Benchmarking miniaturized microscopy against two-photon calcium imaging using single-cell orientation tuning in mouse visual cortex

ECoGScope: An integrated platform for real-time Electrophysiology and fluorescence imaging

In this study, we present ECoGScope, a versatile neural interface platform designed to integrate multiple functions for advancing neural network research. ECoGScope combines an electrocorticography (ECoG) electrode array with a commercial microendoscope, enabling simultaneous recording of ECoG signals and fluorescence imaging. The electrode array, constructed from highly flexible and transparent polymers, ensures conformal contact with the brain surface, allowing unobstructed optical monitoring of neural activity alongside electrophysiological recordings. A key innovation is the compact connection module, which securely integrates the ECoG array and microendoscope while minimizing interference with animal behavior. The device was successfully tested in the visual, somatosensory, and frontal cortex, demonstrating its capability for simultaneous electrophysiological and fluorescent measurements. These results highlight the potential of the ECoGScope platform to advance the development of multifunctional tools for studying brain function and addressing neurological disorders.

Deep-brain optical recording of neural dynamics during behavior

In vivo fluorescence recording techniques have produced landmark discoveries in neuroscience, providing insight into how single cell and circuit-level computations mediate sensory processing and generate complex behaviors. While much attention has been given to recording from cortical brain regions, deep-brain fluorescence recording is more complex because it requires additional measures to gain optical access to harder to reach brain nuclei. Here we discuss detailed considerations and tradeoffs regarding deep-brain fluorescence recording techniques and provide a comprehensive guide for all major steps involved, from project planning to data analysis. The goal is to impart guidance for new and experienced investigators seeking to use in vivo deep fluorescence optical recordings in awake, behaving rodent models.

Advances in cellular resolution microscopy for brain imaging in rats

Rats are used in neuroscience research because of their physiological similarities with humans and accessibility as model organisms, trainability, and behavioral repertoire. In particular, rats perform a wide range of sophisticated social, cognitive, motor, and learning behaviors within the contexts of both naturalistic and laboratory environments. Further progress in neuroscience can be facilitated by using advanced imaging methods to measure the complex neural and physiological processes during behavior in rats. However, compared with the mouse, the rat nervous system offers a set of challenges, such as larger brain size, decreased neuron density, and difficulty with head restraint. Here, we review recent advances in in vivo imaging techniques in rats with a special focus on open-source solutions for calcium imaging. Finally, we provide suggestions for both users and developers of in vivo imaging systems for rats.

An optical design enabling lightweight and large field-of-view head-mounted microscopes

Here we present a fluorescence microscope light path that enables imaging, during free behavior, of thousands of neurons in mice and hundreds of neurons in juvenile songbirds. The light path eliminates traditional illumination optics, allowing for head-mounted microscopes that have both a lower weight and a larger field of view (FOV) than previously possible. Using this light path, we designed two microscopes: one optimized for FOV (~4 mm FOV; 1.4 g), and the other optimized for weight (1.0 mm FOV; 1.0 g).

Anteromedial Thalamus Gates the Selection & Stabilization of Long-Term Memories

Memories initially formed in hippocampus gradually stabilize to cortex, over weeks-to-months, for long-term storage. The mechanistic details of this brain re-organization process remain poorly understood. In this study, we developed a virtual-reality based behavioral task and observed neural activity patterns associated with memory reorganization and stabilization over weeks-long timescales. Initial photometry recordings in circuits that link hippocampus and cortex revealed a unique and prominent neural correlate of memory in anterior thalamus that emerged in training and persisted for several weeks. Inhibition of the anteromedial thalamus-to-anterior cingulate cortex projections during training resulted in substantial memory consolidation deficits, and gain amplification more strikingly, was sufficient to enhance consolidation of otherwise unconsolidated memories. To provide mechanistic insights, we developed a new behavioral task where mice form two memories, of which only the more salient memory is consolidated, and also a technology for simultaneous and longitudinal cellular resolution imaging of hippocampus, thalamus, and cortex throughout the consolidation window. We found that whereas hippocampus equally encodes multiple memories, the anteromedial thalamus forms preferential tuning to salient memories, and establishes inter-regional correlations with cortex, that are critical for synchronizing and stabilizing cortical representations at remote time. Indeed, inhibition of this thalamo-cortical circuit while imaging in cortex reveals loss of contextual tuning and ensemble synchrony in anterior cingulate, together with behavioral deficits in remote memory retrieval. We thus identify a thalamo-cortical circuit that gates memory consolidation and propose a mechanism suitable for the selection and stabilization of hippocampal memories into longer term cortical storage.

Emerging approaches for decoding neuropeptide transmission

Neuropeptides produce robust effects on behavior across species, and recent research has benefited from advances in high-resolution techniques to investigate peptidergic transmission and expression throughout the brain in model systems. Neuropeptides exhibit distinct characteristics which includes their post-translational processing, release from dense core vesicles, and ability to activate G-protein-coupled receptors (GPCRs). These complex properties have driven the need for development of specialized tools that can sense neuropeptide expression, cell activity, and release. Current research has focused on isolating when and how neuropeptide transmission occurs, as well as the conditions in which neuropeptides directly mediate physiological and adaptive behavioral states. Here we describe the current technological landscape in which the field is operating to decode key questions regarding these dynamic neuromodulators.

Calcium imaging: A versatile tool to examine Huntington's disease mechanisms and progression

Huntington's disease (HD) is a fatal, hereditary neurodegenerative disorder that causes chorea, cognitive deficits, and psychiatric symptoms. It is characterized by accumulation of mutant Htt protein, which primarily impacts striatal medium-sized spiny neurons (MSNs), as well as cortical pyramidal neurons (CPNs), causing synapse loss and eventually cell death. Perturbed Ca2+ homeostasis is believed to play a major role in HD, as altered Ca2+ homeostasis often precedes striatal dysfunction and manifestation of HD symptoms. In addition, dysregulation of Ca2+ can cause morphological and functional changes in MSNs and CPNs. Therefore, Ca2+ imaging techniques have the potential of visualizing changes in Ca2+ dynamics and neuronal activity in HD animal models. This minireview focuses on studies using diverse Ca2+ imaging techniques, including two-photon microscopy, fiber photometry, and miniscopes, in combination of Ca2+ indicators to monitor activity of neurons in HD models as the disease progresses. We then discuss the future applications of Ca2+ imaging to visualize disease mechanisms and alterations associated with HD, as well as studies showing how, as a proof-of-concept, Ca2+imaging using miniscopes in freely-behaving animals can help elucidate the differential role of direct and indirect pathway MSNs in HD symptoms.

Large-scale two-photon calcium imaging in freely moving mice

We developed a miniaturized two-photon microscope (MINI2P) for fast, high-resolution, multiplane calcium imaging of over 1,000 neurons at a time in freely moving mice. With a microscope weight below 3 g and a highly flexible connection cable, MINI2P allowed stable imaging with no impediment of behavior in a variety of assays compared to untethered, unimplanted animals. The improved cell yield was achieved through a optical system design featuring an enlarged field of view (FOV) and a microtunable lens with increased z-scanning range and speed that allows fast and stable imaging of multiple interleaved planes, as well as 3D functional imaging. Successive imaging across multiple, adjacent FOVs enabled recordings from more than 10,000 neurons in the same animal. Large-scale proof-of-principle data were obtained from cell populations in visual cortex, medial entorhinal cortex, and hippocampus, revealing spatial tuning of cells in all areas.

Application of optogenetics and in vivo imaging approaches for elucidating the neurobiology of addiction

The neurobiology of addiction has been an intense topic of investigation for more than 50 years. Over this time, technological innovation in methods for studying brain function rapidly progressed, leading to increasingly sophisticated experimental approaches. To understand how specific brain regions, cell types, and circuits are affected by drugs of abuse and drive behaviors characteristic of addiction, it is necessary both to observe and manipulate neural activity in addiction-related behavioral paradigms. In pursuit of this goal, there have been several key technological advancements in in vivo imaging and neural circuit modulation in recent years, which have shed light on the cellular and circuit mechanisms of addiction. Here we discuss some of these key technologies, including circuit modulation with optogenetics, in vivo imaging with miniaturized single-photon microscopy (miniscope) and fiber photometry, and how the application of these technologies has garnered novel insights into the neurobiology of addiction.

Spaced training enhances memory and prefrontal ensemble stability in mice

It is commonly acknowledged that memory is substantially improved when learning is distributed over time, an effect called the "spacing effect". So far it has not been studied how spaced learning affects the neuronal ensembles presumably underlying memory. In the present study, we investigate whether trial spacing increases the stability or size of neuronal ensembles. Mice were trained in the "everyday memory" task, an appetitive, naturalistic, delayed matching-to-place task. Spacing trials by 60 min produced more robust memories than training with shorter or longer intervals. c-Fos labeling and chemogenetic inactivation established the involvement of the dorsomedial prefrontal cortex (dmPFC) in successful memory storage. In vivo calcium imaging of excitatory dmPFC neurons revealed that longer trial spacing increased the similarity of the population activity pattern on subsequent encoding trials and upon retrieval. Conversely, trial spacing did not affect the size of the total neuronal ensemble or the size of subpopulations dedicated to specific task-related behaviors and events. Thus, spaced learning promotes reactivation of prefrontal neuronal ensembles processing episodic-like memories.

Mouse visual cortex areas represent perceptual and semantic features of learned visual categories

Associative memories are stored in distributed networks extending across multiple brain regions. However, it is unclear to what extent sensory cortical areas are part of these networks. Using a paradigm for visual category learning in mice, we investigated whether perceptual and semantic features of learned category associations are already represented at the first stages of visual information processing in the neocortex. Mice learned categorizing visual stimuli, discriminating between categories and generalizing within categories. Inactivation experiments showed that categorization performance was contingent on neuronal activity in the visual cortex. Long-term calcium imaging in nine areas of the visual cortex identified changes in feature tuning and category tuning that occurred during this learning process, most prominently in the postrhinal area (POR). These results provide evidence for the view that associative memories form a brain-wide distributed network, with learning in early stages shaping perceptual representations and supporting semantic content downstream.

Functional interrogation of neural circuits with virally transmitted optogenetic tools

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

Diving into the brain: deep-brain imaging techniques in conscious animals

In most species, survival relies on the hypothalamic control of endocrine axes that regulate critical functions such as reproduction, growth, and metabolism. For decades, the complexity and inaccessibility of the hypothalamic-pituitary axis has prevented researchers from elucidating the relationship between the activity of endocrine hypothalamic neurons and pituitary hormone secretion. Indeed, the study of central control of endocrine function has been largely dominated by 'traditional' techniques that consist of studying in vitro or ex vivo isolated cell types without taking into account the complexity of regulatory mechanisms at the level of the brain, pituitary and periphery. Nowadays, by exploiting modern neuronal transfection and imaging techniques, it is possible to study hypothalamic neuron activity in situ, in real time, and in conscious animals. Deep-brain imaging of calcium activity can be performed through gradient-index lenses that are chronically implanted and offer a 'window into the brain' to image multiple neurons at single-cell resolution. With this review, we aim to highlight deep-brain imaging techniques that enable the study of neuroendocrine neurons in awake animals whilst maintaining the integrity of regulatory loops between the brain, pituitary and peripheral glands. Furthermore, to assist researchers in setting up these techniques, we discuss the equipment required and include a practical step-by-step guide to performing these deep-brain imaging studies.

Ca2+ imaging of neurons in freely moving rats with automatic post hoc histological identification

BACKGROUND

Cognitive neuroscientists aim to understand behavior often based on the underlying activity of individual neurons. Recently developed miniaturized epifluorescence microscopes allow recording of cellular calcium transients, resembling neuronal activity, of individual neurons even in deep brain areas in freely behaving animals. At the same time, molecular markers allow the characterization of diverse neuronal subtypes by post hoc immunohistochemical labeling. Combining both methods would allow researchers to increase insights into how individual neuronal activity and entities contribute to behavior.

NEW METHOD

Here, we present a novel method for identifying the same neurons, recorded with calcium imaging using a miniaturized epifluorescence microscope, post hoc in fixed histological sections. This allows immunohistochemical investigations to detect the molecular signature of in vivo recorded neurons. Our method utilizes the structure of blood vessels for aligning in vivo acquired 2D images with a reconstructed 3D histological model.

RESULTS

We automatically matched, 60 % of all in vivo recorded cells post hoc in histology. Across all animals, we successfully matched 43 % to 89 % of the recorded neurons. We provide a measure for the confidence of matched cells and validated our method by multiple simulation studies.

COMPARISON WITH EXISTING METHODS

To our knowledge, we present the first method for matching cells, recorded with a miniaturized epifluorescence microscope in freely moving animals, post hoc in histological sections.

CONCLUSIONS

Our method allows a comprehensive analysis of how cortical circuits relate to freely moving animal behavior by combining functional activity of individual neurons with their underlying histological profiles.

Design of a high-resolution light field miniscope for volumetric imaging in scattering tissue

Integrating light field microscopy techniques with existing miniscope architectures has allowed for volumetric imaging of targeted brain regions in freely moving animals. However, the current design of light field miniscopes is limited by non-uniform resolution and long imaging path length. In an effort to overcome these limitations, this paper proposes an optimized Galilean-mode light field miniscope (Gali-MiniLFM), which achieves a more consistent resolution and a significantly shorter imaging path than its conventional counterparts. In addition, this paper provides a novel framework that incorporates the anticipated aberrations of the proposed Gali-MiniLFM into the point spread function (PSF) modeling. This more accurate PSF model can then be used in 3D reconstruction algorithms to further improve the resolution of the platform. Volumetric imaging in the brain necessitates the consideration of the effects of scattering. We conduct Monte Carlo simulations to demonstrate the robustness of the proposed Gali-MiniLFM for volumetric imaging in scattering tissue.

CMOS-based bio-image sensor spatially resolves neural activity-dependent proton dynamics in the living brain

Recent studies have shown that protons can function as neurotransmitters in cultured neurons. To further investigate regional and neural activity-dependent proton dynamics in the brain, the development of a device with both wide-area detectability and high spatial-ltemporal resolution is necessary. Therefore, we develop an image sensor with a high spatial-temporal resolution specifically designed for measuring protons in vivo. Here, we demonstrate that spatially deferent neural stimulation by visual stimulation induced distinct patterns of proton changes in the visual cortex. This result indicates that our biosensor can detect micrometer and millisecond scale changes of protons across a wide area. Our study demonstrates that a CMOS-based proton image sensor with high spatial and temporal precision can be used to detect pH changes associated with biological events. We believe that our sensor may have broad applicability in future biological studies.

Protons have been discovered to play a role in neuronal signaling, but current methods to measure pH in the brain of animal models are limited. Here the authors develop a miniaturized proton image sensor that fits into a living mouse brain and can measure pH changes at micrometer and millisecond resolution scales.

Imaging spinal cord activity in behaving animals

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

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

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