Advances in two photon scanning and scanless microscopy technologies for functional neural circuit imaging

Watt-level all polarization-maintaining femtosecond fiber laser source at 1100 nm

We demonstrate a compact watt-level all polarization-maintaining (PM) femtosecond fiber laser source at 1100 nm. The fiber laser source is seeded by an all PM fiber mode-locked laser employing a nonlinear amplifying loop mirror. The seed laser can generate stable pulses at a fundamental repetition rate of 40.71 MHz with a signal-to-noise rate of >100 dB and an integrated relative intensity noise of only ∼0.061%. After two-stage external amplification and pulse compression, an output power of ∼1.47 W (corresponding to a pulse energy of ∼36.1 nJ) and a pulse duration of ∼251 fs are obtained. The 1100 nm femtosecond fiber laser is then employed as the excitation light source for multicolor multi-photon fluorescence microscopy of Chinese hamster ovary (CHO) cells stably expressing red fluorescent proteins.

SmaRT2P: a software for generating and processing smart line recording trajectories for population two-photon calcium imaging

Two-photon fluorescence calcium imaging allows recording the activity of large neural populations with subcellular spatial resolution, but it is typically characterized by low signal-to-noise ratio (SNR) and poor accuracy in detecting single or few action potentials when large number of neurons are imaged. We recently showed that implementing a smart line scanning approach using trajectories that optimally sample the regions of interest increases both the SNR fluorescence signals and the accuracy of single spike detection in population imaging in vivo. However, smart line scanning requires highly specialised software to design recording trajectories, interface with acquisition hardware, and efficiently process acquired data. Furthermore, smart line scanning needs optimized strategies to cope with movement artefacts and neuropil contamination. Here, we develop and validate SmaRT2P, an open-source, user-friendly and easy-to-interface Matlab-based software environment to perform optimized smart line scanning in two-photon calcium imaging experiments. SmaRT2P is designed to interface with popular acquisition software (e.g., ScanImage) and implements novel strategies to detect motion artefacts, estimate neuropil contamination, and minimize their impact on functional signals extracted from neuronal population imaging. SmaRT2P is structured in a modular way to allow flexibility in the processing pipeline, requiring minimal user intervention in parameter setting. The use of SmaRT2P for smart line scanning has the potential to facilitate the functional investigation of large neuronal populations with increased SNR and accuracy in detecting the discharge of single and few action potentials.

Optogenetic Methods to Investigate Brain Alterations in Preclinical Models

Investigating the neuronal dynamics supporting brain functions and understanding how the alterations in these mechanisms result in pathological conditions represents a fundamental challenge. Preclinical research on model organisms allows for a multiscale and multiparametric analysis in vivo of the neuronal mechanisms and holds the potential for better linking the symptoms of a neurological disorder to the underlying cellular and circuit alterations, eventually leading to the identification of therapeutic/rescue strategies. In recent years, brain research in model organisms has taken advantage, along with other techniques, of the development and continuous refinement of methods that use light and optical approaches to reconstruct the activity of brain circuits at the cellular and system levels, and to probe the impact of the different neuronal components in the observed dynamics. These tools, combining low-invasiveness of optical approaches with the power of genetic engineering, are currently revolutionizing the way, the scale and the perspective of investigating brain diseases. The aim of this review is to describe how brain functions can be investigated with optical approaches currently available and to illustrate how these techniques have been adopted to study pathological alterations of brain physiology.

Line-Shaped Illumination: A Promising Configuration for a Flexible Two-Photon Microscopy Setup

An innovative two-photon microscope exploiting a line-shaped illumination has been recently devised and then implemented. Such configuration allows to carry out a real-time detection by means of standard CCD cameras and is able to maintain the same resolution as commonly used point-scanning devices, thus overcoming what is usually regarded as the main limitation of line-scanning microscopes. Here, we provide an overview of the applications in which this device has been tested and has proved to be a flexible and efficient tool, namely imaging of biological samples, in-depth sample reconstruction, two-photon spectra detection, and dye cross-section measurements. These results demonstrate that the considered setup is promising for future developments in many areas of research and applications.

Light-Field Microscopy for Optical Imaging of Neuronal Activity: When Model-Based Methods Meet Data-Driven Approaches

Understanding how networks of neurons process information is one of the key challenges in modern neuroscience. A necessary step to achieve this goal is to be able to observe the dynamics of large populations of neurons over a large area of the brain. Light-field microscopy (LFM), a type of scanless microscope, is a particularly attractive candidate for high-speed three-dimensional (3D) imaging. It captures volumetric information in a single snapshot, allowing volumetric imaging at video frame-rates. Specific features of imaging neuronal activity using LFM call for the development of novel machine learning approaches that fully exploit priors embedded in physics and optics models. Signal processing theory and wave-optics theory could play a key role in filling this gap, and contribute to novel computational methods with enhanced interpretability and generalization by integrating model-driven and data-driven approaches. This paper is devoted to a comprehensive survey to state-of-the-art of computational methods for LFM, with a focus on model-based and data-driven approaches.

Implantable photonic neural probes for light-sheet fluorescence brain imaging

Significance: Light-sheet fluorescence microscopy (LSFM) is a powerful technique for high-speed volumetric functional imaging. However, in typical light-sheet microscopes, the illumination and collection optics impose significant constraints upon the imaging of non-transparent brain tissues. We demonstrate that these constraints can be surmounted using a new class of implantable photonic neural probes. Aim: Mass manufacturable, silicon-based light-sheet photonic neural probes can generate planar patterned illumination at arbitrary depths in brain tissues without any additional micro-optic components. Approach: We develop implantable photonic neural probes that generate light sheets in tissue. The probes were fabricated in a photonics foundry on 200-mm-diameter silicon wafers. The light sheets were characterized in fluorescein and in free space. The probe-enabled imaging approach was tested in fixed, in vitro, and in vivo mouse brain tissues. Imaging tests were also performed using fluorescent beads suspended in agarose. Results: The probes had 5 to 10 addressable sheets and average sheet thicknesses < 16    μ m for propagation distances up to 300    μ m in free space. Imaging areas were as large as ≈ 240    μ m × 490    μ m in brain tissue. Image contrast was enhanced relative to epifluorescence microscopy. Conclusions: The neural probes can lead to new variants of LSFM for deep brain imaging and experiments in freely moving animals.

Place Cells in Head-Fixed Mice Navigating a Floating Real-World Environment

The hippocampal place cell system in rodents has provided a major paradigm for the scientific investigation of memory function and dysfunction. Place cells have been observed in area CA1 of the hippocampus of both freely moving animals, and of head-fixed animals navigating in virtual reality environments. However, spatial coding in virtual reality preparations has been observed to be impaired. Here we show that the use of a real-world environment system for head-fixed mice, consisting of an air-floating track with proximal cues, provides some advantages over virtual reality systems for the study of spatial memory. We imaged the hippocampus of head-fixed mice injected with the genetically encoded calcium indicator GCaMP6s while they navigated circularly constrained or open environments on the floating platform. We observed consistent place tuning in a substantial fraction of cells despite the absence of distal visual cues. Place fields remapped when animals entered a different environment. When animals re-entered the same environment, place fields typically remapped over a time period of multiple days, faster than in freely moving preparations, but comparable with virtual reality. Spatial information rates were within the range observed in freely moving mice. Manifold analysis indicated that spatial information could be extracted from a low-dimensional subspace of the neural population dynamics. This is the first demonstration of place cells in head-fixed mice navigating on an air-lifted real-world platform, validating its use for the study of brain circuits involved in memory and affected by neurodegenerative disorders.

A Systematic Evaluation of Interneuron Morphology Representations for Cell Type Discrimination

Quantitative analysis of neuronal morphologies usually begins with choosing a particular feature representation in order to make individual morphologies amenable to standard statistics tools and machine learning algorithms. Many different feature representations have been suggested in the literature, ranging from density maps to intersection profiles, but they have never been compared side by side. Here we performed a systematic comparison of various representations, measuring how well they were able to capture the difference between known morphological cell types. For our benchmarking effort, we used several curated data sets consisting of mouse retinal bipolar cells and cortical inhibitory neurons. We found that the best performing feature representations were two-dimensional density maps, two-dimensional persistence images and morphometric statistics, which continued to perform well even when neurons were only partially traced. Combining these feature representations together led to further performance increases suggesting that they captured non-redundant information. The same representations performed well in an unsupervised setting, implying that they can be suitable for dimensionality reduction or clustering.

Neuronal Activity at Synapse Resolution: Reporters and Effectors for Synaptic Neuroscience

The development of methods for the activity-dependent tagging of neurons enabled a new way to tackle the problem of engram identification at the cellular level, giving rise to groundbreaking findings in the field of memory studies. However, the resolution of activity-dependent tagging remains limited to the whole-cell level. Notably, events taking place at the synapse level play a critical role in the establishment of new memories, and strong experimental evidence shows that learning and synaptic plasticity are tightly linked. Here, we provide a comprehensive review of the currently available techniques that enable to identify and track the neuronal activity with synaptic spatial resolution. We also present recent technologies that allow to selectively interfere with specific subsets of synapses. Lastly, we discuss how these technologies can be applied to the study of learning and memory.

Design of a multi-modality DMD-based two-photon microscope system

We present the modular design and characterization of a multi-modality video-rate two-photon excitation (TPE) microscope based on integrating a digital micromirror device (DMD), which functions as an ultrafast beam shaper and random-access scanner, with a pair of galvanometric scanners. The TPE microscope system realizes a suite of new imaging functionalities, including (1) multi-layer imaging with 3D programmable imaging planes, (2) DMD-based wavefront correction, and (3) multi-focus optical stimulation (up to 22.7 kHz) with simultaneous TPE imaging, all in real-time. We also report the detailed optomechanical design and software development that achieves high level system automation. To verify the performance of different microscope functions, we have devised and performed imaging experiments on Drosophila brain, mouse kidney and human stem cells. The results not only show improved imaging resolution and depths via the DMD-based adaptive optics, but also demonstrate fast multi-focus stimulation for the first time. With the new imaging capabilities, e.g., tools for optogenetics, the multi-modality TPE microscope may play a critical role in the applications pertinent to neuroscience and biophotonics.

Multiphoton minimal inertia scanning for fast acquisition of neural activity signals

OBJECTIVE

Multi-photon laser scanning microscopy provides a powerful tool for monitoring the spatiotemporal dynamics of neural circuit activity. It is, however, intrinsically a point scanning technique. Standard raster scanning enables imaging at subcellular resolution; however, acquisition rates are limited by the size of the field of view to be scanned. Recently developed scanning strategies such as travelling salesman scanning (TSS) have been developed to maximize cellular sampling rate by scanning only select regions in the field of view corresponding to locations of interest such as somata. However, such strategies are not optimized for the mechanical properties of galvanometric scanners. We thus aimed to develop a new scanning algorithm which produces minimal inertia trajectories, and compare its performance with existing scanning algorithms.

APPROACH

We describe here the adaptive spiral scanning (SSA) algorithm, which fits a set of near-circular trajectories to the cellular distribution to avoid inertial drifts of galvanometer position. We compare its performance to raster scanning and TSS in terms of cellular sampling frequency and signal-to-noise ratio (SNR).

MAIN RESULTS

Using surrogate neuron spatial position data, we show that SSA acquisition rates are an order of magnitude higher than those for raster scanning and generally exceed those achieved by TSS for neural densities comparable with those found in the cortex. We show that this result also holds true for in vitro hippocampal mouse brain slices bath loaded with the synthetic calcium dye Cal-520 AM. The ability of TSS to 'park' the laser on each neuron along the scanning trajectory, however, enables higher SNR than SSA when all targets are precisely scanned. Raster scanning has the highest SNR but at a substantial cost in number of cells scanned. To understand the impact of sampling rate and SNR on functional calcium imaging, we used the Cramér-Rao Bound on evoked calcium traces recorded simultaneously with electrophysiology traces to calculate the lower bound estimate of the spike timing occurrence.

SIGNIFICANCE

The results show that TSS and SSA achieve comparable accuracy in spike time estimates compared to raster scanning, despite lower SNR. SSA is an easily implementable way for standard multi-photon laser scanning systems to gain temporal precision in the detection of action potentials while scanning hundreds of active cells.

Optogenetics in Brain Research: From a Strategy to Investigate Physiological Function to a Therapeutic Tool

Dissecting the functional roles of neuronal circuits and their interaction is a crucial step in basic neuroscience and in all the biomedical field. Optogenetics is well-suited to this purpose since it allows us to study the functionality of neuronal networks on multiple scales in living organisms. This tool was recently used in a plethora of studies to investigate physiological neuronal circuit function in addition to dysfunctional or pathological conditions. Moreover, optogenetics is emerging as a crucial technique to develop new rehabilitative and therapeutic strategies for many neurodegenerative diseases in pre-clinical models. In this review, we discuss recent applications of optogenetics, starting from fundamental research to pre-clinical applications. Firstly, we described the fundamental components of optogenetics, from light-activated proteins to light delivery systems. Secondly, we showed its applications to study neuronal circuits in physiological or pathological conditions at the cortical and subcortical level, in vivo. Furthermore, the interesting findings achieved using optogenetics as a therapeutic and rehabilitative tool highlighted the potential of this technique for understanding and treating neurological diseases in pre-clinical models. Finally, we showed encouraging results recently obtained by applying optogenetics in human neuronal cells in-vitro.

Calcium imaging approaches in investigation of pain mechanism in the spinal cord

The continuous advancement of microscopic imaging techniques combined with the discovery and use of more powerful calcium indicators has made calcium imaging technology much more effective and has increased its use in the study of pain circuitry. Using calcium imaging to study spinal pain mechanisms causes less damage to animals compared to electrophysiological techniques and is also able to observe the firing pattern of spinal neurons and the connections between them on a large scale. These advantages allow any changes in spinal cord circuits caused by pain transmission to be observed more effectively. This review will discuss the development of calcium indicators over the past decades as well as the various applications of calcium imaging, from in vitro to in vivo spinal cord experiments, in the study of pain circuits. We will also discuss possible directions for the study of spinal pain circuits in the future.

Encoding of locomotion kinematics in the mouse cerebellum

The cerebellum is involved in coordinating motor behaviour, but how the cerebellar network regulates locomotion is still not well understood. We characterised the activity of putative cerebellar Purkinje cells, Golgi cells and mossy fibres in awake mice engaged in an active locomotion task, using high-density silicon electrode arrays. Analysis of the activity of over 300 neurons in response to locomotion revealed that the majority of cells (53%) were significantly modulated by phase of the stepping cycle. However, in contrast to studies involving passive locomotion on a treadmill, we found that a high proportion of cells (45%) were tuned to the speed of locomotion, and 19% were tuned to yaw movements. The activity of neurons in the cerebellar vermis provided more information about future speed of locomotion than about past or present speed, suggesting a motor, rather than purely sensory, role. We were able to accurately decode the speed of locomotion with a simple linear algorithm, with only a relatively small number of well-chosen cells needed, irrespective of cell class. Our observations suggest that behavioural state modulates cerebellar sensorimotor integration, and advocate a role for the cerebellar vermis in control of high-level locomotor kinematic parameters such as speed and yaw.

Wide field of view, real time bioimaging apparatus for noninvasive analysis of nanocarrier pharmacokinetics in living model animals

Understanding nanocarrier pharmacokinetics is crucial for the emerging nanopharmacy, which highly demands noninvasive and real-time visualization of the in vivo dynamics of nanocarriers. To this end, we have developed a 2-photon excitation and time-resolved (TPE-TR) bioimaging apparatus for the analysis of the spatial distribution and temporal evolution of nanocarriers in living model animals. The specific polymeric nanocarrier, Eu@pmma-maa doped with Eu-complexes luminescing in long persistence at ∼615 nm upon near-infrared 2-photon excitation, allows the complete rejection of tissue autofluorescence by selective luminescence detection. This together with a unique beam shaping scheme for homogeneous line excitation, a delicate timing strategy for single-shot line scanning, and an equal optical path design for in-plane scan endows the TPE-TR apparatus with the following prominent features: an imaging depth of ∼10 mm, a field of view (FOV) of 32 × 32 mm² along with a horizontal resolution of ∼60 μm, a sub-10 s frame time, and negligible laser heating effect. In addition, a combination of the in-plane line scan with the 3D scan of a model animal offers the convenience for examining an interested FOV with a millimeter vertical resolution. Application of TPE-TR bioimaging to a living mouse reveals rich information on the dynamics of nanocarriers including the spatial distribution and temporal evolution and the kinetics of domains of interest. The noninvasive TPE-TR bioimaging instrumentation with a wide FOV and a large imaging depth will find applications in the pharmaceutical development of nanocarriers and relevant research fields.

High speed functional imaging with source localized multifocal two-photon microscopy

Multifocal two-photon microscopy (MTPM) increases imaging speed over single-focus scanning by parallelizing fluorescence excitation. The imaged fluorescence's susceptibility to crosstalk, however, severely degrades contrast in scattering tissue. Here we present a source-localized MTPM scheme optimized for high speed functional fluorescence imaging in scattering mammalian brain tissue. A rastered line array of beamlets excites fluorescence imaged with a complementary metal-oxide-semiconductor (CMOS) camera. We mitigate scattering-induced crosstalk by temporally oversampling the rastered image, generating grouped images with structured illumination, and applying Richardson-Lucy deconvolution to reassign scattered photons. Single images are then retrieved with a maximum intensity projection through the deconvolved image groups. This method increased image contrast at depths up to 112 μm in scattering brain tissue and reduced functional crosstalk between pixels during neuronal calcium imaging. Source-localization did not affect signal-to-noise ratio (SNR) in densely labeled tissue under our experimental conditions. SNR decreased at low frame rates in sparsely labeled tissue, with no effect at frame rates above 50 Hz. Our non-descanned source-localized MTPM system enables high SNR, 100 Hz capture of fluorescence transients in scattering brain, increasing the scope of MTPM to faster and smaller functional signals.

Progress in automating patch clamp cellular physiology

Patch clamp electrophysiology has transformed research in the life sciences over the last few decades. Since their inception, automatic patch clamp platforms have evolved considerably, demonstrating the capability to address both voltage- and ligand-gated channels, and showing the potential to play a pivotal role in drug discovery and biomedical research. Unfortunately, the cell suspension assays to which early systems were limited cannot recreate biologically relevant cellular environments, or capture higher order aspects of synaptic physiology and network dynamics. In vivo patch clamp electrophysiology has the potential to yield more biologically complex information and be especially useful in reverse engineering the molecular and cellular mechanisms of single-cell and network neuronal computation, while capturing important aspects of human disease mechanisms and possible therapeutic strategies. Unfortunately, it is a difficult procedure with a steep learning curve, which has restricted dissemination of the technique. Luckily, in vivo patch clamp electrophysiology seems particularly amenable to robotic automation. In this review, we document the development of automated patch clamp technology, from early systems based on multi-well plates through to automated planar-array platforms, and modern robotic platforms capable of performing two-photon targeted whole-cell electrophysiological recordings in vivo.

Two-photon laser scanning microscopy with electrowetting-based prism scanning

Laser scanners are an integral part of high resolution biomedical imaging systems such as confocal or 2-photon excitation (2PE) microscopes. In this work, we demonstrate the utility of electrowetting on dielectric (EWOD) prisms as a lateral laser-scanning element integrated in a conventional 2PE microscope. To the best of our knowledge, this is the first such demonstration for EWOD prisms. EWOD devices provide a transmissive, low power consuming, and compact alternative to conventional adaptive optics, and hence this technology has tremendous potential. We demonstrate 2PE microscope imaging of cultured mouse hippocampal neurons with a FOV of 130 × 130 μm² using EWOD prism scanning. In addition, we show simulations of the optical system with the EWOD prism, to evaluate the effect of propagating a Gaussian beam through the EWOD prism on the imaging quality. Based on the simulation results a beam size of 0.91 mm full width half max was chosen to conduct the imaging experiments, resulting in a numerical aperture of 0.17 of the imaging system.

Improving voltage-sensitive dye imaging: with a little help from computational approaches

Voltage-sensitive dye imaging (VSDI) is a key neurophysiological recording tool because it reaches brain scales that remain inaccessible to other techniques. The development of this technique from in vitro to the behaving nonhuman primate has only been made possible thanks to the long-lasting, visionary work of Amiram Grinvald. This work has opened new scientific perspectives to the great benefit to the neuroscience community. However, this unprecedented technique remains largely under-utilized, and many future possibilities await for VSDI to reveal new functional operations. One reason why this tool has not been used extensively is the inherent complexity of the signal. For instance, the signal reflects mainly the subthreshold neuronal population response and is not linked to spiking activity in a straightforward manner. Second, VSDI gives access to intracortical recurrent dynamics that are intrinsically complex and therefore nontrivial to process. Computational approaches are thus necessary to promote our understanding and optimal use of this powerful technique. Here, we review such approaches, from computational models to dissect the mechanisms and origin of the recorded signal, to advanced signal processing methods to unravel new neuronal interactions at mesoscopic scale. Only a stronger development of interdisciplinary approaches can bridge micro- to macroscales.