Aberration correction for confocal imaging in refractive-index-mismatched media

High spatial resolution underwater confocal LiDAR: reduction of optical aberrations in air-water interfaces using a dome port

We study the impact of optical aberrations in underwater scanning confocal inelastic imaging arising from refraction at oblique incidences on a refractive index-mismatched air-glass-water interface. We experimentally demonstrate that optical aberrations at non-normal incidence drastically reduce the intensity of the inelastic signal and deteriorate the system resolution. At a 2.5° incidence angle, the return signal decreases to about 20% of its peak value at normal incidence. We implement passive correction using a spherical glass dome that is co-centered with the pivot point of the scanning mirror to ensure near-normal incidence on the interface irrespective of the scanning angle and depth. This configuration provides a drastic reduction in the optical aberrations within an angular range from -20° to 20°. The optical system is modeled in ray tracing software for validation. The interfacing of a scanning confocal system with a dome port unlocks near-diffraction-limited underwater imaging over wide areas without resorting to complex adaptive wavefront manipulation.

Development of a large volume line scanning, high spectral range and resolution 3D hyperspectral photoluminescence imaging microscope for diamond and other high refractive index materials

Hyperspectral photoluminescence (PL) imaging is a powerful technique that can be used to understand the spatial distribution of emitting species in many materials. Volumetric hyperspectral imaging of weakly emitting color centers often necessitates considerable data collection times when using commercial systems. We report the development of a line-scanning hyperspectral imaging microscope capable of measuring the luminescence emission spectra for diamond volumes up to 2.20 × 30.00 × 6.30 mm with a high lateral spatial resolution of 1-3 µm. In an single X-λ measurement, spectra covering a 711 nm range, in a band from 400-1100 nm, with a spectral resolution up to 0.25 nm can be acquired. Data sets can be acquired with 723 (X) × 643 (Y) × 1172 (λ) pixels at a rate of 6 minutes/planar image slice, allowing for volumetric hyperspectral imaging with high sampling. This instrument demonstrates the ability to detect emission from several different color centers in diamond both at the surface and internally, providing a non-destructive method to probe their 3D spatial distribution, and is currently not achievable with any other commonly used system or technique.

Spatial frequency-based correction of the spherical aberration in living brain imaging

Optical errors, including spherical aberrations, hinder high-resolution imaging of biological samples due to biochemical components and physical properties. We developed the Deep-C microscope system to achieve aberration-free images, employing a motorized correction collar and contrast-based calculations. However, current contrast-maximization techniques, such as the Brenner gradient method, inadequately assess specific frequency bands. The Peak-C method addresses this issue, but its arbitrary neighbor selection and susceptibility to the noise limit its effectiveness. In this paper, we emphasize the importance of a broad spatial frequency range for accurate spherical aberration correction and propose Peak-F. This spatial frequency-based system utilizes a fast Fourier transform as a bandpass filter. This approach overcomes Peak-C's limitations and comprehensively covers the low-frequency domain of image spatial frequencies.

Tracing multiple scattering trajectories for deep optical imaging in scattering media

Multiple light scattering hampers imaging objects in complex scattering media. Approaches used in real practices mainly aim to filter out multiple scattering obscuring the ballistic waves that travel straight through the scattering medium. Here, we propose a method that makes the deterministic use of multiple scattering for microscopic imaging of an object embedded deep within scattering media. The proposed method finds a stack of multiple complex phase plates that generate similar light trajectories as the original scattering medium. By implementing the inverse scattering using the identified phase plates, our method rectifies multiple scattering and amplifies ballistic waves by almost 600 times. This leads to a significant increase in imaging depth-more than three times the scattering mean free path-as well as the correction of image distortions. Our study marks an important milestone in solving the long-standing high-order inverse scattering problems.

Practical strategies for robust and inexpensive imaging of aqueous-cleared tissues

Lightsheet microscopy offers an ideal method for imaging of large (mm-cm scale) biological tissues rendered transparent via optical clearing protocols. However the diversity of clearing technologies and tissue types, and how these are adapted to the microscope can make tissue mounting complicated and somewhat irreproducible. Tissue preparation for imaging can involve glues and or equilibration in a variety of expensive and/or proprietary formulations. Here we present practical advice for mounting and capping cleared tissues in optical cuvettes for macroscopic imaging, providing a standardised 3D cell that can be imaged routinely and relatively inexpensively. We show that acrylic cuvettes cause minimal spherical aberration with objective numerical apertures less than 0.65. Furthermore, we describe methods for aligning and assessing the light sheets, discriminating fluorescence from autofluorescence, identifying chromatic artefacts due to differential scattering and removing streak artefacts such that they do not confound downstream 3D object segmentation analyses, with mouse embryo, liver and heart imaging as demonstrated examples.

Mapping nanoscale topographic features in thick tissues with speckle diffraction tomography

Resolving three-dimensional morphological features in thick specimens remains a significant challenge for label-free imaging. We report a new speckle diffraction tomography (SDT) approach that can image thick biological specimens with ~500 nm lateral resolution and ~1 μm axial resolution in a reflection geometry. In SDT, multiple-scattering background is rejected through spatiotemporal gating provided by dynamic speckle-field interferometry, while depth-resolved refractive index maps are reconstructed by developing a comprehensive inverse-scattering model that also considers specimen-induced aberrations. Benefiting from the high-resolution and full-field quantitative imaging capabilities of SDT, we successfully imaged red blood cells and quantified their membrane fluctuations behind a turbid medium with a thickness of 2.8 scattering mean-free paths. Most importantly, we performed volumetric imaging of cornea inside an ex vivo rat eye and quantified its optical properties, including the mapping of nanoscale topographic features of Dua's and Descemet's membranes that had not been previously visualized.

Dynamic correction of optical aberrations for height-independent selective laser induced etching processing strategies

Optical aberrations are a critical issue for tight focusing and high precision manufacturing with ultrashort pulsed laser radiation in transparent media. Controlling the wave front of ultrashort laser pulses enable the correction of low order phase front distortion and significantly enhances the simplification of laser-based manufacturing of 3D-parts in glass. The influence of system-inherent, dominating aberrations such as spherical and astigmatic aberrations affect the focal area, the beam caustic and therefore the focus intensity distribution. We correct these aberrations by means of a spatial light modulator (SLM) for various processing depths in glass thickness of up to 12 mm. This flexible aberration correction significantly simplifies the process control and scanning strategies for the selective laser induced etching process. The influence on the selectivity is investigated by comparing the three different focus conditions of the intrinsic microscope objective aberration corrected, the aberrated and the SLM aberration corrected beam profile. The previously necessary pulse energy adjustment for different z positions in the glass volume is compensated via SLM aberration correction in the end. Furthermore, the spatial extend of the modified and etched area is investigated. In consequence, a simplified scan strategy and depth-independent processing parameters can be achieved for the selective laser induced etching process.

Efficient framework of solving time-gated reflection matrix for imaging through turbid medium

Imaging through turbid medium is a long pursuit in many research fields, such as biomedicine, astronomy and automatic vehicle, in which the reflection matrix-based method is a promising solution. However, the epi-detection geometry suffers from round-trip distortion and it is challenging to isolate the input and output aberrations in non-ideal cases due to system imperfections and measurement noises. Here, we present an efficient framework based on single scattering accumulation together with phase unwrapping that can accurately separate input and output aberrations from the noise-affected reflection matrix. We propose to only correct the output aberration while suppressing the input aberration by incoherent averaging. The proposed method is faster in convergence and more robust against noise, avoiding precise and tedious system adjustments. In both simulations and experiments, we demonstrate the diffraction-limited resolution capability under optical thickness beyond 10 scattering mean free paths, showing the potential of applications in neuroscience and dermatology.

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.

Experimental Validation of Shifted Position-Diffuse Reflectance Imaging (SP-DRI) on Optical Phantoms

Numerous diseases such as hemorrhage, sepsis or cardiogenic shock induce a heterogeneous perfusion of the capillaries. To detect such alterations in the human blood flow pattern, diagnostic devices must provide an appropriately high spatial resolution. Shifted position-diffuse reflectance imaging (SP-DRI) has the potential to do so; it is an all-optical diagnostic technique. So far, SP-DRI has mainly been developed using Monte Carlo simulations. The present study is therefore validating this algorithm experimentally on realistic optical phantoms with thread structures down to 10 μm in diameter; a SP-DRI sensor prototype was developed and realized by means of additive manufacturing. SP-DRI turned out to be functional within this experimental framework. The position of the structures within the optical phantoms become clearly visible using SP-DRI, and the structure thickness is reflected as modulation in the SP-DRI signal amplitude; this performed well for a shift along the x axis as well as along the y axis. Moreover, SP-DRI successfully masked the pronounced influence of the illumination cone on the data. The algorithm showed significantly superior to a mere raw data inspection. Within the scope of the study, the constructive design of the SP-DRI sensor prototype is discussed and potential for improvement is explored.

Stealth dicing of 1-mm-thick glass with aberration-free axial multi-focus beams

Laser stealth dicing can realize material separation with negligible surface damage, but severe aberrations in thick materials degrade processing quality. This Letter presents a nonlinear point-to-point transformation method combined with spherical aberration compensation to achieve aberration-free axial multi-focus beams. The focus peak intensity increases 7 times at a depth of 0.5 mm after spherical aberration compensation, and reaches 44 times at 3.5 mm. Spherical aberration compensation experiments showed that the width of the heat-affected zone remains almost unchanged at different depths inside the glass, and stealth dicing experiments for 1-mm-thick glass demonstrated that aberration-free 1-focus, 2-foci, and 3-foci stealth dicing can be successfully realized.

Complex-Amplitude-Modulation Vectorial Excitation Beam for High-Resolution Observation of Deep Regions in Two-Photon Microscopy

In two-photon microscopy, aberration correction is an essential technique for realizing high resolution in deep regions. A spatial light modulator (SLM) incorporated into an optical system for two-photon microscopy performs pre-compensation on the wavefront of the excitation beam, restoring the resolution close to the diffraction limit even in the deep region of a biological sample. If a spatial resolution smaller than the diffraction limit can be achieved along with aberration correction, the importance of two-photon microscopy for deep region observation will increase further. In this study, we realize higher resolution observations in the deep region by combining two resolution-enhancement methods and an aberration correction method. Therefore, a z-polarizer is added to the aberration-correction optical system, and the SLM modulates the amplitude and phase of the excitation beam; in other words, complex-amplitude modulation is performed. The lateral resolution is found to be approximately 20% higher than the diffraction limit obtained using a circularly polarized beam. Verification was conducted by simulation and experimentation using model samples and ex vivo biological samples. The proposed method has the potential to be effective for live imaging and photostimulation of the deep region of the sample, although it requires only minor changes to the conventional optical system that performs aberration correction.

Generalised adaptive optics method for high-NA aberration-free refocusing in refractive-index-mismatched media

Phase aberrations are introduced when focusing by a high-numerical aperture (NA) objective lens into refractive-index-mismatched (RIM) media. The axial focus position in these media can be adjusted through either optical remote-focusing or mechanical stage translation. Despite the wide interest in remote-focusing, no generalised control algorithm using Zernike polynomials has been presented that performs independent remote-focusing and RIM correction in combination with mechanical stage translation. In this work, we thoroughly review derivations that model high-NA defocus and RIM aberration. We show through both numerical simulation and experimental results that optical remote-focusing using an adaptive device and mechanical stage translation are not optically equivalent processes, such that one cannot fully compensate for the other without additional aberration compensation. We further establish new orthogonal modes formulated using conventional Zernike modes and discuss its device programming to control high-NA remote-focusing and RIM correction as independent primary modes in combination with mechanical stage translation for aberration-free refocusing. Numerical simulations are performed, and control algorithms are validated experimentally by fabricating graphitic features in diamond using direct laser writing.

2.5D microscopy with polarization independent SLM for enhanced detection efficiency and aberration correction

Fast, volumetric imaging by fluorescence microscopy is essential in studying biological phenomena and cellular functions. Recently, single-shot 2.5D microscopy showed promising results for high-throughput quantitative subcellular analysis via extended depth of field imaging without sequential z-scanning; however, the detection efficiency was limited and it lacked depth-induced aberration correction. Here we report that a spatial light modulator (SLM) in a polarization insensitive configuration can significantly improve the detection efficiency of 2.5D microscopy, while also compensating for aberrations at large imaging depths caused by the refractive index mismatch between the sample and the immersion medium. We highlight the improved efficiency via quantitative single-molecule RNA imaging of mammalian cells with a 2-fold improvement in the fluorescence intensity compared to a conventional SLM-based microscopy. We demonstrate the aberration correction capabilities and extended depth of field by imaging thick specimens with fewer z-scanning steps.

Aberration correction in stimulated emission depletion microscopy to increase imaging depth in living brain tissue

Significance: Stimulated emission depletion (STED) microscopy enables nanoscale imaging of live samples, but it requires a specific spatial beam shaping that is highly sensitive to optical aberrations, limiting its depth penetration. Therefore, there is a need for methods to reduce optical aberrations and improve the spatial resolution of STED microscopy inside thick biological tissue. Aim: The aim of our work was to develop and validate a method based on adaptive optics to achieve an a priori correction of spherical aberrations as a function of imaging depth. Approach: We first measured the aberrations in a phantom sample of gold and fluorescent nanoparticles suspended in an agarose gel with a refractive index closely matching living brain tissue. We then used a spatial light modulator to apply corrective phase shifts and validate this calibration approach by imaging neurons in living brain slices. Results: After quantifying the spatial resolution in depth in phantom samples, we demonstrated that the corrections can substantially increase image quality in living brain slices. Specifically, we could measure structures as small as 80 nm at a depth of 90    μ m inside the biological tissue and obtain a 60% signal increase after correction. Conclusion: We propose a simple and robust approach to calibrate and compensate the distortions of the STED beam profile introduced by spherical aberrations with increasing imaging depth and demonstrated that this method offers significant improvements in microscopy performance for nanoscale cellular imaging in live tissue.

In-situ diagnostic of femtosecond laser probe pulses for high resolution ultrafast imaging

Ultrafast imaging is essential in physics and chemistry to investigate the femtosecond dynamics of nonuniform samples or of phenomena with strong spatial variations. It relies on observing the phenomena induced by an ultrashort laser pump pulse using an ultrashort probe pulse at a later time. Recent years have seen the emergence of very successful ultrafast imaging techniques of single non-reproducible events with extremely high frame rate, based on wavelength or spatial frequency encoding. However, further progress in ultrafast imaging towards high spatial resolution is hampered by the lack of characterization of weak probe beams. For pump-probe experiments realized within solids or liquids, because of the difference in group velocities between pump and probe, the determination of the absolute pump-probe delay depends on the sample position. In addition, pulse-front tilt is a widespread issue, unacceptable for ultrafast imaging, but which is conventionally very difficult to evaluate for the low-intensity probe pulses. Here we show that a pump-induced micro-grating generated from the electronic Kerr effect provides a detailed in-situ characterization of a weak probe pulse. It allows solving the two issues of absolute pump-probe delay determination and pulse-front tilt detection. Our approach is valid whatever the transparent medium with non-negligible Kerr index, whatever the probe pulse polarization and wavelength. Because it is nondestructive and fast to perform, this in-situ probe diagnostic can be repeated to calibrate experimental conditions, particularly in the case where complex wavelength, spatial frequency or polarization encoding is used. We anticipate that this technique will enable previously inaccessible spatiotemporal imaging in a number of fields of ultrafast science at the micro- and nanoscale.

Adaptive Optical Two-Photon Microscopy for Surface-Profiled Living Biological Specimens

We developed adaptive optical (AO) two-photon excitation microscopy by introducing a spatial light modulator (SLM) in a commercially available microscopy system. For correcting optical aberrations caused by refractive index (RI) interfaces at a specimen's surface, spatial phase distributions of the incident excitation laser light were calculated using 3D coordination of the RI interface with a 3D ray-tracing method. Based on the calculation, we applied a 2D phase-shift distribution to a SLM and achieved the proper point spread function. AO two-photon microscopy improved the fluorescence image contrast in optical phantom mimicking biological specimens. Furthermore, it enhanced the fluorescence intensity from tubulin-labeling dyes in living multicellular tumor spheroids and allowed successful visualization of dendritic spines in the cortical layer V of living mouse brains in the secondary motor region with a curved surface. The AO approach is useful for observing dynamic physiological activities in deep regions of various living biological specimens with curved surfaces.

Inhibition and enhancement of linear and nonlinear optical effects by conical phase front shaping for femtosecond laser material processing

The emergence of high-powered femtosecond lasers presents the opportunity for large volume processing inside of transparent materials, wherein a myriad of nonlinear optical and aberration effects typically convolves to distort the focused beam shape. In this paper, convex and concave conical phase fronts were imposed on femtosecond laser beams and focussed into wide-bandgap glass to generate a vortex beam with tuneable Gaussian-Bessel features offset from the focal plane. The influence of Kerr lensing, plasma defocussing, and surface aberration on the conical phase front shaping were examined over low to high pulse energy delivery and for shallow to deep processing tested to 2.5 mm focussing depth. By isolating the underlying processes, the results demonstrate how conical beams can systematically manipulate the degree of nonlinear interaction and surface aberration to facilitate a controllable inhibition or enhancement of Kerr lensing, plasma defocussing, and surface aberration effects. In this way, long and uniform filament tracks have been generated over shallow to deep focussing by harnessing surface aberration and conical beam shaping without the destabilizing Kerr lensing and plasma defocussing effects. A facile means for compressing and stretching of the focal interaction volume is presented for controlling the three-dimensional micro- and nano-structuring of transparent materials.

Compensating deep focusing distortion for femtosecond laser inscription of low-loss optical waveguides

Various beam shaping approaches were examined to counter the negative influence of surface aberration arising when inscribing optical waveguides deeply inside of glass with a femtosecond laser. Aberration correction was found unable to completely recover the low-loss waveguide properties, prompting a comprehensive examination of waveguides formed with focused Gaussian-Bessel beams. Diverging conical phase fronts are presented as a hybrid means of partial aberration correction to improve insertion loss and a new, to the best of our knowledge, means of asymmetric beam shaping. In this way, low-loss waveguides are presented over shallow to deep writing depth (2.8 mm) where morphological and modal properties could be further tuned with conical phase front.

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.

Improved 3D cellular morphometry of Caenorhabditis elegans embryos using a refractive index matching medium

Cell shape change is one of the driving forces of animal morphogenesis, and the model organism Caenorhabditis elegans has played a significant role in analyzing the underlying mechanisms involved. The analysis of cell shape change requires quantification of cellular shape descriptors, a method known as cellular morphometry. However, standard C. elegans live imaging methods limit the capability of cellular morphometry in 3D, as spherical aberrations generated by samples and the surrounding medium misalign optical paths. Here, we report a 3D live imaging method for C. elegans embryos that minimized spherical aberrations caused by refractive index (RI) mismatch. We determined the composition of a refractive index matching medium (RIMM) for C. elegans live imaging. The 3D live imaging with the RIMM resulted in a higher signal intensity in the deeper cell layers. We also found that the obtained images improved the 3D cell segmentation quality. Furthermore, our 3D cellular morphometry and 2D cell shape simulation indicated that the germ cell precursor P4 had exceptionally high cortical tension. Our results demonstrate that the RIMM is a cost-effective solution to improve the 3D cellular morphometry of C. elegans. The application of this method should facilitate understanding of C. elegans morphogenesis from the perspective of cell shape changes.

Dynamic aberration correction via spatial light modulator (SLM) for femtosecond direct laser writing: towards spherical voxels

Optical aberrations are a type of optical defect of imaging systems that hinder femtosecond direct laser write machining by changing voxel size and aspect ratio in different sample depths. We present an approach of compensating such aberrations using a liquid crystal spatial light modulator (SLM). Two methods for correcting are explored. They are based on backward ray tracing and Zernike polynomials. Experiments with a long focal distance lens (F = 25 and 50 mm) and microscope objective (100x, 0.9 NA) have been conducted. Specifically, aberration-free structuring with voxels of a constant aspect ratio of 1-1.5 is carried out throughout a 1 mm thick sample. Results show potential in simplifying direct laser writing and enabling new architectures made possible by near-spherical voxels.

Combining sample expansion and light sheet microscopy for the volumetric imaging of virus-infected cells with super-resolution

Expansion microscopy is a sample preparation technique that enables the optical imaging of biological specimens at super-resolution owing to their physical magnification, which is achieved through water-absorbing polymers. The technique uses readily available chemicals and does not require sophisticated equipment, thus offering super-resolution to laboratories that are not microscopy-specialised. Here we present a protocol combining sample expansion with light sheet microscopy to generate high-contrast, high-resolution 3D reconstructions of whole virus-infected cells. The results are superior to those achievable with comparable imaging modalities and reveal details of the infection cycle that are not discernible before expansion. An image resolution of approximately 95 nm could be achieved in samples labelled in 3 colours. We resolve that the viral nucleoprotein is accumulated at the membrane of vesicular structures within the cell cytoplasm and how these vesicles are positioned relative to cellular structures. We provide detailed guidance and a video protocol for the optimal application of the method and demonstrate its potential to study virus-host cell interactions.

Correction of refractive index mismatch-induced aberrations under radially polarized illumination by deep learning

Radially polarized field under strong focusing has emerged as a powerful manner for fluorescence microscopy. However, the refractive index (RI) mismatch-induced aberrations seriously degrade imaging performance, especially under high numerical aperture (NA). Traditional adaptive optics (AO) method is limited by its tedious procedure. Here, we present a computational strategy that uses artificial neural networks to correct the aberrations induced by RI mismatch. There are no requirements for expensive hardware and complicated wavefront sensing in our framework when the deep network training is completed. The structural similarity index (SSIM) criteria and spatial frequency spectrum analysis demonstrate that our deep-learning-based method has a better performance compared to the widely used Richardson-Lucy (RL) deconvolution method at different imaging depth on simulation data. Additionally, the generalization of our trained network model is tested on new types of samples that are not present in the training procedure to further evaluate the utility of the network, and the performance is also superior to RL deconvolution.

Addressing systematic errors in axial distance measurements in single-emitter localization microscopy

Nanoscale localization of point emitters is critical to several methods in optical fluorescence microscopy, including single-molecule super-resolution imaging and tracking. While the precision of the localization procedure has been the topic of extensive study, localization accuracy has been less emphasized, in part due to the challenge of producing an experimental sample containing unperturbed point emitters at known three-dimensional positions in a relevant geometry. We report a new experimental system which reproduces a widely-adopted geometry in high-numerical aperture localization microscopy, in which molecules are situated in an aqueous medium above a glass coverslip imaged with an oil-immersion objective. We demonstrate a calibration procedure that enables measurement of the depth-dependent point spread function (PSF) for open aperture imaging as well as imaging with engineered PSFs with index mismatch. We reveal the complicated, depth-varying behavior of the focal plane position in this system and discuss the axial localization biases incurred by common approximations of this behavior. We compare our results to theoretical calculations.

Three-Dimensional Single-Molecule Localization Microscopy in Whole-Cell and Tissue Specimens

Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. We focus on three-dimensional single-molecule localization microscopy and review some of the major roadblocks and developing solutions to resolving thick volumes of cells and tissues at the nanoscale in three dimensions. These challenges include background fluorescence, system- and sample-induced aberrations, and information carried by photons, as well as drift correction, volume reconstruction, and photobleaching mitigation. We also highlight examples of innovations that have demonstrated significant breakthroughs in addressing the abovementioned challenges together with their core concepts as well as their trade-offs.

Fluorescence Microscopy of the HIV-1 Envelope

Human immunodeficiency virus (HIV) infection constitutes a major health and social issue worldwide. HIV infects cells by fusing its envelope with the target cell plasma membrane. This process is mediated by the viral Env glycoprotein and depends on the envelope lipid composition. Fluorescent microscopy has been employed to investigate the envelope properties, and the processes of viral assembly and fusion, but the application of this technique to the study of HIV is still limited by a number of factors, such as the small size of HIV virions or the difficulty to label the envelope components. Here, we review fluorescence imaging studies of the envelope lipids and proteins, focusing on labelling strategies and model systems.

Adaptive optics in laser processing

Adaptive optics are becoming a valuable tool for laser processing, providing enhanced functionality and flexibility for a range of systems. Using a single adaptive element, it is possible to correct for aberrations introduced when focusing inside the workpiece, tailor the focal intensity distribution for the particular fabrication task and/or provide parallelisation to reduce processing times. This is particularly promising for applications using ultrafast lasers for three-dimensional fabrication. We review recent developments in adaptive laser processing, including methods and applications, before discussing prospects for the future.

Accurate aberration correction in confocal microscopy based on modal sensorless method

Confocal microscopy has the advantages of high resolution and optical sectioning ability over conventional microscopy. However, aberration induced by the optical system can compromise these advantages and considerably reduce the energy reaching the pointlike detector. We propose an accurate aberration correction method with a liquid-crystal spatial light modulator (LCSLM) in the confocal system. Each coefficient of Zernike aberration modes is calculated by directly measuring the variance of the images with different bias aberration modes. Large-coefficient (>0.7 rad) aberration is compensated first by LCSLM, following which aberrations with small coefficients are measured precisely, minimizing the cross talk between different kinds of aberrations. With this predistortion strategy, the aberration correction is much more accurate, and maximum image intensity in the normal and nonconjugated systems is improved by 2.5 times and 4 times compared to the normal correction method, respectively, demonstrating the effectiveness of our method.

Tailored Sample Mounting for Light-Sheet Fluorescence Microscopy of Clarified Specimens by Polydimethylsiloxane Casting

The combination of biological tissue clearing methods with light-sheet fluorescence microscopy (LSFM) allows acquiring images of specific biological structures of interest at whole organ scale and microscopic resolution. Differently to classical epifluorescence techniques, where the sample is cut into slices, LSFM preserves the whole organ architecture, which is of particular relevance for investigations of long-range neuronal circuits. This imaging modality comes with the need of new protocols for sample mounting. Gel matrix, hooks, tips, glues, and quartz cuvettes have been used to keep whole rodent organs in place during image acquisitions. The last one has the advantage of avoiding sample damage and optical aberrations when using a quartz refractive index (RI) matching solution. However, commercially available quartz cuvettes for such large samples are expensive. We propose the use of polydimethylsiloxane (PDMS) for creating tailor-made cuvettes for sample holding. For validation, we compared PDMS and quartz cuvettes by measuring light transmittance and performing whole mouse-brain imaging with LSFM. Moreover, imaging can be performed using an inexpensive RI matching solution, which further reduces the cost of the imaging process. Worth of note, the RI matching solution used in combination with PDMS leads to a moderate expansion of the sample with respect to its original size, which may represent an advantage when investigating small components, such as neuronal processes. Overall, we found the use of custom-made PDMS cuvettes advantageous in term of cost, image quality, or preservation of sample integrity with respect to other whole-mouse brain mounting strategies adopted for LSFM.

A stage-scanning two-photon microscope equipped with a temporal and a spatial pulse shaper: Enhance fluorescence signal by phase shaping

Here, we present a stage-scanning two-photon microscope (2PM) equipped with a temporal pulse shaper and a spatial light modulator enabling full control over spectral and spatial phases of the exciting laser pulse. We demonstrate the capability of correcting wavefronts and temporal pulse distortions without cross-dependencies induced by optical elements at the same time enhancing the fluorescence signal. We implemented phase resolved interferometric spectral modulation for temporal pulse shaping and the iterative feedback adaptive compensation technique for spatial pulse modulation as iterative techniques. Sample distortions were simulated by cover glass plates in the optical path and by chirping the exciting laser pulses. Optimization of the spectral and spatial phases results in a signal increase of 30% and nearly complete recovery of the losses. Applying a measured spatial compensation phase within a real leaf sample shows the enhancement in contrast due to wavefront shaping with local fluorescence increase up to 75%. The setup allows full independent control over spatial and spectral phases keeping or improving the spatial resolution of our microscope and provides the optimal tool for sensitive non-linear and coherent control microscopy.

Intrinsic refractive index matched 3D dSTORM with two objectives: Comparison of detection techniques

We have built a setup for 3D single molecule localisation microscopy (SMLM) where a very high resolution is achieved by, firstly, the use of two objectives instead of one and, secondly, minimizing optical aberrations by refractive index matching with a glycerol-water mixture as immersion medium in conjunction with glycerol-immersion objectives. Multiple optical paths of the microscope allow to switch between astigmatic and interferometric localisation along the optical axis, thus enabling a direct comparison of the performance of these localisation methods.

Microscope calibration using laser written fluorescence

There is currently no widely adopted standard for the optical characterization of fluorescence microscopes. We used laser written fluorescence to generate two- and three-dimensional patterns to deliver a quick and quantitative measure of imaging performance. We report on the use of two laser written patterns to measure the lateral resolution, illumination uniformity, lens distortion and color plane alignment using confocal and structured illumination fluorescence microscopes.

Aberration correction considering curved sample surface shape for non-contact two-photon excitation microscopy with spatial light modulator

In this paper, excitation light wavefront modulation is performed considering the curved sample surface shape to demonstrate high-quality deep observation using two-photon excitation microscopy (TPM) with a dry objective lens. A large spherical aberration typically occurs when the refractive index (RI) interface between air and the sample is a plane perpendicular to the optical axis. Moreover, the curved sample surface shape and the RI mismatch cause various aberrations, including spherical ones. Consequently, the fluorescence intensity and resolution of the obtained image are degraded in the deep regions. To improve them, we designed a pre-distortion wavefront for correcting the aberration caused by the curved sample surface shape by using a novel, simple optical path length difference calculation method. The excitation light wavefront is modulated to the pre-distortion wavefront by a spatial light modulator incorporated in the TPM system before passing through the interface, where the RI mismatch occurs. Thus, the excitation light is condensed without aberrations. Blood vessels were thereby observed up to an optical depth of 2,000 μm in a cleared mouse brain by using a dry objective lens.

Three dimensional live-cell STED microscopy at increased depth using a water immersion objective

Modern fluorescence superresolution microscopes are capable of imaging living cells on the nanometer scale. One of those techniques is stimulated emission depletion (STED) which increases the microscope's resolution many times in the lateral and the axial directions. To achieve these high resolutions not only close to the coverslip but also at greater depths, the choice of objective becomes crucial. Oil immersion objectives have frequently been used for STED imaging since their high numerical aperture (NA) leads to high spatial resolutions. But during live-cell imaging, especially at great penetration depths, these objectives have a distinct disadvantage. The refractive index mismatch between the immersion oil and the usually aqueous embedding media of living specimens results in unwanted spherical aberrations. These aberrations distort the point spread functions (PSFs). Notably, during z- and 3D-STED imaging, the resolution increase along the optical axis is majorly hampered if at all possible. To overcome this limitation, we here use a water immersion objective in combination with a spatial light modulator for z-STED measurements of living samples at great depths. This compact design allows for switching between objectives without having to adapt the STED beam path and enables on the fly alterations of the STED PSF to correct for aberrations. Furthermore, we derive the influence of the NA on the axial STED resolution theoretically and experimentally. We show under live-cell imaging conditions that a water immersion objective leads to far superior results than an oil immersion objective at penetration depths of 5-180 μm.

Self-interference 3D super-resolution microscopy for deep tissue investigations

Fluorescence localization microscopy has achieved near-molecular resolution capable of revealing ultra-structures, with a broad range of applications, especially in cellular biology. However, it remains challenging to attain such resolution in three dimensions and inside biological tissues beyond the first cell layer. Here we introduce SELFI, a framework for 3D single-molecule localization within multicellular specimens and tissues. The approach relies on self-interference generated within the microscope's point spread function (PSF) to simultaneously encode equiphase and intensity fluorescence signals, which together provide the 3D position of an emitter. We combined SELFI with conventional localization microscopy to visualize F-actin 3D filament networks and reveal the spatial distribution of the transcription factor OCT4 in human induced pluripotent stem cells at depths up to 50 µm inside uncleared tissue spheroids. SELFI paves the way to nanoscale investigations of native cellular processes in intact tissues.

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.

Super-resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices

Three‐dimensional (3D) super‐resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID‐treated slices, and 160‐nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)‐treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high‐NA confocal imaging. Thus, super‐resolution SIM imaging represents a promising high‐throughput method for revealing spine morphologies in single dendrites.

Reduction of chromatic dispersion using multiple carrier frequency patterns in SLM-based microscopy

Typically, spatial light modulator (SLM)-based microscopy is implemented using a carrier frequency in order to avoid disturbances due to the non-ideal modulation behavior of most SLMs. However, in combination with polychromatic light, this leads to strong chromatic aberrations due to the dispersion at the grating formed by the carrier frequency. In this contribution, we introduce a method based on the evaluation of multiple images obtained with different carrier frequency orientations. This way, chromatic aberrations and the limitation concerning the object field can be strongly reduced.

Adaptive optical versus spherical aberration corrections for in vivo brain imaging

Adjusting the objective correction collar is a widely used approach to correct spherical aberrations (SA) in optical microscopy. In this work, we characterized and compared its performance with adaptive optics in the context of in vivo brain imaging with two-photon fluorescence microscopy. We found that the presence of sample tilt had a deleterious effect on the performance of SA-only correction. At large tilt angles, adjusting the correction collar even worsened image quality. In contrast, adaptive optical correction always recovered optimal imaging performance regardless of sample tilt. The extent of improvement with adaptive optics was dependent on object size, with smaller objects having larger relative gains in signal intensity and image sharpness. These observations translate into a superior performance of adaptive optics for structural and functional brain imaging applications in vivo, as we confirmed experimentally.

Recovering fluorophore concentration profiles from confocal images near lateral refractive index step changes

Optical aberrations due to refractive index mismatches occur in various types of microscopy due to refractive differences between the sample and the immersion fluid or within the sample. We study the effects of lateral refractive index differences by fluorescence confocal laser scanning microscopy due to glass or polydimethylsiloxane cuboids and glass cylinders immersed in aqueous fluorescent solution, thereby mimicking realistic imaging situations in the proximity of these materials. The reduction in fluorescence intensity near the embedded objects was found to depend on the geometry and the refractive index difference between the object and the surrounding solution. The observed fluorescence intensity gradients do not reflect the fluorophore concentration in the solution. It is suggested to apply a Gaussian fit or smoothing to the observed fluorescence intensity gradient and use this as a basis to recover the fluorophore concentration in the proximity of the refractive index step change. The method requires that the reference and sample objects have the same geometry and refractive index. The best results were obtained when the sample objects were also used for reference since small differences such as uneven surfaces will result in a different extent of aberration.

Transmissive liquid-crystal device for correcting primary coma aberration and astigmatism in biospecimen in two-photon excitation laser scanning microscopy

All aberrations produced inside a biospecimen can degrade the quality of a three-dimensional image in two-photon excitation laser scanning microscopy. Previously, we developed a transmissive liquid-crystal device to correct spherical aberrations that improved the image quality of a fixed-mouse-brain slice treated with an optical clearing reagent. In this study, we developed a transmissive device that corrects primary coma aberration and astigmatism. The motivation for this study is that asymmetric aberration can be induced by the shape of a biospecimen and/or by a complicated refractive-index distribution in a sample; this can considerably degrade optical performance even near the sample surface. The device’s performance was evaluated by observing fluorescence beads. The device was inserted between the objective lens and microscope revolver and succeeded in improving the spatial resolution and fluorescence signal of a bead image that was originally degraded by asymmetric aberration. Finally, we implemented the device for observing a fixed whole mouse brain with a sloping surface shape and complicated internal refractive-index distribution. The correction with the device improved the spatial resolution and increased the fluorescence signal by ?2.4×. The device can provide a simple approach to acquiring higher-quality images of biospecimens.

Depth profiles in confocal optical microscopy: a simulation approach based on the second Rayleigh-Sommerfeld diffraction integral

A method is presented for recovering the intensity depth profile, by confocal optical microscopy, in transparent and amorphous samples with low scattering. The response function of a confocal Raman microscope has been determined by using the second Rayleigh-Sommerfeld diffraction integral and scalar wave optics within paraxial approximation, taking into account the refractive index mismatch between the sample and the medium surrounding the objective lens. An iterative multi-fitting-scheme, based on the conjugate gradient method and Brent algorithm, allowed to fit several depth profile curves simultaneously and retrieve the beam waist, the signal amplitude and the position of the sample surface. The reliability and accuracy of the theoretical procedure has been investigated through comparison with experimental measurements of the Raman depth profiles for different pinhole diameters. The model is shown to provide accurate description of the effect of the mismatch of the refractive index and of the dependence of the Raman signal on the depth with discrepancies lower than 3%. This procedure constitutes a first step towards the development of a manageable theoretical framework, amenable to a relatively simple numerical implementation, for the solution of the 'inverse' problem of finding the correct reconstruction of unknown profiles of chemical species within the sample, starting from experimental information gathered from micro-Raman depth profiling.

Aberration correction for direct laser written waveguides in a transverse geometry

The depth dependent spherical aberration is investigated for ultrafast laser written waveguides fabricated in a transverse writing geometry using the slit beam shaping technique in the low pulse repetition rate regime. The axial elongation of the focus caused by the aberration leads to a distortion of the refractive index change, and waveguides designed as single mode become multimode. We theoretically estimate a depth range over which the aberration effects can be compensated simply by adjusting the incident laser power. If deeper fabrication is required, it is demonstrated experimentally that the aberration can be successfully removed using adaptive optics to fabricate single mode optical waveguides over a depth range > 1 mm.

Three-dimensional STED microscopy of aberrating tissue using dual adaptive optics

When imaging through tissue, the optical inhomogeneities of the sample generate aberrations that can prevent effective Stimulated Emission Depletion (STED) imaging. This is particularly problematic for 3D-enhanced STED. We present here an adaptive optics implementation that incorporates two adaptive optic elements to enable correction in all beam paths, allowing performance improvement in thick tissue samples. We use this to demonstrate 3D STED imaging of complex structures in Drosophila melanogaster brains.

Correcting spherical aberrations in a biospecimen using a transmissive liquid crystal device in two-photon excitation laser scanning microscopy

Two-photon excitation laser scanning microscopy has enabled the visualization of deep regions in a biospecimen. However, refractive-index mismatches in the optical path cause spherical aberrations that degrade spatial resolution and the fluorescence signal, especially during observation at deeper regions. Recently, we developed transmissive liquid-crystal devices for correcting spherical aberration without changing the basic design of the optical path in a conventional laser scanning microscope. In this study, the device was inserted in front of the objective lens and supplied with the appropriate voltage according to the observation depth. First, we evaluated the device by observing fluorescent beads in single- and two-photon excitation laser scanning microscopes. Using a 25× water-immersion objective lens with a numerical aperture of 1.1 and a sample with a refractive index of 1.38, the device recovered the spatial resolution and the fluorescence signal degraded within a depth of 0.6 mm. Finally, we implemented the device for observation of a mouse brain slice in a two-photon excitation laser scanning microscope. An optical clearing reagent with a refractive index of 1.42 rendered the fixed mouse brain transparent. The device improved the spatial resolution and the yellow fluorescent protein signal within a depth of 0-0.54 mm.

Simple wavefront correction framework for two-photon microscopy of in-vivo brain

We present an easily implemented wavefront correction scheme that has been specifically designed for in-vivo brain imaging. The system can be implemented with a single liquid crystal spatial light modulator (LCSLM), which makes it compatible with existing patterned illumination setups, and provides measurable signal improvements even after a few seconds of optimization. The optimization scheme is signal-based and does not require exogenous guide-stars, repeated image acquisition or beam constraint. The unconstrained beam approach allows the use of Zernike functions for aberration correction and Hadamard functions for scattering correction. Low order corrections performed in mouse brain were found to be valid up to hundreds of microns away from the correction location.

Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) using a genetic algorithm

The resolution of Single Molecule Localization Microscopy (SML) is dependent on the width of the Point Spread Function (PSF) and the number of photons collected. However, biological samples tend to degrade the shape of the PSF due to the heterogeneity of the index of refraction. In addition, there are aberrations caused by imperfections in the optical components and alignment, and the refractive index mismatch between the coverslip and the sample, all of which directly reduce the accuracy of SML. Adaptive Optics (AO) can play a critical role in compensating for aberrations in order to increase the resolution. However the stochastic nature of single molecule emission presents a challenge for wavefront optimization because the large fluctuations in photon emission do not permit many traditional optimization techniques to be used. Here we present an approach that optimizes the wavefront during SML acquisition by combining an intensity independent merit function with a Genetic algorithm (GA) to optimize the PSF despite the fluctuating intensity. We demonstrate the use of AO with GA in tissue culture cells and through ~50µm of tissue in the Drosophila Central Nervous System (CNS) to achieve a 4-fold increase in the localization precision.

Adaptive optics in spinning disk microscopy: improved contrast and brightness by a simple and fast method

Multiconfocal microscopy gives a good compromise between fast imaging and reasonable resolution. However, the low intensity of live fluorescent emitters is a major limitation to this technique. Aberrations induced by the optical setup, especially the mismatch of the refractive index and the biological sample itself, distort the point spread function and further reduce the amount of detected photons. Altogether, this leads to impaired image quality, preventing accurate analysis of molecular processes in biological samples and imaging deep in the sample. The amount of detected fluorescence can be improved with adaptive optics. Here, we used a compact adaptive optics module (adaptive optics box for sectioning optical microscopy), which was specifically designed for spinning disk confocal microscopy. The module overcomes undesired anomalies by correcting for most of the aberrations in confocal imaging. Existing aberration detection methods require prior illumination, which bleaches the sample. To avoid multiple exposures of the sample, we established an experimental model describing the depth dependence of major aberrations. This model allows us to correct for those aberrations when performing a z-stack, gradually increasing the amplitude of the correction with depth. It does not require illumination of the sample for aberration detection, thus minimizing photobleaching and phototoxicity. With this model, we improved both signal-to-background ratio and image contrast. Here, we present comparative studies on a variety of biological samples.

Enhanced resolution through thick tissue with structured illumination and adaptive optics

Structured illumination microscopy provides twice the linear resolution of conventional fluorescence microscopy, but in thick samples, aberrations degrade the performance and limit the resolution. Here, we demonstrate structured illumination microscopy through 35 μm of tissue using adaptive optics (AO) to correct aberrations resulting in images with a resolution of 140 nm. We report a 60% minimum improvement in the signal-to-noise ratio of the structured illumination reconstruction through thick tissue by correction with AO.