Three-dimensional nanometre localization of nanoparticles to enhance super-resolution microscopy

Label-Free Single Nanoparticle Identification and Characterization in Demanding Environment, Including Infectious Emergent Virus

Unknown particle screening-including virus and nanoparticles-are keys in medicine, industry, and also in water pollutant determination. Here, RYtov MIcroscopy for Nanoparticles Identification (RYMINI) is introduced, a staining-free, non-invasive, and non-destructive optical approach that is merging holographic label-free 3D tracking with high-sensitivity quantitative phase imaging into a compact optical setup. Dedicated to the identification and then characterization of single nano-object in solution, it is compatible with highly demanding environments, such as level 3 biological laboratories, with high resilience to external source of mechanical and optical noise. Metrological characterization is performed at the level of each single particle on both absorbing and transparent particles as well as on immature and infectious HIV, SARS-CoV-2 and extracellular vesicles in solution. The capability of RYMINI to determine the nature, concentration, size, complex refractive index and mass of each single particle without knowledge or model of the particles' response is demonstrated. The system surpasses 90% accuracy for automatic identification between dielectric/metallic/biological nanoparticles and ≈80% for intraclass chemical determination of metallic and dielectric. It falls down to 50-70% for type determination inside the biological nanoparticle's class.

A Magnetic Pincher for the Dynamic Measurement of the Actin Cortex Thickness in Live Cells

The actin cortex is an essential element of the cytoskeleton allowing cells to control and modify their shape. It is involved in cell division and migration. However, probing precisely the physical properties of the actin cortex has proved to be challenging: it is a thin and dynamic material, and its location in the cell-directly under the plasma membrane-makes it difficult to study with standard light microscopy and cell mechanics techniques. In this chapter, we present a novel protocol to probe dynamically the thickness of the cortex and its fluctuations using superparamagnetic microbeads in a uniform magnetic field. A bead ingested by the cell and another outside the cell attract each other due to dipolar forces. By tracking their position with nanometer precision, one can measure the thickness of the cortex pinched between two beads and monitor its evolution in time. We first present the set of elements necessary to realize this protocol: a magnetic field generator adapted to a specific imaging setup and the aforementioned superparamagnetic microbeads. Then we detail the different steps of a protocol that can be used on diverse cell types, adherent or not.

openFrame: A modular, sustainable, open microscopy platform with single-shot, dual-axis optical autofocus module providing high precision and long range of operation

'openFrame' is a modular, low-cost, open-hardware microscopy platform that can be configured or adapted to most light microscopy techniques and is easily upgradeable or expandable to multiple modalities. The ability to freely mix and interchange both open-source and proprietary hardware components or software enables low-cost, yet research-grade instruments to be assembled and maintained. It also enables rapid prototyping of advanced or novel microscope systems. For long-term time-lapse image data acquisition, slide-scanning or high content analysis, we have developed a novel optical autofocus incorporating orthogonal cylindrical optics to provide robust single-shot closed-loop focus lock, which we have demonstrated to accommodate defocus up to ±37 μm with <200 nm accuracy, and a two-step autofocus mode which we have shown can operate with defocus up to ±68 μm. We have used this to implement automated single molecule localisation microscopy (SMLM) in a relatively low-cost openFrame-based instrument using multimode diode lasers for excitation and cooled CMOS cameras.

Label-free image scanning microscopy for kHz super-resolution imaging and single particle tracking

We report the modification of a label-free image scanning microscope (ISM) to perform asynchronous 2D imaging at up to 24kHz while keeping the lateral resolution gain and background rejection of a regular label-free ISM setup. Our method uses a resonant mirror oscillating at 12kHz for one-direction scanning and a chromatic line for instantaneous scanning in the other direction. We adapt optical photon reassignment in this scanning regime to perform fully optical super-resolution imaging. We exploit the kHz imaging capabilities of this confocal imaging system for single nanoparticle tracking down to 20 nm for gold and 50 nm for silica particles as well as imaging freely moving Lactobacillus with improved resolution.

Quantitative phase imaging for characterization of single cell growth dynamics

Quantitative phase imaging (QPI) has emerged as an indispensable tool in the field of biomedicine, offering the ability to obtain quantitative maps of phase changes due to optical path length delays without the need for contrast agents. These maps provide valuable information about cellular morphology and dynamics, unperturbed by the introduction of exogenous substances. In this review, a summary of recent studies that have focused on elucidating the growth dynamics of individual cells using QPI is presented. Specifically, investigations into cellular changes occurring during mitosis, the differentiation of cellular organelles, the assessment of distinct cell death processes (i.e., apoptosis, necrosis, and oncosis) and the precise measurement of live cell temperature are explored. Furthermore, the captivating applications of QPI in theragnostics, where its potential for transformative impact is prominently showcased, are highlighted. Finally, the challenges that need to be overcome for its wider adoption and successful integration into biomedical research are outlined.

Physics-informed neural network for phase imaging based on transport of intensity equation

Non-interferometric quantitative phase imaging based on Transport of Intensity Equation (TIE) has been widely used in bio-medical imaging. However, analytic TIE phase retrieval is prone to low-spatial frequency noise amplification, which is caused by the illposedness of inversion at the origin of the spectrum. There are also retrieval ambiguities resulting from the lack of sensitivity to the curl component of the Poynting vector occurring with strong absorption. Here, we establish a physics-informed neural network (PINN) to address these issues, by integrating the forward and inverse physics models into a cascaded deep neural network. We demonstrate that the proposed PINN is efficiently trained using a small set of sample data, enabling the conversion of noise-corrupted 2-shot TIE phase retrievals to high quality phase images under partially coherent LED illumination. The efficacy of the proposed approach is demonstrated by both simulation using a standard image database and experiment using human buccal epitehlial cells. In particular, high image quality (SSIM = 0.919) is achieved experimentally using a reduced size of labeled data (140 image pairs). We discuss the robustness of the proposed approach against insufficient training data, and demonstrate that the parallel architecture of PINN is efficient for transfer learning.

Spectroscopy of individual Brownian nanoparticles in real-time using holographic localization

Individual nanoparticle spectroscopic characterization is fundamental, but challenging in liquids. While confocal selectivity is necessary to isolate a particle in a crowd, Brownian motion constantly offsets the particle from the light collection volume. Here, we present a system able to acquire holograms and reconstruct them to precisely determine the 3D position of a particle in real time. These coordinates drive an adaptive system comprising two galvanometric mirrors (x,y, transverse directions) and a tunable lens (z, longitudinal) which redirect light scattered from the corresponding region of space towards the confocal entrance of a spectrometer, thus allowing long spectral investigations on individual, freely-moving particles. A study of the movements and spectra of individual 100 nm Au nanoparticles undergoing two types of aggregations illustrates the possibilities of the method.

Robust deep learning optical autofocus system applied to automated multiwell plate single molecule localization microscopy

We presenta robust, long-range optical autofocus system for microscopy utilizing machine learning. This can be useful for experiments with long image data acquisition times that may be impacted by defocusing resulting from drift of components, for example due to changes in temperature or mechanical drift. It is also useful for automated slide scanning or multiwell plate imaging where the sample(s) to be imaged may not be in the same horizontal plane throughout the image data acquisition. To address the impact of (thermal or mechanical) fluctuations over time in the optical autofocus system itself, we utilize a convolutional neural network (CNN) that is trained over multiple days to account for such fluctuations. To address the trade-off between axial precision and range of the autofocus, we implement orthogonal optical readouts with separate CNN training data, thereby achieving an accuracy well within the 600 nm depth of field of our 1.3 numerical aperture objective lens over a defocus range of up to approximately +/-100 μm. We characterize the performance of this autofocus system and demonstrate its application to automated multiwell plate single molecule localization microscopy.

3D nanoparticle superlocalization with a thin diffuser

We report on the use of a thin diffuser placed in the close vicinity of a camera sensor as a simple and effective way to superlocalize plasmonic nanoparticles in 3D. This method is based on holographic reconstruction via quantitative phase and intensity measurements of a light field after its interaction with nanoparticles. We experimentally demonstrate that this thin diffuser can be used as a simple add-on to a standard bright-field microscope to allow the localization of 100 nm gold nanoparticles at video rate with nanometer precision (1.3 nm laterally and 6.3 nm longitudinally). We exemplify the approach by revealing the dynamic Brownian trajectory of a gold nanoparticle trapped in various pockets within an agarose gel. The proposed method provides a simple but highly performant way to track nanoparticles in 3D.

Influence of drift correction precision on super-resolution localization microscopy

Super-resolution localization microscopy (SRLM) breaks the diffraction limit successfully and improves the resolution of optical imaging systems by nearly an order of magnitude. However, SRLM typically takes several minutes or longer to collect a sufficient number of image frames that are required for reconstructing a final super-resolution image. During this long image acquisition period, system drift should be tightly controlled to ensure the imaging quality; thus, several drift correction methods have been developed. However, it is still unclear whether the performance of these methods is able to ensure sufficient image quality in SRLM. Without a clear answer to this question, it is hard to choose a suitable drift correction method for a specific SRLM experiment. In this paper, we use both theoretical analysis and simulation to investigate the relationship among drift correction precision, localization precision, and position estimation precision. We propose a concept of relative localization precision for evaluating the effect of drift correction on imaging resolution, which would help to select an appropriate drift correction method for a specific experiment.

Direct Observation of Endocytosis Dynamics of Anti-ErbB Modified Single Nanocargoes

The ErbB receptor family, including the epidermal growth factor receptor (EGFR) and ErbB2/3/4, regulate cell proliferation, differentiation, apoptosis, motility, etc., and their abnormalities can cause cancer and other diseases. Ligand-induced endocytosis of ErbB receptors is the key to various cancer treatment strategies, and different techniques have been developed to study this important process. Among them, single particle tracking (SPT) can reveal the spatiotemporal heterogeneity of ErbB receptors on the live cell membrane and has been used to characterize the EGFR dimerization process. Herein, we studied the endocytosis dynamics of two different ErbB receptors using dark-field microscopy. With anti-ErbB modified plasmonic gold nanorods (AuNRs) as probes, we compared the trajectories of individual anti-EGFR AuNRs (cAuNRs) and anti-ErbB AuNRs (tAuNRs) interacting with MCF-7 cells in situ in real time. The results revealed that the internalization rate of cAuNRs was faster than that of tAuNRs. Detailed SPT analysis suggests that cAuNRs enter cells through EGFR endocytosis pathway, and multiple intracellular transport modes sort the cAuNRs away from the transmembrane site. In contrast, the endocytosis resistance of ErbB2 slows down the cellular uptake rate of tAuNRs and causes some tAuNRs-ErbB2 complexes to be confined on the membrane with "circular" and "rolling circle" motions for a much longer time. Our results provide insights into the endocytosis process of the ErbB receptor family at the nanometer scale and could be potentially useful to develop cancer treatment strategies.

Automatic numerical focus plane estimation in digital holographic microscopy using calibration beads

We present a new method to achieve autofocus in digital holographic microscopy. The method is based on inserting calibrated objects into a sample placed on a slide. Reconstructing a hologram using the inverse problems approach makes it possible to precisely locate and measure the inserted objects and thereby derive the slide plane location. Numerical focusing can then be performed in a plane at any chosen distance from the slide plane of the sample in a reproducible manner and independently of the diversity of the objects in the sample.

Super-Resolution Microscopy for Structural Cell Biology

Super-resolution microscopy techniques, and specifically single-molecule localization microscopy (SMLM), are approaching nanometer resolution inside cells and thus have great potential to complement structural biology techniques such as electron microscopy for structural cell biology. In this review, we introduce the different flavors of super-resolution microscopy, with a special emphasis on SMLM and MINFLUX (minimal photon flux). We summarize recent technical developments that pushed these localization-based techniques to structural scales and review the experimental conditions that are key to obtaining data of the highest quality. Furthermore, we give an overview of different analysis methods and highlight studies that used SMLM to gain structural insights into biologically relevant molecular machines. Ultimately, we give our perspective on what is needed to push the resolution of these techniques even further and to apply them to investigating dynamic structural rearrangements in living cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Three-Dimensional Tracking of Tethered Particles for Probing Nanometer-Scale Single-Molecule Dynamics Using a Plasmonic Microscope

Three-dimensional (3D) tracking of surface-tethered single particles reveals the dynamics of the molecular tether. However, most 3D tracking techniques lack precision, especially in the axial direction, for measuring the dynamics of biomolecules with a spatial scale of several nanometers. Here, we present a plasmonic imaging technique that can track the motion of ∼100 tethered particles in 3D simultaneously with sub-nanometer axial precision and single-digit nanometer lateral precision at millisecond time resolution. By tracking the 3D coordinates of a tethered particle with high spatial resolution, we are able to determine the dynamics of single short DNA and study its interaction with enzymes. We further show that the particle motion pattern can be used to identify specific and nonspecific interactions in immunoassays. We anticipate that our 3D tracking technique can contribute to the understanding of molecular dynamics and interactions at the single-molecule level.

Γ-profilometry: a new paradigm for precise optical metrology

We show that the shape of a surface can be unambiguously determined from investigating the coherence function of a wave-field reflected by the surface and without the requirement of a reference wave. Spatio-temporal sampling facilitates the identification of temporal shifts of the coherence function that correspond to finite height differences of the surface. Evaluating these finite differences allows for the reconstruction of the surface using a numerical integration procedure. Spatial sampling of the coherence function is provided by a shear interferometer whereas temporal sampling is achieved by means of a Soleil-Babinet compensator. This low coherence profiling method allows to determine the shape of an object with sub-micrometer resolution and over a large unambiguity range, although it does not require any isolation against mechanical vibration. The approach therefore opens up a new avenue for precise, rugged optical metrology suitable for industrial in-line applications.

High-precision 3D drift correction with differential phase contrast images

Single molecule localization microscopy (SMLM) usually requires long image acquisition time at the order of minutes and thus suffers from sample drift, which deteriorates image quality. A drift estimation method with high precision is typically used in SMLM, which can be further combined with a drift compensation device to enable active microscope stabilization. Among all the reported methods, the drift estimation method based on bright-field image correlation requires no extra sample preparation or complicated modification to the imaging setup. However, the performance of this method is limited by the contrast of bright-field images, especially for the structures without sufficient features. In this paper, we proposed to use differential phase contrast (DPC) microscopy to enhance the image contrast and presented a 3D drift correction method with higher precision and robustness. This DPC-based drift correction method is suitable even for biological samples without clear morphological features. We demonstrated that this method can achieve a correction precision of < 6 nm in both the lateral direction and axial direction. Using SMLM imaging of microtubules, we verified that this method provides a comparable drift estimation performance as redundant cross-correlation.

A mean shift algorithm for drift correction in localization microscopy

Single-molecule localization microscopy techniques transcend the diffraction limit of visible light by localizing isolated emitters sampled stochastically. This time-lapse imaging necessitates long acquisition times, over which sample drift can become large relative to the localization precision. Here, we present an efficient and robust method for estimating drift, using a simple peak-finding algorithm based on mean shifts that is effective for single-molecule localization microscopy in two or three dimensions.

Fast photothermal spatial light modulation for quantitative phase imaging at the nanoscale

Spatial light modulators have become an essential tool for advanced microscopy, enabling breakthroughs in 3D, phase, and super-resolution imaging. However, continuous spatial-light modulation that is capable of capturing sub-millisecond microscopic motion without diffraction artifacts and polarization dependence is challenging. Here we present a photothermal spatial light modulator (PT-SLM) enabling fast phase imaging for nanoscopic 3D reconstruction. The PT-SLM can generate a step-like wavefront change, free of diffraction artifacts, with a high transmittance and a modulation efficiency independent of light polarization. We achieve a phase-shift > π and a response time as short as 70 µs with a theoretical limit in the sub microsecond range. We used the PT-SLM to perform quantitative phase imaging of sub-diffractional species to decipher the 3D nanoscopic displacement of microtubules and study the trajectory of a diffusive microtubule-associated protein, providing insights into the mechanism of protein navigation through a complex microtubule network.

Supercritical Angle Fluorescence Microscopy and Spectroscopy

Fluorescence detection, either involving propagating or near-field emission, is widely being used in spectroscopy, sensing, and microscopy. Total internal reflection fluorescence (TIRF) confines fluorescence excitation by an evanescent (near) field, and it is a popular contrast generator for surface-selective fluorescence assays. Its emission equivalent, supercritical angle fluorescence (SAF), is comparably less established, although it achieves a similar optical sectioning as TIRF does. SAF emerges when a fluorescing molecule is located very close to an interface and its near-field emission couples to the higher refractive index medium (n2 >n1) and becomes propagative. Then, most fluorescence is detectable on the side of the higher-index substrate, and a large fraction of this fluorescence is emitted into angles forbidden by Snell's law. SAF, as well as the undercritical angle fluorescence (UAF; far-field emission) components, can be collected with microscope objectives having a high-enough detection aperture (numerical aperture >n2) and be separated in the back focal plane by Fourier filtering. The back focal plane image encodes information about the fluorophore radiation pattern, and it can be analyzed to yield precise information about the refractive index in which the emitters are embedded, their nanometric distance from the interface, and their orientation. A SAF microscope can retrieve this near-field information through wide-field optics in a spatially resolved manner, and this functionality can be added to an existing inverted microscope. Here, we describe the potential underpinning of SAF microscopy and spectroscopy, particularly in comparison with TIRF. We review the challenges and opportunities that SAF presents from a biophysical perspective, and we discuss areas in which we see potential.

Effect of Vectashield-induced fluorescence quenching on conventional and super-resolution microscopy

Finding the right combination of a fluorescent dye and a mounting medium is crucial for optimal microscopy of fixed samples. It was recently shown that Vectashield, one of the most commonly used mounting media for conventional microscopy, can also be applied to super-resolution direct stochastic optical reconstruction microscopy (dSTORM). dSTORM utilizes conventional dyes and starts with samples in a fluorescent “ON” state. This helps in identifying structures of interest. Subsequently, labelled samples are induced into blinking, which is necessary for determining the position of single molecules and reconstruction of super-resolution images. This is only possible with certain fluorescent dyes and imaging buffers. One of the most widely used dyes for dSTORM, Alexa Fluor 647 (AF647), blinks in Vectashield. However, after preparing immunocytochemical samples in Vectashield, we noticed that the fluorescence intensity of AF647 is quenched. This is particularly evident for dimmer immunostainings, such as stainings of some components of neuronal cytoskeleton and axonal initial segment. Because structures of interest cannot be identified in quenched samples, loss of fluorescence intensity hinders imaging of AF647 in Vectashield. This has consequences for both conventional and dSTORM imaging. To overcome this, we provide: 1) a quantitative analysis of AF647 intensity in different imaging media, 2) a quantitative analysis of the suitability of Vectashield for dSTORM imaging of high and low-abundance AF647-labelled targets. Furthermore, for the first time, we quantitatively analyse the performance of Alexa Fluor Plus 647, a new variant of AF647-conjugated antibody, in dSTORM imaging.

High-Affinity Bent β2-Integrin Molecules in Arresting Neutrophils Face Each Other through Binding to ICAMs In cis

Leukocyte adhesion requires β₂-integrin activation. Resting integrins exist in a bent-closed conformation-i.e., not extended (E^-) and not high affinity (H^-)-unable to bind ligand. Fully activated E⁺H⁺ integrin binds intercellular adhesion molecules (ICAMs) expressed on the opposing cell in trans. E^-H^- transitions to E⁺H⁺ through E⁺H^- or through E^-H⁺, which binds to ICAMs on the same cell in cis. Spatial patterning of activated integrins is thought to be required for effective arrest, but no high-resolution cell surface localization maps of activated integrins exist. Here, we developed Super-STORM by combining super-resolution microscopy with molecular modeling to precisely localize activated integrin molecules and identify the molecular patterns of activated integrins on primary human neutrophils. At the time of neutrophil arrest, E^-H⁺ integrins face each other to form oriented (non-random) nanoclusters. To address the mechanism causing this pattern, we blocked integrin binding to ICAMs in cis, which significantly relieved the face-to-face orientation.

Axial electrokinetic trapping of anisotropic particles

Anti-Brownian electrokinetic trapping is a method for trapping single particles in liquid based on particle position measurements and the application of feedback voltages. To achieve trapping in the axial direction, information on the axial particle position is required. However, existing strategies for determining the axial position that are based on measuring the size of the first diffraction ring, theory fitting, advanced optical setups or pre-determined axial image stacks are impractical for anisotropic particles. In this work, axial electrokinetic trapping of anisotropic particles is realized in devices with planar, transparent electrodes. The trapping algorithm uses Fourier-Bessel decomposition of standard microscopy images and is learning from the correlation between applied voltages and changes in the particle appearance. No previous knowledge on the particle appearance, theory fitting or advanced optical setup is required. The particle motion in the trap and the influence of screening of the electric field on this motion are analyzed. The axial trapping method opens new possibilities for measuring properties of anisotropic or isotropic particles and forces acting on such particles.

Divide and conquer: real-time maximum likelihood fitting of multiple emitters for super-resolution localization microscopy

Multi-emitter localization has great potential for maximizing the imaging speed of super-resolution localization microscopy. However, the slow image analysis speed of reported multi-emitter localization algorithms limits their usage in mostly off-line image processing with small image size. Here we adopt the well-known divide and conquer strategy in computer science and present a fitting-based method called QC-STORM for fast multi-emitter localization. Using simulated and experimental data, we verify that QC-STORM is capable of providing real-time full image processing on raw images with 100 µm × 100 µm field of view and 10 ms exposure time, with comparable spatial resolution as the popular fitting-based ThunderSTORM and the up-to-date non-iterative WindSTORM. This study pushes the development and practical use of super-resolution localization microscopy in high-throughput or high-content imaging of cell-to-cell differences or discovering rare events in a large cell population.

Quantitative model of the image of a radiating dipole through a microscope

In this paper, we introduce a formalism to determine the relationship between the full vectorial electric field existing at the object plane of a microscope and that existing at the image plane. The model is then used to quantitatively simulate, in both phase and intensity, the image of a radiating electric dipole placed either in a homogeneous medium or in the vicinity of a substrate. These simulations are compared with experimental measurements on single gold nanoparticles carried out by quadriwave lateral shearing interferometry.

Unidirectional scattering exploited transverse displacement sensor with tunable measuring range

We propose a scheme to extend the measuring range of a transverse displacement sensor by exploiting the interaction of an azimuthally polarized beam (APB) with a single metal-dielectric core-shell nanoparticle. The focused APB illumination induces a longitudinal magnetic dipole (MD) in the core-shell nanoparticle, which interferes with the induced transverse electric dipole (ED) to bring forth a transverse unidirectional scattering at a specific position within the focal plane. Emphatically, the rapidly varying electromagnetic field within the focal plane of an APB leads to a remarkable sensitivity of the far-field scattering directivity to nanoscale displacements as the nanoparticle moves away from the optical axis. Moreover, the scattering directivity of the APB illuminated core-shell nanoparticle is also a function of structure-dependent Mie scattering coefficients, rendering the measuring range of the transverse displacement sensor widely tunable. The culmination of all these features enables the continuous tuning of the displacement measuring range from several nanometers to a few micrometers. Thus, we envision the proposed scheme is of high value for modern optical nanometrology.

Wrapping-free numerical refocusing of scalar electromagnetic fields

Numerical refocusing in any plane is one powerful feature granted by measuring both the amplitude and the phase of a coherent light beam. Here, we introduce a method based on the first Rytov approximation of scalar electromagnetic fields that (i) allows numerical propagation without requiring phase unwrapping after propagation and (ii) limits the effect of artificial phase singularities that appear upon numerical defocusing when the measurement noise is mixing with the signal. We demonstrate the feasibility of this method with both scalar electromagnetic field simulations and real acquisitions of microscopic biological samples imaged at high numerical aperture.

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.

Enhancing optical microscopy illumination to enable quantitative imaging

There has been an increasing push to derive quantitative measurements using optical microscopes. While several aspects of microscopy have been identified to enhance quantitative imaging, non-uniform angular illumination asymmetry (ANILAS) across the field-of-view is an important factor that has been largely overlooked. Non-uniform ANILAS results in loss of imaging precision and can lead to, for example, less reliability in medical diagnoses. We use ANILAS maps to demonstrate that objective lens design, illumination wavelength and location of the aperture diaphragm are significant factors that contribute to illumination aberrations. To extract the best performance from an optical microscope, the combination of all these factors must be optimized for each objective lens. This requires the capability to optimally align the aperture diaphragm in the axial direction. Such optimization enhances the quantitative imaging accuracy of optical microscopes and can benefit applications in important areas such as biotechnology, optical metrology, and nanotechnology.

A Simple Marker-Assisted 3D Nanometer Drift Correction Method for Superresolution Microscopy

High-precision fluorescence microscopy such as superresolution imaging or single-particle tracking often requires an online drift correction method to maintain the stability of the three-dimensional (3D) position of the sample at a nanometer precision throughout the entire data acquisition process. Current online drift correction methods require modification of the existing two-dimensional (2D) fluorescence microscope with additional optics and detectors, which can be cumbersome and limit its use in many biological laboratories. Here we report a simple marker-assisted online drift correction method in which all 3D positions can be derived from fiducial markers on the coverslip of the sample on a standard 2D fluorescence microscope without additional optical components. We validate this method by tracking the long-term 3D stability of single-molecule localization microscopy at a precision of <2 and 5 nm in the lateral and axial dimension, respectively. We then provide three examples to evaluate the performance of the marker-assisted drift correction method. Finally, we give an example of a biological application of superresolution imaging of spatiotemporal alteration for a DNA replication structure with both low-abundance newly synthesized DNAs at the early onset of DNA synthesis and gradually condensed DNA structures during DNA replication. Using an isogenic breast cancer progression cell line model that recapitulates normal-like, precancerous, and tumorigenic stages, we characterize a distinction in the DNA replication process in normal, precancerous, and tumorigenic cells.

Optical microscope illumination analysis using through-focus scanning optical microscopy

Misalignment of the aperture diaphragm present in optical microscopes results in angular illumination asymmetry (ANILAS) at the sample plane. Here we show that through-focus propagation of ANILAS results in a lateral image shift with a focus position. This could lead to substantial errors in quantitative results for optical methods that use through-focus images such as three-dimensional nanoparticle tracking, confocal microscopy, and through-focus scanning optical microscopy (TSOM). A correlation exists between ANILAS and the slant in TSOM images. Hence, the slant in the TSOM image can be used to detect, analyze, and rectify the presence of ANILAS.

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.

Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers

Fiducial markers are used to correct the microscope drift and should be photostable, be usable at multiple wavelengths and be compatible for multimodal imaging. Fiducial markers such as beads, gold nanoparticles, microfabricated patterns and organic fluorophores lack one or more of these criteria. Moreover, the localization accuracy and drift correction can be degraded by other fluorophores, instrument noise and artefacts due to image processing and tracking algorithms. Estimating mechanical drift by assuming Gaussian distributed noise is not suitable under these circumstances. Here we present a method that uses fluorescent nanodiamonds as fiducial markers and uses an improved maximum likelihood algorithm to estimate the drift with both accuracy and precision within the range 1.55-5.75 nm.

Quadriwave lateral shearing interferometric microscopy with wideband sensitivity enhancement for quantitative phase imaging in real time

Real-time quantitative phase imaging has tremendous potential in investigating live biological specimens in vitro. Here we report on a wideband sensitivity-enhanced interferometric microscopy for quantitative phase imaging in real time by employing two quadriwave lateral shearing interferometers based on randomly encoded hybrid gratings with different lateral shears. Theoretical framework to analyze the measurement sensitivity is firstly proposed, from which the optimal lateral shear pair for sensitivity enhancement is also derived. To accelerate the phase retrieval algorithm for real-time visualization, we develop a fully vectorized path-independent differential leveling phase unwrapping algorithm ready for parallel computing, and the framerate for retrieving the phase from each pair of two 4 mega pixel interferograms is able to reach 47.85 frames per second. Experiment results demonstrate that the wideband sensitivity-enhanced interferometric microscopy is capable of eliminating all the periodical error caused by spectral leaking problem and reducing the temporal standard deviation to the half level compared with phase directly retrieved by the interferogram. Due to its high adaptability, the wideband sensitivity-enhanced interferometric microscopy is promising in retrofitting existing microscopes to quantitative phase microscopes with high measurement precision and real-time visualization.

Fluorescent probes for nanoscopy: four categories and multiple possibilities

Nanoscopy enables breaking down the light diffraction limit and reveals the nanostructures of objects being studied using light. In 2014, three scientists pioneered the development of nanoscopy and won the Nobel Prize in Chemistry. This recognized the achievement of the past twenty years in the field of nanoscopy. However, fluorescent probes used in the field of nanoscopy are still numbered. Here, we review the currently available four categories of probes and existing methods to improve the performance of probes.

Retrieving the axial position of fluorescent light emitting spots by shearing interferometry

A method for the depth-resolved detection of fluorescent radiation based on imaging of an interference pattern of two intersecting beams and shearing interferometry is presented. The illumination setup provides the local addressing of the excitation of fluorescence and a coarse confinement of the excitation volume in axial and lateral directions. The reconstruction of the depth relies on the measurement of the phase of the fluorescent wave fronts. Their curvature is directly related to the distance of a source to the focus of the imaging system. Access to the phase information is enabled by a lateral shearing interferometer based on a Michelson setup. This allows the evaluation of interference signals even for spatially and temporally incoherent light such as emitted by fluorophors. An analytical signal model is presented and the relations for obtaining the depth information are derived. Measurements of reference samples with different concentrations and spatial distributions of fluorophors and scatterers prove the experimental feasibility of the method. In a setup optimized for flexibility and operating in the visible range, sufficiently large interference signals are recorded for scatterers placed in depths in the range of hundred micrometers below the surface in a material with scattering properties comparable to dental enamel.

Current achievements of nanoparticle applications in developing optical sensing and imaging techniques

Metallic nanostructures have recently been demonstrated to improve the performance of optical sensing and imaging techniques due to their remarkable localization capability of electromagnetic fields. Particularly, the zero-dimensional nanostructure, commonly called a nanoparticle, is a promising component for optical measurement systems due to its attractive features, e.g., ease of fabrication, capability of surface modification and relatively high biocompatibility. This review summarizes the work to date on metallic nanoparticles for optical sensing and imaging applications, starting with the theoretical backgrounds of plasmonic effects in nanoparticles and moving through the applications in Raman spectroscopy and fluorescence biosensors. Various efforts for enhancing the sensitivity, selectivity and biocompatibility are summarized, and the future outlooks for this field are discussed. Convergent studies in optical sensing and imaging have been emerging field for the development of medical applications, including clinical diagnosis and therapeutic applications.

Electrochemistry of Single Nanodomains Revealed by Three-Dimensional Holographic Microscopy

Interest in nanoparticles has vigorously increased over the last 20 years as more and more studies show how their use can potentially revolutionize science and technology. Their applications span many different academically and industrially relevant fields such as catalysis, materials science, health, etc. Until the past decade, however, nanoparticle studies mostly relied on ensemble studies, thus leaving aside their chemical heterogeneity at the single particle level. Over the past few years, powerful new tools appeared to probe nanoparticles individually and in situ. This Account describes how we drew inspiration from the emerging fields of nanoelectrochemistry and plasmonics-based high resolution holographic microscopy to develop a coupled approach capable of analyzing in operando (electro)chemical reaction over one single nanoparticle. A brief overview of selected optical strategies to image NPs in situ with emphasis on scattering based methods is presented. In an electrochemical context, it is necessary to track particle behavior both in solution and near a polarized electrode, which is why 3D optical observation is particularly appealing. These approaches are discussed together with strategies to track NPs beyond the diffraction limit, allowing a much finer description of their trajectories. Then, the holographic setup is used to study electrochemically triggered Ag NP oxidation reaction in the presence of different electrolytes. Holography is shown to be a powerful technique to track and analyze the trajectory of individual NPs in situ, which further sheds light on in operando behaviors such as electrogenerated NP transport, aggregation, or adsorption. We then show that spectroscopy and scattering-based optical methods are reliable and sensitive to the point of being used to investigate and quantify NP (electro)chemical reactions in model cases. However, since real chemical reactions usually take place in an inherently complex environment, approaches based exclusively on optical imaging only reach their limitations. The strategy is then taken one step further by merging together electrochemical nanoimpact experiments with 3D optical monitoring. Previous strategies are validated by showing that in simple cases, these two independent ways of probing NP size and reactivity yield the same results. For more complicated reactions (e.g., multistep reactions), one must go beyond either technique by showing that the two approaches are perfectly complementary and that the two signals contain information of different natures, thus providing a much better characterization of the reaction. This point is illustrated by studying Ag NP oxidation (single or agglomerates) in the presence of a precipitating agent, where the actual oxidation is uncoupled from the dissolution of the particle, thus proving the point of our symbiotic approach.

Control of Transmembrane Protein Diffusion within the Postsynaptic Density Assessed by Simultaneous Single-Molecule Tracking and Localization Microscopy

Postsynaptic transmembrane proteins are critical elements of synapses, mediating trans-cellular contact, sensitivity to neurotransmitters and other signaling molecules, and flux of Ca and other ions. Positioning and mobility of each member of this large class of proteins is critical to their individual function at the synapse. One critical example is that the position of glutamate receptors within the postsynaptic density (PSD) strongly modulates their function by aligning or misaligning them with sites of presynaptic vesicle fusion. In addition, the regulated ability of receptors to move in or out of the synapse is critical for activity-dependent plasticity. However, factors that control receptor mobility within the boundaries of the synapse are not well understood. Notably, PSD scaffold molecules accumulate in domains much smaller than the synapse. Within these nanodomains, the density of proteins is considerably higher than that of the synapse as a whole, so high that steric hindrance is expected to reduce receptor mobility substantially. However, while numerical modeling has demonstrated several features of how the varying protein density across the face of a single PSD may modulate receptor motion, there is little experimental information about the extent of this influence. To address this critical aspect of synaptic organizational dynamics, we performed single-molecule tracking of transmembrane proteins using universal point accumulation-for-imaging-in-nanoscale-topography (uPAINT) over PSDs whose internal structure was simultaneously resolved using photoactivated localization microscopy (PALM). The results provide important experimental confirmation that PSD scaffold protein density strongly influences the mobility of transmembrane proteins. A protein with a cytosolic domain that does not bind PSD-95 was still slowed in regions of high PSD-95 density, suggesting that crowding by scaffold molecules and perhaps other proteins is sufficient to stabilize receptors even in the absence of binding. Because numerous proteins thought to be involved in establishing PSD structure are linked to disorders including autism and depression, this motivates further exploration of how PSD nanostructure is created. The combined application PALM and uPAINT should be invaluable for distinguishing the interactions of mobile proteins with their nano-environment both in synapses and other cellular compartments.

Polarization-controlled directional scattering for nanoscopic position sensing

Controlling the propagation and coupling of light to sub-wavelength antennas is a crucial prerequisite for many nanoscale optical devices. Recently, the main focus of attention has been directed towards high-refractive-index materials such as silicon as an integral part of the antenna design. This development is motivated by the rich spectral properties of individual high-refractive-index nanoparticles. Here we take advantage of the interference of their magnetic and electric resonances to achieve strong lateral directionality. For controlled excitation of a spherical silicon nanoantenna, we use tightly focused radially polarized light. The resultant directional emission depends on the antenna's position relative to the focus. This approach finds application as a novel position sensing technique, which might be implemented in modern nanometrology and super-resolution microscopy set-ups. We demonstrate in a proof-of-concept experiment that a lateral resolution in the Ångström regime can be achieved.