Superpenetration optical microscopy by iterative multiphoton adaptive compensation technique

Adaptive optics in an oblique plane microscope

Adaptive optics (AO) can restore diffraction-limited performance when imaging beyond superficial cell layers in vivo and in vitro, and as such, is of interest for advanced 3D microscopy methods such as light-sheet fluorescence microscopy (LSFM). In a typical LSFM system, the illumination and detection paths are separate and subject to different optical aberrations. To achieve optimal microscope performance, it is necessary to sense and correct these aberrations in both light paths, resulting in a complex microscope system. Here, we show that in an oblique plane microscope (OPM), a type of LSFM with a single primary objective lens, the same deformable mirror can correct both illumination and fluorescence detection. Besides reducing the complexity, we show that AO in OPM also restores the relative alignment of the light-sheet and focal plane, and that a projection imaging mode can stabilize and improve the wavefront correction in a sensorless AO format. We demonstrate OPM with AO on fluorescent nanospheres and by imaging the vasculature and cancer cells in zebrafish embryos embedded in a glass capillary, restoring diffraction limited resolution and improving the signal strength twofold.

Non-invasive and noise-robust light focusing using confocal wavefront shaping

Wavefront-shaping is a promising approach for imaging fluorescent targets deep inside scattering tissue despite strong aberrations. It enables focusing an incoming illumination into a single spot inside tissue, as well as correcting the outgoing light scattered from the tissue. Previously, wavefront shaping modulations have been successively estimated using feedback from strong fluorescent beads, which have been manually added to a sample. However, such algorithms do not generalize to neurons whose emission is orders of magnitude weaker. We suggest a wavefront shaping approach that works with a confocal modulation of both the illumination and imaging arms. Since the aberrations are corrected in the optics before the detector, the low photon budget is directed into a single sensor spot and detected with high signal-noise ratio. We derive a score function for modulation evaluation from mathematical principles, and successfully use it to image fluorescence neurons, despite scattering through thick tissue.

Adaptive Optics in an Oblique Plane Microscope

Adaptive optics (AO) can restore diffraction limited performance when imaging beyond superficial cell layers in vivo and in vitro, and as such is of interest for advanced 3D microscopy methods such as light-sheet fluorescence microscopy (LSFM). In a typical LSFM system, the illumination and detection paths are separate and subject to different optical aberrations. To achieve optimal microscope performance, it is necessary to sense and correct these aberrations in both light paths, resulting in a complex microscope system. Here, we show that in an oblique plane microscope (OPM), a type of LSFM with a single primary objective lens, the same deformable mirror can correct both the illumination and fluorescence detection. Besides reducing the complexity, we show that AO in OPM also restores the relative alignment of the light-sheet and focal plane, and that a projection imaging mode can stabilize and improve the wavefront correction in a sensorless AO format. We demonstrate OPM with AO on fluorescent nanospheres and by imaging the vasculature and cancer cells in zebrafish embryos embedded in a glass capillary, restoring diffraction limited resolution and improving the signal strength twofold.

Speed-enhanced scattering compensation method with sub-Nyquist sampling

A rapid feedback-based scattering compensation method is particularly important for guiding light precisely within turbid tissues, especially the dynamic tissues. However, the huge number of measurements that come from the underutilization of the signal frequency channel greatly limits the modulation speed. This paper introduces a rapid compensation method with the sub-Nyquist sampling which improves the channel utilization and the speed of wavefront shaping. The number of measurements is reduced to ∼1500 with 32 × 32 freedom, and the PBR of the focus reaches ∼200. The system performances are demonstrated by focusing the light through brain slices of different thicknesses.

Geometric transformation adaptive optics (GTAO) for volumetric deep brain imaging through gradient-index lenses

The advance of genetic function indicators has enabled the observation of neuronal activities at single-cell resolutions. A major challenge for the applications on mammalian brains is the limited optical access depth. Currently, the method of choice to access deep brain structures is to insert miniature optical components. Among these validated miniature optics, the gradient-index (GRIN) lens has been widely employed for its compactness and simplicity. However, due to strong fourth-order astigmatism, GRIN lenses suffer from a small imaging field of view, which severely limits the measurement throughput and success rate. To overcome these challenges, we developed geometric transformation adaptive optics (GTAO), which enables adaptable achromatic large-volume correction through GRIN lenses. We demonstrate its major advances through in vivo structural and functional imaging of mouse brains. The results suggest that GTAO can serve as a versatile solution to enable large-volume recording of deep brain structures and activities through GRIN lenses.

Reference-free in situ rapid regional calibration of phase-only spatial light modulators

Spatial light modulators (SLMs) have become an indispensable element in modern optics for their versatile performance in many applications. Among various types of SLMs, such as digital micromirror devices (DMD), liquid crystal-based phase-only spatial light modulators (LC-SLMs), and deformable mirrors (DM), LC-SLMs are often the method of choice due to their high efficiency, precise phase modulation, and abundant number of effective pixels. In general, for research grade applications, an additional SLM calibration step is required due to fabrication imperfection resulting in non-flat liquid crystal panels and varying phase responses over the SLM area. Here, we demonstrate a straightforward approach for reference-free orthogonal calibration of an arbitrary number of SLM subregions which only requires the same measurement time as global calibration. The proposed method requires minimal optical elements and can be applied to any optical setup as is. As a benchmark performance test, we achieved a 2.2-fold enhancement in correction efficiency for wavefront shaping through scattering media utilizing the calibrated 2160 subregions of the SLM, in comparison with a single global look-up table (LUT).

Single-pixel transmission matrix recovery via two-photon fluorescence

Imaging at depth in opaque materials has long been a challenge. Recently, wavefront shaping has enabled notable advance for deep imaging. Nevertheless, most noninvasive wavefront-shaping methods require cameras, lack the sensitivity for deep imaging under weak optical signals, or can only focus on a single "guidestar." Here, we retrieve the transmission matrix (TM) noninvasively using two-photon fluorescence exploiting a single-pixel detection combined with a computational framework, allowing to achieve single-target focus on multiple guidestars spread beyond the memory effect range. In addition, if we assume that memory effect correlations exist in the TM, we are able to substantially reduce the number of measurements needed.

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.

Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing

Two-photon microscopy, combined with the appropriate optical labelling, enables the measurement and tracking of submicrometer structures within brain cells, as well as the spatiotemporal mapping of spikes in individual neurons and of neurotransmitter release in individual synapses. Yet, the spatial resolution of two-photon microscopy rapidly degrades as imaging is attempted at depths of more than a few scattering lengths into tissue, i.e., below the superficial layers that constitute the top 300-400 µm of the neocortex. To obviate this limitation, we shape the focal volume, generated by the excitation beam, by modulating the incident wavefront via guidestar-assisted adaptive optics. Here, we describe the construction, calibration and operation of a two-photon microscope that incorporates adaptive optics to restore diffraction-limited resolution at depths close to 900 µm in the mouse cortex. Our setup detects a guidestar formed by the excitation of a red-shifted dye in blood serum, used to directly measure the wavefront. We incorporate predominantly commercially available optical, optomechanical, mechanical and electronic components, and supply computer-aided design models of other customized components. The resulting adaptive optics two-photon microscope is modular and allows for expanded imaging and optical excitation capabilities. We demonstrate our methodology in the mouse neocortex by imaging the morphology of somatostatin-expressing neurons that lie 700 µm beneath the pia, calcium dynamics of layer 5b projection neurons and thalamocortical glutamate transmission to L4 neurons. The protocol requires ~30 d to complete and is suitable for users with graduate-level expertise in optics.

Universal adaptive optics for microscopy through embedded neural network control

The resolution and contrast of microscope imaging is often affected by aberrations introduced by imperfect optical systems and inhomogeneous refractive structures in specimens. Adaptive optics (AO) compensates these aberrations and restores diffraction limited performance. A wide range of AO solutions have been introduced, often tailored to a specific microscope type or application. Until now, a universal AO solution - one that can be readily transferred between microscope modalities - has not been deployed. We propose versatile and fast aberration correction using a physics-based machine learning assisted wavefront-sensorless AO control (MLAO) method. Unlike previous ML methods, we used a specially constructed neural network (NN) architecture, designed using physical understanding of the general microscope image formation, that was embedded in the control loop of different microscope systems. The approach means that not only is the resulting NN orders of magnitude simpler than previous NN methods, but the concept is translatable across microscope modalities. We demonstrated the method on a two-photon, a three-photon and a widefield three-dimensional (3D) structured illumination microscope. Results showed that the method outperformed commonly-used modal-based sensorless AO methods. We also showed that our ML-based method was robust in a range of challenging imaging conditions, such as 3D sample structures, specimen motion, low signal to noise ratio and activity-induced fluorescence fluctuations. Moreover, as the bespoke architecture encapsulated physical understanding of the imaging process, the internal NN configuration was no-longer a "black box", but provided physical insights on internal workings, which could influence future designs.

Rabies virus-based labeling of layer 6 corticothalamic neurons for two-photon imaging in vivo

Neocortical layer 6 (L6) is less understood than other more superficial layers, largely owing to limitations of performing high-resolution investigations in vivo. Here, we show that labeling with the Challenge Virus Standard (CVS) rabies virus strain enables high-quality imaging of L6 neurons by conventional two-photon microscopes. CVS virus injection into the medial geniculate body can selectively label L6 neurons in the auditory cortex. Only three days after injection, dendrites and cell bodies of L6 neurons could be imaged across all cortical layers. Ca²⁺ imaging in awake mice showed that sound stimulation evokes neuronal responses from cell bodies with minimal contamination from neuropil signals. In addition, dendritic Ca²⁺ imaging revealed significant responses from spines and trunks across all layers. These results demonstrate a reliable method capable of rapid, high-quality labeling of L6 neurons that can be readily extended to other brain regions.

Optofluidic adaptive optics in multi-photon microscopy

Adaptive optics, in combination with multi-photon techniques, is a powerful approach to image deep into a specimen. Remarkably, virtually all adaptive optics schemes today rely on wavefront modulators that are reflective, diffractive or both. This, however, can pose a severe limitation for applications. Here, we present a fast and robust sensorless adaptive optics scheme adapted for transmissive wavefront modulators. We study our scheme in numerical simulations and in experiments with a novel, optofluidic wavefront shaping device that is transmissive, refractive, polarisation-independent, and broadband. We demonstrate scatter correction of two-photon-excited fluorescence images of microbeads as well as brain cells and benchmark our device against a liquid-crystal spatial light modulator. Our method and technology could open new routes for adaptive optics in scenarios where previously, the restriction to reflective and diffractive devices may have staggered innovation and progress.

Adaptive optics for optical microscopy [Invited]

Optical microscopy is widely used to visualize fine structures. When applied to bioimaging, its performance is often degraded by sample-induced aberrations. In recent years, adaptive optics (AO), originally developed to correct for atmosphere-associated aberrations, has been applied to a wide range of microscopy modalities, enabling high- or super-resolution imaging of biological structure and function in complex tissues. Here, we review classic and recently developed AO techniques and their applications in optical microscopy.

Differentiable optimization of the Debye-Wolf integral for light shaping and adaptive optics in two-photon microscopy

Control of light through a microscope objective with a high numerical aperture is a common requirement in applications such as optogenetics, adaptive optics, or laser processing. Light propagation, including polarization effects, can be described under these conditions using the Debye-Wolf diffraction integral. Here, we take advantage of differentiable optimization and machine learning for efficiently optimizing the Debye-Wolf integral for such applications. For light shaping we show that this optimization approach is suitable for engineering arbitrary three-dimensional point spread functions in a two-photon microscope. For differentiable model-based adaptive optics (DAO), the developed method can find aberration corrections with intrinsic image features, for example neurons labeled with genetically encoded calcium indicators, without requiring guide stars. Using computational modeling we further discuss the range of spatial frequencies and magnitudes of aberrations which can be corrected with this approach.

Three-photon excited fluorescence imaging in neuroscience: From principles to applications

The development of three-photon microscopy (3PM) has greatly expanded the capability of imaging deep within biological tissues, enabling neuroscientists to visualize the structure and activity of neuronal populations with greater depth than two-photon imaging. In this review, we outline the history and physical principles of 3PM technology. We cover the current techniques for improving the performance of 3PM. Furthermore, we summarize the imaging applications of 3PM for various brain regions and species. Finally, we discuss the future of 3PM applications for neuroscience.

Robust and adjustable dynamic scattering compensation for high-precision deep tissue optogenetics

The development of high-precision optogenetics in deep tissue is limited due to the strong optical scattering induced by biological tissue. Although various wavefront shaping techniques have been developed to compensate the scattering, it is still a challenge to non-invasively characterize the dynamic scattered optical wavefront inside the living tissue. Here, we present a non-invasive scattering compensation system with fast multidither coherent optical adaptive technique (fCOAT), which allows the rapid wavefront correction and stable focusing in dynamic scattering medium. We achieve subcellular-resolution focusing through 500-μm-thickness brain slices, or even three pieces overlapped mouse skulls after just one iteration with a 589 nm CW laser. Further, focusing through dynamic scattering medium such as live rat ear is also successfully achieved. The formed focus can maintain longer than 60 s, which satisfies the requirements of stable optogenetics manipulation. Moreover, the focus size is adjustable from subcellular level to tens of microns to freely match the various manipulation targets. With the specially designed fCOAT system, we successfully achieve single-cellular optogenetic manipulation through the brain tissue, with a stimulation efficiency enhancement up to 300% compared with that of the speckle.

Guide to the construction and use of an adaptive optics two-photon microscope with direct wavefront sensing

Two-photon microscopy, combined with appropriate optical labeling, has enabled the study of structure and function throughout nervous systems. This methodology enables, for example, the measurement and tracking of sub-micrometer structures within brain cells, the spatio-temporal mapping of spikes in individual neurons, and the spatio-temporal mapping of transmitter release in individual synapses. Yet the spatial resolution of two-photon microscopy rapidly degrades as imaging is attempted at depths more than a few scattering lengths into tissue, i.e., below the superficial layers that constitute the top 300 to 400 µm of neocortex. To obviate this limitation, we measure the wavefront at the focus of the excitation beam and utilize adaptive optics that alters the incident wavefront to achieve an improved focal volume. We describe the constructions, calibration, and operation of a two-photon microscopy that incorporates adaptive optics to restore diffraction-limited resolution throughout the nearly 900 µm depth of mouse cortex. Our realization utilizes a guide star formed by excitation of red-shifted dye within the blood serum to directly measure the wavefront. We incorporate predominantly commercial optical, optomechanical, mechanical, and electronic components; computer aided design models of the exceptional custom components are supplied. The design is modular and allows for expanded imaging and optical excitation capabilities. We demonstrate our methodology in mouse neocortex by imaging the morphology of somatostatin-expressing neurons at 700 µm beneath the pia, calcium dynamics of layer 5b projection neurons, and glutamate transmission to L4 neurons.

Light scattering control with the two-step focusing method based on neural networks and multi-pixel coding

Focusing light through scattering media is essential for high-resolution optical imaging and deep penetration. Here, a two-step focusing method based on neural networks (NNs) and multi-pixel coding is proposed to achieve high-quality focusing with theoretical maximum enhancement. In the first step, a single-layer neural network (SLNN) is used to obtain the initial mask, which can be used to focus with a moderate enhancement. In the second step, we use multi-pixel coding to encode the initial mask. The coded masks and their corresponding speckle patterns are used to train another SLNN to get the final mask and achieve high-quality focusing. In this experiment, for a mask of 16 × 16 modulation units, in the case of using 8 pixels in a modulation unit, focus with the enhancement of 40.3 (only 0.44 less than the theoretical value) has been achieved with 3000 pictures (1000 pictures in the first step and 2000 pictures in the second step). Compared with the case of employing only the initial mask and the direct multi-pixel encoded mask, the enhancement is increased by 220% and 24%. The proposed method provides a new idea for improving the focusing effect through the scattering media using NNs.

High-speed single-exposure time-reversed ultrasonically encoded optical focusing against dynamic scattering

Focusing light deep inside live scattering tissue promises to revolutionize biophotonics by enabling deep tissue noninvasive optical imaging, manipulation, and therapy. By combining with guide stars, wavefront shaping is emerging as a powerful tool to make scattering media optically transparent. However, for in vivo biomedical applications, the speeds of existing techniques are still too slow to accommodate the fast speckle decorrelation of live tissue. To address this key bottleneck, we develop a quaternary phase encoding scheme to enable single-exposure time-reversed ultrasonically encode optical focusing with full-phase modulations. Specifically, we focus light inside dynamic scattering media with an average mode time down to 29 ns, which indicates that more than 10⁴ effective spatial modes can be controlled within 1 millisecond. With this technique, we demonstrate in vivo light focusing in between a highly opaque adult zebrafish of 5.1 millimeters in thickness and a ground glass diffuser. Our work presents an important step toward in vivo deep tissue applications of wavefront shaping.

Scattering correcting wavefront shaping for three-photon microscopy

Three-photon (3P) microscopy is getting traction due to its superior performance in deep tissues. Yet, aberrations and light scattering still pose one of the main limitations in the attainable depth ranges for high-resolution imaging. Here, we show scattering correcting wavefront shaping with a simple continuous optimization algorithm, guided by the integrated 3P fluorescence signal. We demonstrate focusing and imaging behind scattering layers and investigate convergence trajectories for different sample geometries and feedback non-linearities. Furthermore, we show imaging through a mouse skull and demonstrate a novel, to the best of our knowledge, fast phase estimation scheme that substantially increases the speed at which the optimal correction can be found.

Deep tissue multi-photon imaging using adaptive optics with direct focus sensing and shaping

High-resolution optical imaging deep in tissues is challenging because of optical aberrations and scattering of light caused by the complex structure of living matter. Here we present an adaptive optics three-photon microscope based on analog lock-in phase detection for focus sensing and shaping (ALPHA-FSS). ALPHA-FSS accurately measures and effectively compensates for both aberrations and scattering induced by specimens and recovers subcellular resolution at depth. A conjugate adaptive optics configuration with remote focusing enables in vivo imaging of fine neuronal structures in the mouse cortex through the intact skull up to a depth of 750 µm below the pia, enabling near-non-invasive high-resolution microscopy in cortex. Functional calcium imaging with high sensitivity and high-precision laser-mediated microsurgery through the intact skull were also demonstrated. Moreover, we achieved in vivo high-resolution imaging of the deep cortex and subcortical hippocampus up to 1.1 mm below the pia within the intact brain.

Coherent enhancement of optical remission in diffusive media

Remitted waves are used for sensing and imaging in diverse diffusive media from the Earth's crust to the human brain. Separating the source and detector increases the penetration depth of light, but the signal strength decreases rapidly, leading to a poor signal-to-noise ratio. Here, we show, experimentally and numerically, that wavefront shaping a laser beam incident on a diffusive sample enables an enhancement of remission by an order of magnitude at depths of up to 10 transport mean free paths. We develop a theoretical model which predicts the maximal remission enhancement. Our analysis reveals a significant improvement in the sensitivity of remitted waves to local changes of absorption deep inside diffusive media. This work illustrates the potential of coherent wavefront control for noninvasive diffuse wave imaging applications, such as diffuse optical tomography and functional near-infrared spectroscopy.

In vivo super-resolution of the brain - How to visualize the hidden nanoplasticity?

Super-resolution fluorescence microscopy has entered most biological laboratories worldwide and its benefit is undisputable. Its application to brain imaging, for example in living mice, enables the study of sub-cellular structural plasticity and brain function directly in a living mammal. The demands of brain imaging on the different super-resolution microscopy techniques (STED, RESOLFT, SIM, ISM) and labeling strategies are discussed here as well as the challenges of the required cranial window preparation. Applications of super-resolution in the anesthetized mouse brain enlighten the stability and plasticity of synaptic nanostructures. These studies show the potential of in vivo super-resolution imaging and justify its application more widely in vivo to investigate the role of nanostructures in memory and learning.

The Lattice Geometry of Walsh-Function-Based Adaptive Optics

We show that there is an intrinsic link between the use of Walsh aberration modes in adaptive optics (AO) and the mathematics of lattices. The discrete and binary nature of these modes means that there are infinite combinations of Walsh mode coefficients that can optimally correct the same aberration. Finding such a correction is hence a poorly conditioned optimisation problem that can be difficult to solve. This can be mitigated by confining the AO correction space defined in Walsh mode coefficients to the fundamental Voronoi cell of a lattice. By restricting the correction space in this way, one can ensure there is only one set of Walsh coefficients that corresponds to the optimum correction aberration. This property is used to enable the design of efficient estimation algorithms to solve the inverse problem of finding correction aberrations from a sequence of measurements in a wavefront sensorless AO system. The benefit of this approach is illustrated using a neural-network-based estimator.

Wavefront shaping: A versatile tool to conquer multiple scattering in multidisciplinary fields

Optical techniques offer a wide variety of applications as light-matter interactions provide extremely sensitive mechanisms to probe or treat target media. Most of these implementations rely on the usage of ballistic or quasi-ballistic photons to achieve high spatial resolution. However, the inherent scattering nature of light in biological tissues or tissue-like scattering media constitutes a critical obstacle that has restricted the penetration depth of non-scattered photons and hence limited the implementation of most optical techniques for wider applications. In addition, the components of an optical system are usually designed and manufactured for a fixed function or performance. Recent advances in wavefront shaping have demonstrated that scattering- or component-induced phase distortions can be compensated by optimizing the wavefront of the input light pattern through iteration or by conjugating the transmission matrix of the scattering medium. This offers unprecedented opportunities in many applications to achieve controllable optical delivery or detection at depths or dynamically configurable functionalities by using scattering media to substitute conventional optical components. In this article, the recent progress of wavefront shaping in multidisciplinary fields is reviewed, from optical focusing and imaging with scattering media, functionalized devices, modulation of mode coupling, and nonlinearity in multimode fiber to multimode fiber-based applications. Apart from insights into the underlying principles and recent advances in wavefront shaping implementations, practical limitations and roadmap for future development are discussed in depth. Looking back and looking forward, it is believed that wavefront shaping holds a bright future that will open new avenues for noninvasive or minimally invasive optical interactions and arbitrary control inside deep tissues. The high degree of freedom with multiple scattering will also provide unprecedented opportunities to develop novel optical devices based on a single scattering medium (generic or customized) that can outperform traditional optical components.

Three-Photon Adaptive Optics for Mouse Brain Imaging

Three-photon microscopy (3PM) was shown to allow deeper imaging than two-photon microscopy (2PM) in scattering biological tissues, such as the mouse brain, since the longer excitation wavelength reduces tissue scattering and the higher-order non-linear excitation suppresses out-of-focus background fluorescence. Imaging depth and resolution can further be improved by aberration correction using adaptive optics (AO) techniques where a spatial light modulator (SLM) is used to correct wavefront aberrations. Here, we present and analyze a 3PM AO system for in vivo mouse brain imaging. We use a femtosecond source at 1300 nm to generate three-photon (3P) fluorescence in yellow fluorescent protein (YFP) labeled mouse brain and a microelectromechanical (MEMS) SLM to apply different Zernike phase patterns. The 3P fluorescence signal is used as feedback to calculate the amount of phase correction without direct phase measurement. We show signal improvement in the cortex and the hippocampus at greater than 1 mm depth and demonstrate close to diffraction-limited imaging in the cortical layers of the brain, including imaging of dendritic spines. In addition, we characterize the effective volume for AO correction within brain tissues, and discuss the limitations of AO correction in 3PM of mouse brain.

Quantification of bone marrow interstitial pH and calcium concentration by intravital ratiometric imaging

The fate of hematopoietic stem cells (HSCs) can be directed by microenvironmental factors including extracellular calcium ion concentration ([Ca2+]e), but the local [Ca2+]e around individual HSCs in vivo remains unknown. Here we develop intravital ratiometric analyses to quantify the absolute pH and [Ca2+]e in the mouse calvarial bone marrow, taking into account the pH sensitivity of the calcium probe and the wavelength-dependent optical loss through bone. Unexpectedly, the mean [Ca2+]e in the bone marrow (1.0 ± 0.54 mM) is not significantly different from the blood serum, but the HSCs are found in locations with elevated local [Ca2+]e (1.5 ± 0.57 mM). With aging, a significant increase in [Ca2+]e is found in M-type cavities that exclusively support clonal expansion of activated HSCs. This work thus establishes a tool to investigate [Ca2+]e and pH in the HSC niche with high spatial resolution and can be broadly applied to other tissue types.

Improvement of spatial resolution in photoacoustic microscopy using transmissive adaptive optics with a low-frequency ultrasound transducer

Maintaining a high spatial resolution in photoacoustic microscopy (PAM) of deep tissues is difficult due to large aberration in an objective lens with high numerical aperture and photoacoustic wave attenuation. To address the issue, we integrate transmission-type adaptive optics (AO) in high-resolution PAM with a low-frequency ultrasound transducer (UT), which increases the photoacoustic wave detection efficiency. AO improves lateral resolution and depth discrimination in PAM, even for low-frequency ultrasound waves by focusing a beam spot in deep tissues. Using the proposed PAM, we increased the lateral resolution and depth discrimination for blood vessels in mouse ears.

Imaging deeper than the transport mean free path with multiphoton microscopy

Multiphoton fluorescence microscopy enables deep in vivo imaging by using long excitation wavelengths to increase the penetration depth of ballistic photons and nonlinear excitation to suppress the out-of-focus fluorescence. However, the imaging depth of multiphoton microscopy is limited by tissue scattering and absorption. This fundamental depth limit for two-photon microscopy has been studied theoretically and experimentally. Long wavelength three-photon fluorescence microscopy was developed to image beyond the depth limit of two-photon microscopy and has achieved unprecedented in vivo imaging depth. Here we extend the theoretical framework for characterizing the depth limit of two-photon microscopy to three-photon microscopy. We further verify the theoretical predictions with experimental results from tissue phantoms. We demonstrate experimentally that high spatial resolution diffraction-limited imaging at a depth of 10 scattering mean free paths, which is nearly twice the transport mean free path, is possible with multiphoton microscopy. Our results indicate that the depth limit of three-photon microscopy is significantly beyond what has been achieved in biological tissues so far, and further technological development is required to reach the full potential of three-photon microscopy.

Simultaneous scattering compensation at multiple points in multi-photon microscopy

The two-photon fluorescence imaging depth has been significantly improved in recent years by compensating for tissue scattering with wavefront correction. However, in most approaches the wavefront corrections are valid only over a small sample region on the order of 1 to 10 µm. In samples where most scattering structures are confined to a single plane, sample conjugate correction geometries can increase the observable field to a few tens of µm. Here, we apply a recently introduced fast converging scheme for sensor-less scattering correction termed "Dynamic Adaptive Scattering compensation Holography" (DASH) in a sample conjugate configuration with a high pixel count nematic liquid crystal spatial light modulator (LC-SLM). Using a large SLM allows us to simultaneously correct for scattering at multiple field points, which can be distributed over the entire field of view provided by the objective lens. Despite the comparably slow refresh time of LC-SLMs, we achieve correction times on the order of 10 s per field point, which we show is sufficiently fast to counteract scattering at multiple sites in living mouse hippocampal tissue slices.

Non-line-of-sight optical information transmission through turbid water

In this paper, a new and robust method is proposed to realize high-fidelity non-line-of-sight (NLOS) optical information transmission through turbid water around a corner. A series of 2D random amplitude-only patterns are generated by using the zero-frequency modulation method, which are used as optical information carriers. The laser beam modulated by random amplitude-only patterns propagates through turbid water, and the wave diffused by turbid water is further reflected around a corner. A single-pixel detector is used to collect light intensity at the receiving end. To demonstrate feasibility and effectiveness of the proposed NLOS free-space optical information transmission system, many optical experiments are conducted. The proposed method is fully verified by using different turbid water conditions, different separation distances around a corner and different detection angles of the single-pixel detector. Optical experimental results demonstrate that the proposed method is able to achieve high fidelity and high robustness for free-space optical information transmission through turbid water. Even when there is an obstacle behind turbid water, high-fidelity free-space optical information transmission is still realized by using the proposed method. In addition, the proposed method possesses a wide detection range at the receiving end, which is of great significance in practical applications. The proposed method is a promising application for NLOS free-space optical information transmission.

Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging

To understand neural circuit mechanisms underlying behavior, it is crucial to observe the dynamics of neuronal structure and function in different regions of the brain. Since current noninvasive imaging technologies allow cellular-resolution imaging of neurons only within ~1 mm below the cortical surface, the majority of mouse brain tissue remains inaccessible. While miniature optical imaging probes allow access to deep brain regions, cellular-resolution imaging is typically restricted to a small tissue volume. To increase the tissue access volume, we developed a clear optically matched panoramic access channel technique (COMPACT). With probe dimensions comparable to those of common gradient-index lenses, COMPACT enables a two to three orders of magnitude greater tissue access volume. We demonstrated the capabilities of COMPACT by multiregional calcium imaging in mice during sleep. We believe that large-volume in vivo imaging with COMPACT will be valuable to a variety of deep tissue imaging applications.

Intravital fluorescence microscopy with negative contrast

Advances in intravital microscopy (IVM) have enabled the studies of cellular organization and dynamics in the native microenvironment of intact organisms with minimal perturbation. The abilities to track specific cell populations and monitor their interactions have opened up new horizons for visualizing cell biology in vivo, yet the success of standard fluorescence cell labeling approaches for IVM comes with a "dark side" in that unlabeled cells are invisible, leaving labeled cells or structures to appear isolated in space, devoid of their surroundings and lacking proper biological context. Here we describe a novel method for "filling in the void" by harnessing the ubiquity of extracellular (interstitial) fluid and its ease of fluorescence labelling by commonly used vascular and lymphatic tracers. We show that during routine labeling of the vasculature and lymphatics for IVM, commonly used fluorescent tracers readily perfuse the interstitial spaces of the bone marrow (BM) and the lymph node (LN), outlining the unlabeled cells and forming negative contrast images that complement standard (positive) cell labeling approaches. The method is simple yet powerful, offering a comprehensive view of the cellular landscape such as cell density and spatial distribution, as well as dynamic processes such as cell motility and transmigration across the vascular endothelium. The extracellular localization of the dye and the interstitial flow provide favorable conditions for prolonged Intravital time lapse imaging with minimal toxicity and photobleaching.

Fast holographic scattering compensation for deep tissue biological imaging

Scattering in biological tissues is a major barrier for in vivo optical imaging of all but the most superficial structures. Progress toward overcoming the distortions caused by scattering in turbid media has been made by shaping the excitation wavefront to redirect power into a single point in the imaging plane. However, fast, non-invasive determination of the required wavefront compensation remains challenging. Here, we introduce a quickly converging algorithm for non-invasive scattering compensation, termed DASH, in which holographic phase stepping interferometry enables new phase information to be updated after each measurement. This leads to rapid improvement of the wavefront correction, forming a focus after just one measurement iteration and achieving an order of magnitude higher signal enhancement at this stage than the previous state-of-the-art. Using DASH, we demonstrate two-photon fluorescence imaging of microglia cells in highly turbid mouse hippocampal tissue down to a depth of 530 μm.

Dynamic mutation enhanced particle swarm optimization for optical wavefront shaping

Particle swarm optimization (PSO) is a well-known iterative algorithm commonly adopted in wavefront shaping for focusing light through or inside scattering media. The performance is, however, limited by premature convergence in an unstable environment. Therefore, we aim to solve this problem and enhance the focusing performance by adding a dynamic mutation operation into the plain PSO. With dynamic mutation, the "particles," or the optimized masks, are mutated with quantifiable discrepancy between the current and theoretical optimal solution, i.e., the "error rate." Gauged by that, the diversity of the "particles" is effectively expanded, and the adaptability of the algorithm to noise and instability is significantly promoted, yielding optimization approaching the theoretical optimum. The simulation and experimental results show that PSO with dynamic mutation demonstrates considerably better performance than PSO without mutation or with a constant mutation, especially under a noisy environment.

Guidestar-free image-guided wavefront shaping

Optical imaging through scattering media is a fundamental challenge in many applications. Recently, breakthroughs such as imaging through biological tissues and looking around corners have been obtained via wavefront-shaping approaches. However, these require an implanted guidestar for determining the wavefront correction, controlled coherent illumination, and most often raster scanning of the shaped focus. Alternative novel computational approaches that exploit speckle correlations avoid guidestars and wavefront control but are limited to small two-dimensional objects contained within the "memory-effect" correlation range. Here, we present a new concept, image-guided wavefront shaping, allowing widefield noninvasive, guidestar-free, incoherent imaging through highly scattering layers, without illumination control. The wavefront correction is found even for objects that are larger than the memory-effect range, by blindly optimizing image quality metrics. We demonstrate imaging of extended objects through highly scattering layers and multicore fibers, paving the way for noninvasive imaging in various applications, from microscopy to endoscopy.

High-pulse-energy multiphoton imaging of neurons and oligodendrocytes in deep murine brain with a fiber laser

Here we demonstrate high-pulse-energy multiphoton microscopy (MPM) for intravital imaging of neurons and oligodendrocytes in the murine brain. Pulses with an order of magnitude higher energy (~ 10 nJ) were employed from a ytterbium doped fiber laser source at a 1-MHz repetition rate, as compared to the standard 80-MHz Ti:Sapphire laser. Intravital imaging was performed on mice expressing common fluorescent proteins, including green (GFP) and yellow fluorescent proteins (YFP), and TagRFPt. One fifth of the average power could be used for superior depths of MPM imaging, as compared to the Ti:Sapphire laser: A depth of ~ 860 µm was obtained by imaging the Thy1-YFP brain in vivo with 6.5 mW, and cortical myelin as deep as 400 µm ex vivo by intrinsic third-harmonic generation using 50 mW. The substantially higher pulse energy enables novel regimes of photophysics to be exploited for microscopic imaging. The limitation from higher order phototoxicity is also discussed.

Learned adaptive multiphoton illumination microscopy for large-scale immune response imaging

Multiphoton microscopy is a powerful technique for deep in vivo imaging in scattering samples. However, it requires precise, sample-dependent increases in excitation power with depth in order to generate contrast in scattering tissue, while minimizing photobleaching and phototoxicity. We show here how adaptive imaging can optimize illumination power at each point in a 3D volume as a function of the sample's shape, without the need for specialized fluorescent labeling. Our method relies on training a physics-based machine learning model using cells with identical fluorescent labels imaged in situ. We use this technique for in vivo imaging of immune responses in mouse lymph nodes following vaccination. We achieve visualization of physiologically realistic numbers of antigen-specific T cells (~2 orders of magnitude lower than previous studies), and demonstrate changes in the global organization and motility of dendritic cell networks during the early stages of the immune response. We provide a step-by-step tutorial for implementing this technique using exclusively open-source hardware and software.

Wavefront Shaping Concepts for Application in Optical Coherence Tomography-A Review

Optical coherence tomography (OCT) enables three-dimensional imaging with resolution on the micrometer scale. The technique relies on the time-of-flight gated detection of light scattered from a sample and has received enormous interest in applications as versatile as non-destructive testing, metrology and non-invasive medical diagnostics. However, in strongly scattering media such as biological tissue, the penetration depth and imaging resolution are limited. Combining OCT imaging with wavefront shaping approaches significantly leverages the capabilities of the technique by controlling the scattered light field through manipulation of the field incident on the sample. This article reviews the main concepts developed so far in the field and discusses the latest results achieved with a focus on signal enhancement and imaging.

Long-range remote focusing by image-plane aberration correction

Laser scanning plays an important role in a broad range of applications. Toward 3D aberration-free scanning, a remote focusing technique has been developed for high-speed imaging applications. However, the implementation of remote focusing often suffers from a limited axial scan range as a result of unknown aberration. Through simple analysis, we show that the sample-to-image path length conservation is crucially important to the remote focusing performance. To enhance the axial scan range, we propose and demonstrate an image-plane aberration correction method. Using a static correction, we can effectively improve the focus quality over a large defocusing range. Experimentally, we achieved ∼three times greater defocusing range than that of conventional methods. This technique can broadly benefit the implementations of high-speed large-volume 3D imaging.

Adaptive optics via pupil ring segmentation improves spherical aberration correction for two-photon imaging of optically cleared tissues

Optical clearing methods reduce the optical scattering of biological samples and thereby extend optical imaging penetration depth. However, refractive index mismatch between the immersion media of objectives and clearing reagents induces spherical aberration (SA), causing significant degradation of fluorescence intensity and spatial resolution. We present an adaptive optics method based on pupil ring segmentation to correct SA in optically cleared samples. Our method demonstrates superior SA correction over a modal-based adaptive optics method and restores the fluorescence intensity and resolution at high imaging depth. Moreover, the method can derive an SA correction map for the whole imaging volume based on three representative measurements. It facilitates SA correction during image acquisition without intermittent SA measurements. We applied this method in mouse brain tissues treated with different optical clearing methods. The results illustrate that the synaptic structures of neurons within 900 μm depth can be clearly resolved after SA correction.

Adaptive optics two-photon endomicroscopy enables deep-brain imaging at synaptic resolution over large volumes

Optical deep-brain imaging in vivo at high resolution has remained a great challenge over the decades. Two-photon endomicroscopy provides a minimally invasive approach to image buried brain structures, once it is integrated with a gradient refractive index (GRIN) lens embedded in the brain. However, its imaging resolution and field of view are compromised by the intrinsic aberrations of the GRIN lens. Here, we develop a two-photon endomicroscopy by adding adaptive optics based on direct wavefront sensing, which enables recovery of diffraction-limited resolution in deep-brain imaging. A new precompensation strategy plays a critical role to correct aberrations over large volumes and achieve rapid random-access multiplane imaging. We investigate the neuronal plasticity in the hippocampus, a critical deep brain structure, and reveal the relationship between the somatic and dendritic activity of pyramidal neurons.

Disordered Optics: Exploiting Multiple Light Scattering and Wavefront Shaping for Nonconventional Optical Elements

Advances in diverse areas such as inspection, imaging, manufacturing, telecommunications, and information processing have been stimulated by novel optical devices. Conventional material ingredients for these devices are typically made of homogeneous refractive or diffractive materials and require sophisticated design and fabrication, which results in practical limitations related to their form and functional figures of merit. To overcome such limitations, recent developments in the application of disordered materials as novel optical elements have indicated great potential in enabling functionalities that go beyond their conventional counterparts, while the materials exhibit potential advantages with respect to reduced form factors. Combined with wavefront shaping, disordered materials enable dynamic transitions between multiple functionalities in a single active optical device. Recent progress in this field is summarized to gain insight into the physical principles behind disordered optics with regard to their advantages in various applications as well as their limitations compared to conventional optics.

Second harmonic generation characterization of collagen in whole bone

Bone is a unique biological composite material made up of a highly structured collagen mesh matrix and mineral deposits. Although mineral provides stiffness, collagen's secondary organization provides a critical role in bone elasticity. Here, we performed polarimetric analysis of bone collagen fibers using second harmonic generation (SHG) imaging to evaluate lamella sheets and collagen fiber integrity in intact cranial bone. Our polarimetric data was fitted to a model accounting for diattenuation, polarization cross-talk, and birefringence. We compared our data to the fitted model and found no significant difference between our polarimetric observation and the representation of these scattering properties up to 70 µm deep. We also observed a loss of resolution as we imaged up to 70 µm deep into bone but a conservation of polarimetric response. Polarimetric SHG allows for the discrimination of collagen lamellar sheet structures in intact bone. Our work could allow for label-free identification of disease states and monitor the efficacy of therapies for bone disorders.

Aberration-free 3D imaging via DMD-based two-photon microscopy and sensorless adaptive optics

In this Letter, we present a new, to our knowledge, aberration-free 3D imaging technique based on digital micromirror device (DMD)-based two-photon microscopy and sensorless adaptive optics (AO), where 3D random-access scanning and modal wavefront correction are realized using a single DMD chip at 22.7 kHz. Specifically, the DMD is simultaneously used as a deformable mirror to modulate a distorted wavefront and a fast scanner to maneuver the laser focus in a 3D space by designed binary holograms. As such, aberration-free 3D imaging is realized by superposing the wavefront correction and 3D scanning holograms. Compared with conventional AO devices and methods, the DMD system can apply optimal wavefront correction information to different imaging regions or even individual pixels without compromising the scanning speed and device resolution. In the experiments, we first focus the laser through a diffuser and apply sensorless AO to retrieve a corrected focus. After that, the DMD performs 3D scanning on a Drosophila brain labeled with green fluorescent protein. The two-photon imaging results, where optimal wavefront correction information is applied to 3×3 separate regions, demonstrate significantly improved resolution and image quality. The new DMD-based imaging solution presents a compact, low-cost, and effective solution for aberration-free two-photon deep tissue imaging, which may find important applications in the field of biophotonics.

Real-time frequency-encoded spatiotemporal focusing through scattering media using a programmable 2D ultrafine optical frequency comb

Optical wavefront shaping is a powerful tool for controlling photons in strongly scattering media. Its speed, however, has been the bottleneck for in vivo applications. Moreover, unlike spatial focusing, temporal focusing from a continuous-wave source has rarely been exploited yet is highly desired for nonlinear photonics. Here, we present a novel real-time frequency-encoded spatiotemporal (FEST) focusing technology. FEST focusing uses a novel programmable two-dimensional optical frequency comb with an ultrafine linewidth to perform single-shot wavefront measurements, with a fast single-pixel detector. This technique enables simultaneous spatial and temporal focusing at microsecond scales through thick dynamic scattering media. This technology also enabled us to discover the large-scale temporal shift, a new phenomenon that, with the conventional spatial memory effect, establishes a space-time duality. FEST focusing opens a new avenue for high-speed wavefront shaping in the field of photonics.

Reliability of wavefront shaping based on coherent optical adaptive technique in deep tissue focusing

Wavefront shaping can compensate the wavefront distortions in deep tissue focusing, leading to an improved penetration depth. However, when using the backscattered signals as the feedback, unexpected compensation bias may be introduced, resulting in focusing position deviations or even no focus in the illumination focal plane. Here we investigated the reliability of wavefront shaping based on coherent optical adaptive technique in deep tissue focusing by measuring the position deviations between the foci in the illumination focal plane and the epi-detection plane. The experimental results show that when the penetration depth reaches 150 μm in mouse brain tissue (with scattering coefficient ~22.42 mm^-1 ) using a 488 nm laser and an objective lens with 0.75 numerical aperture, the center of the real focus will deviate out of one radius range of the Airy disk while the optimized focus in the epi-detection plane maintained basically at the center. With the penetration depth increases, the peak to background ratio of the focus in the illumination focal plane decreases faster than that in the epi-detection plane. The results indicate that when the penetration depth reaches 150 μm, feedback based on backscattered signals will make wavefront shaping lose its reliability, which may provide a guidance for applications of non-invasive precise optogenetics or deep tissue optical stimulation using wavefront shaping methods. A, Intensity distribution in the epi-detection plane and the illumination focal plane before and after correction, corresponding to brain sections with 250 and 300 μm thickness, respectively. Scale bar is 2 μm. B, Averaged focusing deviations in the epi-detection plane (optimized) and the illumination focal plane (monitored) after compensation. The unit of the ordinate is one Airy disk diameter. Black dashed line represents one Airy disk radius. Bars represent the SE of each measurement set.

Dynamic conjugate F-SHARP microscopy

Optical microscopy is an indispensable tool in biomedical sciences, but its reach in deep tissues is limited due to aberrations and scattering. This problem can be overcome by wavefront-shaping techniques, albeit at limited fields of view (FOVs). Inspired by astronomical imaging, conjugate wavefront shaping can lead to an increased field of view in microscopy, but this correction is limited to a set depth and cannot be dynamically adapted. Here, we present a conjugate wavefront-shaping scheme based on focus scanning holographic aberration probing (F-SHARP). We combine it with a compact implementation that can be readily adapted to a variety of commercial and home-built two-photon microscopes. We demonstrate the power of the method by imaging with high resolution over extended FOV (>80 µm) deeper than 400 μm inside a mouse brain through a thinned skull.

A Digital-Enhanced Chip-Scale Photoacoustic Sensor System for Blood Core Temperature Monitoring and In Vivo Imaging

Monolithic integration of photoacoustic (PA) sensor with compact size, lightweight, and low power consumption is attractive to be implemented on wearable medical devices for in vivo blood metabolic sensing and imaging. This work presents a miniaturized chip-scale mixed-signal photoacoustic sensor system which can achieve coherent lock-in function to detect weak target PA signals noninvasively at in vivo scenarios of poor signal to noise ratio (SNR) and strong interferences. A low-noise amplifier (LNA), a 3rd order Butterworth low-pass filter (LPF), and a variable-gain amplifier (VGA) chain with 10 MHz cutoff frequency are implemented on-chip to attain a high-quality sensing performance with 50-dB dynamic range. A Gilbert-cell type multiplier is integrated on-chip to fulfill the coherent lock-in process on acquired PA signals in a closed-loop process with an embedded FPGA system. Fabricated in 65-nm CMOS technology, the prototype PA sensor system demonstrated 50 μV sensitivity. The functions of the chip-scale PA sensor system enhanced by coherent lock-in process were validated through the experiments on temperature monitoring and vessel imaging. The PA receiver chip occupies an area of 0.6 mm² and consumes 20 mW at a 1.8-V supply.

Tissue-Clearing Technique and Cutaneous Nerve Biopsies: Quantification of the Intraepidermal Nerve-Fiber Density Using Active Clarity Technique-Pressure Related Efficient and Stable Transfer of Macromolecules Into Organs

Background and Purpose

Cutaneous nerve biopsies based on two-dimensional analysis have been regarded as a creditable assessment tool for diagnosing peripheral neuropathies. However, advancements in methodological imaging are required for the analysis of intact structures of peripheral nerve fibers. A tissue-clearing and labeling technique facilitates three-dimensional imaging of internal structures in unsectioned, whole biological tissues without excessive time or labor costs. We sought to establish whether a tissue-clearing and labeling technique could be used for the diagnostic evaluation of peripheral neuropathies.

Methods

Five healthy individuals and four patients with small-fiber neuropathy (SFN) and postherpetic neuralgia (PHN) were prospectively enrolled. The conventional methods of indirect immunofluorescence (IF) and bright-field immunohistochemistry (IHC) were adopted in addition to the tissue-clearing and labeling method called active clarity technique-pressure related efficient and stable transfer of macromolecules into organs (ACT-PRESTO) to quantify the intraepidermal nerve-fiber density (IENFD).

Results

The mean IENFD values obtained by IF, bright-field IHC, and ACT-PRESTO in the healthy control group were 6.54, 6.44, and 90.19 fibers/mm², respectively; the corresponding values in the patients with SFN were 1.99, 2.32, and 48.12 fibers/mm², respectively, and 3.06, 2.87, and 47.21 fibers/mm², respectively, in the patients with PHN.

Conclusions

This study has shown that a tissue-clearing method provided not only rapid and highly reproducible three-dimensional images of cutaneous nerve fibers but also yielded reliable quantitative IENFD data. Quantification of the IENFD using a tissue-clearing and labeling technique is a promising way to improve conventional cutaneous nerve biopsies.