The Three-Dimensional Signal Collection Field for Fiber Photometry in Brain Tissue

Vibrational fiber photometry: label-free and reporter-free minimally invasive Raman spectroscopy deep in the mouse brain

Optical approaches to monitor neural activity are transforming neuroscience, owing to a fast-evolving palette of genetically encoded molecular reporters. However, the field still requires robust and label-free technologies to monitor the multifaceted biomolecular changes accompanying brain development, aging or disease. Here, we have developed vibrational fiber photometry as a low-invasive method for label-free monitoring of the biomolecular content of arbitrarily deep regions of the mouse brain in vivo through spontaneous Raman spectroscopy. Using a tapered fiber probe as thin as 1 µm at its tip, we elucidate the cytoarchitecture of the mouse brain, monitor molecular alterations caused by traumatic brain injury, as well as detect markers of brain metastasis with high accuracy. We view our approach, which introduces a deep learning algorithm to suppress probe background, as a promising complement to the existing palette of tools for the optical interrogation of neural function, with application to fundamental and preclinical investigations of the brain and other organs.

Distinct spatially organized striatum-wide acetylcholine dynamics for the learning and extinction of Pavlovian associations

Striatal acetylcholine (ACh) signaling has been proposed to counteract reinforcement signals to promote extinction and behavioral flexibility. ACh dips to cues and rewards may open a temporal window for associative plasticity to occur, while elevations may promote extinction. Changes in multi-phasic striatal ACh signals have been widely reported during learning, but how and where signals are distributed to enable region-specific plasticity for the learning and degradation of cue-reward associations is poorly understood. We used array fiber photometry in mice to investigate how ACh release across the striatum evolves during learning and extinction of Pavlovian associations. We report a topographic organization of opposing changes in ACh release to cues, rewards, and consummatory actions across distinct striatum regions. We localized reward prediction error encoding in particular phases of the ACh dynamics to a specific region of the anterior dorsal striatum (aDS). Positive prediction errors in the aDS were expressed in ACh dips, and negative prediction errors in long latency ACh elevations. Silencing aDS ACh release impaired behavioral extinction, suggesting a role for ACh elevations in down-regulating cue-reward associations. Dopamine release in aDS dipped for cues during extinction, but glutamate input onto cholinergic interneurons did not change, suggesting an intrastriatal mechanism for the emergence of ACh elevations. Our large scale measurements indicate how and where ACh dynamics can shape region-specific plasticity to gate learning and promote extinction of Pavlovian associations.

Low-NA two-photon lithography patterning of metal/dielectric tapered optical fibers for depth-selective, volumetric optical neural interfaces

Optical neural implants allow neuroscientists to access deep brain regions, enabling to decipher complex patterns of neural activity. In this field, the use of optical fibers is rapidly increasing, and the ability to generate high-quality metal patterns on their non-planar surface would further extend their application. Here, we propose to use alternating metal shielding and dielectric confinement to engineer the mode-division properties of tapered optical fiber neural implants. This is accomplished through an unconventional application of two-photon lithography (TPL), which employs a low-numerical aperture objective to pattern extensive waveguide sections at both low and high curvature radii. The low-NA TPL is used to polymerize a mask of photoresist, while the rest of the taper undergoes wet metal etching. This implies no direct destructive interaction between the laser beam and the metal to be removed, preserving the optical properties of the dielectric waveguide and of the metal coating. The advantages provided by the presented fabrication method, combined with the intrinsic modal properties of the dielectric waveguide, enable the engineering of the light guiding mechanisms, achieving depth-selective light delivery with a high extinction ratio. The device's light emission and collection properties were investigated in quasi-transparent media and highly scattering brain slices, finding that our proposed method facilitates 360° symmetric light collection around the dielectric-confined section with depth resolution. This opens a perspective for the realization of optical neural implants that can interface the implant axis all-around, with low-NA TPL that can also be applied on other types of non-planar surfaces.

Fiber photometry in neuroscience research: principles, applications, and future directions

In recent years, fluorescent sensors are enjoying a surge of popularity in the field of neuroscience. Through the development of novel genetically encoded sensors as well as improved methods of detection and analysis, fluorescent sensing has risen as a new major technique in neuroscience alongside molecular, electrophysiological, and imaging methods, opening up new avenues for research. Combined with multiphoton microscopy and fiber photometry, these sensors offer unique advantages in terms of cellular specificity, access to multiple targets - from calcium dynamics to neurotransmitter release to intracellular processes - as well as high capability for in vivo interrogation of neurobiological mechanisms underpinning behavior. Here, we provide a brief overview of the method, present examples of its integration with other tools in recent studies ranging from cellular to systems neuroscience, and discuss some of its principles and limitations, with the aim of introducing new potential users to this rapidly developing and potent technique.

Role of the Nucleus Accumbens in Signaled Avoidance Actions

Animals, humans included, navigate their environments guided by sensory cues, responding adaptively to potential dangers and rewards. Avoidance behaviors serve as adaptive strategies in the face of signaled threats, but the neural mechanisms orchestrating these behaviors remain elusive. Current circuit models of avoidance behaviors indicate that the nucleus accumbens (NAc) in the ventral striatum plays a key role in signaled avoidance behaviors, but the nature of this engagement is unclear. Evolving perspectives propose the NAc as a pivotal hub for action selection, integrating cognitive and affective information to heighten the efficiency of both appetitive and aversive motivated behaviors. To unravel the engagement of the NAc during active and passive avoidance, we used calcium imaging fiber photometry to examine NAc GABAergic neuron activity in ad libitum moving mice performing avoidance behaviors. We then probed the functional significance of NAc neurons using optogenetics and genetically targeted or electrolytic lesions. We found that NAc neurons code contraversive orienting movements and avoidance actions. However, direct optogenetic inhibition or lesions of NAc neurons did not impair active or passive avoidance behaviors, challenging the notion of their purported pivotal role in adaptive avoidance. The findings emphasize that while the NAc encodes avoidance movements, it is not required for avoidance behaviors, highlighting the distinction between behavior encoding or representation and mediation or generation.

Photonic neural probe enabled microendoscopes for light-sheet light-field computational fluorescence brain imaging

Significance

Light-sheet fluorescence microscopy is widely used for high-speed, high-contrast, volumetric imaging. Application of this technique to in vivo brain imaging in non-transparent organisms has been limited by the geometric constraints of conventional light-sheet microscopes, which require orthogonal fluorescence excitation and collection objectives. We have recently demonstrated implantable photonic neural probes that emit addressable light sheets at depth in brain tissue, miniaturizing the excitation optics. Here, we propose a microendoscope consisting of a light-sheet neural probe packaged together with miniaturized fluorescence collection optics based on an image fiber bundle for lensless, light-field, computational fluorescence imaging.

Aim

Foundry-fabricated, silicon-based, light-sheet neural probes can be packaged together with commercially available image fiber bundles to form microendoscopes for light-sheet light-field fluorescence imaging at depth in brain tissue.

Approach

Prototype microendoscopes were developed using light-sheet neural probes with five addressable sheets and image fiber bundles. Fluorescence imaging with the microendoscopes was tested with fluorescent beads suspended in agarose and fixed mouse brain tissue.

Results

Volumetric light-sheet light-field fluorescence imaging was demonstrated using the microendoscopes. Increased imaging depth and enhanced reconstruction accuracy were observed relative to epi-illumination light-field imaging using only a fiber bundle.

Conclusions

Our work offers a solution toward volumetric fluorescence imaging of brain tissue with a compact size and high contrast. The proof-of-concept demonstrations herein illustrate the operating principles and methods of the imaging approach, providing a foundation for future investigations of photonic neural probe enabled microendoscopes for deep-brain fluorescence imaging in vivo.

Acute and chronic alcohol modulation of extended amygdala calcium dynamics

The central amygdala (CeA) and bed nucleus of the stria terminalis (BNST) are reciprocally connected nodes of the extended amygdala thought to play an important role in alcohol consumption. Studies of immediate-early genes indicate that BNST and CeA are acutely activated following alcohol drinking and may signal alcohol reward in nondependent drinkers, while stress signaling in the extended amygdala following chronic alcohol exposure drives increased drinking via negative reinforcement. However, the temporal dynamics of neuronal activation in these regions during drinking behavior are poorly understood. In this study, we used fiber photometry and the genetically encoded calcium sensor GCaMP6s to assess acute changes in neuronal activity during alcohol consumption in BNST and CeA before and after a chronic drinking paradigm. Activity was examined in the pan-neuronal population and separately in dynorphinergic neurons. BNST and CeA showed increased pan-neuronal activity during acute consumption of alcohol and other fluid tastants of positive and negative valence, as well as highly palatable chow. Responses were greatest during initial consummatory bouts and decreased in amplitude with repeated consumption of the same tastant, suggesting modulation by stimulus novelty. Dynorphin neurons showed similar consumption-associated calcium increases in both regions. Following three weeks of continuous alcohol access (CA), calcium increases in dynorphin neurons during drinking were maintained, but pan-neuronal activity and BNST-CeA coherence were altered in a sex-specific manner. These results indicate that BNST and CeA, and dynorphin neurons specifically, are engaged during drinking behavior, and activity dynamics are influenced by stimulus novelty and chronic alcohol.

Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior

Neural population dynamics relevant to behavior vary over multiple spatial and temporal scales across three-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice, enabling the investigation of cell-type- and neurotransmitter-specific signals over arbitrary 3D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum, revealing distinct, modality-specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and the spatial localization of behavioral function across large circuits.

Lights, fiber, action! A primer on in vivo fiber photometry

Fiber photometry is a key technique for characterizing brain-behavior relationships in vivo. Initially, it was primarily used to report calcium dynamics as a proxy for neural activity via genetically encoded indicators. This generated new insights into brain functions including movement, memory, and motivation at the level of defined circuits and cell types. Recently, the opportunity for discovery with fiber photometry has exploded with the development of an extensive range of fluorescent sensors for biomolecules including neuromodulators and peptides that were previously inaccessible in vivo. This critical advance, combined with the new availability of affordable "plug-and-play" recording systems, has made monitoring molecules with high spatiotemporal precision during behavior highly accessible. However, while opening exciting new avenues for research, the rapid expansion in fiber photometry applications has occurred without coordination or consensus on best practices. Here, we provide a comprehensive guide to help end-users execute, analyze, and suitably interpret fiber photometry studies.

Zona incerta distributes a broad movement signal that modulates behavior

The zona incerta is a subthalamic nucleus made up mostly of GABAergic neurons. It has wide-ranging inputs and outputs and is believed to have many integrative functions that link sensory stimuli with motor responses to guide behavior. However, its role is not well established perhaps because few studies have measured the activity of zona incerta neurons in behaving animals under different conditions. To record the activity of zona incerta neurons during exploratory and cue-driven goal-directed behaviors, we used electrophysiology in head-fixed mice moving on a spherical treadmill and fiber photometry in freely moving mice. We found two groups of neurons based on their sensitivity to movement, with a minority of neurons responding to whisker stimuli. Furthermore, zona incerta GABAergic neurons robustly code the occurrence of exploratory and goal-directed movements, but not their direction. To understand the function of these activations, we performed genetically targeted lesions and optogenetic manipulations of zona incerta GABAergic neurons during exploratory and goal-directed behaviors. The results showed that the zona incerta has a role in modulating the movement associated with these behaviors, but this has little impact on overall performance. Zona incerta neurons distribute a broad corollary signal of movement occurrence to their diverse projection sites, which regulates behavior.

Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior

Neural population dynamics relevant for behavior vary over multiple spatial and temporal scales across 3-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array and imaging approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice. We developed a semi-automated micro-CT based strategy to precisely localize positions of each optical fiber. This highly-customizable approach enables investigation of multi-scale spatial and temporal patterns of cell-type and neurotransmitter specific signals over arbitrary 3-D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum volume which revealed distinct, modality specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics through our fiber arrays enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and spatial localization of behavioral function across large circuits.

Acute and chronic alcohol modulation of extended amygdala calcium dynamics

The central amygdala (CeA) and bed nucleus of the stria terminalis (BNST) are reciprocally connected nodes of the extended amygdala thought to play an important role in alcohol consumption. Studies of immediate-early genes indicate that BNST and CeA are acutely activated following alcohol drinking and may signal alcohol reward in nondependent drinkers, while increased stress signaling in the extended amygdala following chronic alcohol exposure drives increased drinking via negative reinforcement. However, the temporal dynamics of neuronal activation in these regions during drinking behavior are poorly understood. In this study, we used fiber photometry and the genetically encoded calcium sensor GCaMP6s to assess acute changes in neuronal activity during alcohol consumption in BNST and CeA before and after a chronic drinking paradigm. Activity was examined in the pan-neuronal population and separately in dynorphinergic neurons. BNST and CeA showed increased pan-neuronal activity during acute consumption of alcohol and other fluid tastants of positive and negative valence, as well as highly palatable chow. Responses were greatest during initial consummatory bouts and decreased in amplitude with repeated consumption of the same tastant, suggesting modulation by stimulus novelty. Dynorphin neurons showed similar consumption-associated calcium increases in both regions. Following three weeks of continuous alcohol access (CA), calcium increases in dynorphin neurons during drinking were maintained, but pan-neuronal activity and BNST-CeA coherence were altered in a sex-specific manner. These results indicate that BNST and CeA, and dynorphin neurons specifically, are engaged during drinking behavior, and activity dynamics are influenced by stimulus novelty and chronic alcohol.

A High-Density Raman Photometry for Tracking and Quantifying of AchE Activity in The Brain of Freely Moving Animals with Network

A high-density Raman photometry based on a dual-recognition strategy is created for accurately quantifying acetylcholinesterase (AchE) activity in 24 brain regions of free-moving animals with network. A series of 5-ethynyl-1,2,3,3-tetramethyl-based molecules with different conjugated structures and substitute groups are designed and synthesized for specific recognition of AchE by Raman spectroscopy. After systematically evaluating the recognition ability toward AchE, 2-(4-((4-(dimethylamino)benzoyl)oxy)styryl)-5-ethynyl-1,3,3-trimethyl-3H-indol-1-ium (ET-5) is finally optimized for AchE determination, which shows the highest selectivity, the greatest sensitivity, and the fastest response time among the investigated seven molecules. More interestingly, using the developed probe for AchE with high accuracy and sensitivity, the optimized AchE regulated by nitric oxide (NO) is discovered for promoting the neurogenesis of neural stem cells (NSCs). Benefiting from the high-density photometry, it is found that the activity and distribution of AchE varied in 24 brain regions, and the levels of AchE activity in 24 brain regions of Alzheimer's mice (AD) are lower than those of normal mice. It is the first time that a functional network of AchE in 24 brain regions is established. It is also found that the loss of AchE functional network in AD mice is restored and reconstructed by the controlled release of AchE regulated by NO.

Unique functional responses differentially map onto genetic subtypes of dopamine neurons

Dopamine neurons are characterized by their response to unexpected rewards, but they also fire during movement and aversive stimuli. Dopamine neuron diversity has been observed based on molecular expression profiles; however, whether different functions map onto such genetic subtypes remains unclear. In this study, we established that three genetic dopamine neuron subtypes within the substantia nigra pars compacta, characterized by the expression of Slc17a6 (Vglut2), Calb1 and Anxa1, each have a unique set of responses to rewards, aversive stimuli and accelerations and decelerations, and these signaling patterns are highly correlated between somas and axons within subtypes. Remarkably, reward responses were almost entirely absent in the Anxa1+ subtype, which instead displayed acceleration-correlated signaling. Our findings establish a connection between functional and genetic dopamine neuron subtypes and demonstrate that molecular expression patterns can serve as a common framework to dissect dopaminergic functions.

PhAT: A Flexible Open-Source GUI-Driven Toolkit for Photometry Analysis

Photometry approaches detect sensor-mediated changes in fluorescence as a proxy for rapid molecular changes within the brain. As a flexible technique with a relatively low cost to implement, photometry is rapidly being incorporated into neuroscience laboratories. Yet, although multiple data acquisition systems for photometry now exist, robust analytical pipelines for the resulting data remain limited. Here we present the Photometry Analysis Toolkit (PhAT)-a free open-source analysis pipeline that provides options for signal normalization, incorporation of multiple data streams to align photometry data with behavior and other events, calculation of event-related changes in fluorescence, and comparison of similarity across fluorescent traces. A graphical user interface (GUI) enables use of this software without prior coding knowledge. In addition to providing foundational analytical tools, PhAT is designed to readily incorporate community-driven development of new modules for more bespoke analyses, and enables data to be easily exported to enable subsequent statistical testing and/or code-based analyses. In addition, we provide recommendations regarding technical aspects of photometry experiments, including sensor selection and validation, reference signal considerations, and best practices for experimental design and data collection. We hope that the distribution of this software and protocols will lower the barrier to entry for new photometry users and improve the quality of collected data, increasing transparency and reproducibility in photometry analyses. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Software and environment installation Alternate Protocol 1: Software and environment update Basic Protocol 2: GUI-driven fiber photometry analysis Support Protocol 1: Examining signal quality Support Protocol 2: Interacting with graphs Basic Protocol 3: Adding modules to PhAT Alternate Protocol 2: Creating functions for use in Jupyter Notebook.

A flexible and versatile system for multi-color fiber photometry and optogenetic manipulation

Here, we present simultaneous fiber photometry recordings and optogenetic stimulation based on a multimode fused fiber coupler for both light delivery and collection without the need for dichroic beam splitters. In combination with a multi-color light source and appropriate optical filters, our approach offers remarkable flexibility in experimental design and facilitates the exploration of new molecular tools in vivo at minimal cost. We demonstrate straightforward re-configuration of the setup to operate with green, red, and near-infrared calcium indicators with or without simultaneous optogenetic stimulation and further explore the multi-color photometry capabilities of the system. The ease of assembly, operation, characterization, and customization of this platform holds the potential to foster the development of experimental strategies for multi-color fused fiber photometry combined with optogenetics far beyond its current state.

The Orienting Reflex Reveals Behavioral States Set by Demanding Contexts: Role of the Superior Colliculus

Sensory stimuli can trigger an orienting reflex (response) by which animals move the head to position their sensors (e.g., eyes, pinna, whiskers). Orienting responses may be important to evaluate stimuli that call for action (e.g., approach, escape, ignore), but little is known about the dynamics of orienting responses in the context of goal-directed actions. Using mice of either sex, we found that, during a signaled avoidance action, the orienting response evoked by the conditioned stimulus (CS) consisted of a fast head movement containing rotational and translational components that varied substantially as a function of the behavioral and underlying brain states of the animal set by different task contingencies. Larger CS-evoked orienting responses were associated with high-intensity auditory stimuli, failures to produce the appropriate signaled action, and behavioral states resulting from uncertain or demanding situations and the animal's ability to cope with them. As a prototypical orienting neural circuit, we confirmed that the superior colliculus controls and codes the direction of spontaneous exploratory orienting movements. In addition, superior colliculus activity correlated with CS-evoked orienting responses, and either its optogenetic inhibition or excitation potentiated CS-evoked orienting responses, which are likely generated downstream in the medulla. CS-evoked orienting responses may be a useful probe to assess behavioral and related brain states, and state-dependent modulation of orienting responses may involve the superior colliculus.SIGNIFICANCE STATEMENT Humans and other animals produce an orienting reflex (also known as orienting response) by which they rapidly orient their head and sensors to evaluate novel or salient stimuli. Spontaneous orienting movements also occur during exploration of the environment in the absence of explicit, salient stimuli. We monitored stimulus-evoked orienting responses in mice performing signaled avoidance behaviors and found that these responses reflect the behavioral state of the animal set by contextual demands and the animal's ability to cope with them. Various experiments involving the superior colliculus revealed a well-established role in spontaneous orienting but only an influencing effect over orienting responses. Stimulus-evoked orienting responses may be a useful probe of behavioral and related brain states.

Simultaneous dynamic glucose-enhanced (DGE) MRI and fiber photometry measurements of glucose in the healthy mouse brain

Glucose is the main energy source in the brain and its regulated uptake and utilization are important biomarkers of pathological brain function. Glucose Chemical Exchange Saturation Transfer (GlucoCEST) and its time-resolved version Dynamic Glucose-Enhanced MRI (DGE) are promising approaches to monitor glucose and detect tumors, since they are radioactivity-free, do not require ¹³C labeling and are is easily translatable to the clinics. The main principle of DGE is clear. However, what remains to be established is to which extent the signal reflects vascular, extracellular or intracellular glucose. To elucidate the compartmental contributions to the DGE signal, we coupled it with FRET-based fiber photometry of genetically encoded sensors, a technique that combines quantitative glucose readout with cellular specificity. The glucose sensor FLIIP was used with fiber photometry to measure astrocytic and neuronal glucose changes upon injection of D-glucose, 3OMG and L-glucose, in the anaesthetized murine brain. By correlating the kinetic profiles of the techniques, we demonstrate the presence of a vascular contribution to the signal, especially at early time points after injection. Furthermore, we show that, in the case of the commonly used contrast agent 3OMG, the DGE signal actually anticorrelates with the glucose concentration in neurons and astrocytes.

Multiscale imaging informs translational mouse modeling of neurological disease

Multiscale neurophysiology reveals that simple motor actions are associated with changes in neuronal firing in virtually every brain region studied. Accordingly, the assessment of focal pathology such as stroke or progressive neurodegenerative diseases must also extend widely across brain areas. To derive mechanistic information through imaging, multiple resolution scales and multimodal factors must be included, such as the structure and function of specific neurons and glial cells and the dynamics of specific neurotransmitters. Emerging multiscale methods in preclinical animal studies that span micro- to macroscale examinations fill this gap, allowing a circuit-based understanding of pathophysiological mechanisms. Combined with high-performance computation and open-source data repositories, these emerging multiscale and large field-of-view techniques include live functional ultrasound, multi- and single-photon wide-scale light microscopy, video-based miniscopes, and tissue-penetrating fiber photometry, as well as variants of post-mortem expansion microscopy. We present these technologies and outline use cases and data pipelines to uncover new knowledge within animal models of stroke, Alzheimer's disease, and movement disorders.

Multiregion neuronal activity: the forest and the trees

The past decade has witnessed remarkable advances in the simultaneous measurement of neuronal activity across many brain regions, enabling fundamentally new explorations of the brain-spanning cellular dynamics that underlie sensation, cognition and action. These recently developed multiregion recording techniques have provided many experimental opportunities, but thoughtful consideration of methodological trade-offs is necessary, especially regarding field of view, temporal acquisition rate and ability to guarantee cellular resolution. When applied in concert with modern optogenetic and computational tools, multiregion recording has already made possible fundamental biological discoveries - in part via the unprecedented ability to perform unbiased neural activity screens for principles of brain function, spanning dozens of brain areas and from local to global scales.

Spectral fiber photometry derives hemoglobin concentration changes for accurate measurement of fluorescent sensor activity

Fiber photometry is an emerging technique for recording fluorescent sensor activity in the brain. However, significant hemoglobin absorption artifacts in fiber photometry data may be misinterpreted as sensor activity changes. Because hemoglobin exists widely in the brain, and its concentration varies temporally, such artifacts could impede the accuracy of photometry recordings. Here we present use of spectral photometry and computational methods to quantify photon absorption effects by using activity-independent fluorescence signals, which can be used to derive oxy- and deoxy-hemoglobin concentration changes. Although these changes are often temporally delayed compared with the fast-responding fluorescence spikes, we found that erroneous interpretation may occur when examining pharmacology-induced sustained changes and that sometimes hemoglobin absorption could flip the GCaMP signal polarity. We provide hemoglobin-based correction methods to restore fluorescence signals and compare our results with other commonly used approaches. We also demonstrated the utility of spectral fiber photometry for delineating regional differences in hemodynamic response functions.

Adaptive polymer fiber neural device for drug delivery and enlarged illumination angle for neuromodulation

OBJECTIVE

Optical fiber devices constitute significant tools for the modulation and interrogation of neuronal circuitry in the mid and deep brain regions. The illuminated brain area during neuromodulation has a direct impact on the spatio-temporal properties of the brain activity and depends solely on the material and geometrical characteristics of the optical fibers. In the present work, we developed two different flexible polymer optical fibers (POFs) with integrated microfluidic channels (MFCs) and an ultra-high numerical aperture (UHNA) for enlarging the illumination angle to achieve efficient neuromodulation.

APPROACH

Three distinct thermoplastic polymers: polysulfone (PSU), polycarbonate (PC), and fluorinated ethylene propylene (FEP) were used to fabricate two step-index UHNA POF neural devices using a scalable thermal drawing process. The POFs were characterized in terms of their illumination map as well as their fluid delivery capability in phantom and adult rat brain slices.

MAIN RESULTS

A 100-fold reduced bending stiffness of the proposed fiber devices compared to their commercially available counterparts has been found. The integrated MFCs can controllably deliver dye (trypan blue) on-demand over a wide range of injection rates spanning from 10 nL/min to 1000 nL/min. Compared with commercial silica fibers, the proposed UHNA POFs exhibited an increased illumination area by 17% and 21% under 470 and 650 nm wavelength, respectively. In addition, a fluorescent light recording experiment has been conducted to demonstrate the ability of our UHNA POFs to be used as optical waveguides in fiber photometry.

SIGNIFICANCE

Our results overcome the current technological limitations of fiber implants that have limited illumination area and we suggest that soft neural fiber devices can be developed using different custom designs for illumination, collection, and photometry applications. We anticipate our work to pave the way towards the development of next-generation functional optical fibers for neuroscience.

Orthogonalization of far-field detection in tapered optical fibers for depth-selective fiber photometry in brain tissue

The field of implantable optical neural interfaces has recently enabled the interrogation of neural circuitry with both cell-type specificity and spatial resolution in sub-cortical structures of the mouse brain. This generated the need to integrate multiple optical channels within the same implantable device, motivating the requirement of multiplexing and demultiplexing techniques. In this article, we present an orthogonalization method of the far-field space to introduce mode-division demultiplexing for collecting fluorescence from the implantable tapered optical fibers. This is achieved by exploiting the correlation between the transversal wavevector k t of the guided light and the position of the fluorescent sources along the implant, an intrinsic property of the taper waveguide. On these bases, we define a basis of orthogonal vectors in the Fourier space, each of which is associated with a depth along the taper, to simultaneously detect and demultiplex the collected signal when the probe is implanted in fixed mouse brain tissue. Our approach complements the existing multiplexing techniques used in silicon-based photonics probes with the advantage of a significant simplification of the probe itself.

Numerical Calculation of the Light Propagation in Tapered Optical Fibers for Optical Neural Interfaces

As implantable optical systems recently enabled new approaches to study the brain with optical radiations, tapered optical fibers emerged as promising implantable waveguides to deliver and collect light from sub-cortical structures of the mouse brain. They rely on a specific feature of multimodal fiber optics: as the waveguide narrows, the number of guided modes decreases and the radiation can gradually couple with the environment. This happens along a taper segment whose length can be tailored to match with the depth of functional structures of the mouse brain, and can extend for a few millimeters. This anatomical requirement results in optical systems which have an active area that is very long compared to the wavelength of the light they guide and their behavior is typically estimated by ray tracing simulations, because finite element methods are too computationally demanding. Here we present a computational technique that exploits the beam-envelope method and the cylindrical symmetry of the fibers to provide an efficient and exact calculation of the electric field along the fibers, which may enable the design of neural interfaces optimized to meet different goals.

Noradrenergic terminal short-term potentiation enables modality-selective integration of sensory input and vigilance state

Recent years have seen compelling demonstrations of the importance of behavioral state on sensory processing and attention. Arousal plays a dominant role in controlling brain-wide neural activity patterns, particularly through modulation by norepinephrine. Noradrenergic brainstem nuclei, including locus coeruleus, can be activated by stimuli of multiple sensory modalities and broadcast modulatory signals via axonal projections throughout the brain. This organization might suggest proportional brain-wide norepinephrine release during states of heightened vigilance. Here, however, we have found that low-intensity, nonarousing visual stimuli enhanced vigilance-dependent noradrenergic signaling locally in visual cortex, revealed using dual-site fiber photometry to monitor noradrenergic Ca²⁺ responses of astroglia simultaneously in cerebellum and visual cortex and two-photon microscopy to monitor noradrenergic axonal terminal Ca²⁺ dynamics. Nitric oxide, following N-methyl-d-aspartate receptor activation in neuronal nitric oxide synthase-positive interneurons, mediated transient acceleration of norepinephrine-dependent astroglia Ca²⁺ activation. These findings reveal a candidate cortical microcircuit for sensory modality-selective modulation of attention.

Contribution of animal models toward understanding resting state functional connectivity

Functional connectivity, which reflects the spatial and temporal organization of intrinsic activity throughout the brain, is one of the most studied measures in human neuroimaging research. The noninvasive acquisition of resting state functional magnetic resonance imaging (rs-fMRI) allows the characterization of features designated as functional networks, functional connectivity gradients, and time-varying activity patterns that provide insight into the intrinsic functional organization of the brain and potential alterations related to brain dysfunction. Functional connectivity, hence, captures dimensions of the brain's activity that have enormous potential for both clinical and preclinical research. However, the mechanisms underlying functional connectivity have yet to be fully characterized, hindering interpretation of rs-fMRI studies. As in other branches of neuroscience, the identification of the neurophysiological processes that contribute to functional connectivity largely depends on research conducted on laboratory animals, which provide a platform where specific, multi-dimensional investigations that involve invasive measurements can be carried out. These highly controlled experiments facilitate the interpretation of the temporal correlations observed across the brain. Indeed, information obtained from animal experimentation to date is the basis for our current understanding of the underlying basis for functional brain connectivity. This review presents a compendium of some of the most critical advances in the field based on the efforts made by the animal neuroimaging community.

Influence of the anatomical features of different brain regions on the spatial localization of fiber photometry signals

Fiber photometry is widely used in neuroscience labs for in vivo detection of functional fluorescence from optical indicators of neuronal activity with a simple optical fiber. The fiber is commonly placed next to the region of interest to both excite and collect the fluorescence signal. However, the path of both excitation and fluorescence photons is altered by the uneven optical properties of the brain, due to local variation of the refractive index, different cellular types, densities and shapes. Nonetheless, the effect of the local anatomy on the actual shape and extent of the volume of tissue that interfaces with the fiber has received little attention so far. To fill this gap, we measured the size and shape of fiber photometry efficiency field in the primary motor and somatosensory cortex, in the hippocampus and in the striatum of the mouse brain, highlighting how their substructures determine the detected signal and the depth at which photons can be mined. Importantly, we show that the information on the spatial expression of the fluorescent probes alone is not sufficient to account for the contribution of local subregions to the overall collected signal, and it must be combined with the optical properties of the tissue adjacent to the fiber tip.

Population calcium responses of Purkinje cells in the oculomotor cerebellum driven by non-visual input

The climbing fiber input to the cerebellum conveys instructive signals that can induce synaptic plasticity and learning by triggering complex spikes accompanied by large calcium transients in Purkinje cells. In the cerebellar flocculus, which supports oculomotor learning, complex spikes are driven by image motion on the retina, which could indicate an oculomotor error. In the same neurons, complex spikes also can be driven by non-visual signals. It has been shown that the calcium transients accompanying each complex spike can vary in amplitude, even within a given cell, therefore, we compared the calcium responses associated with the visual and non-visual inputs to floccular Purkinje cells. The calcium indicator GCaMP6f was selectively expressed in Purkinje cells, and fiber photometry was used to record the calcium responses from a population of Purkinje cells in the flocculus of awake behaving mice. During visual (optokinetic) stimuli and pairing of vestibular and visual stimuli, the calcium level increased during contraversive retinal image motion. During performance of the vestibulo-ocular reflex in the dark, calcium increased during contraversive head rotation and the associated ipsiverse eye movements. The amplitude of this non-visual calcium response was comparable to that during conditions with retinal image motion present that induce oculomotor learning. Thus, population calcium responses of Purkinje cells in the cerebellar flocculus to visual and non-visual input are similar to what has been reported previously for complex spikes, suggesting that multimodal instructive signals control the synaptic plasticity supporting oculomotor learning.

Eavesdropping wires: Recording activity in axons using genetically encoded calcium indicators

Neurons broadcast electrical signals to distal brain regions through extensive axonal arbors. Genetically encoded calcium sensors permit the direct observation of action potential activity at axonal terminals, providing unique insights on the organization and function of neural projections. Here, we consider what information can be gleaned from axonal recordings made at scales ranging from the summed activity extracted from multi-cell axon projections to single boutons. In particular, we discuss the application of different recently developed multi photon and fiber photometry methods for recording neural activity in axons of rodents. We define experimental difficulties associated with imaging approaches in the axonal compartment and highlight the latest methodological advances for addressing these issues. Finally, we reflect on ways in which new technologies can be used in conjunction with axon calcium imaging to address current questions in neurobiology.

Triboelectric Nanogenerators for Therapeutic Electrical Stimulation

Current solutions developed for the purpose of in and on body (IOB) electrical stimulation (ES) lack autonomous qualities necessary for comfortable, practical, and self-dependent use. Consequently, recent focus has been placed on developing self-powered IOB therapeutic devices capable of generating therapeutic ES for human use. With the recent invention of the triboelectric nanogenerator (TENG), harnessing passive human biomechanical energy to develop self-powered systems has allowed for the introduction of novel therapeutic ES solutions. TENGs are especially effective at providing ES for IOB therapeutic systems given their bioconformability, low cost, simple manufacturability, and self-powering capabilities. Due to the key role of naturally induced electrical signals in many physiological functions, TENG-induced ES holds promise to provide a novel paradigm in therapeutic interventions. The aim here is to detail research on IOB TENG devices applied for ES-based therapy in the fields of regenerative medicine, neurology, rehabilitation, and pharmaceutical engineering. Furthermore, considering TENG-produced ES can be measured for sensing applications, this technology is paving the way to provide a fully autonomous personalized healthcare system, capable of IOB energy generation, sensing, and therapeutic intervention. Considering these grounds, it seems highly relevant to review TENG-ES research and applications, as they could constitute the foundation and future of personalized healthcare.

A Signaled Locomotor Avoidance Action Is Fully Represented in the Neural Activity of the Midbrain Tegmentum

Animals, including humans, readily learn to avoid harmful and threatening situations by moving in response to cues that predict the threat (e.g., fire alarm, traffic light). During a negatively reinforced sensory-guided locomotor action, known as signaled active avoidance, animals learn to avoid a harmful unconditioned stimulus (US) by moving away when signaled by a harmless conditioned stimulus (CS) that predicts the threat. CaMKII-expressing neurons in the pedunculopontine tegmentum area (PPT) of the midbrain locomotor region have been shown to play a critical role in the expression of this learned behavior, but the activity of these neurons during learned behavior is unknown. Using calcium imaging fiber photometry in freely behaving mice, we show that PPT neurons sharply activate during presentation of the auditory CS that predicts the threat before onset of avoidance movement. PPT neurons activate further during the succeeding CS-driven avoidance movement, or during the faster US-driven escape movement. PPT neuron activation was weak during slow spontaneous movements but correlated sharply with movement speed and, therefore, with the urgency of the behavior. Moreover, using optogenetics, we found that these neurons must discharge during the signaled avoidance interval for naive mice to effectively learn the active avoidance behavior. As an essential hub for signaled active avoidance, neurons in the midbrain tegmentum process the conditioned cue that predicts the threat and discharge sharply relative to the speed or apparent urgency of the avoidance (learned) and escape (innate) responses.SIGNIFICANCE STATEMENT During signaled active avoidance behavior, subjects move away to avoid a threat when directed by an innocuous sensory stimulus. Using imaging methods in freely behaving mice, we found that the activity of neurons in a part of the midbrain, known as the pedunculopontime tegmentum, increases during the presentation of the innocuous sensory stimulus that predicts the threat and also during the expression of the learned behavior as mice move away to avoid the threat. In addition, inhibiting these neurons abolishes the ability of mice to learn the behavior. Thus, neurons in this part of the midbrain code and are essential for signaled active avoidance behavior.

Multimode Optical Fibers for Optical Neural Interfaces

Although multiphoton microscopy enables optical control and monitoring of neural activity with single cells resolution over a depth of several hundreds of micrometers, the scattering nature of the brain tissue requires implantable optical neural interfaces to access subcortical structures. If micro light-emitting devices (μLEDs) and solid-state waveguides represent important technological advancements for the field, multimodal optical fibers (MMFs) are still the most diffused tool in neuroscience labs to interface with deep regions of the brain. At a first glance, MMFs can be seen as very limited systems. However, new studies and discoveries in optics, photonics, and technological solutions for their application to neuroscience research have enabled applications of MMF where competing technologies fail. In this framework, the chapter starts with a description of optical neural interfaces based on MMF, with specific reference on recent works analyzing the performances of this approach to deliver and collect light from scattering tissue. The discussion then focuses on how peculiar features of MMFs can be exploited to obtain unconventional applications, including brain imaging through a single multimode fiber, multifunctional neural interfaces, and depth-resolved light delivery and functional fluorescence collection.

pMAT: An open-source software suite for the analysis of fiber photometry data

The combined development of new technologies for neuronal recordings and the development of novel sensors for recording both cellular activity and neurotransmitter binding has ushered in a new era for the field of neuroscience. Among these new technologies is fiber photometry, a technique wherein an implanted fiber optic is used to record signals from genetically encoded fluorescent sensors in bulk tissue. Fiber photometry has been widely adapted due to its cost-effectiveness, ability to examine the activity of neurons with specific anatomical or genetic identities, and the ability to use these highly modular systems to record from one or more sensors or brain sites in both superficial and deep-brain structures. Despite these many benefits, one major hurdle for laboratories adopting this technique is the steep learning curve associated with the analysis of fiber photometry data. This has been further complicated by a lack of standardization in analysis pipelines. In the present communication, we present pMAT, a 'photometry modular analysis tool' that allows users to accomplish common analysis routines through the use of a graphical user interface. This tool can be deployed in MATLAB and edited by more advanced users, but is also available as an independently deployable, open-source application.

Comparative study of autofluorescence in flat and tapered optical fibers towards application in depth-resolved fluorescence lifetime photometry in brain tissue

As the scientific community seeks efficient optical neural interfaces with sub-cortical structures of the mouse brain, a wide set of technologies and methods is being developed to monitor cellular events through fluorescence signals generated by genetically encoded molecules. Among these technologies, tapered optical fibers (TFs) take advantage of the modal properties of narrowing waveguides to enable both depth-resolved and wide-volume light collection from scattering tissue, with minimized invasiveness with respect to standard flat fiber stubs (FFs). However, light guided in patch cords as well as in FFs and TFs can result in autofluorescence (AF) signal, which can act as a source of time-variable noise and limit their application to probe fluorescence lifetime in vivo. In this work, we compare the AF signal of FFs and TFs, highlighting the influence of the cladding composition on AF generation. We show that the autofluorescence signal generated in TFs has a peculiar coupling pattern with guided modes, and that far-field detection can be exploited to separate functional fluorescence from AF. On these bases, we provide evidence that TFs can be employed to implement depth-resolved fluorescence lifetime photometry, potentially enabling the extraction of a new set of information from deep brain regions, as time-correlating single photon counting starts to be applied in freely-moving animals to monitor the intracellular biochemical state of neurons.

Evolution of in vivo dopamine monitoring techniques

The brain dopamine system is central to numerous behavioral processes, including movement, learning, and motivation. Accordingly, disruptions of this neural system underlie numerous neurological and psychiatric disorders. Current understanding of how dopamine neurotransmission contributes to behavior and its dysfunction has been driven by technological advancements that permit spatiotemporally-defined measurements of dopaminergic signaling in behaving animals. In this review, we will discuss the evolution of in vivo neural monitoring technologies for measuring dopamine neuron function. We focus on the dopamine system for two reasons: (1) the central role of dopamine neurotransmission in normal behavior and disease, and (2) dopamine neuron measurements have long been at the forefront of in vivo neural monitoring technologies. We will provide a brief overview of standard techniques for monitoring dopamine function, including electrophysiology, microdialysis, and voltammetry. Then, we will discuss recent advancements in optical technologies using genetically-encoded fluorescent proteins (GEFPs), including a critical evaluation of their advantages and limitations.

Basal Forebrain Cholinergic Activity Modulates Isoflurane and Propofol Anesthesia

Cholinergic neurons in the basal forebrain (BF) have long been considered to be the key neurons in the regulation of cortical and behavioral arousal, and cholinergic activation in the downstream region of the BF can arouse anesthetized rats. However, whether the activation of BF cholinergic neurons can induce behavior and electroencephalogram (EEG) recovery from anesthesia is unclear. In this study, based on a transgenic mouse line expressing ChAT-IRES-Cre, we applied a fiber photometry system combined with GCaMPs expression in the BF and found that both isoflurane and propofol inhibit the activity of BF cholinergic neurons, which is closely related to the consciousness transition. We further revealed that genetic lesion of BF cholinergic neurons was associated with a markedly increased potency of anesthetics, while designer receptor exclusively activated by designer drugs (DREADD)-activated BF cholinergic neurons was responsible for slower induction and faster recovery of anesthesia. We also documented a significant increase in δ power bands (1-4 Hz) and a decrease in β (12-25 Hz) power bands in BF cholinergic lesioned mice, while there was a clearly noticeable decline in EEG δ power of activated BF cholinergic neurons. Moreover, sensitivity to anesthetics was reduced after optical stimulation of BF cholinergic cells, yet it failed to restore wake-like behavior in constantly anesthetized mice. Our results indicate a functional role of BF cholinergic neurons in the regulation of general anesthesia. Inhibition of BF cholinergic neurons mediates the formation of unconsciousness induced by general anesthetics, and their activation promotes recovery from the anesthesia state.

nNOS-expressing interneurons control basal and behaviorally evoked arterial dilation in somatosensory cortex of mice

Cortical neural activity is coupled to local arterial diameter and blood flow. However, which neurons control the dynamics of cerebral arteries is not well understood. We dissected the cellular mechanisms controlling the basal diameter and evoked dilation in cortical arteries in awake, head-fixed mice. Locomotion drove robust arterial dilation, increases in gamma band power in the local field potential (LFP), and increases calcium signals in pyramidal and neuronal nitric oxide synthase (nNOS)-expressing neurons. Chemogenetic or pharmocological modulation of overall neural activity up or down caused corresponding increases or decreases in basal arterial diameter. Modulation of pyramidal neuron activity alone had little effect on basal or evoked arterial dilation, despite pronounced changes in the LFP. Modulation of the activity of nNOS-expressing neurons drove changes in the basal and evoked arterial diameter without corresponding changes in population neural activity.

Two-photon fluorescence-assisted laser ablation of non-planar metal surfaces: fabrication of optical apertures on tapered fibers for optical neural interfaces

We propose a feedback-assisted direct laser writing method to perform laser ablation of fiber optic devices in which their light-collection signal is used to optimize their properties. A femtosecond-pulsed laser beam is used to ablate a metal coating deposited around a tapered optical fiber, employed to show the suitability of the approach to pattern devices with a small radius of curvature. During processing, the same pulses generate two-photon fluorescence in the surrounding environment and the signal is monitored to identify different patterning regimes over time through spectral analysis. The employed fs beam mostly interacts with the metal coating, leaving almost intact the underlying silica and enabling fluorescence to couple with a specific subset of guided modes, as verified by far-field analysis. Although the method is described here for tapered optical fibers used to obtain efficient light collection in the field of optical neural interfaces, it can be easily extended to other waveguide-based devices and represents a general approach to support the implementation of a closed-loop laser ablation system of fiber optics.

Ray tracing models for estimating light collection properties of microstructured tapered optical fibers for optical neural interfaces

Tapered optical fibers (TFs) were recently employed for depth-resolved monitoring of functional fluorescence in subcortical brain structures, enabling light collection from groups of a few cells through small optical windows located on the taper edge [Pisano et al., Nat. Methods16, 1185 (2019)1548-709110.1038/s41592-019-0581-x]. Here we present a numerical model to estimate light collection properties of microstructured TFs implanted in scattering brain tissue. Ray tracing coupled with the Henyey-Greenstein scattering model enables the estimation of both light collection and fluorescence excitation fields in three dimensions, whose combination is employed to retrieve the volume of tissue probed by the device.

Simultaneous Electrophysiology and Fiber Photometry in Freely Behaving Mice

In vivo electrophysiology is the gold standard technique used to investigate sub-second neural dynamics in freely behaving animals. However, monitoring cell-type-specific population activity is not a trivial task. Over the last decade, fiber photometry based on genetically encoded calcium indicators (GECIs) has been widely adopted as a versatile tool to monitor cell-type-specific population activity in vivo. However, this approach suffers from low temporal resolution. Here, we combine these two approaches to monitor both sub-second field potentials and cell-type-specific population activity in freely behaving mice. By developing an economical custom-made system and constructing a hybrid implant of an electrode and a fiber optic cannula, we simultaneously monitor artifact-free mesopontine field potentials and calcium transients in cholinergic neurons across the sleep-wake cycle. We find that mesopontine cholinergic activity co-occurs with sub-second pontine waves, called P-waves, during rapid eye movement sleep. Given the simplicity of our approach, simultaneous electrophysiological recording and cell-type-specific imaging provides a novel and valuable tool for interrogating state-dependent neural circuit dynamics in vivo.

Cue-Evoked Dopamine Promotes Conditioned Responding during Learning

Dopamine neurons mediate the association of conditioned stimuli (CS) with reward (unconditioned stimuli, US) by signaling the discrepancy between predicted and actual reward during the US. Some theoretical models suggest that learning is also influenced by the salience or associability of the CS. A hallmark of CS associability models is that they can explain latent inhibition, i.e., the observation that novel CS are more effectively learned than familiar CS. Novel CS are known to activate dopamine neurons, but whether those responses affect associative learning has not been investigated. Here, we used fiber photometry to characterize dopamine responses to inconsequential familiar and novel stimuli. Using bidirectional optogenetic modulation during conditioning, we then show that CS-evoked dopamine promotes conditioned responses. This suggests that Pavlovian conditioning is influenced by CS dopamine, in addition to US reward prediction errors. Accordingly, the absence of dopamine responses to familiar CS might explain their slower learning in latent inhibition.

Depth-resolved fiber photometry with a single tapered optical fiber implant

Fiber photometry is increasingly utilized to monitor fluorescent sensors of neural activity in the brain. However, most implementations are based on flat-cleaved optical fibers that can only interface with shallow tissue volumes adjacent to the fiber. We exploit modal properties of tapered optical fibers (TFs) to enable light collection over an extent of up to 2 mm of tissue and multisite photometry along the taper. Using a single TF, we simultaneously observed distinct dopamine transients in dorsal and ventral striatum in freely moving mice performing a simple, operant conditioning task. Collection volumes from TFs can also be engineered in both shape and size by microstructuring the nonplanar surface of the taper, to optically target multiple sites not only in the deep brain but, in general, in any biological system or organ in which light collection is beneficial but challenging because of light scattering and absorption.

Single-cell micro- and nano-photonic technologies

Since the advent of optogenetics, the technology development has focused on new methods to optically interact with single nerve cells. This gave rise to the field of photonic neural interfaces, intended as the set of technologies that can modify light radiation in either a linear or non-linear fashion to control and/or monitor cellular functions. This set includes the use of plasmonic effects, up-conversion, electron transfer and integrated light steering, with some of them already implemented in vivo. This article will review available approaches in this framework, with a particular emphasis on methods operating at the single-unit level or having the potential to reach single-cell resolution.