Aberrations in stimulated emission depletion (STED) microscopy

Nanoparticles and plants: A focus on analytical characterization techniques

Nanotechnology has brought about significant progress through the use of goods based on nanomaterials. However, concerns remain about the accumulation of these materials in the environment and their potential toxicity to living organisms. Plants have the ability to take in nanomaterials (NMs), which can cause changes in their physiology and morphology. On the other hand, nanoparticles (NPs) have been used to increase plant development and control pests in agriculture by including them into agrochemicals. The challenges of the interaction, internalization, and accumulation of NMs within plant tissues are enormous, mainly because of the various characteristics of NMs and the absence of reliable analytical tools. As our knowledge of the interactions between NMs and plant cells expands, we are able to create novel NMs that are tailored, targeted, and designed to be safe, thus minimizing the environmental consequences of nanomaterials. This review provides a thorough examination and comparison of the main microscopy techniques, spectroscopic methods, and far-field super-resolution methodologies used to examine nanomaterials within the cell walls of plants.

STED super-resolution microscopy of mitochondrial translocases

The mitochondrial translocases of the outer membrane (TOM) and of the inner membrane (TIM) act together to facilitate the import of nuclear-encoded proteins across the mitochondrial membranes. Stimulated Emission Depletion (STED) super-resolution microscopy enables the in situ imaging of such complexes in single cells at sub-diffraction resolution. STED microscopy requires only conventional sample preparation techniques and provides super-resolved raw data without the need for further image processing. In this chapter, we provide a detailed example protocol for STED microscopy of TOM20 and mitochondrial DNA in fixed mammalian cells. The protocol includes instructions on sample preparation for immunolabeling, including cell line selection, fixation, permeabilization, blocking, labeling and mounting, but also recommendations for sample and microscope performance evaluation. The protocol is supplemented by considerations on key factors that influence the quality of the final image and also includes some considerations for the analysis of the acquired images. While the protocol described here is aimed at imaging TOM20 and DNA, it contains all the information for an immediate adaptation to other cellular targets.

Impact of a tilted coverslip on two-photon and STED microscopy

The advent of super-resolution microscopy has opened up new avenues to unveil brain structures with unprecedented spatial resolution in the living state. Yet, its application to live animals remains a genuine challenge. Getting optical access to the brain in vivo requires the use of a 'cranial window', whose mounting greatly influences image quality. Indeed, the coverslip used for the cranial window should lie as orthogonal as possible to the optical axis of the objective, or else significant optical aberrations occur. In this work, we assess the effect of the tilt angle of the coverslip on STED and two-photon microscopy, in particular, image brightness and spatial resolution. We then propose an approach to measure and reduce the tilt using a simple device added to the microscope, which can ensure orthogonality with a precision of 0.07°.

Adaptive optics in super-resolution microscopy

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

Stimulated Emission Depletion Spectroscopy of Color Centers in Hexagonal Boron Nitride

We demonstrate the use of Stimulated Emission Depletion (STED) spectroscopy to map the electron-optical-phonon sideband of the ground state of the radiative transition of color centers in hexagonal boron nitride emitting at 2.0-2.2 eV, with in-plane linear polarization. The measurements are compared to photoluminescence of excitation (PLE) spectra that maps the electron-optical-phonon sideband of the excited state. The main qualitative difference is a red-shift in the longitudinal optical phonon peak associated with E _1u symmetry at the zone center. We compare our results to theoretical work on different defect species in hBN and find they are consistent with a carbon-based defect.

Background Reduction in STED-FCS Using a Bivortex Phase Mask

Fluorescence correlation spectroscopy (FCS) is a valuable tool to study the molecular dynamics in living cells. When used together with a super-resolution stimulated emission depletion (STED) microscope, STED-FCS can measure diffusion processes on the nanoscale in living cells. In two-dimensional (2D) systems like the cellular plasma membrane, a ring-shaped depletion focus is most commonly used to increase the lateral resolution, leading to more than 25-fold decrease in the observation volume, reaching the relevant scale of supramolecular arrangements. However, STED-FCS faces severe limitations when measuring diffusion in three dimensions (3D), largely due to the spurious background contributions from undepleted areas of the excitation focus that reduce the signal quality and ultimately limit the resolution. In this paper, we investigate how different STED confinement modes can mitigate this issue. By simulations as well as experiments with fluorescent probes in solution and in cells, we demonstrate that the coherent-hybrid (CH) depletion pattern created by a bivortex phase mask reduces background most efficiently and thus provides superior signal quality under comparable reduction of the observation volume. Featuring also the highest robustness to common optical aberrations, CH-STED can be considered the method of choice for reliable STED-FCS-based investigations of 3D diffusion on the subdiffraction scale.

High photon count rates improve the quality of super-resolution fluorescence fluctuation spectroscopy

Probing the diffusion of molecules has become a routine measurement across the life sciences, chemistry and physics. It provides valuable insights into reaction dynamics, oligomerisation, molecular (re-)organisation or cellular heterogeneities. Fluorescence correlation spectroscopy (FCS) is one of the widely applied techniques to determine diffusion dynamics in two and three dimensions. This technique relies on the temporal autocorrelation of intensity fluctuations but recording these fluctuations has thus far been limited by the detection electronics, which could not efficiently and accurately time-tag photons at high count rates. This has until now restricted the range of measurable dye concentrations, as well as the data quality of the FCS recordings, especially in combination with super-resolution stimulated emission depletion (STED) nanoscopy. Here, we investigate the applicability and reliability of (STED-)FCS at high photon count rates (average intensities of more than 1 MHz) using novel detection equipment, namely hybrid detectors and real-time gigahertz sampling of the photon streams implemented on a commercial microscope. By measuring the diffusion of fluorophores in solution and cytoplasm of live cells, as well as in model and cellular membranes, we show that accurate diffusion and concentration measurements are possible in these previously inaccessible high photon count regimes. Specifically, it offers much greater flexibility of experiments with biological samples with highly variable intensity, e.g. due to a wide range of expression levels of fluorescent proteins. In this context, we highlight the independence of diffusion properties of cytosolic GFP in a concentration range of approx. 0.01-1 µm. We further show that higher photon count rates also allow for much shorter acquisition times, and improved data quality. Finally, this approach also pronouncedly increases the robustness of challenging live cell STED-FCS measurements of nanoscale diffusion dynamics, which we testify by confirming a free diffusion pattern for a fluorescent lipid analogue on the apical membrane of adherent cells.

Numerically Enhanced Stimulated Emission Depletion Microscopy with Adaptive Optics for Deep-Tissue Super-Resolved Imaging

In stimulated emission depletion (STED) nanoscopy, the major origin of decreased signal-to-noise ratio within images can be attributed to sample photobleaching and strong optical aberrations. This is due to STED utilizing a high-power depletion laser (increasing the risk of photodamage), while the depletion beam is very sensitive to sample-induced aberrations. Here, we demonstrate a custom-built STED microscope with automated aberration correction that is capable of 3D super-resolution imaging through thick, highly aberrating tissue. We introduce and investigate a state of the art image denoising method by block-matching and collaborative 3D filtering (BM3D) to numerically enhance fine object details otherwise mixed with noise and further enhance the image quality. Numerical denoising provides an increase in the final effective resolution of the STED imaging of 31% using the well established Fourier ring correlation metric. Results achieved through the combination of aberration correction and tailored image processing are experimentally validated through super-resolved 3D imaging of axons in differentiated induced pluripotent stem cells growing under an 80 μm thick layer of tissue with lateral and axial resolution of 204 and 310 nm, respectively.

Adaptive optics allows STED-FCS measurements in the cytoplasm of living cells

Fluorescence correlation spectroscopy in combination with super-resolution stimulated emission depletion microscopy (STED-FCS) is a powerful tool to investigate molecular diffusion with sub-diffraction resolution. It has been of particular use for investigations of two dimensional systems like cell membranes, but has so far seen very limited applications to studies of three-dimensional diffusion. One reason for this is the extreme sensitivity of the axial (z) STED depletion pattern to optical aberrations. We present here an adaptive optics-based correction method that compensates for these aberrations and allows STED-FCS measurements in the cytoplasm of living cells.

Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens

Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions.

Fight against background noise in stimulated emission depletion nanoscopy

STimulated emission depletion (STED) nanoscopy has been proposed to extend greatly our capability of using light to study a variety of biological problems with nanometer-scale resolution. However, in practice the unwanted background noise degrades the STED image quality and precludes quantitative analysis. Here, we discuss the underlying sources of the background noise in STED images, and review current approaches to alleviate this problem, such as time-gating, anti-Stokes excitation removal, and off-focus incomplete depletion suppression. Progress in correcting uncorrelated background photons in fluorescence correlation spectroscopy combined with STED (STED-FCS) will also be discussed.

A special three-layer step-index fiber for building compact STED systems

Up to now, most of stimulated-emission-depletion (STED) systems were lens-based bulky systems. Exchanging some spatial light paths with optical fiber components will make the systems more flexible and will benefit various fields. A big problem to achieve this goal is that the STED beam generated by the traditional method of bulky systems cannot be maintained in an optical fiber due to its birefringence. In this article, we will introduce a type of special optical fiber. With the special fiber, a dark hollow beam with doughnut-shaped focal spot and a concentric beam with Gaussian-shaped focal spot can be generated at the same time. Parameters of a sample and a compact STED system based on it are demonstrated.

Full volume super-resolution imaging of thick mitotic spindle using 3D AO STED microscope

Stimulated emission depletion (STED) nanoscopy is one of a suite of modern optical microscopy techniques capable of bypassing the conventional diffraction limit in fluorescent imaging. STED makes use of a spiral phase mask to enable 2D super-resolution imaging whereas to achieve full volumetric 3D super-resolution an additional bottle-beam phase mask must be applied. The resolution achieved in biological samples 10 µm or thicker is limited by aberrations induced mainly by scattering due to refractive index heterogeneity in the sample. These aberrations impact the fidelity of both types of phase mask, and have limited the application of STED to thicker biological systems. Here we apply an automated adaptive optics solution to correct the performance of both STED masks, enhancing robustness and expanding the capabilities of this nanoscopic technique. Corroboration in terms of successful high-quality imaging of the full volume of a 15µm mitotic spindle with resolution of 50nm x 50nm x 150nm achieved in all three dimensions is presented.

Coherent-hybrid STED: high contrast sub-diffraction imaging using a bi-vortex depletion beam

Stimulated emission depletion (STED) fluorescence microscopy squeezes an excited spot well below the wavelength scale using a doughnut-shaped depletion beam. To generate a doughnut, a scale-free vortex phase modulation (2D-STED) is often used because it provides maximal transverse confinement and radial-aberration immunity (RAI) to the central dip. However, RAI also means blindness to a defocus term, making the axial origin of fluorescence photons uncertain within the wavelength scale provided by the confocal detection pinhole. Here, to reduce the uncertainty, we perturb the 2D-STED phase mask so as to change the sign of the axial concavity near focus, creating a dilated dip. By providing laser depletion power, the dip can be compressed back in three dimensions to retrieve lateral resolution, now at a significantly higher contrast. We test this coherent-hybrid STED (CH-STED) mode in x-y imaging of complex biological structures, such as the dividing cell. The proposed strategy creates an orthogonal direction in the STED parametric space that uniquely allows independent tuning of resolution and contrast using a single depletion beam in a conventional (circular polarization-based) STED setup.

Effects of aberrations on effective point spread function in STED microscopy

Like other imaging techniques, stimulated emission depletion (STED) microscopy suffers from aberrations. While their effects on depletion patterns have been explicitly investigated, the study on how aberrations affect the effective point spread function (PSF) in STED microscopy is still missing. For STED researchers, however, this study is beneficial, as it directly bridges image qualities and aberrations. In this paper, we quantitatively analyze the effects of primary aberrations, including astigmatism, coma, trefoil, and spherical aberration, in two-dimensional (2D) and three-dimensional (3D) STED microscopy, and further discuss the corresponding aberration tolerance. Specifically, attention is given to the modification of the shape, the size, and the peak intensity of the effective PSF in the presence of these aberrations.