Post hoc immunostaining of GABAergic neuronal subtypes following in vivo two-photon calcium imaging in mouse neocortex

Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

Head-mounted miniscopes have allowed for functional fluorescence imaging in freely moving animals. However, current capabilities of state-of-the-art technology can record only up to two, spectrally distinct fluorophores. This severely limits the number of cell types identifiable in a functional imaging experiment. Here we present a pipeline that enables the distinction of nine neuronal subtypes from regions defined by behaviorally relevant cells during in vivo GCaMP imaging. These subtypes are identified utilizing unique fluorophores that are co-expressed with GCaMP, unmixed by spectral imaging on a confocal microscope and co-registering these spectral fingerprints with functional data obtained on miniaturized microscopes. This method facilitates detailed analyses of circuit-level encoding of behavior.

Chasing cortical behavior: designing multiphoton microscopes for imaging neuronal populations in freely moving rodents

Imaging in the freely moving animal gives unparalleled access to circuit activity as the animal interacts with its environment in a self-guided way. Over the past few years, new imaging technologies have enabled the interrogation of neuronal populations located at any depth of the cortex in freely moving mice while preserving the animal's behavioral repertoire. This commentary gives an updated overview of the recent advances that have enabled the link between behavior and the underlying neuronal activity to be explored.

Light-guided sectioning for precise in situ localization and tissue interface analysis for brain-implanted optical fibers and GRIN lenses

Optical implants to control and monitor neuronal activity in vivo have become foundational tools of neuroscience. Standard two-dimensional histology of the implant location, however, often suffers from distortion and loss during tissue processing. To address that, we developed a three-dimensional post hoc histology method called “light-guided sectioning” (LiGS), which preserves the tissue with its optical implant in place and allows staining and clearing of a volume up to 500 μm in depth. We demonstrate the use of LiGS to determine the precise location of an optical fiber relative to a deep brain target and to investigate the implant-tissue interface. We show accurate cell registration of ex vivo histology with single-cell, two-photon calcium imaging, obtained through gradient refractive index (GRIN) lenses, and identify subpopulations based on immunohistochemistry. LiGS provides spatial information in experimental paradigms that use optical fibers and GRIN lenses and could help increase reproducibility through identification of fiber-to-target localization and molecular profiling.

Kahan et al. describe a 3D histology method (LiGS) to investigate with high fidelity the vicinity of an intact optical implant (e.g., GRIN lenses and optical fibers). LiGS is compatible with immunohistochemistry and single-molecule imaging. With the use of two-photon microscopy, LiGS can also link the functional properties of cells to their molecular identity.

Large-Scale 3D Two-Photon Imaging of Molecularly Identified CA1 Interneuron Dynamics in Behaving Mice

Cortical computations are critically reliant on their local circuit, GABAergic cells. In the hippocampus, a large body of work has identified an unprecedented diversity of GABAergic interneurons with pronounced anatomical, molecular, and physiological differences. Yet little is known about the functional properties and activity dynamics of the major hippocampal interneuron classes in behaving animals. Here we use fast, targeted, three-dimensional (3D) two-photon calcium imaging coupled with immunohistochemistry-based molecular identification to retrospectively map in vivo activity onto multiple classes of interneurons in the mouse hippocampal area CA1 during head-fixed exploration and goal-directed learning. We find examples of preferential subtype recruitment with quantitative differences in response properties and feature selectivity during key behavioral tasks and states. These results provide new insights into the collective organization of local inhibitory circuits supporting navigational and mnemonic functions of the hippocampus.

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.

Ancestral Circuits for the Coordinated Modulation of Brain State

Internal states of the brain profoundly influence behavior. Fluctuating states such as alertness can be governed by neuromodulation, but the underlying mechanisms and cell types involved are not fully understood. We developed a method to globally screen for cell types involved in behavior by integrating brain-wide activity imaging with high-content molecular phenotyping and volume registration at cellular resolution. We used this method (MultiMAP) to record from 22 neuromodulatory cell types in behaving zebrafish during a reaction-time task that reports alertness. We identified multiple monoaminergic, cholinergic, and peptidergic cell types linked to alertness and found that activity in these cell types was mutually correlated during heightened alertness. We next recorded from and controlled homologous neuromodulatory cells in mice; alertness-related cell-type dynamics exhibited striking evolutionary conservation and modulated behavior similarly. These experiments establish a method for unbiased discovery of cellular elements underlying behavior and reveal an evolutionarily conserved set of diverse neuromodulatory systems that collectively govern internal state.

Cell type specificity of neurovascular coupling in cerebral cortex

Identification of the cellular players and molecular messengers that communicate neuronal activity to the vasculature driving cerebral hemodynamics is important for (1) the basic understanding of cerebrovascular regulation and (2) interpretation of functional Magnetic Resonance Imaging (fMRI) signals. Using a combination of optogenetic stimulation and 2-photon imaging in mice, we demonstrate that selective activation of cortical excitation and inhibition elicits distinct vascular responses and identify the vasoconstrictive mechanism as Neuropeptide Y (NPY) acting on Y1 receptors. The latter implies that task-related negative Blood Oxygenation Level Dependent (BOLD) fMRI signals in the cerebral cortex under normal physiological conditions may be mainly driven by the NPY-positive inhibitory neurons. Further, the NPY-Y1 pathway may offer a potential therapeutic target in cerebrovascular disease.

Inference of neuronal network spike dynamics and topology from calcium imaging data

Two-photon calcium imaging enables functional analysis of neuronal circuits by inferring action potential (AP) occurrence ("spike trains") from cellular fluorescence signals. It remains unclear how experimental parameters such as signal-to-noise ratio (SNR) and acquisition rate affect spike inference and whether additional information about network structure can be extracted. Here we present a simulation framework for quantitatively assessing how well spike dynamics and network topology can be inferred from noisy calcium imaging data. For simulated AP-evoked calcium transients in neocortical pyramidal cells, we analyzed the quality of spike inference as a function of SNR and data acquisition rate using a recently introduced peeling algorithm. Given experimentally attainable values of SNR and acquisition rate, neural spike trains could be reconstructed accurately and with up to millisecond precision. We then applied statistical neuronal network models to explore how remaining uncertainties in spike inference affect estimates of network connectivity and topological features of network organization. We define the experimental conditions suitable for inferring whether the network has a scale-free structure and determine how well hub neurons can be identified. Our findings provide a benchmark for future calcium imaging studies that aim to reliably infer neuronal network properties.

Imaging neuronal populations in behaving rodents: paradigms for studying neural circuits underlying behavior in the mammalian cortex

Understanding the neural correlates of behavior in the mammalian cortex requires measurements of activity in awake, behaving animals. Rodents have emerged as a powerful model for dissecting the cortical circuits underlying behavior attributable to the convergence of several methods. Genetically encoded calcium indicators combined with viral-mediated or transgenic tools enable chronic monitoring of calcium signals in neuronal populations and subcellular structures of identified cell types. Stable one- and two-photon imaging of neuronal activity in awake, behaving animals is now possible using new behavioral paradigms in head-fixed animals, or using novel miniature head-mounted microscopes in freely moving animals. This mini-symposium will highlight recent applications of these methods for studying sensorimotor integration, decision making, learning, and memory in cortical and subcortical brain areas. We will outline future prospects and challenges for identifying the neural underpinnings of task-dependent behavior using cellular imaging in rodents.

Studying synaptic efficiency by post-hoc immunolabelling

Background

In terms of vesicular recycling, synaptic efficiency is a key determinant of the fidelity of synaptic transmission. The ability of a presynaptic terminal to reuse its vesicular content is thought to be a signature of synaptic maturity and this process depends on the activity of several proteins that govern exo/endocytosis. Upon stimulation, individual terminals in networks of cultured cerebellar granule neurons exhibit heterogeneous exocytic responses, which reflect the distinct states of maturity and plasticity intrinsic to individual synaptic terminals. This dynamic scenario serves as the substrate for processes such as scaling, plasticity and synaptic weight redistribution. Presynaptic strength has been associated with the activity of several types of proteins, including the scaffolding proteins that form the active zone cytomatrix and the proteins involved in presynaptic exocytosis.

Methods

We have combined fluorescence imaging techniques using the styryl dye FM1-43 in primary cultures of cerebellar granule cells with subsequent post-hoc immunocytochemistry in order to study synaptic efficiency in terms of vesicular release. We describe a protocol to easily quantify these results with minimal user intervention.

Results

In this study we describe a technique that specifically correlates presynaptic activity with the levels of presynaptic markers. This method involves the use of the styryl dye FM1-43 to estimate the release capacity of a synaptic terminal, and the subsequent post-hoc immunolabelling of thousands of individual nerve terminals. We observed a strong correlation between the release capacity of the nerve terminal and the levels of the RIM1α but not the Munc13-1 protein in the active zone.

Conclusions

Our findings support those of previous studies and point out to RIM1α as a crucial factor in determining synaptic efficiency. These results also demonstrate that this technique is a useful tool to analyse the molecular differences underlying the heterogeneous responses exhibited by neuronal networks.

Steady or changing? Long-term monitoring of neuronal population activity

Stability and flexibility are both hallmarks of brain function that allow animals to thrive in ever-changing environments. Investigating how a balance between these opposing features is achieved with a dynamic array of cellular and molecular constituents requires long-term tracking of activity from individual neurons. Here, we review in vivo chronic extracellular recording studies and recent long-term two-photon calcium-imaging investigations that address the question of stability and plasticity of neuronal population activity in the mammalian brain. Overall, spiking activity is heterogeneously distributed among neurons in local populations and largely remains stable for individual cells over time. Tuning properties appear more flexible and may be adaptively stabilized, possibly by neuromodulators, to encode reliably and specifically salient stimuli or behaviors.

HelioScan: a software framework for controlling in vivo microscopy setups with high hardware flexibility, functional diversity and extendibility

Intravital microscopy such as in vivo imaging of brain dynamics is often performed with custom-built microscope setups controlled by custom-written software to meet specific requirements. Continuous technological advancement in the field has created a need for new control software that is flexible enough to support the biological researcher with innovative imaging techniques and provide the developer with a solid platform for quickly and easily implementing new extensions. Here, we introduce HelioScan, a software package written in LabVIEW, as a platform serving this dual role. HelioScan is designed as a collection of components that can be flexibly assembled into microscope control software tailored to the particular hardware and functionality requirements. Moreover, HelioScan provides a software framework, within which new functionality can be implemented in a quick and structured manner. A specific HelioScan application assembles at run-time from individual software components, based on user-definable configuration files. Due to its component-based architecture, HelioScan can exploit synergies of multiple developers working in parallel on different components in a community effort. We exemplify the capabilities and versatility of HelioScan by demonstrating several in vivo brain imaging modes, including camera-based intrinsic optical signal imaging for functional mapping of cortical areas, standard two-photon laser-scanning microscopy using galvanometric mirrors, and high-speed in vivo two-photon calcium imaging using either acousto-optic deflectors or a resonant scanner. We recommend HelioScan as a convenient software framework for the in vivo imaging community.

Finding a Needle in a Haystack: Identification of EGFP Tagged Neurons during Calcium Imaging by Means of Two-Photon Spectral Separation

The combination of two-photon in vivo imaging and genetic labeling of specific cell types in the mouse brain is a powerful method to refine our understanding of brain circuitry and to dissect the contribution of specific neural classes to cortical function. The synthetic calcium indicators are the best fluorescent reporters for cellular activity that are presently available but their spectral proprieties are often overlapped with those of the fluorescent proteins used for genetic labeling. Such is the case of Oregon Green BAPTA1 and EGFP, the most widely used fluorophores for targeted two-photon imaging. The emission spectra of these molecules are virtually identical, precluding their separation by narrow band filters at the detector side. However, even if their one photon excitation spectra are very similar, their two-photon excitation spectra differ significantly: here we show how it is possible to exploit this difference to separate the relative contributions of EGFP and Oregon Green to the total fluorescence signal. This approach addresses two different issues: the unbiased detection of cells expressing EGFP in a cortical volume injected with Oregon Green, and the computation of the Ca(2+) insensitive fluorescence background. The latter data is essential for the quantitative comparison of the relative changes in Ca(2+) concentration between different cells, containing variable concentrations of EGFP. This strategy can be easily extended to any couple of fluorophores provided that have a different two-photon excitation spectra.

Reliable in vivo identification of both GABAergic and glutamatergic neurons using Emx1-Cre driven fluorescent reporter expression

The development of genetically modified mice in which subpopulations of cortical neurons are labelled by fluorescent proteins has greatly facilitated single-cellular imaging and electrophysiology studies in vitro and in vivo. However, the parallel visualization of both inhibitory and excitatory neocortical neurons remains problematic. We here provide an alternative approach to identify GABAergic neurons in the context of in vivo calcium imaging. The method relies on the Emx1(IREScre) recombinase driven expression of a red fluorescent protein in excitatory neurons and glia. We quantitatively examined the upper layers of the visual neocortex in vivo and found that due to pronounced neuropil staining Emx1(IREScre)-negative and Emx1(IREScre)-positive neurons can be reliably differentiated based on negative and positive contrast, respectively. Immunohistochemical analyses confirmed that the entire population of GABAergic interneurons is represented by Emx1(IREScre)-negative cells. The potential usefulness of the method is exemplified by calcium imaging of sensory-evoked responses in the primary visual cortex. We conclude that the proposed method extends the repertoire of strategies aimed at discriminating two major neocortical neuron populations in situ.

Imaging microcircuit function in healthy and diseased brain

Neural microcircuits are the computational units of the mammalian brain. Recent evidence suggests that they are not composed exclusively of neurons but also involve other cell types such as astrocytes and microglia. In the healthy brain microglia, the resident immune cell, closely interacts with synapses and is likely to be involved in their structural plasticity. The interaction between the nervous and the immune systems is even more prominent under pathological conditions such as brain injury, inflammation and neurodegenerative diseases. This review discusses the techniques for high resolution imaging of microcircuit function in health and disease by focusing on some of the most recent advances in the field of in vivo calcium imaging of neurons, astrocytes and microglia.