Fast optical recording of neuronal activity by three-dimensional custom-access serial holography

Two-photon all-optical neurophysiology for the dissection of larval zebrafish brain functional and effective connectivity

One of the most audacious goals of modern neuroscience is unraveling the complex web of causal relations underlying the activity of neuronal populations on a whole-brain scale. This endeavor, which was prohibitive only a couple of decades ago, has recently become within reach owing to the advancements in optical methods and the advent of genetically encoded indicators/actuators. These techniques, applied to the translucent larval zebrafish have enabled recording and manipulation of the activity of extensive neuronal populations spanning the entire vertebrate brain. Here, we present a custom two-photon optical system that couples light-sheet imaging and 3D excitation with acousto-optic deflectors for simultaneous high-speed volumetric recording and optogenetic stimulation. By employing a zebrafish line with pan-neuronal expression of both the calcium reporter GCaMP6s and the red-shifted opsin ReaChR, we implemented a crosstalk-free, noninvasive all-optical approach and applied it to reconstruct the functional and effective connectivity of the left habenula.

Neurophotonics beyond the surface: unmasking the brain's complexity exploiting optical scattering

The intricate nature of the brain necessitates the application of advanced probing techniques to comprehensively study and understand its working mechanisms. Neurophotonics offers minimally invasive methods to probe the brain using optics at cellular and even molecular levels. However, multiple challenges persist, especially concerning imaging depth, field of view, speed, and biocompatibility. A major hindrance to solving these challenges in optics is the scattering nature of the brain. This perspective highlights the potential of complex media optics, a specialized area of study focused on light propagation in materials with intricate heterogeneous optical properties, in advancing and improving neuronal readouts for structural imaging and optical recordings of neuronal activity. Key strategies include wavefront shaping techniques and computational imaging and sensing techniques that exploit scattering properties for enhanced performance. We discuss the potential merger of the two fields as well as potential challenges and perspectives toward longer term in vivo applications.

Demixing fluorescence time traces transmitted by multimode fibers

Optical methods based on thin multimode fibers (MMFs) are promising tools for measuring neuronal activity in deep brain regions of freely moving mice thanks to their small diameter. However, current methods are limited: while fiber photometry provides only ensemble activity, imaging techniques using of long multimode fibers are very sensitive to bending and have not been applied to unrestrained rodents yet. Here, we demonstrate the fundamentals of a new approach using a short MMF coupled to a miniscope. In proof-of-principle in vitro experiments, we disentangled spatio-temporal fluorescence signals from multiple fluorescent sources transmitted by a thin (200 µm) and short (8 mm) MMF, using a general unconstrained non-negative matrix factorization algorithm directly on the raw video data. Furthermore, we show that low-cost open-source miniscopes have sufficient sensitivity to image the same fluorescence patterns seen in our proof-of-principle experiment, suggesting a new avenue for novel minimally invasive deep brain studies using multimode fibers in freely behaving mice.

Deep Learning Enhanced Label-Free Action Potential Detection Using Plasmonic-Based Electrochemical Impedance Microscopy

Measuring neuronal electrical activity, such as action potential propagation in cells, requires the sensitive detection of the weak electrical signal with high spatial and temporal resolution. None of the existing tools can fulfill this need. Recently, plasmonic-based electrochemical impedance microscopy (P-EIM) was demonstrated for the label-free mapping of the ignition and propagation of action potentials in neuron cells with subcellular resolution. However, limited by the signal-to-noise ratio in the high-speed P-EIM video, action potential mapping was achieved by averaging 90 cycles of signals. Such extensive averaging is not desired and may not always be feasible due to factors such as neuronal desensitization. In this study, we utilized advanced signal processing techniques to detect action potentials in P-EIM extracted signals with fewer averaged cycles. Matched filtering successfully detected action potential signals with as few as averaging five cycles of signals. Long short-term memory (LSTM) recurrent neural network achieved the best performance and was able to detect single-cycle stimulated action potential successfully [satisfactory area under the receiver operating characteristic curve (AUC) equal to 0.855]. Therefore, we show that deep learning-based signal processing can dramatically improve the usability of P-EIM mapping of neuronal electrical signals.

Scanless two-photon voltage imaging

Two-photon voltage imaging has long been heralded as a transformative approach capable of answering many long-standing questions in modern neuroscience. However, exploiting its full potential requires the development of novel imaging approaches well suited to the photophysical properties of genetically encoded voltage indicators. We demonstrate that parallel excitation approaches developed for scanless two-photon photostimulation enable high-SNR two-photon voltage imaging. We use whole-cell patch-clamp electrophysiology to perform a thorough characterization of scanless two-photon voltage imaging using three parallel illumination approaches and lasers with different repetition rates and wavelengths. We demonstrate voltage recordings of high-frequency spike trains and sub-threshold depolarizations from neurons expressing the soma-targeted genetically encoded voltage indicator JEDI-2P-Kv. Using a low repetition-rate laser, we perform multi-cell recordings from up to fifteen targets simultaneously. We co-express JEDI-2P-Kv and the channelrhodopsin ChroME-ST and capitalize on their overlapping two-photon absorption spectra to simultaneously evoke and image action potentials using a single laser source. We also demonstrate in vivo scanless two-photon imaging of multiple cells simultaneously up to 250 µm deep in the barrel cortex of head-fixed, anaesthetised mice.

Acousto-optic holography for pseudo-two-dimensional dynamic light patterning

Optical systems use acousto-optic deflectors (AODs) mostly for fast angular scanning and spectral filtering of laser beams. However, AODs may transform laser light in much broader ways. When time-locked to the pulsing of low repetition rate laser amplifiers, AODs permit the holographic reconstruction of 1D and pseudo-two-dimensional (ps2D) intensity objects of rectangular shape by controlling the amplitude and phase of the light field at high (20-200 kHz) rates for microscopic light patterning. Using iterative Fourier transformations (IFTs), we searched for AOD-compatible holograms to reconstruct the given ps2D target patterns through either phase-only or complex light field modulation. We previously showed that phase-only holograms can adequately render grid-like patterns of diffraction-limited points with non-overlapping diffraction orders, while side lobes to the target pattern can be cured with an apodization mask. Dense target patterns, in contrast, are typically encumbered by apodization-resistant speckle noise. Here, we show the denoised rendering of dense ps2D objects by complex acousto-optic holograms deriving from simultaneous optimization of the amplitude and phase of the light field. Target patterns lacking ps2D symmetry, although not translatable into single holograms, were accessed by serial holography based on a segregation into ps2D-compatible components. The holograms retrieved under different regularizations were experimentally validated in an AOD random-access microscope. IFT regularizations characterized in this work extend the versatility of acousto-optic holography for fast dynamic light patterning.

Fast wavefront shaping for two-photon brain imaging with multipatch correction

Nonlinear fluorescence microscopy promotes in-vivo optical imaging of cellular structure at diffraction-limited resolution deep inside scattering biological tissues. Active compensation of tissue-induced aberrations and light scattering through adaptive wavefront correction further extends the accessible depth by restoring high resolution at large depth. However, those corrections are only valid over a very limited field of view within the angular memory effect. To overcome this limitation, we introduce an acousto-optic light modulation technique for fluorescence imaging with simultaneous wavefront correction at pixel scan speed. Biaxial wavefront corrections are first learned by adaptive optimization at multiple locations in the image field. During image acquisition, the learned corrections are then switched on the fly according to the position of the excitation focus during the raster scan. The proposed microscope is applied to in vivo transcranial neuron imaging and demonstrates multi-patch correction of thinned skull-induced aberrations and scattering at 40-kHz data acquisition speed.

Recent strategies for neural dynamics observation at a larger scale and wider scope

The tremendous technical progress in neuroscience offers opportunities to observe a more minor or/and broader dynamic picture of the brain. Moreover, the large-scale neural activity of individual neurons enables the dissection of detailed mechanistic links between neural populations and behaviors. To measure neural activity in-vivo, multi-neuron recording, and neuroimaging techniques are employed and developed to acquire more neurons. The tools introduced concurrently recorded dozens to hundreds of neurons in the coordinated brain regions and elucidated the neuronal ensembles from a massive population perspective of diverse neurons at cellular resolution. In particular, the increasing spatiotemporal resolution of neuronal monitoring across the whole brain dramatically facilitates our understanding of additional nervous system functions in health and disease. Here, we will introduce state-of-the-art neuroscience tools involving large-scale neural population recording and the long-range connections spanning multiple brain regions. Their synergic effects provide to clarify the controversial circuitry underlying neuroscience. These challenging neural tools present a promising outlook for the fundamental dynamic interplay across levels of synaptic cellular, circuit organization, and brain-wide. Hence, more observations of neural dynamics will provide more clues to elucidate brain functions and push forward innovative technology at the intersection of neural engineering disciplines. We hope this review will provide insight into the use or development of recent neural techniques considering spatiotemporal scales of brain observation.

Multi-neuronal recording in unrestrained animals with all acousto-optic random-access line-scanning two-photon microscopy

To understand how neural activity encodes and coordinates behavior, it is desirable to record multi-neuronal activity in freely behaving animals. Imaging in unrestrained animals is challenging, especially for those, like larval Drosophila melanogaster, whose brains are deformed by body motion. A previously demonstrated two-photon tracking microscope recorded from individual neurons in freely crawling Drosophila larvae but faced limits in multi-neuronal recording. Here we demonstrate a new tracking microscope using acousto-optic deflectors (AODs) and an acoustic GRIN lens (TAG lens) to achieve axially resonant 2D random access scanning, sampling along arbitrarily located axial lines at a line rate of 70 kHz. With a tracking latency of 0.1 ms, this microscope recorded activities of various neurons in moving larval Drosophila CNS and VNC including premotor neurons, bilateral visual interneurons, and descending command neurons. This technique can be applied to the existing two-photon microscope to allow for fast 3D tracking and scanning.

Polarization-based idler elimination: enhancing the efficiency of optical parametric amplification

This study presents a novel way to increase the energy conversion efficiency of optical parametric amplification by eliminating the idler wave from the interaction using consecutive type-I and type-II amplification processes. By using the aforementioned straightforward approach the wavelength tunable narrow-bandwidth amplification with exceptionally high 40% peak pump-to-signal conversion efficiency and 68% peak pump depletion was achieved in the short-pulse regime, while preserving the beam quality factor of less than 1.4. The same optical layout can also serve as an enhanced idler amplification scheme.

Two-photon synthetic aperture microscopy for minimally invasive fast 3D imaging of native subcellular behaviors in deep tissue

Holistic understanding of physio-pathological processes requires noninvasive 3D imaging in deep tissue across multiple spatial and temporal scales to link diverse transient subcellular behaviors with long-term physiogenesis. Despite broad applications of two-photon microscopy (TPM), there remains an inevitable tradeoff among spatiotemporal resolution, imaging volumes, and durations due to the point-scanning scheme, accumulated phototoxicity, and optical aberrations. Here, we harnessed the concept of synthetic aperture radar in TPM to achieve aberration-corrected 3D imaging of subcellular dynamics at a millisecond scale for over 100,000 large volumes in deep tissue, with three orders of magnitude reduction in photobleaching. With its advantages, we identified direct intercellular communications through migrasome generation following traumatic brain injury, visualized the formation process of germinal center in the mouse lymph node, and characterized heterogeneous cellular states in the mouse visual cortex, opening up a horizon for intravital imaging to understand the organizations and functions of biological systems at a holistic level.

Two-photon calcium imaging of neuronal activity

In vivo two-photon calcium imaging (2PCI) is a technique used for recording neuronal activity in the intact brain. It is based on the principle that, when neurons fire action potentials, intracellular calcium levels rise, which can be detected using fluorescent molecules that bind to calcium. This Primer is designed for scientists who are considering embarking on experiments with 2PCI. We provide the reader with a background on the basic concepts behind calcium imaging and on the reasons why 2PCI is an increasingly powerful and versatile technique in neuroscience. The Primer explains the different steps involved in experiments with 2PCI, provides examples of what ideal preparations should look like and explains how data are analysed. We also discuss some of the current limitations of the technique, and the types of solutions to circumvent them. Finally, we conclude by anticipating what the future of 2PCI might look like, emphasizing some of the analysis pipelines that are being developed and international efforts for data sharing.

Single-shot quantitative aberration and scattering length measurements in mouse brain tissues using an extended-source Shack-Hartmann wavefront sensor

Deep fluorescence imaging in mammalian brain tissues remains challenging due to scattering and optical aberration-induced loss in signal and resolution. Correction of aberrations using adaptive optics (AO) requires their reliable measurement in the tissues. Here, we show that an extended-source Shack-Hartmann wavefront sensor (ESSH) allows quantitative aberration measurements through fixed brain slices with a thickness up to four times their scattering length. We demonstrate in particular that this wavefront measurement method based on image correlation is more robust to scattering compared to the standard centroid-based approach. Finally, we obtain a measurement of the tissue scattering length taking advantage of the geometry of a Shack-Hartmann sensor.