Field of view advantage of conjugate adaptive optics in microscopy applications

Closed-loop experiments and brain machine interfaces with multiphoton microscopy

In the field of neuroscience, the importance of constructing closed-loop experimental systems has increased in conjunction with technological advances in measuring and controlling neural activity in live animals. We provide an overview of recent technological advances in the field, focusing on closed-loop experimental systems where multiphoton microscopy-the only method capable of recording and controlling targeted population activity of neurons at a single-cell resolution in vivo-works through real-time feedback. Specifically, we present some examples of brain machine interfaces (BMIs) using in vivo two-photon calcium imaging and discuss applications of two-photon optogenetic stimulation and adaptive optics to real-time BMIs. We also consider conditions for realizing future optical BMIs at the synaptic level, and their possible roles in understanding the computational principles of the brain.

Adaptive optical imaging with entangled photons

Adaptive optics (AO) has revolutionized imaging in fields from astronomy to microscopy by correcting optical aberrations. In label-free microscopes, however, conventional AO faces limitations because of the absence of a guide star and the need to select an optimization metric specific to the sample and imaging process. Here, we propose an AO approach leveraging correlations between entangled photons to directly correct the point spread function. This guide star-free method is independent of the specimen and imaging modality. We demonstrate the imaging of biological samples in the presence of aberrations using a bright-field imaging setup operating with a source of spatially entangled photon pairs. Our approach performs better than conventional AO in correcting specific aberrations, particularly those involving substantial defocus. Our work improves AO for label-free microscopy and could play a major role in the development of quantum microscopes.

Tandem aberration correction optics (TACO) in wide-field structured illumination microscopy

Structured illumination microscopy (SIM) is a powerful super-resolution imaging technique that uses patterned illumination to down-modulate high spatial-frequency information of samples. However, the presence of spatially-dependent aberrations can severely disrupt the illumination pattern, limiting the quality of SIM imaging. Conventional adaptive optics (AO) techniques that employ wavefront correctors at the pupil plane are not capable of effectively correcting these spatially-dependent aberrations. We introduce the Tandem Aberration Correction Optics (TACO) approach that combines both pupil AO and conjugate AO for aberration correction in SIM. TACO incorporates a deformable mirror (DM) for pupil AO in the detection path to correct for global aberrations, while a spatial light modulator (SLM) is placed at the plane conjugate to the aberration source near the sample plane, termed conjugate AO, to compensate spatially-varying aberrations in the illumination path. Our numerical simulations and experimental results show that the TACO approach can recover the illumination pattern close to an ideal condition, even when severely misshaped by aberrations, resulting in high-quality super-resolution SIM reconstruction. The TACO approach resolves a critical traditional shortcoming of aberration correction for structured illumination. This advance significantly expands the application of SIM imaging in the study of complex, particularly biological, samples and should be effective in other wide-field microscopies.

Large field of view aberrations correction with deformable lenses and multi conjugate adaptive optics

Optical microscopes can have limited resolution due to aberrations caused by samples and sample holders. Using deformable mirrors and wavefront sensorless optimization algorithms can correct these aberrations, but the correction is limited to a small area of the field of view. This study presents an adaptive optics method that uses a series of plug-and-play deformable lenses for large field of view wavefront correction. A direct wavefront measurement method using the spinning sub-pupil aberration measurement technique is combined with correction based on the deformable lenses. Experimental results using fluorescence microscopy with a wide field and a light sheet fluorescence microscope show that the proposed method can achieve detection and correction over an extended field of view with a compact transmissive module placed in the detection path of the microscope. This method could improve the resolution and accuracy of imaging in a variety of fields, including biology and materials science.

Three-dimensional ultrasound matrix imaging

Matrix imaging paves the way towards a next revolution in wave physics. Based on the response matrix recorded between a set of sensors, it enables an optimized compensation of aberration phenomena and multiple scattering events that usually drastically hinder the focusing process in heterogeneous media. Although it gave rise to spectacular results in optical microscopy or seismic imaging, the success of matrix imaging has been so far relatively limited with ultrasonic waves because wave control is generally only performed with a linear array of transducers. In this paper, we extend ultrasound matrix imaging to a 3D geometry. Switching from a 1D to a 2D probe enables a much sharper estimation of the transmission matrix that links each transducer and each medium voxel. Here, we first present an experimental proof of concept on a tissue-mimicking phantom through ex-vivo tissues and then, show the potential of 3D matrix imaging for transcranial applications.

Aberration free synthetic aperture second harmonic generation holography

Second harmonic generation (SHG) microscopy is a valuable tool for optical microscopy. SHG microscopy is normally performed as a point scanning imaging method, which lacks phase information and is limited in spatial resolution by the spatial frequency support of the illumination optics. In addition, aberrations in the illumination are difficult to remove. We propose and demonstrate SHG holographic synthetic aperture holographic imaging in both the forward (transmission) and backward (epi) imaging geometries. By taking a set of holograms with varying incident angle plane wave illumination, the spatial frequency support is increased and the input and output pupil phase aberrations are estimated and corrected - producing diffraction limited SHG imaging that combines the spatial frequency support of the input and output optics. The phase correction algorithm is computationally efficient and robust and can be applied to any set of measured field imaging data.

Adaptive inverse mapping: a model-free semi-supervised learning approach towards robust imaging through dynamic scattering media

Imaging through scattering media is a useful and yet demanding task since it involves solving for an inverse mapping from speckle images to object images. It becomes even more challenging when the scattering medium undergoes dynamic changes. Various approaches have been proposed in recent years. However, none of them are able to preserve high image quality without either assuming a finite number of sources for dynamic changes, assuming a thin scattering medium, or requiring access to both ends of the medium. In this paper, we propose an adaptive inverse mapping (AIP) method, which requires no prior knowledge of the dynamic change and only needs output speckle images after initialization. We show that the inverse mapping can be corrected through unsupervised learning if the output speckle images are followed closely. We test the AIP method on two numerical simulations: a dynamic scattering system formulated as an evolving transmission matrix and a telescope with a changing random phase mask at a defocused plane. Then we experimentally apply the AIP method to a multimode-fiber-based imaging system with a changing fiber configuration. Increased robustness in imaging is observed in all three cases. AIP method's high imaging performance demonstrates great potential in imaging through dynamic scattering media.

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.

Ultrasound Matrix Imaging-Part II: The Distortion Matrix for Aberration Correction Over Multiple Isoplanatic Patches

This is the second article in a series of two which report on a matrix approach for ultrasound imaging in heterogeneous media. This article describes the quantification and correction of aberration, i.e. the distortion of an image caused by spatial variations in the medium speed-of-sound. Adaptive focusing can compensate for aberration, but is only effective over a restricted area called the isoplanatic patch. Here, we use an experimentally-recorded matrix of reflected acoustic signals to synthesize a set of virtual transducers. We then examine wave propagation between these virtual transducers and an arbitrary correction plane. Such wave-fronts consist of two components: (i) An ideal geometric wave-front linked to diffraction and the input focusing point, and; (ii) Phase distortions induced by the speed-of-sound variations. These distortions are stored in a so-called distortion matrix, the singular value decomposition of which gives access to an optimized focusing law at any point. We show that, by decoupling the aberrations undergone by the outgoing and incoming waves and applying an iterative strategy, compensation for even high-order and spatially-distributed aberrations can be achieved. After a numerical validation of the process, ultrasound matrix imaging (UMI) is applied to the in-vivo imaging of a gallbladder. A map of isoplanatic modes is retrieved and is shown to be strongly correlated with the arrangement of tissues constituting the medium. The corresponding focusing laws yield an ultrasound image with drastically improved contrast and transverse resolution. UMI thus provides a flexible and powerful route towards computational ultrasound.

Space-variant Shack-Hartmann wavefront sensing based on affine transformation estimation

The space-variant wavefront reconstruction problem inherently exists in deep tissue imaging. In this paper, we propose a framework of Shack-Hartmann wavefront space-variant sensing with extended source illumination. The space-variant wavefront is modeled as a four-dimensional function where two dimensions are in the spatial domain and two are in the Fourier domain with priors that both gently vary. Here, the affine transformation is used to characterize the wavefront space-variant function. Correspondingly, the zonal and modal methods are both escalated to adapt to four-dimensional representation and reconstruction. Experiments and simulations show double to quadruple improvements in space-variant wavefront reconstruction accuracy compared to the conventional space-invariant correlation method.

Recent advances in optical imaging through deep tissue: imaging probes and techniques

Optical imaging has been essential for scientific observations to date, however its biomedical applications has been restricted due to its poor penetration through tissues. In living tissue, signal attenuation and limited imaging depth caused by the wave distortion occur because of scattering and absorption of light by various molecules including hemoglobin, pigments, and water. To overcome this, methodologies have been proposed in the various fields, which can be mainly categorized into two stategies: developing new imaging probes and optical techniques. For example, imaging probes with long wavelength like NIR-II region are advantageous in tissue penetration. Bioluminescence and chemiluminescence can generate light without excitation, minimizing background signals. Afterglow imaging also has high a signal-to-background ratio because excitation light is off during imaging. Methodologies of adaptive optics (AO) and studies of complex media have been established and have produced various techniques such as direct wavefront sensing to rapidly measure and correct the wave distortion and indirect wavefront sensing involving modal and zonal methods to correct complex aberrations. Matrix-based approaches have been used to correct the high-order optical modes by numerical post-processing without any hardware feedback. These newly developed imaging probes and optical techniques enable successful optical imaging through deep tissue. In this review, we discuss recent advances for multi-scale optical imaging within deep tissue, which can provide reseachers multi-disciplinary understanding and broad perspectives in diverse fields including biophotonics for the purpose of translational medicine and convergence science.

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.

Diffractive optical system design by cascaded propagation

Modern design of complex optical systems relies heavily on computational tools. These frequently use geometrical optics as well as Fourier optics. Fourier optics is typically used for designing thin diffractive elements, placed in the system's aperture, generating a shift-invariant Point Spread Function (PSF). A major bottleneck in applying Fourier Optics in many cases of interest, e.g. when dealing with multiple, or out-of-aperture elements, comes from numerical complexity. In this work, we propose and implement an efficient and differentiable propagation model based on the Collins integral, which enables the optimization of diffractive optical systems with unprecedented design freedom using backpropagation. We demonstrate the applicability of our method, numerically and experimentally, by engineering shift-variant PSFs via thin plate elements placed in arbitrary planes inside complex imaging systems, performing cascaded optimization of multiple planes, and designing optimal machine-vision systems by deep learning.

Aberration measurement and correction on a large field of view in fluorescence microscopy

The aberrations induced by the sample and/or by the sample holder limit the resolution of optical microscopes. Wavefront correction can be achieved using a deformable mirror with wavefront sensorless optimization algorithms but, despite the complexity of these systems, the level of correction is often limited to a small area in the field of view of the microscope. In this work, we present a plug and play module for aberration measurement and correction. The wavefront correction is performed through direct wavefront reconstruction using the spinning-pupil aberration measurement and controlling a deformable lens in closed loop. The lens corrects the aberrations in the center of the field of view, leaving residual aberrations at the margins, that are removed by anisoplanatic deconvolution. We present experimental results obtained in fluorescence microscopy, with a wide field and a light sheet fluorescence microscope. These results indicate that detection and correction over the full field of view can be achieved with a compact transmissive module placed in the detection path of the fluorescence microscope.

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.

In vivo volumetric imaging of calcium and glutamate activity at synapses with high spatiotemporal resolution

Studying neuronal activity at synapses requires high spatiotemporal resolution. For high spatial resolution in vivo imaging at depth, adaptive optics (AO) is required to correct sample-induced aberrations. To improve temporal resolution, Bessel focus has been combined with two-photon fluorescence microscopy (2PFM) for fast volumetric imaging at subcellular lateral resolution. To achieve both high-spatial and high-temporal resolution at depth, we develop an efficient AO method that corrects the distorted wavefront of Bessel focus at the objective focal plane and recovers diffraction-limited imaging performance. Applying AO Bessel focus scanning 2PFM to volumetric imaging of zebrafish larval and mouse brains down to 500 µm depth, we demonstrate substantial improvements in the sensitivity and resolution of structural and functional measurements of synapses in vivo. This enables volumetric measurements of synaptic calcium and glutamate activity at high accuracy, including the simultaneous recording of glutamate activity of apical and basal dendritic spines in the mouse cortex.

High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy

Multiphoton microscopy has become a powerful tool with which to visualize the morphology and function of neural cells and circuits in the intact mammalian brain. However, tissue scattering, optical aberrations and motion artifacts degrade the imaging performance at depth. Here we describe a minimally invasive intravital imaging methodology based on three-photon excitation, indirect adaptive optics (AO) and active electrocardiogram gating to advance deep-tissue imaging. Our modal-based, sensorless AO approach is robust to low signal-to-noise ratios as commonly encountered in deep scattering tissues such as the mouse brain, and permits AO correction over large axial fields of view. We demonstrate near-diffraction-limited imaging of deep cortical spines and (sub)cortical dendrites up to a depth of 1.4 mm (the edge of the mouse CA1 hippocampus). In addition, we show applications to deep-layer calcium imaging of astrocytes, including fibrous astrocytes that reside in the highly scattering corpus callosum.

Adaptive optics in super-resolution microscopy

Fluorescence microscopy has become a routine tool in biology for interrogating life activities with minimal perturbation. While the resolution of fluorescence microscopy is in theory governed only by the diffraction of light, the resolution obtainable in practice is also constrained by the presence of optical aberrations. The past two decades have witnessed the advent of super-resolution microscopy that overcomes the diffraction barrier, enabling numerous biological investigations at the nanoscale. Adaptive optics, a technique borrowed from astronomical imaging, has been applied to correct for optical aberrations in essentially every microscopy modality, especially in super-resolution microscopy in the last decade, to restore optimal image quality and resolution. In this review, we briefly introduce the fundamental concepts of adaptive optics and the operating principles of the major super-resolution imaging techniques. We highlight some recent implementations and advances in adaptive optics for active and dynamic aberration correction in super-resolution microscopy.

Adaptive optics with spatio-temporal lock-in detection for temporal focusing microscopy

Wavefront distortion in temporal focusing microscopy (TFM) results in a distorted temporal profile of the excitation pulses owing to spatio-temporal coupling. Since the pulse duration is dramatically changed in the excitation volume, it is difficult to correct the temporal profile for a thick sample. Here, we demonstrate adaptive optics (AO) correction in a thick sample. We apply structured illumination microscopy (SIM) to an AO correction in wide-field TFM to decrease the change in the pulse duration in the signal detection volume. The AO correction with SIM was very successful in a thick sample for which AO correction with TFM failed.

Manifestation of aberrations in full-field optical coherence tomography

We report on a theoretical model for image formation in full-field optical coherence tomography (FFOCT). Because the spatial incoherence of the illumination acts as a virtual confocal pinhole in FFOCT, its imaging performance is equivalent to a scanning time-gated coherent confocal microscope. In agreement with optical experiments enabling a precise control of aberrations, FFOCT is shown to have nearly twice the resolution of standard imaging at moderate aberration level. Beyond a rigorous study on the sensitivity of FFOCT with respect to aberrations, this theoretical model paves the way towards an optimized design of adaptive optics and computational tools for high-resolution and deep imaging of biological tissues.

Spinning pupil aberration measurement for anisoplanatic deconvolution

The aberrations in an optical microscope are commonly measured and corrected at one location in the field of view, within the so-called isoplanatic patch. Full-field correction is desirable for high-resolution imaging of large specimens. Here we present, to the best of our knowledge, a novel wavefront detector, based on pupil sampling with subapertures, measuring the aberrated wavefront phase at each position of the specimen. Based on this measurement, we propose a region-wise deconvolution that provides an anisoplanatic reconstruction of the sample image. Our results indicate that the measurement and correction of the aberrations can be performed in a wide-field fluorescence microscope over its entire field of view.

Adaptive optics for high-resolution imaging

Adaptive optics (AO) is a technique that corrects for optical aberrations. It was originally proposed to correct for the blurring effect of atmospheric turbulence on images in ground-based telescopes and was instrumental in the work that resulted in the Nobel prize-winning discovery of a supermassive compact object at the centre of our galaxy. When AO is used to correct for the eye's imperfect optics, retinal changes at the cellular level can be detected, allowing us to study the operation of the visual system and to assess ocular health in the microscopic domain. By correcting for sample-induced blur in microscopy, AO has pushed the boundaries of imaging in thick tissue specimens, such as when observing neuronal processes in the brain. In this primer, we focus on the application of AO for high-resolution imaging in astronomy, vision science and microscopy. We begin with an overview of the general principles of AO and its main components, which include methods to measure the aberrations, devices for aberration correction, and how these components are linked in operation. We present results and applications from each field along with reproducibility considerations and limitations. Finally, we discuss future directions.

Adaptive-glasses time-domain FFOCT for wide-field high-resolution retinal imaging with increased SNR

The highest three-dimensional (3D) resolution possible in in vivo retinal imaging is achieved by combining optical coherence tomography (OCT) and adaptive optics. However, this combination brings important limitations, such as small field-of-view and complex, cumbersome systems, preventing so far the translation of this technology from the research lab to clinics. In this Letter, we mitigate these limitations by combining our compact time-domain full-field OCT (FFOCT) with a multi-actuator adaptive lens positioned just in front of the eye, in a technique we call the adaptive-glasses wavefront sensorless approach. Through this approach, we demonstrate that ocular aberrations can be corrected, increasing the FFOCT signal-to-noise ratio (SNR) and enabling imaging of different retinal layers with a 3D cellular resolution over a 5^∘×5^∘ field-of-view, without apparent anisoplanatism.

Model-based wavefront shaping microscopy

Wavefront shaping is increasingly being used in modern microscopy to obtain high-resolution images deep inside inhomogeneous media. Wavefront shaping methods typically rely on the presence of a "guide star" to find the optimal wavefront to mitigate the scattering of light. However, the use of guide stars poses severe limitations. Notably, only objects in the close vicinity of the guide star can be imaged. Here, we introduce a guide-star-free wavefront shaping method in which the optimal wavefront is computed using a digital model of the sample. The refractive index model of the sample, that serves as the input for the computation, is constructed in situ by the microscope itself. In a proof of principle imaging experiment, we demonstrate a large improvement in the two-photon fluorescence signal through a diffuse medium, outperforming state-of-the-art wavefront shaping by a factor of two in imaging depth.

Plug-and-play adaptive optics for commercial laser scanning fluorescence microscopes based on an adaptive lens

In this Letter, we present a solution for simple implementation of adaptive optics in any existing laser scanning fluorescence microscope. Adaptive optics are implemented by the introduction of a multiactuator adaptive lens between the microscope body and the objective lens. Correction is performed with a sensorless method by optimizing the quality of the images presented on screen by the microscope software. We present the results acquired on both a commercial linear excitation confocal microscope and a custom-made multiphoton excitation microscope.

Distortion matrix concept for deep optical imaging in scattering media

In optical imaging, light propagation is affected by the inhomogeneities of the medium. Sample-induced aberrations and multiple scattering can strongly degrade the image resolution and contrast. On the basis of a dynamic correction of the incident and/or reflected wavefronts, adaptive optics has been used to compensate for those aberrations. However, it only applies to spatially invariant aberrations or to thin aberrating layers. Here, we propose a global and noninvasive approach based on the distortion matrix concept. This matrix basically connects any focusing point of the image with the distorted part of its wavefront in reflection. A singular value decomposition of the distortion matrix allows to correct for high-order aberrations and forward multiple scattering over multiple isoplanatic modes. Proof-of-concept experiments are performed through biological tissues including a turbid cornea. We demonstrate a Strehl ratio enhancement up to 2500 and recover a diffraction-limited resolution until a depth of 10 scattering mean free paths.

Distortion matrix approach for ultrasound imaging of random scattering media

Focusing waves inside inhomogeneous media is a fundamental problem for imaging. Spatial variations of wave velocity can strongly distort propagating wave fronts and degrade image quality. Adaptive focusing can compensate for such aberration but is only effective over a restricted field of view. Here, we introduce a full-field approach to wave imaging based on the concept of the distortion matrix. This operator essentially connects any focal point inside the medium with the distortion that a wave front, emitted from that point, experiences due to heterogeneities. A time-reversal analysis of the distortion matrix enables the estimation of the transmission matrix that links each sensor and image voxel. Phase aberrations can then be unscrambled for any point, providing a full-field image of the medium with diffraction-limited resolution. Importantly, this process is particularly efficient in random scattering media, where traditional approaches such as adaptive focusing fail. Here, we first present an experimental proof of concept on a tissue-mimicking phantom and then, apply the method to in vivo imaging of human soft tissues. While introduced here in the context of acoustics, this approach can also be extended to optical microscopy, radar, or seismic imaging.

Anisoplanatic adaptive optics in parallelized laser scanning microscopy

Inhomogeneities in the refractive index of a biological microscopy sample can introduce phase aberrations, severely impairing the quality of images. Adaptive optics can be employed to correct for phase aberrations and improve image quality. However, conventional adaptive optics can only correct a single phase aberration for the whole field of view (isoplanatic correction) while, due to the highly heterogeneous nature of biological tissues, the sample induced aberrations in microscopy often vary throughout the field of view (anisoplanatic aberration), limiting significantly the effectiveness of adaptive optics. This paper reports on a new approach for aberration correction in laser scanning confocal microscopy, in which a spatial light modulator is used to generate multiple excitation points in the sample to simultaneously scan different portions of the field of view with completely independent correction, achieving anisoplanatic compensation of sample induced aberrations, in a significantly shorter time compared to sequential isoplanatic correction of multiple image subregions. The method was tested in whole Drosophila brains and in larval Zebrafish, each showing a dramatic improvement in resolution and sharpness when compared to conventional isoplanatic adaptive optics.

Extended field-of-view adaptive optics in microscopy via numerical field segmentation

Sample-induced optical aberrations in microscopy are, in general, field dependent, limiting their correction via pupil adaptive optics (AO) to the center of the available field-of-view (FoV). This is a major hindrance, particularly for deep tissue imaging, where AO has a significant impact. We present a new wide-field AO microscopy scheme, in which the deformable element is located at the pupil plane of the objective. To maintain high-quality correction across its entirety, the FoV is partitioned into small segments, and a separate aberration estimation is performed for each via a modal-decomposition-based indirect wavefront sensing algorithm. A final full-field image is synthesized by stitching of the partitions corrected consecutively and independently via their respective measured aberrations. The performance and limitations of the method are experimentally explored on synthetic samples imaged via a custom-developed AO fluorescence microscope featuring an optofluidic refractive wavefront modulator.

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.

Aberration corrections of doughnut beam by adaptive optics in the turbid medium

The doughnut beam is a spatially structured beam which has been widely used in super-resolution microscopy, laser trapping and so on. However, when it passes through thick scattering medium, aberrations will seriously affect its performance. Currently, adaptive optics (AO) has become one of the most powerful tools to compensate aberrations. However, conventional AO always suffers from limited corrected field of view (FOV). Here, we propose a method with conjugate AO system based on coherent optical adaptive technique. The results show that the corrected FOV can be improved effectively. For a wide range of the optical applications with doughnut beam, our method has potentials in correcting aberrations with high speed in turbid media.(A) Mouse brain slice, (B) the distribution of r _PAO , (C) the distribution of r _CAO . The vortex beam focus of the blue point in (B) and (C) among a 137.5 × 137.5 μm FOV (D1) ideally, (D2) with scattering, (D3) in pupil AO system and (D4) in conjugate AO system.

Adaptive optics microspectrometer for cross-correlation measurement of microfluidic flows

Mapping flows in vivo is essential for the investigation of cardiovascular pathologies in animal models. The limitation of optical-based methods, such as space-time cross correlation, is the scattering of light by the connective and fat components and the direct wave front distortion by large inhomogeneities in the tissue. Nonlinear excitation of the sample fluorescence helps us by reducing light scattering in excitation. However, there is still a limitation on the signal-background due to the wave front distortion. We develop a diffractive optical microscope based on a single spatial light modulator (SLM) with no movable parts. We combine the correction of wave front distortions to the cross-correlation analysis of the flow dynamics. We use the SLM to shine arbitrary patterns of spots on the sample, to correct their optical aberrations, to shift the aberration corrected spot array on the sample for the collection of fluorescence images, and to measure flow velocities from the cross-correlation functions computed between couples of spots. The setup and the algorithms are tested on various microfluidic devices. By applying the adaptive optics correction algorithm, it is possible to increase up to 5 times the signal-to-background ratio and to reduce approximately of the same ratio the uncertainty of the flow speed measurement. By working on grids of spots, we can correct different aberrations in different portions of the field of view, a feature that allows for anisoplanatic aberrations correction. Finally, being more efficient in the excitation, we increase the accuracy of the speed measurement by employing a larger number of spots in the grid despite the fact that the two-photon excitation efficiency scales as the fourth power of this number: we achieve a twofold decrease of the uncertainty and a threefold increase of the accuracy in the evaluation of the flow speed.

Large field of view correction by using conjugate adaptive optics with multiple guide stars

Adaptive optics has been widely used in the optical microscopy to recover high-resolution images deep into the sample. However, the corrected field of view (FOV) with a single correction is generally limited, which seriously restricts the imaging speed. In this article, we demonstrate a high-speed wavefront correction method by using the conjugate adaptive optical correction with multiple guide stars (CAOMG) based on the coherent optical adaptive technique. The results show that the CAOMG method can greatly improve the corrected FOV. For 120-μm-thick mouse brain tissue, the corrected FOV can be improved up to ~243 times of the conventional pupil adaptive optics (PAO) without additional time consumption. Therefore, this study shows the potential of high-speed imaging through scattering medium in biological science.

Fourier conjugate adaptive optics for deep-tissue large field of view imaging

Light microscopy enables multifunctional imaging of biological specimens at unprecedented depths and resolutions. However, the performance of all optical methods degrades with the imaging depth due to sample-induced aberrations. Methods of adaptive optics (AO), which are aimed at pre-compensation of these distortions, still suffer from a limited field of view and imaging depth as well as inconvenient microscope design. Here, I propose and investigate a new approach to overcome these limitations: Fourier image plane conjugate AO. Two experimental designs of the new approach are carefully studied, and an accurate comparison between different methods of AO is presented. Fourier conjugate AO provides a larger field of view, which can only be limited by the angular memory effect, and allows the optimal use of the spatial light modulator. Moreover, theoretically possible imaging depth of Fourier conjugate AO is limited only by the working distance of the objective and not by the microscope design.

Extended-image-based correction of aberrations using a deformable mirror with hysteresis

With a view to the next generation of large space telescopes, we investigate guide-star-free, image-based aberration correction using a unimorph deformable mirror in a plane conjugate to the primary mirror. We designed and built a high-resolution imaging testbed to evaluate control algorithms. In this paper we use an algorithm based on the heuristic hill climbing technique and compare the correction in three different domains, namely the voltage domain, the domain of the Zernike modes, and the domain of the singular modes of the deformable mirror. Through our systematic experimental study, we found that successive control in two domains effectively counteracts uncompensated hysteresis of the deformable mirror.

Brillouin micro-spectroscopy through aberrations via sensorless adaptive optics

Brillouin spectroscopy is a powerful optical technique for non-contact viscoelastic characterizations which has recently found applications in three-dimensional mapping of biological samples. Brillouin spectroscopy performances are rapidly degraded by optical aberrations and have therefore been limited to homogenous transparent samples. In this work, we developed an adaptive optics (AO) configuration designed for Brillouin scattering spectroscopy to engineer the incident wavefront and correct for aberrations. Our configuration does not require direct wavefront sensing and the injection of a "guide-star"; hence, it can be implemented without the need for sample pre-treatment. We used our AO-Brillouin spectrometer in aberrated phantoms and biological samples and obtained improved precision and resolution of Brillouin spectral analysis; we demonstrated 2.5-fold enhancement in Brillouin signal strength and 1.4-fold improvement in axial resolution because of the correction of optical aberrations.

High precision wavefront control in point spread function engineering for single emitter localization

Point spread function (PSF) engineering is used in single emitter localization to measure the emitter position in 3D and possibly other parameters such as the emission color or dipole orientation as well. Advanced PSF models such as spline fits to experimental PSFs or the vectorial PSF model can be used in the corresponding localization algorithms in order to model the intricate spot shape and deformations correctly. The complexity of the optical architecture and fit model makes PSF engineering approaches particularly sensitive to optical aberrations. Here, we present a calibration and alignment protocol for fluorescence microscopes equipped with a spatial light modulator (SLM) with the goal of establishing a wavefront error well below the diffraction limit for optimum application of complex engineered PSFs. We achieve high-precision wavefront control, to a level below 20 mλ wavefront aberration over a 30 minute time window after the calibration procedure, using a separate light path for calibrating the pixel-to-pixel variations of the SLM, and alignment of the SLM with respect to the optical axis and Fourier plane within 3 μm (x/y) and 100 μm (z) error. Aberrations are retrieved from a fit of the vectorial PSF model to a bead z-stack and compensated with a residual wavefront error comparable to the error of the SLM calibration step. This well-calibrated and corrected setup makes it possible to create complex '3D+λ' PSFs that fit very well to the vectorial PSF model. Proof-of-principle bead experiments show precisions below 10 nm in x, y, and λ, and below 20 nm in z over an axial range of 1 μm with 2000 signal photons and 12 background photons.

Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking

Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information on single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems.

Large-field-of-view imaging by multi-pupil adaptive optics

For in vivo deep imaging at high spatiotemporal resolutions, we developed Multi-Pupil Adaptive Optics (MPAO) which enables simultaneous wavefront correction over a large imaging field-of-view. The current implementation improves correction area by nine times over that of conventional methods. MPAO’s capability of spatially independent wavefront control further enables 3D nonplanar imaging. We applied MPAO to in vivo structural and functional imaging of biological dynamics in mammalian brain.

Three-dimensional focusing through scattering media using conjugate adaptive optics with remote focusing (CAORF)

The small correction volume for conventional wavefront shaping methods limits their application in biological imaging through scattering media. We demonstrate large volume wavefront shaping through a scattering layer with a single correction by conjugate adaptive optics and remote focusing (CAORF). The remote focusing module can maintain the conjugation between the adaptive optical (AO) element and the scattering layer during three-dimensional scanning. This new configuration provides a wider correction volume by better utilization of the memory effect in a fast three-dimensional laser scanning microscope. Our results show that the proposed system can provide 10 times wider axial field of view compared with a conventional conjugate AO system when 16,384 segments are used on a spatial light modulator. We also demonstrate three-dimensional fluorescence imaging, multi-spot patterning through a scattering layer and two-photon imaging through mouse skull tissue.

Magnetic Fluid Deformable Mirror with a Two-Layer Layout of Actuators †

In this paper, a new type of magnetic fluid deformable mirror (MFDM) with a two-layer layout of actuators is proposed to improve the correction performance for full-order aberrations with a high spatial resolution. The shape of the magnetic fluid surface is controlled by the combined magnetic field generated by the Maxwell coil and the two-layer array of miniature coils. The upper-layer actuators which have a small size and high density are used to compensate for small-amplitude high-order aberrations and the lower-layer actuators which have a big size and low density are used to correct large-amplitude low-order aberrations. The analytical model of this deformable mirror is established and the aberration correction performance is verified by the experimental results. As a new kind of wavefront corrector, the MFDM has major advantages such as large stroke, low cost, and easy scalability and fabrication.

Adaptive optics full-field optical coherence tomography

We describe a simple and compact full-field optical coherence tomography (FFOCT) setup coupled to a transmissive liquid crystal spatial light modulator (LCSLM) to induce or correct aberrations. To reduce the system complexity, strict pupil conjugation was abandoned because low-order aberrations are often dominant. We experimentally confirmed a recent theoretical and experimental demonstration that the image resolution was almost insensitive to aberrations that mostly induce a reduction of the signal level. As a consequence, an image-based algorithm was applied for the optimization process by using the FFOCT image intensity as the metric. Aberration corrections were demonstrated with both an USAF resolution target and biological samples for LCSLM-induced and sample-induced wavefront distortions.

Widefield fluorescence microscopy with sensor-based conjugate adaptive optics using oblique back illumination

We describe a wavefront sensor strategy for the implementation of adaptive optics (AO) in microscope applications involving thick, scattering media. The strategy is based on the exploitation of multiple scattering to provide oblique back illumination of the wavefront-sensor focal plane, enabling a simple and direct measurement of the flux-density tilt angles caused by aberrations at this plane. Advantages of the sensor are that it provides a large measurement field of view (FOV) while requiring no guide star, making it particularly adapted to a type of AO called conjugate AO, which provides a large correction FOV in cases when sample-induced aberrations arise from a single dominant plane (e.g., the sample surface). We apply conjugate AO here to widefield (i.e., nonscanning) fluorescence microscopy for the first time and demonstrate dynamic wavefront correction in a closed-loop implementation.

Separation of ballistic and diffusive fluorescence photons in confocal Light-Sheet Microscopy of Arabidopsis roots

Image quality in light-sheet fluorescence microscopy is strongly affected by the shape of the illuminating laser beam inside embryos, plants or tissue. While the phase of Gaussian or Bessel beams propagating through thousands of cells can be partly controlled holographically, the propagation of fluorescence light to the detector is difficult to control. With each scatter process a fluorescence photon loses information necessary for the image generation. Using Arabidopsis root tips we demonstrate that ballistic and diffusive fluorescence photons can be separated by analyzing the image spectra in each plane without a priori knowledge. We introduce a theoretical model allowing to extract typical scattering parameters of the biological material. This allows to attenuate image contributions from diffusive photons and to amplify the relevant image contributions from ballistic photons through a depth dependent deconvolution. In consequence, image contrast and resolution are significantly increased and scattering artefacts are minimized especially for Bessel beams with confocal line detection.

Characterisation of the effects of optical aberrations in single molecule techniques

Optical aberrations degrade image quality in fluorescence microscopy, including for single-molecule based techniques. These depend on post-processing to localize individual molecules in an image series. Using simulated data, we show the impact of optical aberrations on localization success, accuracy and precision. The peak intensity and the proportion of successful localizations strongly reduces when the aberration strength is greater than 1.0 rad RMS, while the precision of each of those localisations is halved. The number of false-positive localisations exceeded 10% of the number of true-positive localisations at an aberration strength of only ~0.6 rad RMS when using the ThunderSTORM package, but at greater than 1.0 rad RMS with the Radial Symmetry package. In the presence of coma, the localization error reaches 100 nm at ~0.6 rad RMS of aberration strength. The impact of noise and of astigmatism for axial resolution are also considered. Understanding the effect of aberrations is crucial when deciding whether the addition of adaptive optics to a single-molecule microscope could significantly increase the information obtainable from an image series.

Sensorless adaptive optics implementation in widefield optical sectioning microscopy inside in vivo Drosophila brain

We present an implementation of a sensorless adaptive optics loop in a widefield fluorescence microscope. This setup is designed to compensate for aberrations induced by the sample on both excitation and emission pathways. It allows fast optical sectioning inside a living Drosophila brain. We present a detailed characterization of the system performances. We prove that the gain brought to optical sectioning by realizing structured illumination microscopy with adaptive optics down to 50 μm deep inside living Drosophila brain.

In vivo volumetric imaging of biological dynamics in deep tissue via wavefront engineering

Biological systems undergo dynamical changes continuously which span multiple spatial and temporal scales. To study these complex biological dynamics in vivo, high-speed volumetric imaging that can work at large imaging depth is highly desired. However, deep tissue imaging suffers from wavefront distortion, resulting in reduced Strehl ratio and image quality. Here we combine the two wavefront engineering methods developed in our lab, namely the optical phase-locked ultrasound lens based volumetric imaging and the iterative multiphoton adaptive compensation technique, and demonstrate in vivo volumetric imaging of microglial and mitochondrial dynamics at large depth in mouse brain cortex and lymph node, respectively.

Axial range of conjugate adaptive optics in two-photon microscopy

We describe an adaptive optics technique for two-photon microscopy in which the deformable mirror used for aberration compensation is positioned in a plane conjugate to the plane of the aberration. We demonstrate in a proof-of-principle experiment that this technique yields a large field of view advantage in comparison to standard pupil-conjugate adaptive optics. Further, we show that the extended field of view in conjugate AO is maintained over a relatively large axial translation of the deformable mirror with respect to the conjugate plane. We conclude with a discussion of limitations and prospects for the conjugate AO technique in two-photon biological microscopy.

High-resolution in vivo imaging of mouse brain through the intact skull

Multiphoton microscopy is the current method of choice for in vivo deep-tissue imaging. The long laser wavelength suffers less scattering, and the 3D-confined excitation permits the use of scattered signal light. However, the imaging depth is still limited because of the complex refractive index distribution of biological tissue, which scrambles the incident light and destroys the optical focus needed for high resolution imaging. Here, we demonstrate a wavefront-shaping scheme that allows clear imaging through extremely turbid biological tissue, such as the skull, over an extended corrected field of view (FOV). The complex wavefront correction is obtained and directly conjugated to the turbid layer in a noninvasive manner. Using this technique, we demonstrate in vivo submicron-resolution imaging of neural dendrites and microglia dynamics through the intact skulls of adult mice. This is the first observation, to our knowledge, of dynamic morphological changes of microglia through the intact skull, allowing truly noninvasive studies of microglial immune activities free from external perturbations.