Deciphering Brain Function by Miniaturized Fluorescence Microscopy in Freely Behaving Animals

Brain-implantable needle-type CMOS imaging device enables multi-layer dissection of seizure calcium dynamics in the hippocampus

Objective: Current neuronal imaging methods mostly use bulky lenses that either impede animal behavior or prohibit multi-depth imaging. To overcome these limitations, we developed a lightweight lensless biophotonic system for neuronal imaging, enabling compact and simultaneous visualization of multiple brain layers.Approach: Our developed 'CIS-NAIST' device integrates a micro-CMOS image sensor, thin-film fluorescence filter, micro-LEDs, and a needle-shaped flexible printed circuit. With this device, we monitored neuronal calcium dynamics during seizures across the different layers of the hippocampus and employed machine learning techniques for seizure classification and prediction.Main results: The CIS-NAIST device revealed distinct calcium activity patterns across the CA1, molecular interlayer, and dentate gyrus. Our findings indicated an elevated calcium amplitude activity specifically in the dentate gyrus compared to other layers. Then, leveraging the multi-layer data obtained from the device, we successfully classified seizure calcium activity and predicted seizure behavior using Long Short-Term Memory and Hidden Markov models.Significance: Taken together, our 'CIS-NAIST' device offers an effective and minimally invasive method of seizure monitoring that can help elucidate the mechanisms of temporal lobe epilepsy.

CRASH2p: Closed-loop Two Photon Imaging in Freely Moving Animals

Direct measurement of neural activity in freely moving animals is essential for understanding how the brain controls and represents behaviors. Genetically encoded calcium indicators report neural activity as changes in fluorescence intensity, but brain motion confounds quantitative measurement of fluorescence. Translation, rotation, and deformation of the brain and the movements of intervening scattering or auto-fluorescent tissue all alter the amount of fluorescent light captured by a microscope. Compared to single-photon approaches, two photon microscopy is less sensitive to scattering and off-target fluorescence, but more sensitive to motion, and two photon imaging has always required anchoring the microscope to the brain. We developed a closed-loop resonant axial-scanning high-speed two photon (CRASH2p) microscope for real-time 3D motion correction in unrestrained animals, without implantation of reference markers. We complemented CRASH2p with a novel scanning strategy and a multistage registration pipeline. We performed volumetric ratiometrically corrected functional imaging in the CNS of freely moving Drosophila larvae and discovered previously unknown neural correlates of behavior.

Cell Signaling in the Circadian Pacemaker: New Insights from in vivo Imaging

BACKGROUND

"One for all, and all for one," the famous rallying cry of the Three Musketeers, in Alexandre Dumas's popular novel, certainly applies to the 20,000 cells composing the suprachiasmatic nuclei (SCN). These cells work together to form the central clock that coordinates body rhythms in tune with the day-night cycle. Like virtually every body cell, individual SCN cells exhibit autonomous circadian oscillations, but this rhythmicity only reaches a high level of precision and robustness when the cells are coupled with their neighbors. Therefore, understanding the functional network organization of SCN cells beyond their core rhythmicity is an important issue in circadian biology.

SUMMARY

The present review summarizes the main results from our recent study demonstrating the feasibility of recording SCN cells in freely moving mice and the significance of variations in intracellular calcium over several timescales.

KEY MESSAGE

We discuss how in vivo imaging at the cell level will be pivotal to interrogate the mammalian master clock, in an integrated context that preserves the SCN network organization, with intact inputs and outputs.

Overcoming the field-of-view to diameter trade-off in microendoscopy via computational optrode-array microscopy

High-resolution microscopy of deep tissue with large field-of-view (FOV) is critical for elucidating organization of cellular structures in plant biology. Microscopy with an implanted probe offers an effective solution. However, there exists a fundamental trade-off between the FOV and probe diameter arising from aberrations inherent in conventional imaging optics (typically, FOV < 30% of diameter). Here, we demonstrate the use of microfabricated non-imaging probes (optrodes) that when combined with a trained machine-learning algorithm is able to achieve FOV of 1x to 5x the probe diameter. Further increase in FOV is achieved by using multiple optrodes in parallel. With a 1 × 2 optrode array, we demonstrate imaging of fluorescent beads (including 30 FPS video), stained plant stem sections and stained living stems. Our demonstration lays the foundation for fast, high-resolution microscopy with large FOV in deep tissue via microfabricated non-imaging probes and advanced machine learning.

A miniature fluorescence microscope for multi-plane imaging

Miniature fluorescence microscopes are becoming an increasingly established tool to investigate neural circuits in freely moving animals. In this work we present a lightweight one-photon microscope capable of imaging at different focal depths. The focal plane can be changed dynamically by modulating the pulse width of the control signal to a variable focus liquid lens, which is synchronized to the image sensor to enable changing focal plane between frames. The system was tested by imaging GCaMP7f expressing neurons in the mouse medial prefrontal cortex (mPFC) in vivo during open field test. Results showed that with the proposed design it is possible to image neurons across an axial scan of ~ 60 μm, resulting in a ~ 40% increase of total neurons imaged compared to single plane imaging.

Scan-less machine-learning-enabled incoherent microscopy for minimally-invasive deep-brain imaging

Deep-brain microscopy is strongly limited by the size of the imaging probe, both in terms of achievable resolution and potential trauma due to surgery. Here, we show that a segment of an ultra-thin multi-mode fiber (cannula) can replace the bulky microscope objective inside the brain. By creating a self-consistent deep neural network that is trained to reconstruct anthropocentric images from the raw signal transported by the cannula, we demonstrate a single-cell resolution (< 10μm), depth sectioning resolution of 40 μm, and field of view of 200 μm, all with green-fluorescent-protein labelled neurons imaged at depths as large as 1.4 mm from the brain surface. Since ground-truth images at these depths are challenging to obtain in vivo, we propose a novel ensemble method that averages the reconstructed images from disparate deep-neural-network architectures. Finally, we demonstrate dynamic imaging of moving GCaMp-labelled C. elegans worms. Our approach dramatically simplifies deep-brain microscopy.

Emerging imaging methods to study whole-brain function in rodent models

In the past decade, the idea that single populations of neurons support cognition and behavior has gradually given way to the realization that connectivity matters and that complex behavior results from interactions between remote yet anatomically connected areas that form specialized networks. In parallel, innovation in brain imaging techniques has led to the availability of a broad set of imaging tools to characterize the functional organization of complex networks. However, each of these tools poses significant technical challenges and faces limitations, which require careful consideration of their underlying anatomical, physiological, and physical specificity. In this review, we focus on emerging methods for measuring spontaneous or evoked activity in the brain. We discuss methods that can measure large-scale brain activity (directly or indirectly) with a relatively high temporal resolution, from milliseconds to seconds. We further focus on methods designed for studying the mammalian brain in preclinical models, specifically in mice and rats. This field has seen a great deal of innovation in recent years, facilitated by concomitant innovation in gene-editing techniques and the possibility of more invasive recordings. This review aims to give an overview of currently available preclinical imaging methods and an outlook on future developments. This information is suitable for educational purposes and for assisting scientists in choosing the appropriate method for their own research question.

In vivo live imaging of postnatal neural stem cells

Neural stem cells (NSCs) are maintained in specific regions of the postnatal brain and contribute to its structural and functional plasticity. However, the long-term renewal potential of NSCs and their mode of division remain elusive. The use of advanced in vivo live imaging approaches may expand our knowledge of NSC physiology and provide new information for cell replacement therapies. In this Review, we discuss the in vivo imaging methods used to study NSC dynamics and recent live-imaging results with respect to specific intracellular pathways that allow NSCs to integrate and decode different micro-environmental signals. Lastly, we discuss future directions that may provide answers to unresolved questions regarding NSC physiology.

Live imaging of adult neural stem cells in freely behaving mice using mini-endoscopes

During adulthood, the activation of adult neural stem cells (NSCs) has been mostly studied ex vivo in post-mortem tissues or in vivo in anesthetized animals. This protocol presents an approach that allows for the long-term and minimally invasive investigation of adult NSC activation and physiology in freely behaving animals. By combining specific NSC labeling and mini-endoscopic microscopy, live imaging of NSC division and Ca²⁺ activity can be performed continuously for 2–3 days and even up to several months.

For complete details on the use and execution of this protocol, please refer to Gengatharan et al. (2021).

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A protocol for mini-endoscopic imaging of adult neural stem cells (NSCs)

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Live imaging of NSCs activation in freely behaving mice

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In vivo mini-endoscopic imaging and analysis of Ca²⁺ dynamics in NSCs

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A protocol for labeling adult NSCs based on coincident activity of two promoters

Photoacoustic Neuroimaging - Perspectives on a Maturing Imaging Technique and its Applications in Neuroscience

A prominent goal of neuroscience is to improve our understanding of how brain structure and activity interact to produce perception, emotion, behavior, and cognition. The brain's network activity is inherently organized in distinct spatiotemporal patterns that span scales from nanometer-sized synapses to meter-long nerve fibers and millisecond intervals between electrical signals to decades of memory storage. There is currently no single imaging method that alone can provide all the relevant information, but intelligent combinations of complementary techniques can be effective. Here, we thus present the latest advances in biomedical and biological engineering on photoacoustic neuroimaging in the context of complementary imaging techniques. A particular focus is placed on recent advances in whole-brain photoacoustic imaging in rodent models and its influential role in bridging the gap between fluorescence microscopy and more non-invasive techniques such as magnetic resonance imaging (MRI). We consider current strategies to address persistent challenges, particularly in developing molecular contrast agents, and conclude with an overview of potential future directions for photoacoustic neuroimaging to provide deeper insights into healthy and pathological brain processes.

Long term intravital single cell tracking under multiphoton microscopy

Visualizing and tracking cells over time in a living organism has been a much-coveted dream before the invention of intravital microscopy. The opaque nature of tissue was a major hurdle that was remedied by the multiphoton microscopy. With the advancement of optical imaging and fluorescent labeling tools, intravital high resolution imaging has become increasingly accessible over the past few years. Long-term intravital tracking of single cells (LIST) under multiphoton microscopy provides a unique opportunity to gain insight into the longitudinal changes in the morphology, migration, or function of cells or subcellular structures. It is particularly suitable for studying slow-evolving cellular and molecular events during normal development or disease progression, without losing the opportunity of catching fast events such as calcium signals. Here, we review the application of LIST under 2-photon microscopy in various fields of neurobiology and discuss challenges and new directions in labeling and imaging methods for LIST. Overall, this review provides an overview of current applications of LIST in mammals, which is an emerging field that will contribute to a better understanding of essential molecular and cellular events in health and disease.

Evolution of in vivo dopamine monitoring techniques

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