concentration, enables detection of in vivo neuronal firing activity. Various GECIs have been developed and can be chosen for diverse purposes. These GECI-based signals can be acquired by several tools including two-photon microscopy and microendoscopy for precise or wide imaging at cellular to synaptic levels. In addition, the images from GECI signals can be analyzed with open source codes including constrained non-negative matrix factorization for endoscopy data (CNMF_E) and miniscope 1-photon-based calcium imaging signal extraction pipeline (MIN1PIPE), and considering parameters of the imaged brain regions (e.g., diameter or shape of soma or the resolution of recorded images), the real-time activity of each cell can be acquired and linked with animal behaviors. As a result, GECI signal analysis can be a powerful tool for revealing the functions of neuronal circuits related to specific behaviors.

Wide and Deep Imaging of Neuronal Activities by a Wearable NeuroImager Reveals Premotor Activity in the Whole Motor Cortex

Wearable technologies for functional whole brain imaging in freely moving animals would advance our understanding of cognitive processing and adaptive behavior. Fluorescence imaging can visualize the activity of individual neurons in real time, but conventional microscopes have limited sample coverage in both the width and depth of view. Here we developed a novel head-mounted laser camera (HLC) with macro and deep-focus lenses that enable fluorescence imaging at cellular resolution for comprehensive imaging in mice expressing a layer- and cell type-specific calcium probe. We visualized orientation selectivity in individual excitatory neurons across the whole visual cortex of one hemisphere, and cell assembly expressing the premotor activity that precedes voluntary movement across the motor cortex of both hemispheres. Including options for multiplex and wireless interfaces, our wearable, wide- and deep-imaging HLC technology could enable simple and economical mapping of neuronal populations underlying cognition and behavior.

Imaging spinal cord activity in behaving animals

The spinal cord is the primary neurological link between the brain and peripheral organs. How important it is in everyday life is apparent in patients with spinal cord injury or motoneuron disease, who have dramatically reduced musculoskeletal control or capacity to sense their environment. Despite its crucial role in sensory and motor processing little is known about the cellular and molecular signaling events that underlie spinal cord function under naturalistic conditions. While genetic, electrophysiological, pharmacological, and circuit tracing studies have revealed important roles for different molecularly defined neurons, these approaches insufficiently describe the moment-to-moment neuronal and non-neuronal activity patterns that underlie sensory-guided motor behaviors in health and disease. The recent development of imaging methods for real-time interrogation of cellular activity in the spinal cord of behaving mice has removed longstanding technical obstacles to spinal cord research and allowed new insight into how different cell types encode sensory information from mechanoreceptors and nociceptors in the skin. Here, we review the current state-of-the-art in interrogating cellular and microcircuit function in the spinal cord of behaving mammals and discuss current opportunities and technological challenges.

Differences in colonic crypt morphology of spontaneous and colitis-associated murine models via second harmonic generation imaging to quantify colon cancer development

Background

Colorectal cancer remains the second leading cause of cancer death in the United States, and increased risk in patients with ulcerative colitis (a subset of inflammatory bowel disease) has motivated studies into early markers of dysplasia. The development of clinically translatable multiphoton imaging systems has allowed for the potential of in vivo label-free imaging of epithelial crypt structures via autofluorescence and/or second harmonic generation (SHG). SHG has been used to investigate collagen structures in various types of cancer, though the changes that colorectal epithelial collagen structures undergo during tumor development, specifically colitis-associated tumors, have not been fully investigated.

Methods

This study used two murine models, using A/J mice, one for spontaneous carcinoma and one for colitis-associated carcinoma, to investigate and quantify SHG image features that could potentially inform future study designs of endoscopic multiphoton imaging systems. The spontaneous tumor model comprised a series of six weekly injections of azoxymethane (AOM model). The colitis-associated tumor model comprised a single injection of AOM, followed by cycles of drinking water with dissolved dextran sodium sulfate salt (AOM-DSS model). SHG images of freshly resected murine colon were acquired with a multiphoton imaging system, and image features, such as crypt size, shape and distribution, were quantified using an automated algorithm.

Results

The comparison of quantified features of crypt morphology demonstrated the ability of our quantitative image feature algorithms to detect differences between spontaneous (AOM model) and colitis-associated (AOM-DSS model) murine colorectal tissue specimens. There were statistically significant differences in the mean and standard deviation of nearest neighbor (distance between crypts) and circularity between the Control cohort, AOM and AOM-DSS cohorts. We also saw significance between AOM and AOM-DSS cohorts when calculating nearest neighbor in images acquired at fixed depths.

Conclusion

The results provide insight into the ability of SHG imaging to yield relevant data about the crypt microstructure in colorectal epithelium, specifically the potential to distinguish between spontaneous and colitis-associated murine models using quantification of crypt shape and distribution, informing future design of translational multiphoton imaging systems and protocols.

Electronic supplementary material

The online version of this article (10.1186/s12885-019-5639-8) contains supplementary material, which is available to authorized users.

Microstructured Optical Waveguide-Based Endoscopic Probe Coated with Silica Submicron Particles

Microstructured optical waveguides (MOW) are of great interest for chemical and biological sensing. Due to the high overlap between a guiding light mode and an analyte filling of one or several fiber capillaries, such systems are able to provide strong sensitivity with respect to variations in the refractive index and the thickness of filling materials. Here, we introduce a novel type of functionalized MOWs whose capillaries are coated by a layer-by-layer (LBL) approach, enabling the alternate deposition of silica particles (SiO₂) at different diameters—300 nm, 420 nm, and 900 nm—and layers of poly(diallyldimethylammonium chloride) (PDDA). We demonstrate up to three covering bilayers consisting of 300-nm silica particles. Modifications in the MOW transmission spectrum induced by coating are measured and analyzed. The proposed technique of MOW functionalization allows one to reach novel sensing capabilities, including an increase in the effective sensing area and the provision of a convenient scaffold for the attachment of long molecules such as proteins.

Circuit Investigations With Open-Source Miniaturized Microscopes: Past, Present and Future

The ability to simultaneously image the spatiotemporal activity signatures from many neurons during unrestrained vertebrate behaviors has become possible through the development of miniaturized fluorescence microscopes, or miniscopes, sufficiently light to be carried by small animals such as bats, birds and rodents. Miniscopes have permitted the study of circuits underlying song vocalization, action sequencing, head-direction tuning, spatial memory encoding and sleep to name a few. The foundation for these microscopes has been laid over the last two decades through academic research with some of this work resulting in commercialization. More recently, open-source initiatives have led to an even broader adoption of miniscopes in the neuroscience community. Open-source designs allow for rapid modification and extension of their function, which has resulted in a new generation of miniscopes that now permit wire-free or wireless recording, concurrent electrophysiology and imaging, two-color fluorescence detection, simultaneous optical actuation and read-out as well as wide-field and volumetric light-field imaging. These novel miniscopes will further expand the toolset of those seeking affordable methods to probe neural circuit function during naturalistic behaviors. Here, we will discuss the early development, present use and future potential of miniscopes.

Fabrication and characterization of large numerical aperture, high-resolution optical fiber bundles based on high-contrast pairs of soft glasses for fluorescence imaging

Fabrication and characterization of flexible optical fiber bundles (FBs) with in-house synthesized high-index and low-index thermally matched glasses are presented. The FBs composed of around 15000 single-core fibers with pixel sizes between 1.1 and 10 μm are fabricated using the stack-and-draw technique from sets of thermally matched zirconium-silicate ZR3, borosilicate SK222, sodium-silicate K209, and F2 glasses. With high refractive index contrast pair of glasses ZR3/SK222 and K209/F2, FBs with numerical apertures (NAs) of 0.53 and 0.59 are obtained, respectively. Among the studied glass materials, ZR3, SK222, and K209 are in-house synthesized, while F2 is commercially acquired. Seven different FBs with varying pixel sizes and bundle diameters are characterized. Brightfield imaging of a micro-ruler and a Convallaria majalis sample and fluorescence imaging of a dye-stained paper tissue and a cirrhotic mice liver tissue are demonstrated using these FBs, demonstrating their good potential for microendoscopic imaging. Brightfield and fluorescence imaging performance of the studied FBs are compared. For both sets of glass compositions, good imaging performance is observed for FBs, with core diameter and core-to-core distance values larger than 1.6 μm and 2.3 μm, respectively. FBs fabricated with K209/F2 glass pairs revealed better performance in fluorescence imaging due to their higher NA of 0.59.

Lissajous Scanning Two-photon Endomicroscope for In vivo Tissue Imaging

An endomicroscope opens new frontiers of non-invasive biopsy for in vivo imaging applications. Here we report two-photon laser scanning endomicroscope for in vivo cellular and tissue imaging using a Lissajous fiber scanner. The fiber scanner consists of a piezoelectric (PZT) tube, a single double-clad fiber (DCF) with high fluorescence collection, and a micro-tethered-silicon-oscillator (MTSO) for the separation of biaxial resonant scanning frequencies. The endomicroscopic imaging exhibits 5 frames/s with 99% in scanning density by using the selection rule of scanning frequencies. The endomicroscopic scanner was compactly packaged within a stainless tube of 2.6 mm in diameter with a high NA gradient-index (GRIN) lens, which can be easily inserted into the working channel of a conventional laparoscope. The lateral and axial resolutions of the endomicroscope are 0.70 µm and 7.6 μm, respectively. Two-photon fluorescence images of a stained kidney section and miscellaneous ex vivo and in vivo organs from wild type and green fluorescent protein transgenic (GFP-TG) mice were successfully obtained by using the endomicroscope. The endomicroscope also obtained label free images including autofluorescence and second-harmonic generation of an ear tissue of Thy1-GCaMP6 (GP5.17) mouse. The Lissajous scanning two-photon endomicroscope can provide a compact handheld platform for in vivo tissue imaging or optical biopsy applications.

Leveraging calcium imaging to illuminate circuit dysfunction in addiction

Alcohol and drug use can dysregulate neural circuit function to produce a wide range of neuropsychiatric disorders, including addiction. To understand the neural circuit computations that mediate behavior, and how substances of abuse may transform them, we must first be able to observe the activity of circuits. While many techniques have been utilized to measure activity in specific brain regions, these regions are made up of heterogeneous sub-populations, and assessing activity from neuronal populations of interest has been an ongoing challenge. To fully understand how neural circuits mediate addiction-related behavior, we must be able to reveal the cellular granularity within brain regions and circuits by overlaying functional information with the genetic and anatomical identity of the cells involved. The development of genetically encoded calcium indicators, which can be targeted to populations of interest, allows for in vivo visualization of calcium dynamics, a proxy for neuronal activity, thus providing an avenue for real-time assessment of activity in genetically and anatomically defined populations during behavior. Here, we highlight recent advances in calcium imaging technology, compare the current technology with other state-of-the-art approaches for in vivo monitoring of neural activity, and discuss the strengths, limitations, and practical concerns for observing neural circuit activity in preclinical addiction models.

MEMS Actuators for Optical Microendoscopy

Growing demands for affordable, portable, and reliable optical microendoscopic imaging devices are attracting research institutes and industries to find new manufacturing methods. However, the integration of microscopic components into these subsystems is one of today's challenges in manufacturing and packaging. Together with this kind of miniaturization more and more functional parts have to be accommodated in ever smaller spaces. Therefore, solving this challenge with the use of microelectromechanical systems (MEMS) fabrication technology has opened the promising opportunities in enabling a wide variety of novel optical microendoscopy to be miniaturized. MEMS fabrication technology enables abilities to apply batch fabrication methods with high-precision and to include a wide variety of optical functionalities to the optical components. As a result, MEMS technology has enabled greater accessibility to advance optical microendoscopy technology to provide high-resolution and high-performance imaging matching with traditional table-top microscopy. In this review the latest advancements of MEMS actuators for optical microendoscopy will be discussed in detail.

Imaging Neural Activity in the Primary Somatosensory Cortex Using Thy1-GCaMP6s Transgenic Mice

The mammalian brain exhibits marked symmetry across the sagittal plane. However, detailed description of neural dynamics in symmetric brain regions in adult mammalian animals remains elusive. In this study, we describe an experimental procedure for measuring calcium dynamics through dual optical windows above bilateral primary somatosensory corticies (S1) in Thy1-GCaMP6s transgenic mice using 2-photon (2P) microscopy. This method enables recordings and quantifications of neural activity in bilateral mouse brain regions one at a time in the same experiment for a prolonged period in vivo. Key aspects of this method, which can be completed within an hour, include minimally invasive surgery procedures for creating dual optical windows, and the use of 2P imaging. Although we only demonstrate the technique in the S1 area, the method can be applied to other regions of the living brain facilitating the elucidation of structural and functional complexities of brain neural networks.

All the light that we can see: a new era in miniaturized microscopy

One major challenge in neuroscience is to uncover how defined neural circuits in the brain encode, store, modify, and retrieve information. Meeting this challenge comprehensively requires tools capable of recording and manipulating the activity of intact neural networks in naturally behaving animals. Head-mounted miniature microscopes are emerging as a key tool to address this challenge. Here we discuss recent work leading to the miniaturization of neural imaging tools, the current state of the art in this field, and the importance and necessity of open-source options. We finish with a discussion on what the future may hold for miniature microscopy.

Dual-axis confocal microscopy for point-of-care pathology

Dual-axis confocal (DAC) microscopy is an optical imaging modality that utilizes simple low-numerical aperture (NA) lenses to achieve effective optical sectioning and superior image contrast in biological tissues. The unique architecture of DAC microscopy also provides some advantages for miniaturization, facilitating the development of endoscopic and handheld DAC systems for in vivo imaging. This article reviews the principles of DAC microscopy, including its differences from conventional confocal microscopy, and surveys several variations of DAC microscopy that have been developed and investigated as non-invasive real-time alternatives to conventional biopsy and histopathology.

Improving collection efficiency in two-photon endoscopy with reflective waveguiding

Two-photon endoscopy based on a gradient-index lens has been widely utilized for studying cellular behaviors in deep-lying tissues with minimal invasiveness in vivo. Although the efficient collection of emitted light is critical to attain high-contrast spatiotemporal information, the intrinsic low numerical aperture of the endoscopic probe poses a physical limitation. We report a simple solution to overcome this limit by incorporating a reflective waveguide ensheathing the endoscopic probe, which improves the collection efficiency by approximately two-fold. We describe its principle, fabrication procedure, optical characterization, and utilities in biological tissues.

Optimization of frequency-doubled Er-doped fiber laser for miniature multiphoton endoscopy

Frequency-doubled femtosecond Er-doped fiber laser is a low-cost and portable excitation source suitable for multiphoton endoscopy. The frequency-doubled wavelength at 780 nm is used to excite the intrinsic fluorescence signal. The frequency-doubling with a periodically poled MgO  :  LiNbO3 (PPLN) is integrated in the distal end of the imaging head to achieve fiber connection. The imaging speed is further improved by optimizing the excitation laser source. A 0.3-mm length of PPLN crystal is selected and the Er-doped fiber laser is manipulated to match its bandwidth with the acceptance bandwidth of the PPLN. Through this optimization, a reduced pulsewidth of 80 fs of the frequency-doubled pulse is achieved. All-fiber dispersion compensation and pulse compression by single mode fiber is conducted, which makes the fiber laser directly fiber-coupled to the imaging head. An imaging speed of 4  frames  /  s is demonstrated on ex vivo imaging of unstained biological tissues, which is 10 times faster than our previous study using a 1-mm-long PPLN. The results show that miniature multiphoton endoscopy using frequency-doubled Er-doped fiber laser has great potential for clinical applications.

Open-field PET: Simultaneous brain functional imaging and behavioural response measurements in freely moving small animals

A comprehensive understanding of how the brain responds to a changing environment requires techniques capable of recording functional outputs at the whole-brain level in response to external stimuli. Positron emission tomography (PET) is an exquisitely sensitive technique for imaging brain function but the need for anaesthesia to avoid motion artefacts precludes concurrent behavioural response studies. Here, we report a technique that combines motion-compensated PET with a robotically-controlled animal enclosure to enable simultaneous brain imaging and behavioural recordings in unrestrained small animals. The technique was used to measure in vivo displacement of [¹¹C]raclopride from dopamine D2 receptors (D2R) concurrently with changes in the behaviour of awake, freely moving rats following administration of unlabelled raclopride or amphetamine. The timing and magnitude of [¹¹C]raclopride displacement from D2R were reliably estimated and, in the case of amphetamine, these changes coincided with a marked increase in stereotyped behaviours and hyper-locomotion. The technique, therefore, allows simultaneous measurement of changes in brain function and behavioural responses to external stimuli in conscious unrestrained animals, giving rise to important applications in behavioural neuroscience.

The Virtual-Environment-Foraging Task enables rapid training and single-trial metrics of attention in head-fixed mice

Attention - the flexible allocation of processing resources based on behavioural demands - is essential to survival. Mouse research offers unique tools to dissect the underlying pathways, but is hampered by the difficulty of accurately measuring attention in mice. Current attention tasks for mice face several limitations: Binary (hit/miss), temporally imprecise metrics, behavioural confounds and overtraining. Thus, despite the increasing scope of neuronal population measurements, insights are limited without equally precise behavioural measures. Here we present a virtual-environment task for head-fixed mice based on 'foraging-like' navigation. The task requires animals to discriminate gratings at orientation differences from 90° to 5°, and can be learned in only 3-5 sessions (<550 trials). It yields single-trial, non-binary metrics of response speed and accuracy, which generate secondary metrics of choice certainty, visual acuity, and most importantly, of sustained and cued attention - two attentional components studied extensively in humans. This allows us to examine single-trial dynamics of attention in mice, independently of confounds like rule learning. With this approach, we show that C57/BL6 mice have better visual acuity than previously measured, that they rhythmically alternate between states of high and low alertness, and that they can be prompted to adopt different performance strategies using minute changes in reward contingencies.

Imaging Cortical Dynamics in GCaMP Transgenic Rats with a Head-Mounted Widefield Macroscope

Widefield imaging of calcium dynamics is an emerging method for mapping regional neural activity but is currently limited to restrained animals. Here we describe cScope, a head-mounted widefield macroscope developed to image large-scale cortical dynamics in rats during natural behavior. cScope provides a 7.8 × 4 mm field of view and dual illumination paths for both fluorescence and hemodynamic correction and can be fabricated at low cost using readily attainable components. We also report the development of Thy-1 transgenic rat strains with widespread neuronal expression of the calcium indicator GCaMP6f. We combined these two technologies to image large-scale calcium dynamics in the dorsal neocortex during a visual evidence accumulation task. Quantitative analysis of task-related dynamics revealed multiple regions having neural signals that encode behavioral choice and sensory evidence. Our results provide a new transgenic resource for calcium imaging in rats and extend the domain of head-mounted microscopes to larger-scale cortical dynamics. VIDEO ABSTRACT.

Miniscope GRIN Lens System for Calcium Imaging of Neuronal Activity from Deep Brain Structures in Behaving Animals

Visualizing neural activity from deep brain regions in freely behaving animals through miniature fluorescent microscope (miniscope) systems is becoming more important for understanding neural encoding mechanisms underlying cognitive functions. Here we present our custom-designed miniscope GRadient INdex (GRIN) lens system that enables simultaneously recording from hundreds of neurons for months. This article includes miniscope design, the surgical procedure for GRIN lens implantation, miniscope mounting on the head of a mouse, and data acquisition and analysis. First, a target brain region is labeled with virus expressing GCaMP6; second, a GRIN lens is implanted above the target brain region; third, following mouse surgical recovery, a miniscope is mounted on the head of the mouse above the GRIN lens; and finally, neural activity is recorded from the freely behaving mouse. This system can be applied to recording the same population of neurons longitudinally, enabling the elucidation of neural mechanisms underlying behavioral control. © 2018 by John Wiley & Sons, Inc.

Two-wavelength oximetry of tissue microcirculation based on sidestream dark-field imaging

Monitoring oxygen saturation (SO2) in microcirculation is effective for understanding disease dynamics. We have developed an SO2 estimation method, sidestream dark-field (SDF) oximetry, based on SDF imaging. SDF imaging is a noninvasive and clinically applicable technique to observe microcirculation. We report the first in vivo experiment observing the changes in SO2 of microcirculation using SDF oximetry. First, heat from the light-emitting diodes used for the SDF imaging might affect hemodynamics in microcirculation, hence, we performed an experiment to evaluate the influence of that on the SDF oximetry. The result suggested that SDF oximetry had enough stability for long-term experiments. Then, to evaluate the sensitivity of SDF oximetry to alterations in the hemodynamics of the microcirculation, we observed the time-lapsed SO2 changes in the dermis microcirculation of rats under hypoxic stimulation. We confirmed that the SO2 estimated by SDF oximetry was in accordance with changes in the fraction of inspired oxygen (FiO2). Thus, SDF oximetry is considered to be able to observe SO2 changes that occur in accordance with alteration of the microcirculation.

Spectro-temporal dispersion management of femtosecond pulses for fiber-optic two-photon endomicroscopy

The emerging fiber-optic two-photon endomicroscopy technology holds a strong promise for enabling translational applications of nonlinear optical imaging. Effective femtosecond pulse dispersion management is critical for achieving high-quality imaging. Here we report systematic analyses and performance characterization of a dual-fiber spectro-temporal dispersion management scheme involving a grating pair as the pulse stretcher. Compared with conventional linear-only compensation, the grating-based spectro-temporal compensation also takes into account nonlinear effects and enhances the two-photon signal by ~3-fold as experimentally demonstrated. Numerical simulations were carried out to systematically investigate the influence of several key design parameters on the overall compensation efficacy. Furthermore, comprehensive performance comparison with an ideal grism-pair counterpart reveals that a grating-pair stretcher affords much higher power throughput and thus is preferable for portable endomicroscopy systems with limited laser source power.

Two-Photon Microscopy with a Double-Wavelength Metasurface Objective Lens

Two-photon microscopy is a key imaging technique in life sciences due to its superior deep-tissue imaging capabilities. Light-weight and compact two-photon microscopes are of great interest because of their applications for in vivo deep brain imaging. Recently, dielectric metasurfaces have enabled a new category of small and lightweight optical elements, including objective lenses. Here we experimentally demonstrate two-photon microscopy using a double-wavelength metasurface lens. It is specifically designed to focus 820 and 605 nm light, corresponding to the excitation and emission wavelengths of the measured fluorophors, to the same focal distance. The captured two-photon images are qualitatively comparable to the ones taken by a conventional objective lens. Our metasurface lens can enable ultracompact two-photon microscopes with similar performance compared to current systems that are usually based on graded-index-lenses. In addition, further development of tunable metasurface lenses will enable fast axial scanning for volumetric imaging.

Multiphoton Intravital Calcium Imaging

Multiphoton intravital calcium imaging is a powerful technique that enables high-resolution longitudinal monitoring of cellular and subcellular activity hundreds of microns deep in the living organism. This unit addresses the application of 2-photon microscopy to imaging of genetically encoded calcium indicators (GECIs) in the mouse brain. The protocols in this unit enable real-time intravital imaging of intracellular calcium concentration simultaneously in hundreds of neurons, or at the resolution of single synapses, as mice respond to sensory stimuli or perform behavioral tasks. Protocols are presented for implantation of a cranial imaging window to provide optical access to the brain and for 2-photon image acquisition. Protocols for implantation of both open skull and thinned skull windows for single or multi-session imaging are described. © 2018 by John Wiley & Sons, Inc.

Tracking the Same Neurons across Multiple Days in Ca2+ Imaging Data

Ca²⁺ imaging techniques permit time-lapse recordings of neuronal activity from large populations over weeks. However, without identifying the same neurons across imaging sessions (cell registration), longitudinal analysis of the neural code is restricted to population-level statistics. Accurate cell registration becomes challenging with increased numbers of cells, sessions, and inter-session intervals. Current cell registration practices, whether manual or automatic, do not quantitatively evaluate registration accuracy, possibly leading to data misinterpretation. We developed a probabilistic method that automatically registers cells across multiple sessions and estimates the registration confidence for each registered cell. Using large-scale Ca²⁺ imaging data recorded over weeks from the hippocampus and cortex of freely behaving mice, we show that our method performs more accurate registration than previously used routines, yielding estimated error rates <5%, and that the registration is scalable for many sessions. Thus, our method allows reliable longitudinal analysis of the same neurons over long time periods.

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A method for tracking neurons across days (cell registration) in Ca²⁺ imaging data

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The method is probabilistic and quantitatively evaluates registration accuracy

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The method is applicable to various imaging techniques and cell detection algorithms

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Registration accuracy remains high with an increased number of registered sessions

Three dimensional two-photon brain imaging in freely moving mice using a miniature fiber coupled microscope with active axial-scanning

We present a miniature head mounted two-photon fiber-coupled microscope (2P-FCM) for neuronal imaging with active axial focusing enabled using a miniature electrowetting lens. We show three-dimensional two-photon imaging of neuronal structure and record neuronal activity from GCaMP6s fluorescence from multiple focal planes in a freely-moving mouse. Two-color simultaneous imaging of GFP and tdTomato fluorescence is also demonstrated. Additionally, dynamic control of the axial scanning of the electrowetting lens allows tilting of the focal plane enabling neurons in multiple depths to be imaged in a single plane. Two-photon imaging allows increased penetration depth in tissue yielding a working distance of 450 μm with an additional 180 μm of active axial focusing. The objective NA is 0.45 with a lateral resolution of 1.8 μm, an axial resolution of 10 μm, and a field-of-view of 240 μm diameter. The 2P-FCM has a weight of only ~2.5 g and is capable of repeatable and stable head-attachment. The 2P-FCM with dynamic axial scanning provides a new capability to record from functionally distinct neuronal layers, opening new opportunities in neuroscience research.