In vivo widefield calcium imaging of the mouse cortex for analysis of network connectivity in health and brain disease

Attention-based CNN-BiLSTM for sleep state classification of spatiotemporal wide-field calcium imaging data

BACKGROUND

Wide-field calcium imaging (WFCI) with genetically encoded calcium indicators allows for spatiotemporal recordings of neuronal activity in mice. When applied to the study of sleep, WFCI data are manually scored into the sleep states of wakefulness, non-REM (NREM) and REM by use of adjunct EEG and EMG recordings. However, this process is time-consuming, invasive and often suffers from low inter- and intra-rater reliability. Therefore, an automated sleep state classification method that operates on spatiotemporal WFCI data is desired.

NEW METHOD

A hybrid network architecture consisting of a convolutional neural network (CNN) to extract spatial features of image frames and a bidirectional long short-term memory network (BiLSTM) with attention mechanism to identify temporal dependencies among different time points was proposed to classify WFCI data into states of wakefulness, NREM and REM sleep.

RESULTS

Sleep states were classified with an accuracy of 84 % and Cohen's κ of 0.64. Gradient-weighted class activation maps revealed that the frontal region of the cortex carries more importance when classifying WFCI data into NREM sleep while posterior area contributes most to the identification of wakefulness. The attention scores indicated that the proposed network focuses on short- and long-range temporal dependency in a state-specific manner.

COMPARISON WITH EXISTING METHOD

On a held out, repeated 3-hour WFCI recording, the CNN-BiLSTM achieved a κ of 0.67, comparable to a κ of 0.65 corresponding to the human EEG/EMG-based scoring.

CONCLUSIONS

The CNN-BiLSTM effectively classifies sleep states from spatiotemporal WFCI data and will enable broader application of WFCI in sleep research.

Imaging the large-scale and cellular response to focal traumatic brain injury in mouse neocortex

Traumatic brain injury (TBI) affects neural function at the local injury site and also at distant, connected brain areas. However, the real-time neural dynamics in response to injury and subsequent effects on sensory processing and behavior are not fully resolved, especially across a range of spatial scales. We used in vivo calcium imaging in awake, head-restrained male and female mice to measure large-scale and cellular resolution neuronal activation, respectively, in response to a mild/moderate TBI induced by focal controlled cortical impact (CCI) injury of the motor cortex (M1). Widefield imaging revealed an immediate CCI-induced activation at the injury site, followed by a massive slow wave of calcium signal activation that traveled across the majority of the dorsal cortex within approximately 30 s. Correspondingly, two-photon calcium imaging in primary somatosensory cortex (S1) found strong activation of neuropil and neuronal populations during the CCI-induced traveling wave. A depression of calcium signals followed the wave, during which we observed atypical activity of a sparse population of S1 neurons. Longitudinal imaging in the hours and days after CCI revealed increases in the area of whisker-evoked sensory maps at early time points, in parallel to decreases in cortical functional connectivity and behavioral measures. Neural and behavioral changes mostly recovered over hours to days in our M1-TBI model, with a more lasting decrease in the number of active S1 neurons. Our results in unanesthetized mice describe novel spatial and temporal neural adaptations that occur at cortical sites remote to a focal brain injury.

Updated Toolbox for Assessing Neuronal Network Reconstruction after Cell Therapy

Cell therapy has proven to be a promising treatment for a range of neurological disorders, including Parkinson Disease, drug-resistant epilepsy, and stroke, by restoring function after brain damage. Nevertheless, evaluating the true effectiveness of these therapeutic interventions requires a deep understanding of the functional integration of grafted cells into existing neural networks. This review explores a powerful arsenal of molecular techniques revolutionizing our ability to unveil functional integration of grafted cells within the host brain. From precise manipulation of neuronal activity to pinpoint the functional contribution of transplanted cells by using opto- and chemo-genetics, to real-time monitoring of neuronal dynamics shedding light on functional connectivity within the reconstructed circuits by using genetically encoded (calcium) indicators in vivo. Finally, structural reconstruction and mapping communication pathways between grafted and host neurons can be achieved by monosynaptic tracing with viral vectors. The cutting-edge toolbox presented here holds immense promise for elucidating the impact of cell therapy on neural circuitry and guiding the development of more effective treatments for neurological disorders.

Real-time monitoring of cortical brain activity in response to acute pain using wide-area Ca2+ imaging

Previous human and rodent studies indicated that nociceptive stimuli activate many brain regions that is involved in the somatosensory and emotional sensation. Although these studies have identified several important brain regions involved in pain perception, it has been a challenge to observe neural activity directly and simultaneously in these multiple brain regions during pain perception. Using a transgenic mouse expressing G-CaMP7 in majority of astrocytes and a subpopulation of excitatory neurons, we recorded the brain activity in the mouse cerebral cortex during acute pain stimulation. Both of hind paw pinch and intraplantar administration of formalin caused strong transient increase of the fluorescence in several cortical regions, including primary somatosensory, motor and retrosplenial cortex. This increase of the fluorescence intensity was attenuated by the pretreatment with morphine. The present study provides important insight into the cortico-cortical network during pain perception.

A Siamese Convolutional Neural Network for Identifying Mild Traumatic Brain Injury and Predicting Recovery

Timely diagnosis of mild traumatic brain injury (mTBI) remains challenging due to the rapid recovery of acute symptoms and the absence of evidence of injury in static neuroimaging scans. Furthermore, while longitudinal tracking of mTBI is essential in understanding how the diseases progresses/regresses over time for enhancing personalized patient care, a standardized approach for this purpose is not yet available. Recent functional neuroimaging studies have provided evidence of brain function alterations following mTBI, suggesting mTBI-detection models can be built based on these changes. Most of these models, however, rely on manual feature engineering, but the optimal set of features for detecting mTBI may be unknown. Data-driven approaches, on the other hand, may uncover hidden relationships in an automated manner, making them suitable for the problem of mTBI detection. This paper presents a data-driven framework based on Siamese Convolutional Neural Network (SCNN) to detect mTBI and to monitor the recovery state from mTBI over time. The proposed framework is tested on the cortical images of Thy1-GCaMP6s mice, obtained via widefield calcium imaging, acquired in a longitudinal study. Results show that the proposed model achieves a classification accuracy of 96.5%. To track the state of the injured brain over time, a reference distance map is constructed, which together with the SCNN model, are employed to assess the recovery state in subsequent sessions after injury, revealing that the recovery progress varies among subjects. The promising results of this work suggest that a similar approach could be potentially applicable for monitoring recovery from mTBI, in humans.

Aberrant cortical activity, functional connectivity, and neural assembly architecture after photothrombotic stroke in mice

Despite substantial progress in mapping the trajectory of network plasticity resulting from focal ischemic stroke, the extent and nature of changes in neuronal excitability and activity within the peri-infarct cortex of mice remains poorly defined. Most of the available data have been acquired from anesthetized animals, acute tissue slices, or infer changes in excitability from immunoassays on extracted tissue, and thus may not reflect cortical activity dynamics in the intact cortex of an awake animal. Here, in vivo two-photon calcium imaging in awake, behaving mice was used to longitudinally track cortical activity, network functional connectivity, and neural assembly architecture for 2 months following photothrombotic stroke targeting the forelimb somatosensory cortex. Sensorimotor recovery was tracked over the weeks following stroke, allowing us to relate network changes to behavior. Our data revealed spatially restricted but long-lasting alterations in somatosensory neural network function and connectivity. Specifically, we demonstrate significant and long-lasting disruptions in neural assembly architecture concurrent with a deficit in functional connectivity between individual neurons. Reductions in neuronal spiking in peri-infarct cortex were transient but predictive of impairment in skilled locomotion measured in the tapered beam task. Notably, altered neural networks were highly localized, with assembly architecture and neural connectivity relatively unaltered a short distance from the peri-infarct cortex, even in regions within 'remapped' forelimb functional representations identified using mesoscale imaging with anaesthetized preparations 8 weeks after stroke. Thus, using longitudinal two-photon microscopy in awake animals, these data show a complex spatiotemporal relationship between peri-infarct neuronal network function and behavioral recovery. Moreover, the data highlight an apparent disconnect between dramatic functional remapping identified using strong sensory stimulation in anaesthetized mice compared to more subtle and spatially restricted changes in individual neuron and local network function in awake mice during stroke recovery.

Low-cost reversible tandem lens mesoscope for brain imaging in rodents

Significance

The development of imaging systems that are cost-efficient and modular is essential for modern neuroscience research.

Aim

In the current study, we designed, developed, and characterized a low-cost reversible tandem lens mesoscope for brain imaging in rodents.

Approach

Using readily available components, we assembled a robust imaging system that is highly efficient and cost-effective. We developed a mesoscope that offers high-resolution structural and functional imaging with cost-effective lenses and CMOS camera.

Results

The reversible tandem lens configuration of the mesoscope offers two fields of view (FOVs), which can be achieved by swapping the objective and imaging lenses. The large FOV configuration of 12.6 × 10.5    mm provides a spatial resolution up to 4.92    μ m , and the small FOV configuration of 6 × 5    mm provides a resolution of up to 2.46    μ m . We demonstrate the efficiency of our system for imaging neuronal calcium activity in both rat and mouse brains in vivo.

Conclusions

The careful selection of the mesoscope components ensured its compactness, portability, and versatility, meaning that different types of samples and sample holders can be easily accommodated, enabling a range of different experiments both in vivo and in vitro. The custom-built reversible FOV mesoscope is cost-effective and was developed for under US$10,000 with excellent performance.

Rethinking Remapping: Circuit Mechanisms of Recovery after Stroke

Stroke is one of the most common causes of disability, and there are few treatments that can improve recovery after stroke. Therapeutic development has been hindered because of a lack of understanding of precisely how neural circuits are affected by stroke, and how these circuits change to mediate recovery. Indeed, some of the hypotheses for how the CNS changes to mediate recovery, including remapping, redundancy, and diaschisis, date to more than a century ago. Recent technological advances have enabled the interrogation of neural circuits with ever greater temporal and spatial resolution. These techniques are increasingly being applied across animal models of stroke and to human stroke survivors, and are shedding light on the molecular, structural, and functional changes that neural circuits undergo after stroke. Here we review these studies and highlight important mechanisms that underlie impairment and recovery after stroke. We begin by summarizing knowledge about changes in neural activity that occur in the peri-infarct cortex, specifically considering evidence for the functional remapping hypothesis of recovery. Next, we describe the importance of neural population dynamics, disruptions in these dynamics after stroke, and how allocation of neurons into spared circuits can restore functionality. On a more global scale, we then discuss how effects on long-range pathways, including interhemispheric interactions and corticospinal tract transmission, contribute to post-stroke impairments. Finally, we look forward and consider how a deeper understanding of neural circuit mechanisms of recovery may lead to novel treatments to reduce disability and improve recovery after stroke.

Identifying properties of pattern completion neurons in a computational model of the visual cortex

Neural ensembles are found throughout the brain and are believed to underlie diverse cognitive functions including memory and perception. Methods to activate ensembles precisely, reliably, and quickly are needed to further study the ensembles' role in cognitive processes. Previous work has found that ensembles in layer 2/3 of the visual cortex (V1) exhibited pattern completion properties: ensembles containing tens of neurons were activated by stimulation of just two neurons. However, methods that identify pattern completion neurons are underdeveloped. In this study, we optimized the selection of pattern completion neurons in simulated ensembles. We developed a computational model that replicated the connectivity patterns and electrophysiological properties of layer 2/3 of mouse V1. We identified ensembles of excitatory model neurons using K-means clustering. We then stimulated pairs of neurons in identified ensembles while tracking the activity of the entire ensemble. Our analysis of ensemble activity quantified a neuron pair's power to activate an ensemble using a novel metric called pattern completion capability (PCC) based on the mean pre-stimulation voltage across the ensemble. We found that PCC was directly correlated with multiple graph theory parameters, such as degree and closeness centrality. To improve selection of pattern completion neurons in vivo, we computed a novel latency metric that was correlated with PCC and could potentially be estimated from modern physiological recordings. Lastly, we found that stimulation of five neurons could reliably activate ensembles. These findings can help researchers identify pattern completion neurons to stimulate in vivo during behavioral studies to control ensemble activation.

Virtual reality-based real-time imaging reveals abnormal cortical dynamics during behavioral transitions in a mouse model of autism

Functional connectivity (FC) can provide insight into cortical circuit dysfunction in neuropsychiatric disorders. However, dynamic changes in FC related to locomotion with sensory feedback remain to be elucidated. To investigate FC dynamics in locomoting mice, we develop mesoscopic Ca2+ imaging with a virtual reality (VR) environment. We find rapid reorganization of cortical FC in response to changing behavioral states. By using machine learning classification, behavioral states are accurately decoded. We then use our VR-based imaging system to study cortical FC in a mouse model of autism and find that locomotion states are associated with altered FC dynamics. Furthermore, we identify FC patterns involving the motor area as the most distinguishing features of the autism mice from wild-type mice during behavioral transitions, which might correlate with motor clumsiness in individuals with autism. Our VR-based real-time imaging system provides crucial information to understand FC dynamics linked to behavioral abnormality of neuropsychiatric disorders.

Neurovascular coupling is preserved in chronic stroke recovery after targeted photothrombosis

Functional neuroimaging, which measures hemodynamic responses to brain activity, has great potential for monitoring recovery in stroke patients and guiding rehabilitation during recovery. However, hemodynamic responses after stroke are almost always altered relative to responses in healthy subjects and it is still unclear if these alterations reflect the underlying brain physiology or if the alterations are purely due to vascular injury. In other words, we do not know the effect of stroke on neurovascular coupling and are therefore limited in our ability to use functional neuroimaging to accurately interpret stroke pathophysiology. To address this challenge, we simultaneously captured neural activity, through fluorescence calcium imaging, and hemodynamics, through intrinsic optical signal imaging, during longitudinal stroke recovery. Our data suggest that neurovascular coupling was preserved in the chronic phase of recovery (2 weeks and 4 weeks post-stoke) and resembled pre-stroke neurovascular coupling. This indicates that functional neuroimaging faithfully represents the underlying neural activity in chronic stroke. Further, neurovascular coupling in the sub-acute phase of stroke recovery was predictive of long-term behavioral outcomes. Stroke also resulted in increases in global brain oscillations, which showed distinct patterns between neural activity and hemodynamics. Increased neural excitability in the contralesional hemisphere was associated with increased contralesional intrahemispheric connectivity. Additionally, sub-acute increases in hemodynamic oscillations were associated with improved sensorimotor outcomes. Collectively, these results support the use of hemodynamic measures of brain activity post-stroke for predicting functional and behavioral outcomes.

To be and not to be: wide-field Ca2+ imaging reveals neocortical functional segmentation combines stability and flexibility

The stability and flexibility of the functional parcellation of the cerebral cortex is fundamental to how familiar and novel information is both represented and stored. We leveraged new advances in Ca2+ sensors and microscopy to understand the dynamics of functional segmentation in the dorsal cerebral cortex. We performed wide-field Ca2+ imaging in head-fixed mice and used spatial independent component analysis (ICA) to identify independent spatial sources of Ca2+ fluorescence. The imaging data were evaluated over multiple timescales and discrete behaviors including resting, walking, and grooming. When evaluated over the entire dataset, a set of template independent components (ICs) were identified that were common across behaviors. Template ICs were present across a range of timescales, from days to 30 seconds, although with lower occurrence probability at shorter timescales, highlighting the stability of the functional segmentation. Importantly, unique ICs emerged at the shorter duration timescales that could act to transiently refine the cortical network. When data were evaluated by behavior, both common and behavior-specific ICs emerged. Each behavior is composed of unique combinations of common and behavior-specific ICs. These observations suggest that cerebral cortical functional segmentation exhibits considerable spatial stability over time and behaviors while retaining the flexibility for task-dependent reorganization.

New imaging instrument in animal models: Two-photon miniature microscope and large field of view miniature microscope for freely behaving animals

Over the past decade, novel optical imaging tools have been developed for imaging neuronal activities along with the evolution of fluorescence indicators with brighter expression and higher sensitivity. Miniature microscopes, as revolutionary approaches, enable the imaging of large populations of neuron ensembles in freely behaving rodents and mammals, which allows exploring the neural basis of behaviors. Recent progress in two-photon miniature microscopes and mesoscale single-photon miniature microscopes further expand those affordable methods to navigate neural activities during naturalistic behaviors. In this review article, two-photon miniature microscopy techniques are summarized historically from the first documented attempt to the latest ones, and comparisons are made. The driving force behind and their potential for neuroscientific inquiries are also discussed. Current progress in terms of the mesoscale, i.e., the large field-of-view miniature microscopy technique, is addressed as well. Then, pipelines for registering single cells from the data of two-photon and large field-of-view miniature microscopes are discussed. Finally, we present the potential evolution of the techniques.

The Evolving Role of Animal Models in the Discovery and Development of Novel Treatments for Psychiatric Disorders

Historically, animal models have been routinely used in the characterization of novel chemical entities (NCEs) for various psychiatric disorders. Animal models have been essential in the in vivo validation of novel drug targets, establishment of lead compound pharmacokinetic to pharmacodynamic relationships, optimization of lead compounds through preclinical candidate selection, and development of translational measures of target occupancy and functional target engagement. Yet, with decades of multiple NCE failures in Phase II and III efficacy trials for different psychiatric disorders, the utility and value of animal models in the drug discovery process have come under intense scrutiny along with the widespread withdrawal of the pharmaceutical industry from psychiatric drug discovery. More recently, the development and utilization of animal models for the discovery of psychiatric NCEs has undergone a dynamic evolution with the application of the Research Domain Criteria (RDoC) framework for better design of preclinical to clinical translational studies combined with innovative genetic, neural circuitry-based, and automated testing technologies. In this chapter, the authors will discuss this evolving role of animal models for improving the different stages of the discovery and development in the identification of next generation treatments for psychiatric disorders.

Wide-Field Optical Imaging in Mouse Models of Ischemic Stroke

Functional neuroimaging is a powerful tool for evaluating how local and global brain circuits evolve after focal ischemia and how these changes relate to functional recovery. For example, acutely after stroke, changes in functional brain organization relate to initial deficit and are predictive of recovery potential. During recovery, the reemergence and restoration of connections lost due to stroke correlate with recovery of function. Thus, information gleaned from functional neuroimaging can be used as a proxy for behavior and inform on the efficacy of interventional strategies designed to affect plasticity mechanisms after injury. And because these findings are consistently observed across species, bridge measurements can be made in animal models to enrich findings in human stroke populations. In mice, genetic engineering techniques have provided several new opportunities for extending optical neuroimaging methods to more direct measures of neuronal activity. These developments are especially useful in the context of stroke where neurovascular coupling can be altered, potentially limiting imaging measures based on hemodynamic activity alone. This chapter is designed to give an overview of functional wide-field optical imaging (WFOI) for applications in rodent models of stroke, primarily in the mouse. The goal is to provide a protocol for laboratories that want to incorporate an affordable functional neuroimaging assay into their current research thrusts, but perhaps lack the background knowledge or equipment for developing a new arm of research in their lab. Within, we offer a comprehensive guide developing and applying WFOI technology with the hope of facilitating accessibility of neuroimaging technology to other researchers in the stroke field.

Transcranial cortex-wide Ca2+ imaging for the functional mapping of cortical dynamics

Visualization and tracking of the information flow in the broader brain area are essential because nerve cells make a vast network in the brain. Fluorescence Ca²⁺ imaging is a simultaneous visualization of brain cell activities in a wide area. Instead of classical chemical indicators, developing various types of transgenic animals that express Ca²⁺-sensitive fluorescent proteins enables us to observe brain activities in living animals at a larger scale for a long time. Multiple kinds of literature have reported that transcranial imaging of such transgenic animals is practical for monitoring the wide-field information flow across the broad brain regions, although it has a lower spatial resolution. Notably, this technique is helpful for the initial evaluation of cortical function in disease models. This review will introduce fully intact transcranial macroscopic imaging and cortex-wide Ca²⁺ imaging as practical applications.

REM sleep is associated with distinct global cortical dynamics and controlled by occipital cortex

The cerebral cortex is spontaneously active during sleep, yet it is unclear how this global cortical activity is spatiotemporally organized, and whether such activity not only reflects sleep states but also contributes to sleep state switching. Here we report that cortex-wide calcium imaging in mice revealed distinct sleep stage-dependent spatiotemporal patterns of global cortical activity, and modulation of such patterns could regulate sleep state switching. In particular, elevated activation in the occipital cortical regions (including the retrosplenial cortex and visual areas) became dominant during rapid-eye-movement (REM) sleep. Furthermore, such pontogeniculooccipital (PGO) wave-like activity was associated with transitions to REM sleep, and optogenetic inhibition of occipital activity strongly promoted deep sleep by suppressing the NREM-to-REM transition. Thus, whereas subcortical networks are critical for initiating and maintaining sleep and wakefulness states, distinct global cortical activity also plays an active role in controlling sleep states.

Wide-Field Calcium Imaging of Neuronal Network Dynamics In Vivo

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

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.

Review of data processing of functional optical microscopy for neuroscience

Functional optical imaging in neuroscience is rapidly growing with the development of optical systems and fluorescence indicators. To realize the potential of these massive spatiotemporal datasets for relating neuronal activity to behavior and stimuli and uncovering local circuits in the brain, accurate automated processing is increasingly essential. We cover recent computational developments in the full data processing pipeline of functional optical microscopy for neuroscience data and discuss ongoing and emerging challenges.

Astrocyte calcium dysfunction causes early network hyperactivity in Alzheimer's disease

Dysfunctions of network activity and functional connectivity (FC) represent early events in Alzheimer’s disease (AD), but the underlying mechanisms remain unclear. Astrocytes regulate local neuronal activity in the healthy brain, but their involvement in early network hyperactivity in AD is unknown. We show increased FC in the human cingulate cortex several years before amyloid deposition. We find the same early cingulate FC disruption and neuronal hyperactivity in App^NL-F mice. Crucially, these network disruptions are accompanied by decreased astrocyte calcium signaling. Recovery of astrocytic calcium activity normalizes neuronal hyperactivity and FC, as well as seizure susceptibility and day/night behavioral disruptions. In conclusion, we show that astrocytes mediate initial features of AD and drive clinically relevant phenotypes.

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The cingulate cortex of humans and mice shows early functional deficits in AD

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Astrocyte calcium signaling is decreased before the presence of amyloid plaques

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Recovery of astrocyte calcium signals mitigates neuronal hyperactivity

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Recovery of astrocytes normalizes cingulate connectivity and behavior disruptions

Ca2+-based neural activity recording for rapidly screening behavioral correlates of the claustrum in freely behaving mice

The claustrum has been hypothesized to participate in high-order brain functions, but experimental studies to demonstrate these functions are currently lacking. Neural activity recording of the claustrum in freely-behaving animals allows for correlating claustral activities with specific behaviors. However, previously utilized methods for studying the claustrum make it difficult to monitor neural activity patterns of freely-behaving animals in real time. Here we applied fiber photometry to monitor Ca²⁺ activity in the claustrum of freely-behaving mice. Using this method, we were able to achieve Ca²⁺ activity recording in both anesthetized and freely-behaving mice. We found that the dynamics of Ca²⁺ activity depended on anesthesia levels. As compared to the use of genetically encoded Ca²⁺ indicators that requires a few weeks of virus-dependent expression, we used a synthetic fluorescent Ca²⁺-sensitive dye, Oregon green 488 BAPTA-1, that allows for rapidly screening neural activity of interest within a few hours that relates to certain behaviors. In this way, we found the correlation between Ca²⁺ activity and specific behaviors, such as approaching an object. Our work offers an effective method for recording neural activity in the claustrum and thus for rapidly screening any behavioral relevance of the claustrum in freely-behaving mice.

Homotopic contralesional excitation suppresses spontaneous circuit repair and global network reconnections following ischemic stroke

Understanding circuit-level manipulations that affect the brain's capacity for plasticity will inform the design of targeted interventions that enhance recovery after stroke. Following stroke, increased contralesional activity (e.g. use of the unaffected limb) can negatively influence recovery, but it is unknown which specific neural connections exert this influence, and to what extent increased contralesional activity affects systems- and molecular-level biomarkers of recovery. Here, we combine optogenetic photostimulation with optical intrinsic signal imaging to examine how contralesional excitatory activity affects cortical remodeling after stroke in mice. Following photothrombosis of left primary somatosensory forepaw (S1FP) cortex, mice either recovered spontaneously or received chronic optogenetic excitation of right S1FP over the course of 4 weeks. Contralesional excitation suppressed perilesional S1FP remapping and was associated with abnormal patterns of stimulus-evoked activity in the unaffected limb. This maneuver also prevented the restoration of resting-state functional connectivity (RSFC) within the S1FP network, RSFC in several networks functionally distinct from somatomotor regions, and resulted in persistent limb-use asymmetry. In stimulated mice, perilesional tissue exhibited transcriptional changes in several genes relevant for recovery. Our results suggest that contralesional excitation impedes local and global circuit reconnection through suppression of cortical activity and several neuroplasticity-related genes after stroke, and highlight the importance of site selection for targeted therapeutic interventions after focal ischemia.

Altered dorsal functional connectivity after post-weaning social isolation and resocialization in mice

BACKGROUND

Social isolation (SI) leads to various mental health disorders. Despite abundant studies on behavioral and neurobiological changes induced by post-weaning SI, the characterization of its imaging correlates, such as resting-state functional connectivity (RSFC), is critically lacking. In addition, the effects of resocialization after isolation remain unclear. Therefore, this study aimed to explore the effects of 1) SI on cortical functional connectivity and 2) subsequent resocialization on behavior and functional connectivity.

METHODS

Behavioral tests were conducted to validate the post-weaning SI mouse model, which is isolated during the juvenile period. Wide-field optical mapping was performed to observe both neuronal and hemodynamic signals in the cortex under anesthesia. Using seed-based and graph theoretical analyses, RSFC was analyzed. SI mice were then resocialized and the array of behavior and imaging tests was conducted.

RESULTS

Behaviorally, SI mice showed elevated anxiety, social preference, and aggression. RSFC analyses using the seed-based approach revealed decreased cortical functional connectivity in SI mice, especially in the frontal region. Graph network analyses demonstrated significant reduction in network segregation measures. After resocialization, mice exhibited recovered anxiogenic and aggressive behavior, but RSFC data did not show significant changes.

CONCLUSIONS

We observed an overall decrease in functional connectivity in SI mice. Moreover, resocialization restored the disruptions in behavioral patterns but functional connectivity was not recovered. To our knowledge, this is the first study to report that, despite the recovering tendencies of behavior in resocialized mice, similar changes in RSFC were not observed. This suggests that disruptions in functional connectivity caused by social isolation remain as long-term sequelae.

High-resolution fluorescence-guided transcranial ultrasound mapping in the live mouse brain

Understanding the physiological impact of transcranial ultrasound in rodent brains may offer an important preclinical model for human scale magnetic resonance–guided focused ultrasound methods. However, precision tools for high-resolution transcranial ultrasound targeting and real-time in vivo tracking of its effects at the mouse brain scale are currently lacking. We report a versatile bidirectional hybrid fluorescence-ultrasound (FLUS) system incorporating a 0.35-mm precision spherical-phased array ultrasound emission with a fiberscope-based wide-field fluorescence imaging. We show how the marriage between cortex-wide functional imaging and targeted ultrasound delivery can be used to transcranially map previously undocumented localized fluorescence events caused by reversible thermal processes and perform high-speed large-scale recording of neural activity induced by focused ultrasound. FLUS thus naturally harnesses the extensive toolbox of fluorescent tags and ultrasound’s localized bioeffects toward visualizing and causally perturbing a plethora of normal and pathophysiological processes in the living murine brain.

Disrupted population coding in the prefrontal cortex underlies pain aversion

The prefrontal cortex (PFC) regulates a wide range of sensory experiences. Chronic pain is known to impair normal neural response, leading to enhanced aversion. However, it remains unknown how nociceptive responses in the cortex are processed at the population level and whether such processes are disrupted by chronic pain. Using in vivo endoscopic calcium imaging, we identify increased population activity in response to noxious stimuli and stable patterns of functional connectivity among neurons in the prelimbic (PL) PFC from freely behaving rats. Inflammatory pain disrupts functional connectivity of PFC neurons and reduces the overall nociceptive response. Interestingly, ketamine, a well-known neuromodulator, restores the functional connectivity among PL-PFC neurons in the inflammatory pain model to produce anti-aversive effects. These results suggest a dynamic resource allocation mechanism in the prefrontal representations of pain and indicate that population activity in the PFC critically regulates pain and serves as an important therapeutic target.

Li et al. reveal that inflammatory pain disrupts the functional connectivity of neurons in the prelimbic prefrontal cortex (PL-PFC) and the overall nociceptive response. Ketamine, meanwhile, restores the functional connectivity of neurons in the PL-PFC in the inflammatory pain state to produce anti-aversive effects.

The gut microbiota modulates brain network connectivity under physiological conditions and after acute brain ischemia

The gut microbiome has been implicated as a key regulator of brain function in health and disease. But the impact of gut microbiota on functional brain connectivity is unknown. We used resting-state functional magnetic resonance imaging in germ-free and normally colonized mice under naive conditions and after ischemic stroke. We observed a strong, brain-wide increase of functional connectivity in germ-free animals. Graph theoretical analysis revealed significant higher values in germ-free animals, indicating a stronger and denser global network but with less structural organization. Breakdown of network function after stroke equally affected germ-free and colonized mice. Results from histological analyses showed changes in dendritic spine densities, as well as an immature microglial phenotype, indicating impaired microglia-neuron interaction in germ-free mice as potential cause of this phenomenon. These results demonstrate the substantial impact of bacterial colonization on brain-wide function and extend our so far mainly (sub) cellular understanding of the gut-brain axis.

Chronic T cell proliferation in brains after stroke could interfere with the efficacy of immunotherapies

Neuroinflammation is an emerging focus of translational stroke research. Preclinical studies have demonstrated a critical role for brain-invading lymphocytes in post-stroke pathophysiology. Reducing cerebral lymphocyte invasion by anti-CD49d antibodies consistently improves outcome in the acute phase after experimental stroke models. However, clinical trials testing this approach failed to show efficacy in stroke patients for the chronic outcome 3 mo after stroke. Here, we identify a potential mechanistic reason for this phenomenon by detecting chronic T cell accumulation-evading the systemic therapy-in the post-ischemic brain. We observed a persistent accumulation of T cells in mice and human autopsy samples for more than 1 mo after stroke. Cerebral T cell accumulation in the post-ischemic brain was driven by increased local T cell proliferation rather than by T cell invasion. This observation urges re-evaluation of current immunotherapeutic approaches, which target circulating lymphocytes for promoting recovery after stroke.

Go with the FLOW: visualizing spatiotemporal dynamics in optical widefield calcium imaging

Widefield calcium imaging has recently emerged as a powerful experimental technique to record coordinated large-scale brain activity. These measurements present a unique opportunity to characterize spatiotemporally coherent structures that underlie neural activity across many regions of the brain. In this work, we leverage analytic techniques from fluid dynamics to develop a visualization framework that highlights features of flow across the cortex, mapping wavefronts that may be correlated with behavioural events. First, we transform the time series of widefield calcium images into time-varying vector fields using optic flow. Next, we extract concise diagrams summarizing the dynamics, which we refer to as FLOW (flow lines in optical widefield imaging) portraits. These FLOW portraits provide an intuitive map of dynamic calcium activity, including regions of initiation and termination, as well as the direction and extent of activity spread. To extract these structures, we use the finite-time Lyapunov exponent technique developed to analyse time-varying manifolds in unsteady fluids. Importantly, our approach captures coherent structures that are poorly represented by traditional modal decomposition techniques. We demonstrate the application of FLOW portraits on three simple synthetic datasets and two widefield calcium imaging datasets, including cortical waves in the developing mouse and spontaneous cortical activity in an adult mouse.

Chronic, cortex-wide imaging of specific cell populations during behavior

Measurements of neuronal activity across brain areas are important for understanding the neural correlates of cognitive and motor processes such as attention, decision-making and action selection. However, techniques that allow cellular resolution measurements are expensive and require a high degree of technical expertise, which limits their broad use. Wide-field imaging of genetically encoded indicators is a high-throughput, cost-effective and flexible approach to measure activity of specific cell populations with high temporal resolution and a cortex-wide field of view. Here we outline our protocol for assembling a wide-field macroscope setup, performing surgery to prepare the intact skull and imaging neural activity chronically in behaving, transgenic mice. Further, we highlight a processing pipeline that leverages novel, cloud-based methods to analyze large-scale imaging datasets. The protocol targets laboratories that are seeking to build macroscopes, optimize surgical procedures for long-term chronic imaging and/or analyze cortex-wide neuronal recordings. The entire protocol, including steps for assembly and calibration of the macroscope, surgical preparation, imaging and data analysis, requires a total of 8 h. It is designed to be accessible to laboratories with limited expertise in imaging methods or interest in high-throughput imaging during behavior.

Multi-scale network imaging in a mouse model of amyloidosis

The adult neocortex is not hard-wired but instead retains the capacity to reorganise across multiple spatial scales long into adulthood. Plastic reorganisation occurs at the level of mesoscopic sensory maps, functional neuronal assemblies and synaptic ensembles and is thought to be a critical feature of neuronal network function. Here, we describe a series of approaches that use calcium imaging to measure network reorganisation across multiple spatial scales in vivo. At the mesoscopic level, we demonstrate that sensory activity can be measured in animals undergoing longitudinal behavioural assessment involving automated touchscreen tasks. At the cellular level, we show that network dynamics can be longitudinally measured at both stable and transient functional assemblies. At the level of single synapses, we show that functional subcellular calcium imaging approaches can be used to measure synaptic ensembles of dendritic spines in vivo. Finally, we demonstrate that all three levels of imaging can be spatially related to local pathology in a preclinical rodent model of amyloidosis. We propose that multi-scale in vivo calcium imaging can be used to measure parallel plasticity processes operating across multiple spatial scales in both the healthy brain and preclinical models of disease.

Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI

Achieving a comprehensive understanding of brain function requires multiple imaging modalities with complementary strengths. We present an approach for concurrent widefield optical and functional magnetic resonance imaging. By merging these modalities, we can simultaneously acquire whole-brain blood-oxygen-level-dependent (BOLD) and whole-cortex calcium-sensitive fluorescent measures of brain activity. In a transgenic murine model, we show that calcium predicts the BOLD signal, using a model that optimizes a gamma-variant transfer function. We find consistent predictions across the cortex, which are best at low frequency (0.009-0.08 Hz). Furthermore, we show that the relationship between modality connectivity strengths varies by region. Our approach links cell-type-specific optical measurements of activity to the most widely used method for assessing human brain function.

Mesoscopic Imaging: Shining a Wide Light on Large-Scale Neural Dynamics

Optical imaging has revolutionized our ability to monitor brain activity, spanning spatial scales from synapses to cells to circuits. Here, we summarize the rapid development and application of mesoscopic imaging, a widefield fluorescence-based approach that balances high spatiotemporal resolution with extraordinarily large fields of view. By leveraging the continued expansion of fluorescent reporters for neuronal activity and novel strategies for indicator expression, mesoscopic analysis enables measurement and correlation of network dynamics with behavioral state and task performance. Moreover, the combination of widefield imaging with cellular resolution methods such as two-photon microscopy and electrophysiology is bridging boundaries between cellular and network analyses. Overall, mesoscopic imaging provides a powerful option in the optical toolbox for investigation of brain function.

Detecting mTBI by Learning Spatio-temporal Characteristics of Widefield Calcium Imaging Data Using Deep Learning

Early diagnosis of mild traumatic brain injury (mTBI) is of great interest to the neuroscience and medical communities. Widefield optical imaging of neuronal populations over the cerebral cortex in animals provides a unique opportunity to study injury-induced alternations in brain function. Using this technique, along with deep learning, the goal of this paper is to develop a framework for the detection of mTBI. Cortical activities in transgenic calcium reporter mice expressing GCaMP6s are obtained using widefield imaging from 8 mice before and after inducing an injury. Two deep learning models for differentiating mTBI from normal conditions are proposed. One model is based on the convolutional neural network-long short term memory (CNN-LSTM), and the second model is based on a 3D-convolutional neural network (3D-CNN). These two models offer the ability to capture features both in the spatial and temporal domains. Results for the average classification accuracy for the CNN-LSTM and the 3D-CNN are 97.24% and 91.34%, respectively. These results are notably higher than the case of using the classical machine learning methods, demonstrating the importance of utilizing both the spatial and temporal information for early detection of mTBI.

A Review of Exercise-Induced Neuroplasticity in Ischemic Stroke: Pathology and Mechanisms

After ischemic stroke, survivors experience motor dysfunction and deterioration of memory and cognition. These symptoms are associated with the disruption of normal neuronal function, i.e., the secretion of neurotrophic factors, interhemispheric connections, and synaptic activity, and hence the disruption of the normal neural circuit. Exercise is considered an effective and feasible rehabilitation strategy for improving cognitive and motor recovery following ischemic stroke through the facilitation of neuroplasticity. In this review, our aim was to discuss the mechanisms by which exercise-induced neuroplasticity improves motor function and cognitive ability after ischemic stroke. The associated mechanisms include increases in neurotrophins, improvements in synaptic structure and function, the enhancement of interhemispheric connections, the promotion of neural regeneration, the acceleration of neural function reorganization, and the facilitation of compensation beyond the infarcted tissue. We also discuss some common exercise strategies and a novel exercise therapy, robot-assisted movement, which might be widely applied in the clinic to help stroke patients in the future.

Low-Dimensional Spatiotemporal Dynamics Underlie Cortex-wide Neural Activity

Cognition arises from the dynamic flow of neural activity through the brain. To capture these dynamics, we used mesoscale calcium imaging to record neural activity across the dorsal cortex of awake mice. We found that the large majority of variance in cortex-wide activity (∼75%) could be explained by a limited set of ∼14 "motifs" of neural activity. Each motif captured a unique spatiotemporal pattern of neural activity across the cortex. These motifs generalized across animals and were seen in multiple behavioral environments. Motif expression differed across behavioral states, and specific motifs were engaged by sensory processing, suggesting the motifs reflect core cortical computations. Together, our results show that cortex-wide neural activity is highly dynamic but that these dynamics are restricted to a low-dimensional set of motifs, potentially allowing for efficient control of behavior.

Short-Chain Fatty Acids Improve Poststroke Recovery via Immunological Mechanisms

Recovery after stroke is a multicellular process encompassing neurons, resident immune cells, and brain-invading cells. Stroke alters the gut microbiome, which in turn has considerable impact on stroke outcome. However, the mechanisms underlying gut-brain interaction and implications for long-term recovery are largely elusive. Here, we tested the hypothesis that short-chain fatty acids (SCFAs), key bioactive microbial metabolites, are the missing link along the gut-brain axis and might be able to modulate recovery after experimental stroke. SCFA supplementation in the drinking water of male mice significantly improved recovery of affected limb motor function. Using in vivo wide-field calcium imaging, we observed that SCFAs induced altered contralesional cortex connectivity. This was associated with SCFA-dependent changes in spine and synapse densities. RNA sequencing of the forebrain cortex indicated a potential involvement of microglial cells in contributing to the structural and functional remodeling. Further analyses confirmed a substantial impact of SCFAs on microglial activation, which depended on the recruitment of T cells to the infarcted brain. Our findings identified that microbiota-derived SCFAs modulate poststroke recovery via effects on systemic and brain resident immune cells.SIGNIFICANCE STATEMENT Previous studies have shown a bidirectional communication along the gut-brain axis after stroke. Stroke alters the gut microbiota composition, and in turn, microbiota dysbiosis has a substantial impact on stroke outcome by modulating the immune response. However, until now, the mediators derived from the gut microbiome affecting the gut-immune-brain axis and the molecular mechanisms involved in this process were unknown. Here, we demonstrate that short-chain fatty acids, fermentation products of the gut microbiome, are potent and proregenerative modulators of poststroke neuronal plasticity at various structural levels. We identified that this effect was mediated via circulating lymphocytes on microglial activation. These results identify short-chain fatty acids as a missing link along the gut-brain axis and as a potential therapeutic to improve recovery after stroke.

Microglia monitor and protect neuronal function through specialized somatic purinergic junctions

Microglia are the main immune cells in the brain and have roles in brain homeostasis and neurological diseases. Mechanisms underlying microglia-neuron communication remain elusive. Here, we identified an interaction site between neuronal cell bodies and microglial processes in mouse and human brain. Somatic microglia-neuron junctions have a specialized nanoarchitecture optimized for purinergic signaling. Activity of neuronal mitochondria was linked with microglial junction formation, which was induced rapidly in response to neuronal activation and blocked by inhibition of P2Y12 receptors. Brain injury-induced changes at somatic junctions triggered P2Y12 receptor-dependent microglial neuroprotection, regulating neuronal calcium load and functional connectivity. Thus, microglial processes at these junctions could potentially monitor and protect neuronal functions.