Head-mounted microendoscopic calcium imaging in dorsal premotor cortex of behaving rhesus macaque

CalliCog is an open-source cognitive neuroscience toolkit for freely behaving nonhuman primates

Nonhuman primates (NHPs) are pivotal for unlocking the complexities of human cognition, yet traditional cognitive studies remain constrained to specialized laboratories. To address this gap, we present CalliCog: an open-source, scalable in-cage platform tailored for experiments in small freely behaving primate species such as the common marmoset (Callithrix jacchus). CalliCog includes modular operant chambers that operate autonomously and integrate seamlessly with home cages, eliminating human intervention. Our results showcase the power of CalliCog to train experimentally naive marmosets in touchscreen-based cognitive tasks. Across two independent facilities, marmosets achieved touchscreen proficiency within 2 weeks and successfully completed tasks probing behavioral flexibility and working memory. Moreover, CalliCog enabled precise synchronization of behavioral data with electrocorticography (ECoG) recordings from freely moving animals, opening new frontiers for neurobehavioral research. By making CalliCog openly accessible, we aim to democratize cognitive experimentation with small NHPs, narrowing the translational gap between preclinical models and human cognition.

Protocol for in vivo recording of neural activity in deep structures of mice brain via gradient lenses by calcium imaging

Calcium (Ca2+) imaging is a viable approach for imaging neuronal activity patterns in local brain circuits in living animals. Here, we present a protocol for gradient lens implantation in deep brain structures followed by in vivo Ca2+ imaging. We describe in detail the steps for surgery preparation, followed by lens implantation, setup for awake head-fixed imaging, and the recording process. For complete details on the use and execution of this protocol, please refer to Cherepanov et al.1.

Miniscope Imaging of Nucleus Accumbens Neural Activity in Freely Behaving Rats: Virus Injection, Gradient Index Lens Implantation, Recording Strategies, and Analytical Methods

In vivo calcium imaging in freely moving rats using miniscopes provides valuable information about the neural mechanisms of behavior in real time. A gradient index (GRIN) lens can be implanted in deep brain structures to relay activity from single neurons. While such procedures have been successful in mice, few reports provide detailed procedures for successful surgery and long-term imaging in rats, which are better suited for studying complex human behaviors. We present a robotic surgical protocol for same-day virus injection and GRIN lens implantation into the rat nucleus accumbens core. Our procedure utilizes a direct lens insertion without tissue aspiration and produces quality image retention for months of recording. We also describe daily recording strategies to minimize damage and promote long-term imaging. Finally, we present custom protective strategies to eliminate the need to remove miniscopes between sessions. This methodology protects rats from repeated isoflurane exposure and ensures a consistent focal plane for the entirety of the experiment. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Craniotomy Basic Protocol 2: Virus injection Basic Protocol 3: GRIN lens implantation Basic Protocol 4: Baseplate mounting and assessment of the anesthetized rat Basic Protocol 5: Assessment of the awake, behaving rat Support Protocol 1: Protective miniscope cone fabrication Support Protocol 2: Miniscope cable fabrication.

CalliCog: an open-source cognitive neuroscience toolkit for freely behaving nonhuman primates

Nonhuman primates (NHPs) are pivotal for unlocking the complexities of human cognition, yet traditional cognitive studies remain constrained to specialized laboratories. To revolutionize this paradigm, we present CalliCog : an open-source, scalable in-cage platform tailored for freely behaving experiments in small primate species such as the common marmoset ( Callithrix jacchus ). CalliCog includes modular operant chambers that operate autonomously and integrate seamlessly with home cages, eliminating human intervention. Our results showcase the power of CalliCog to train experimentally naïve marmosets in touchscreen-based cognitive tasks. Remarkably, across two independent facilities, marmosets achieved touchscreen proficiency within two weeks and successfully completed tasks probing behavioral flexibility and working memory. Moreover, CalliCog enabled precise synchronization of behavioral data with electrocorticography (ECoG) recordings from freely moving animals, opening new frontiers for neurobehavioral research. By making CalliCog openly accessible, we aim to democratize cognitive experimentation with small NHPs, narrowing the translational gap between preclinical models and human cognition.

Motivation

Cognitive neuroscience research involving nonhuman primates (NHPs) has traditionally been confined to a few highly specialized laboratories equipped with advanced infrastructure, expert knowledge, and specialized resources for housing and testing these animals. The common marmoset ( Callithrix jacchus ), a small NHP species, has gained popularity in cognitive research due to its ability to address some of these challenges. However, behavioral studies in marmosets remain labor-intensive and restricted mainly to experts in the field, making them less accessible to the broader scientific community. To address these barriers, we introduce an open and accessible platform designed for automated cognitive experiments in home cage settings with marmosets. This system supports the integration of cognitive behavioral analysis with wireless neural recordings, is cost-effective, and requires minimal technical expertise to build and operate.

ARViS: a bleed-free multi-site automated injection robot for accurate, fast, and dense delivery of virus to mouse and marmoset cerebral cortex

Genetically encoded fluorescent sensors continue to be developed and improved. If they could be expressed across multiple cortical areas in non-human primates, it would be possible to measure a variety of spatiotemporal dynamics of primate-specific cortical activity. Here, we develop an Automated Robotic Virus injection System (ARViS) for broad expression of a biosensor. ARViS consists of two technologies: image recognition of vasculature structures on the cortical surface to determine multiple injection sites without hitting them, and robotic control of micropipette insertion perpendicular to the cortical surface with 50 μm precision. In mouse cortex, ARViS sequentially injected virus solution into 100 sites over a duration of 100 min with a bleeding probability of only 0.1% per site. Furthermore, ARViS successfully achieved 266-site injections over the frontoparietal cortex of a female common marmoset. We demonstrate one-photon and two-photon calcium imaging in the marmoset frontoparietal cortex, illustrating the effective expression of biosensors delivered by ARViS.

Dynamics of directional motor tuning in the primate premotor and primary motor cortices during sensorimotor learning

Sensorimotor learning requires reorganization of neuronal activity in the premotor cortex (PM) and primary motor cortex (M1). To reveal PM- and M1-specific reorganization in a primate, we conducted calcium imaging in common marmosets while they learned a two-target reaching (pull/push) task after mastering a one-target reaching (pull) task. Throughout learning of the two-target reaching task, the dorsorostral PM (PMdr) showed peak activity earlier than the dorsocaudal PM (PMdc) and M1. During learning, the reaction time in pull trials increased and correlated strongly with the peak timing of PMdr activity. PMdr showed decreasing representation of newly introduced (push) movement, whereas PMdc and M1 maintained high representation of pull and push movements. Many task-related neurons in PMdc and M1 exhibited a strong preference to either movement direction. PMdc neurons dynamically switched their preferred direction depending on their performance in push trials in the early learning stage, whereas M1 neurons stably retained their preferred direction and high similarity of preferred direction between neighbors. These results suggest that in primate sensorimotor learning, dynamic directional motor tuning in PMdc converts the sensorimotor association formed in PMdr to the stable and specific motor representation of M1.

The selfish network: how the brain preserves behavioral function through shifts in neuronal network state

Neuronal networks possess the ability to regulate their activity states in response to disruptions. How and when neuronal networks turn from physiological into pathological states, leading to the manifestation of neuropsychiatric disorders, remains largely unknown. Here, we propose that neuronal networks intrinsically maintain network stability even at the cost of neuronal loss. Despite the new stable state being potentially maladaptive, neural networks may not reverse back to states associated with better long-term outcomes. These maladaptive states are often associated with hyperactive neurons, marking the starting point for activity-dependent neurodegeneration. Transitions between network states may occur rapidly, and in discrete steps rather than continuously, particularly in neurodegenerative disorders. The self-stabilizing, metastable, and noncontinuous characteristics of these network states can be mathematically described as attractors. Maladaptive attractors may represent a distinct pathophysiological entity that could serve as a target for new therapies and for fostering resilience.

Low frequency independent components: Internal neuromarkers linking cortical LFPs to behavior

Local field potentials (LFPs) in the primate motor cortex have been shown to reflect information related to volitional movements. However, LFPs are composite signals that receive contributions from multiple neural sources, producing a complex mix of component signals. Using a blind source separation approach, we examined the components of neural activity recorded using multielectrode arrays in motor areas of macaque monkeys during a grasping and lifting task. We found a set of independent components in the low-frequency LFP with high temporal and spatial consistency associated with each task stage. We observed that ICs often arise from electrodes distributed across multiple cortical areas and provide complementary information to external behavioral markers, specifically in task stage detection and trial alignment. Taken together, our results show that it is possible to separate useful independent components of the LFP associated with specific task-related events, potentially representing internal markers of transition between cortical network states.

Mesoscopic calcium imaging in a head-unrestrained male non-human primate using a lensless microscope

Mesoscopic calcium imaging enables studies of cell-type specific neural activity over large areas. A growing body of literature suggests that neural activity can be different when animals are free to move compared to when they are restrained. Unfortunately, existing systems for imaging calcium dynamics over large areas in non-human primates (NHPs) are table-top devices that require restraint of the animal's head. Here, we demonstrate an imaging device capable of imaging mesoscale calcium activity in a head-unrestrained male non-human primate. We successfully miniaturize our system by replacing lenses with an optical mask and computational algorithms. The resulting lensless microscope can fit comfortably on an NHP, allowing its head to move freely while imaging. We are able to measure orientation columns maps over a 20 mm2 field-of-view in a head-unrestrained macaque. Our work establishes mesoscopic imaging using a lensless microscope as a powerful approach for studying neural activity under more naturalistic conditions.

A Neural Implant Design Toolbox for Nonhuman Primates

This paper describes an in-house method of 3D brain and skull modeling from magnetic resonance imaging (MRI) tailored for nonhuman primate (NHP) neurosurgical planning. This automated, computational software-based technique provides an efficient way of extracting brain and skull features from MRI files as opposed to traditional manual extraction techniques using imaging software. Furthermore, the procedure provides a method for visualizing the brain and craniotomized skull together for intuitive, virtual surgical planning. This generates a drastic reduction in time and resources from those required by past work, which relied on iterative 3D printing. The skull modeling process creates a footprint that is exported into modeling software to design custom-fit cranial chambers and headposts for surgical implantation. Custom-fit surgical implants minimize gaps between the implant and the skull that could introduce complications, including infection or decreased stability. By implementing these pre-surgical steps, surgical and experimental complications are reduced. These techniques can be adapted for other surgical processes, facilitating more efficient and effective experimental planning for researchers and, potentially, neurosurgeons.

Calcium imaging: a technique to monitor calcium dynamics in biological systems

Calcium ion (Ca2+) is a multifaceted signaling molecule that acts as an important second messenger. During the course of evolution, plants and animals have developed Ca2+ signaling in order to respond against diverse stimuli, to regulate a large number of physiological and developmental pathways. Our understanding of Ca2+ signaling and its components in physiological phenomena ranging from lower to higher organisms, and from single cell to multiple tissues has grown exponentially. The generation of Ca2+ transients or signatures for various stress factor is a well-known mechanism adopted in plant and animal systems. However, the decoding of such remarkable signatures is an uphill task and is always an interesting goal for the scientific community. In the past few decades, studies on the concentration and dynamics of intracellular Ca2+ are significantly increasing and have become a trend in modern biology. The advancement in approaches from Ca2+ binding dyes to in vivo Ca2+ imaging through the use of Ca2+ biosensors to achieve spatio-temporal resolution in micro and milliseconds range, provide us phenomenal opportunities to study live cell Ca2+ imaging or dynamics. Here, we describe the usage, improvement and advancement of Ca2+ based dyes, genetically encoded probes and sensors to achieve extraordinary Ca2+ imaging in plants and animals.

Graphical abstract

Emergence of task-related spatiotemporal population dynamics in transplanted neurons

Loss of nervous system tissue after severe brain injury is a main determinant of poor functional recovery. Cell transplantation is a promising method to restore lost tissue and function, yet it remains unclear if transplanted neurons can demonstrate the population level dynamics important for movement control. Here we present a comprehensive approach for long-term single neuron monitoring and manipulation of transplanted embryonic cortical neurons after cortical injury in adult male mice performing a prehension task. The observed patterns of population activity in the transplanted network strongly resembled that of healthy networks. Specifically, the task-related spatiotemporal activity patterns of transplanted neurons could be represented by latent factors that evolve within a low dimensional manifold. We also demonstrate reliable modulation of the transplanted networks using minimally invasive epidural stimulation. Our approach may allow greater insight into how restoration of cell-type specific network dynamics in vivo can restore motor function.

Motor actions are spatially organized in motor and dorsal premotor cortex

Frontal motor areas are central to controlling voluntary movements. In non-human primates, the motor areas contain independent, somatotopic, representations of the forelimb (i.e., motor maps). But are the neural codes for actions spatially organized within those forelimb representations? Addressing this question would provide insight into the poorly understood structure-function relationships of the cortical motor system. Here, we tackle the problem using high-resolution optical imaging and motor mapping in motor (M1) and dorsal premotor (PMd) cortex. Two macaque monkeys performed an instructed reach-to-grasp task while cortical activity was recorded with intrinsic signal optical imaging (ISOI). The spatial extent of activity in M1 and PMd was then quantified in relation to the forelimb motor maps, which we obtained from the same hemisphere with intracortical microstimulation. ISOI showed that task-related activity was concentrated in patches that collectively overlapped <40% of the M1 and PMd forelimb representations. The spatial organization of the patches was consistent across task conditions despite small variations in forelimb use. Nevertheless, the largest condition differences in forelimb use were reflected in the magnitude of cortical activity. Distinct time course profiles from patches in arm zones and patches in hand zones suggest functional differences within the forelimb representations. The results collectively support an organizational framework wherein the forelimb representations contain subzones enriched with neurons tuned for specific actions. Thus, the often-overlooked spatial dimension of neural activity appears to be an important organizing feature of the neural code in frontal motor areas.

2-Photon imaging of fluorescent proteins in living swine

A common point of failure in translation of preclinical neurological research to successful clinical trials comes in the giant leap from rodent models to humans. Non-human primates are phylogenetically close to humans, but cost and ethical considerations prohibit their widespread usage in preclinical trials. Swine have large, gyrencencephalic brains, which are biofidelic to human brains. Their classification as livestock makes them a readily accessible model organism. However, their size has precluded experiments involving intravital imaging with cellular resolution. Here, we present a suite of techniques and tools for in vivo imaging of porcine brains with subcellular resolution. Specifically, we describe surgical techniques for implanting a synthetic, flexible, transparent dural window for chronic optical access to the neocortex. We detail optimized parameters and methods for injecting adeno-associated virus vectors through the cranial imaging window to express fluorescent proteins. We introduce a large-animal 2-photon microscope that was constructed with off-the shelf components, has a gantry design capable of accommodating animals > 80 kg, and is equipped with a high-speed digitizer for digital fluorescence lifetime imaging. Finally, we delineate strategies developed to mitigate the substantial motion artifact that complicates high resolution imaging in large animals, including heartbeat-triggered high-speed image stack acquisition. The effectiveness of this approach is demonstrated in sample images acquired from pigs transduced with the chloride-sensitive fluorescent protein SuperClomeleon.

Large-scale high-density brain-wide neural recording in nonhuman primates

High-density, integrated silicon electrodes have begun to transform systems neuroscience, by enabling large-scale neural population recordings with single cell resolution. Existing technologies, however, have provided limited functionality in nonhuman primate species such as macaques, which offer close models of human cognition and behavior. Here, we report the design, fabrication, and performance of Neuropixels 1.0-NHP, a high channel count linear electrode array designed to enable large-scale simultaneous recording in superficial and deep structures within the macaque or other large animal brain. These devices were fabricated in two versions: 4416 electrodes along a 45 mm shank, and 2496 along a 25 mm shank. For both versions, users can programmatically select 384 channels, enabling simultaneous multi-area recording with a single probe. We demonstrate recording from over 3000 single neurons within a session, and simultaneous recordings from over 1000 neurons using multiple probes. This technology represents a significant increase in recording access and scalability relative to existing technologies, and enables new classes of experiments involving fine-grained electrophysiological characterization of brain areas, functional connectivity between cells, and simultaneous brain-wide recording at scale.

Intravenous functional gene transfer throughout the brain of non-human primates using AAV

Adeno-associated viruses (AAVs) promise robust gene delivery to the brain through non-invasive, intravenous delivery. However, unlike in rodents, few neurotropic AAVs efficiently cross the blood-brain barrier in non-human primates (NHPs). Here we describe AAV.CAP-Mac, an engineered variant identified by screening in adult marmosets and newborn macaques with improved efficiency in the brain of multiple NHP species: marmoset, rhesus macaque, and green monkey. CAP-Mac is neuron-biased in infant Old World primates, exhibits broad tropism in adult rhesus macaques, and is vasculature-biased in adult marmosets. We demonstrate applications of a single, intravenous dose of CAP-Mac to deliver (1) functional GCaMP for ex vivo calcium imaging across multiple brain areas, and (2) a cocktail of fluorescent reporters for Brainbow-like labeling throughout the macaque brain, circumventing the need for germline manipulations in Old World primates. Given its capabilities for systemic gene transfer in NHPs, CAP-Mac promises to help unlock non-invasive access to the brain.

Head-mounted optical imaging and optogenetic stimulation system for use in behaving primates

Advances in optical technology have revolutionized studies of brain function in freely behaving mice. Here, we describe an optical imaging and stimulation device for use in primates that easily attaches to an intracranial chamber. It consists of affordable commercially available or 3D-printed components: a monochromatic camera, a small standard lens, a wireless μLED stimulator powered by an induction coil, and an LED array for illumination. We show that the intrinsic imaging performance of this device is comparable to a standard benchtop system in revealing the functional organization of the visual cortex for awake macaques in a primate chair or under anesthesia. Imaging revealed neural modulatory effects of wireless focal optogenetic stimulation aimed at identified functional domains. With a 1 to 2 cm field of view, 100× larger than previously used in primates without head restraint, our device permits widefield optical imaging and optogenetic stimulation for ethological studies in primates.

Visualizing advances in the future of primate neuroscience research

Future neuroscience and biomedical projects involving non-human primates (NHPs) remain essential in our endeavors to understand the complexities and functioning of the mammalian central nervous system. In so doing, the NHP neuroscience researcher must be allowed to incorporate state-of-the-art technologies, including the use of novel viral vectors, gene therapy and transgenic approaches to answer continuing and emerging research questions that can only be addressed in NHP research models. This perspective piece captures these emerging technologies and some specific research questions they can address. At the same time, we highlight some current caveats to global NHP research and collaborations including the lack of common ethical and regulatory frameworks for NHP research, the limitations involving animal transportation and exports, and the ongoing influence of activist groups opposed to NHP research.

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.

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.

Large-volume and deep brain imaging in rabbits and monkeys using COMPACT two-photon microscopy

In vivo imaging has been widely used for investigating the structure and function of neurons typically located within ~ 800 μm below the cortical surface. Due to light scattering and absorption, it has been difficult to perform in-vivo imaging of neurons in deep cortical and subcortical regions of large animals with two-photon microscopy. Here, we combined a thin-wall quartz capillary with a GRIN lens attached to a prism for large-volume structural and calcium imaging of neurons located 2 mm below the surface of rabbit and monkey brains. The field of view was greatly expanded by rotating and changing the depth of the imaging probe inside a quartz capillary. Calcium imaging of layer 5/6 neurons in the rabbit motor cortex revealed differential activity of these neurons between quiet wakefulness and slow wave sleep. The method described here provides an important tool for studying the structure and function of neurons located deep in the brains of large animals.

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.

An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy

Single-photon-based head-mounted microscopy is widely used to record the brain activities of freely-moving animals. However, during data acquisition, the free movement of animals will cause shaking in the field of view, which deteriorates subsequent neural signal analyses. Existing motion correction methods applied to calcium imaging data either focus on offline analyses or lack sufficient accuracy in real-time processing for single-photon data. In this study, we proposed an open-source real-time motion correction (RTMC) plug-in for single-photon calcium imaging data acquisition. The RTMC plug-in is a real-time subpixel registration algorithm that can run GPUs in UCLA Miniscope data acquisition software. When used with the UCLA Miniscope, the RTMC algorithm satisfies real-time processing requirements in terms of speed, memory, and accuracy. We tested the RTMC algorithm by extending a manual neuron labeling function to extract calcium signals in a real experimental setting. The results demonstrated that the neural calcium dynamics and calcium events can be restored with high accuracy from the calcium data that were collected by the UCLA Miniscope system embedded with our RTMC plug-in. Our method could become an essential component in brain science research, where real-time brain activity is needed for closed-loop experiments.

Dissecting the Prefrontal Network With Pathway-Selective Manipulation in the Macaque Brain-A Review

Macaque monkeys are prime animal models for studying the neural mechanisms of decision-making because of their close kinship with humans. Manipulation of neural activity during decision-making tasks is essential for approaching the causal relationship between the brain and its functions. Conventional manipulation methods used in macaque studies are coarse-grained, and have worked indiscriminately on mutually intertwined neural pathways. To systematically dissect neural circuits responsible for a variety of functions, it is essential to analyze changes in behavior and neural activity through interventions in specific neural pathways. In recent years, an increasing number of studies have applied optogenetics and chemogenetics to achieve fine-grained pathway-selective manipulation in the macaque brain. Here, we review the developments in macaque studies involving pathway-selective operations, with a particular focus on applications to the prefrontal network. Pathway selectivity can be achieved using single viral vector transduction combined with local light stimulation or ligand administration directly into the brain or double-viral vector transduction combined with systemic drug administration. We discuss the advantages and disadvantages of these methods. We also highlight recent technological developments in viral vectors that can effectively infect the macaque brain, as well as the development of methods to deliver photostimulation or ligand drugs to a wide area to effectively manipulate behavior. The development and dissemination of such pathway-selective manipulations of macaque prefrontal networks will enable us to efficiently dissect the neural mechanisms of decision-making and innovate novel treatments for decision-related psychiatric disorders.

A versatile toolbox for studying cortical physiology in primates

Lesioning and neurophysiological studies have facilitated the elucidation of cortical functions and mechanisms of functional recovery following injury. Clinical translation of such studies is contingent on their employment in non-human primates (NHPs), yet tools for monitoring and modulating cortical physiology are incompatible with conventional lesioning techniques. To address these challenges, we developed a toolbox validated in seven macaques. We introduce the photothrombotic method for inducing focal cortical lesions, a quantitative model for designing experiment-specific lesion profiles and optical coherence tomography angiography (OCTA) for large-scale (~5 cm2) monitoring of vascular dynamics. We integrate these tools with our electrocorticographic array for large-scale monitoring of neural dynamics and testing stimulation-based interventions. Advantageously, this versatile toolbox can be incorporated into established chronic cranial windows. By combining optical and electrophysiological techniques in the NHP cortex, we can enhance our understanding of cortical functions, investigate functional recovery mechanisms, integrate physiological and behavioral findings, and develop neurorehabilitative treatments. MOTIVATION The primate neocortex encodes for complex functions and behaviors, the physiologies of which are yet to be fully understood. Such an understanding in both healthy and diseased states can be crucial for the development of effective neurorehabilitative strategies. However, there is a lack of a comprehensive and adaptable set of tools that enables the study of multiple physiological phenomena in healthy and injured brains. Therefore, we developed a toolbox with the capability to induce targeted cortical lesions, monitor dynamics of underlying cortical microvasculature, and record and stimulate neural activity. With this toolbox, we can enhance our understanding of cortical functions, investigate functional recovery mechanisms, test stimulation-based interventions, and integrate physiological and behavioral findings.

Fluorescence imaging of large-scale neural ensemble dynamics

Recent progress in fluorescence imaging allows neuroscientists to observe the dynamics of thousands of individual neurons, identified genetically or by their connectivity, across multiple brain areas and for extended durations in awake behaving mammals. We discuss advances in fluorescent indicators of neural activity, viral and genetic methods to express these indicators, chronic animal preparations for long-term imaging studies, and microscopes to monitor and manipulate the activity of large neural ensembles. Ca2+ imaging studies of neural activity can track brain area interactions and distributed information processing at cellular resolution. Across smaller spatial scales, high-speed voltage imaging reveals the distinctive spiking patterns and coding properties of targeted neuron types. Collectively, these innovations will propel studies of brain function and dovetail with ongoing neuroscience initiatives to identify new neuron types and develop widely applicable, non-human primate models. The optical toolkit's growing sophistication also suggests that "brain observatory" facilities would be useful open resources for future brain-imaging studies.

Operating principles of the cerebral cortex as a six-layered network in primates: beyond the classic canonical circuit model

The cerebral cortex performs its computations with many six-layered fundamental units, collectively spreading along the cortical sheet. What is the local network structure and the operating dynamics of such a fundamental unit? Previous investigations of primary sensory areas revealed a classic "canonical" circuit model, leading to an expectation of similar circuit organization and dynamics throughout the cortex. This review clarifies the different circuit dynamics at play in the higher association cortex of primates that implements computation for high-level cognition such as memory and attention. Instead of feedforward processing of response selectivity through Layers 4 to 2/3 that the classic canonical circuit stipulates, memory recall in primates occurs in Layer 5/6 with local backward projection to Layer 2/3, after which the retrieved information is sent back from Layer 6 to lower-level cortical areas for further retrieval of nested associations of target attributes. In this review, a novel "dynamic multimode module (D3M)" in the primate association cortex is proposed, as a new "canonical" circuit model performing this operation.

Modelling behaviors relevant to brain disorders in the nonhuman primate: Are we there yet?

Recent years have seen a profound resurgence of activity with nonhuman primates (NHPs) to model human brain disorders. From marmosets to macaques, the study of NHP species offers a unique window into the function of primate-specific neural circuits that are impossible to examine in other models. Examining how these circuits manifest into the complex behaviors of primates, such as advanced cognitive and social functions, has provided enormous insights to date into the mechanisms underlying symptoms of numerous neurological and neuropsychiatric illnesses. With the recent optimization of modern techniques to manipulate and measure neural activity in vivo, such as optogenetics and calcium imaging, NHP research is more well-equipped than ever to probe the neural mechanisms underlying pathological behavior. However, methods for behavioral experimentation and analysis in NHPs have noticeably failed to keep pace with these advances. As behavior ultimately lies at the junction between preclinical findings and its translation to clinical outcomes for brain disorders, approaches to improve the integrity, reproducibility, and translatability of behavioral experiments in NHPs requires critical evaluation. In this review, we provide a unifying account of existing brain disorder models using NHPs, and provide insights into the present and emerging contributions of behavioral studies to the field.

Miniature microscopes for manipulating and recording in vivo brain activity

Here we describe the development and application of miniature integrated microscopes (miniscopes) paired with microendoscopes that allow for the visualization and manipulation of neural circuits in superficial and subcortical brain regions in freely behaving animals. Over the past decade the miniscope platform has expanded to include simultaneous optogenetic capabilities, electrically-tunable lenses that enable multi-plane imaging, color-corrected optics, and an integrated data acquisition platform that streamlines multimodal experiments. Miniscopes have given researchers an unprecedented ability to monitor hundreds to thousands of genetically-defined neurons from weeks to months in both healthy and diseased animal brains. Sophisticated algorithms that take advantage of constrained matrix factorization allow for background estimation and reliable cell identification, greatly improving the reliability and scalability of source extraction for large imaging datasets. Data generated from miniscopes have empowered researchers to investigate the neural circuit underpinnings of a wide array of behaviors that cannot be studied under head-fixed conditions, such as sleep, reward seeking, learning and memory, social behaviors, and feeding. Importantly, the miniscope has broadened our understanding of how neural circuits can go awry in animal models of progressive neurological disorders, such as Parkinson's disease. Continued miniscope development, including the ability to record from multiple populations of cells simultaneously, along with continued multimodal integration of techniques such as electrophysiology, will allow for deeper understanding into the neural circuits that underlie complex and naturalistic behavior.

Circuit Investigation of Social Interaction and Substance Use Disorder Using Miniscopes

Substance use disorder (SUD) is comorbid with devastating health issues, social withdrawal, and isolation. Successful clinical treatments for SUD have used social interventions. Neurons can encode drug cues, and drug cues can trigger relapse. It is important to study how the activity in circuits and embedded cell types that encode drug cues develop in SUD. Exploring shared neurobiology between social interaction (SI) and SUD may explain why humans with access to social treatments still experience relapse. However, circuitry remains poorly characterized due to technical challenges in studying the complicated nature of SI and SUD. To understand the neural correlates of SI and SUD, it is important to: (1) identify cell types and circuits associated with SI and SUD, (2) record and manipulate neural activity encoding drug and social rewards over time, (3) monitor unrestrained animal behavior that allows reliable drug self-administration (SA) and SI. Miniaturized fluorescence microscopes (miniscopes) are ideally suited to meet these requirements. They can be used with gradient index (GRIN) lenses to image from deep brain structures implicated in SUD. Miniscopes can be combined with genetically encoded reporters to extract cell-type specific information. In this mini-review, we explore how miniscopes can be leveraged to uncover neural components of SI and SUD and advance potential therapeutic interventions.

Optical deep-cortex exploration in behaving rhesus macaques

Two papers published in June 2021 used a two-photon microscope or one-photon miniature microscope to interrogate the motor cortex in behaving macaque monkeys. The imaging was performed over several months, and the direction of natural arm reaching was decoded from the population activity.

Windows and periscopes into primate behavior

Calcium imaging of neurons in monkeys making reaches is complicated by brain movements and limited by shallow imaging depth. In a pair of recent studies, Trautmann et al., 2021 and Bollimunta et al. (2021) present complementary solutions to these problems.

Dendritic calcium signals in rhesus macaque motor cortex drive an optical brain-computer interface

Calcium imaging is a powerful tool for recording from large populations of neurons in vivo. Imaging in rhesus macaque motor cortex can enable the discovery of fundamental principles of motor cortical function and can inform the design of next generation brain-computer interfaces (BCIs). Surface two-photon imaging, however, cannot presently access somatic calcium signals of neurons from all layers of macaque motor cortex due to photon scattering. Here, we demonstrate an implant and imaging system capable of chronic, motion-stabilized two-photon imaging of neuronal calcium signals from macaques engaged in a motor task. By imaging apical dendrites, we achieved optical access to large populations of deep and superficial cortical neurons across dorsal premotor (PMd) and gyral primary motor (M1) cortices. Dendritic signals from individual neurons displayed tuning for different directions of arm movement. Combining several technical advances, we developed an optical BCI (oBCI) driven by these dendritic signalswhich successfully decoded movement direction online. By fusing two-photon functional imaging with CLARITY volumetric imaging, we verified that many imaged dendrites which contributed to oBCI decoding originated from layer 5 output neurons, including a putative Betz cell. This approach establishes new opportunities for studying motor control and designing BCIs via two photon imaging.