Efficient multi-site two-photon functional imaging of neuronal circuits

Two-site microendoscopic imaging probe for simultaneous three-dimensional imaging at two anatomic locations in tissues

Systems that can image in three dimensions at cellular resolution and across different locations within an organism may enable insights into complex biological processes, such as immune responses, for which a single location measurement may be insufficient. In this Letter, we describe an in vivo two-site imaging probe (TIP) that can simultaneously image two anatomic sites with a maximum separation of a few centimeters. The TIP consists of two identical bendable graded index (GRIN) lenses and is demonstrated by a two-photon two-color fluorescence imaging system. Each GRIN lens has a field of view of 162 × 162 × 170 µm3, a nominal numerical aperture of 0.5, a magnification of 0.7, and working distances of 0.2 mm in air for both ends. A blind linear unmixing algorithm is applied to suppress bleedthrough between channels. We use this system to successfully demonstrate two-site two-photon two-color imaging of two biomedically relevant samples, i.e., (1) a mixture of two autofluorescent anti-cancer drugs and (2) a live hybrid tumor consisting of two spectrally distinct fluorescent cell lines.

Holographic microscope and its biological application

Holographic structured illumination combined with optogenetics enables patterned stimulation of neurons and glial cells in an intact living brain. Moreover, in vivo functional imaging of cellular activity with recent advanced microscope technologies allows for visualization of the cellular responses during learning, emotion and cognition. Integrating these techniques can be used to verify the link between cell function and behavior output. However, there are technical limitations to stimulate multiple cells with high spatial and temporal resolution with available techniques of optogenetic stimulation. Here, we summarized a two-photon microscope combined with holographic system to stimulate multiple cells with high spatial and temporal resolution for living mice and their biological application.

Spatio-temporal parameters for optical probing of neuronal activity

The challenge to understand the complex neuronal circuit functions in the mammalian brain has brought about a revolution in light-based neurotechnologies and optogenetic tools. However, while recent seminal works have shown excellent insights on the processing of basic functions such as sensory perception, memory, and navigation, understanding more complex brain functions is still unattainable with current technologies. We are just scratching the surface, both literally and figuratively. Yet, the path towards fully understanding the brain is not totally uncertain. Recent rapid technological advancements have allowed us to analyze the processing of signals within dendritic arborizations of single neurons and within neuronal circuits. Understanding the circuit dynamics in the brain requires a good appreciation of the spatial and temporal properties of neuronal activity. Here, we assess the spatio-temporal parameters of neuronal responses and match them with suitable light-based neurotechnologies as well as photochemical and optogenetic tools. We focus on the spatial range that includes dendrites and certain brain regions (e.g., cortex and hippocampus) that constitute neuronal circuits. We also review some temporal characteristics of some proteins and ion channels responsible for certain neuronal functions. With the aid of the photochemical and optogenetic markers, we can use light to visualize the circuit dynamics of a functioning brain. The challenge to understand how the brain works continue to excite scientists as research questions begin to link macroscopic and microscopic units of brain circuits.

Localization of Fluorescent Targets in Deep Tissue With Expanded Beam Illumination for Studies of Cancer and the Brain

Imaging fluorescence through millimeters or centimeters of tissue has important in vivo applications, such as guiding surgery and studying the brain. Often, the important information is the location of one of more optical reporters, rather than the specifics of the local geometry, motivating the need for a localization method that provides this information. We present an optimization approach based on a diffusion model for the fast localization of fluorescent inhomogeneities in deep tissue with expanded beam illumination that simplifies the experiment and the reconstruction. We show that the position of a fluorescent inhomogeneity can be estimated while assuming homogeneous tissue parameters and without having to model the excitation profile, reducing the computational burden and improving the utility of the method. We perform two experiments as a demonstration. First, a tumor in a mouse is localized using a near infrared folate-targeted fluorescent agent (OTL38). This result shows that localization can quickly provide tumor depth information, which could reduce damage to healthy tissue during fluorescence-guided surgery. Second, another near infrared fluorescent agent (ATTO647N) is injected into the brain of a rat, and localized through the intact skull and surface tissue. This result will enable studies of protein aggregation and neuron signaling.

3D Localization for Light-Field Microscopy via Convolutional Sparse Coding on Epipolar Images

Light-field microscopy (LFM) is a type of all-optical imaging system that is able to capture 4D geometric information of light rays and can reconstruct a 3D model from a single snapshot. In this paper, we propose a new 3D localization approach to effectively detect 3D positions of neuronal cells from a single light-field image with high accuracy and outstanding robustness to light scattering. This is achieved by constructing a depth-aware dictionary and by combining it with convolutional sparse coding. Specifically, our approach includes 3 key parts: light-field calibration, depth-aware dictionary construction, and localization based on convolutional sparse coding (CSC). In the first part, an observed raw light-field image is calibrated and then decoded into a two-plane parameterized 4D format which leads to the epi-polar plane image (EPI). The second part involves simulating a set of light-fields using a wave-optics forward model for a ball-shaped volume that is located at different depths. Then, a depth-aware dictionary is constructed where each element is a synthetic EPI associated to a specific depth. Finally, by taking full advantage of the sparsity prior and shift-invariance property of EPI, 3D localization is achieved via convolutional sparse coding on an observed EPI with respect to the depth-aware EPI dictionary. We evaluate our approach on both non-scattering specimen (fluorescent beads suspended in agarose gel) and scattering media (brain tissues of genetically encoded mice). Extensive experiments demonstrate that our approach can reliably detect the 3D positions of granular targets with small Root Mean Square Error (RMSE), high robustness to optical aberration and light scattering in mammalian brain tissues.

High-Accuracy Detection of Neuronal Ensemble Activity in Two-Photon Functional Microscopy Using Smart Line Scanning

Two-photon functional imaging using genetically encoded calcium indicators (GECIs) is one prominent tool to map neural activity. Under optimized experimental conditions, GECIs detect single action potentials in individual cells with high accuracy. However, using current approaches, these optimized conditions are never met when imaging large ensembles of neurons. Here, we developed a method that substantially increases the signal-to-noise ratio (SNR) of population imaging of GECIs by using galvanometric mirrors and fast smart line scan (SLS) trajectories. We validated our approach in anesthetized and awake mice on deep and dense GCaMP6 staining in the mouse barrel cortex during spontaneous and sensory-evoked activity. Compared to raster population imaging, SLS led to increased SNR, higher probability of detecting calcium events, and more precise identification of functional neuronal ensembles. SLS provides a cheap and easily implementable tool for high-accuracy population imaging of neural GCaMP6 signals by using galvanometric-based two-photon microscopes.

Measurement and visualization of stimulus-evoked tissue dynamics in mouse barrel cortex using phase-sensitive optical coherence tomography

We describe a method to measure tissue dynamics in mouse barrel cortex during functional activation via phase-sensitive optical coherence tomography (PhS-OCT). The method measures the phase changes in OCT signals, which are induced by the tissue volume change, upon which to localize the activated tissue region. Phase unwrapping, compensation and normalization are applied to increase the dynamic range of the OCT phase detection. To guide the OCT scanning, intrinsic optical signal imaging (IOSI) system equipped with a green light laser source (532 nm) is integrated with the PhS-OCT system to provide a full field time-lapsed images of the reflectance that is used to identify the transversal 2D localized tissue response in the mouse brain. The OCT results show a localized decrease in the OCT phase signal in the activated region of the mouse brain tissue. The decrease in the phase signal may be originated from the brain tissue compression caused by the vasodilatation in the activated region. The activated region revealed in the cross-sectional OCT image is consistent with that identified by the IOSI imaging, indicating the phase change in the OCT signals may associate with the changes in the corresponding hemodynamics. In vivo localized tissue dynamics in the barrel cortex at depth during whisker stimulation is observed and monitored in this study.

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.