Orientational effects in the excitation and de-excitation of single molecules interacting with donut-mode laser beams

Improving STED microscopy with SUPPOSe: enhancing resolution from a single-image

Here we apply the SUPPOSe algorithm on images acquired using Stimulated Emission Depletion (STED) microscopy with the aim of improving the resolution limit achieved. We processed images of the nuclear pore complex (NPC) from cell lines in which the Nup96 nucleoporin was endogenously labeled. This reference protein forms a ring whose diameter is ∼107 nm with 8 corners ∼42 nm apart from each other. The stereotypic arrangement of proteins in the NPC has been used as reference structures to characterize the performance of a variety of microscopy techniques. STED microscopy images resolve the ring arrangement but not the eightfold symmetry of the NPC. After applying the SUPPOSe algorithm to the STED images, we were able to solve the octagonal structure of the NPC. After processing 562 single NPC, the average radius of the NPC was found to beR= 54.2 ± 2.9 nm, being consistent with the theoretical distances of this structure. To verify that the solutions obtained are compatible with a NPC-type geometry, we rotate the solutions to optimally fit an eightfold-symmetric pattern and we count the number of corners that contain at least one localization. Fitting a probabilistic model to the histogram of the number of bright corners gives an effective labeling efficiency of 31%, which is in agreement with the values reported in for other cell lines and ligands used in Single Molecule Localization microscopy, showing that SUPPOSe can reliably retrieve sub-resolution, nanoscale objects from single acquisitions even in noisy conditions.

Direct generation of vortex beams from a double-end polarized pumped Yb:KYW laser

Double-end polarized pumping scheme combined with off-axis pumping technique has been first introduced to generate vortex beams in a z-type cavity. By employing double-end pumping, two different transverse modes can be excited simultaneously. The phase delay between these two modes can be finely tuned by manipulating the cavity structure. Direct emission of a chirality controllable Laguerre Gaussian LG₀₁ vortex beam with slope efficiency of more than 40% has been realized by a double-end polarized pumped Yb:KYW laser. Other modes, such as dual-LG₀₁ mode, cross-shaped mode, and LG₁₀ mode, have also been demonstrated from our laser setup.

Single molecule optical measurements of orientation and rotations of biological macromolecules

Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.

Plasmonic gratings with nano-protrusions made by glancing angle deposition for single-molecule super-resolution imaging

Super-resolution imaging has been advantageous in studying biological and chemical systems, but the required equipment and platforms are expensive and unable to observe single-molecules at the high (μM) fluorophore concentrations required to study protein interaction and enzymatic activity. Here, a plasmonic platform was designed that utilized an inexpensively fabricated plasmonic grating in combination with a scalable glancing angle deposition (GLAD) technique using physical vapor deposition. The GLAD creates an abundance of plasmonic nano-protrusion probes that combine the surface plasmon resonance (SPR) from the periodic gratings with the localized SPR of these nano-protrusions. The resulting platform enables simultaneous imaging of a large area without point-by-point scanning or bulk averaging for the detection of single Cyanine-5 molecules in dye concentrations ranging from 50 pM to 10 μM using epifluorescence microscopy. Combining the near-field plasmonic nano-protrusion probes and super-resolution technique using localization microscopy, we demonstrate the ability to resolve grain sizes down to 65 nm. This plasmonic GLAD grating is a cost-effective super-resolution imaging substrate with potential applications in high-speed biomedical imaging over a wide range of fluorescent concentrations.

isoSTED nanoscopy with intrinsic beam alignment

Despite the need for isotropic optical resolution in a growing number of applications, the majority of super-resolution fluorescence microscopy setups still do not attain an axial resolution comparable to that in the lateral dimensions. Three-dimensional (3D) nanoscopy implementations that employ only a single objective lens typically feature a trade-off between axial and lateral resolution. 4Pi arrangements, in which the sample is illuminated coherently through two opposing lenses, have proven their potential for rendering the resolution isotropic. However, instrument complexity due to a large number of alignment parameters has so far thwarted the dissemination of this approach. Here, we present a 4Pi-STED setup combination, also called isoSTED nanoscope, where the STED and excitation beams are intrinsically co-aligned. A highly robust and convenient 4Pi cavity allows easy handling without the need for readjustments during imaging experiments.

Ryanodine receptor cluster fragmentation and redistribution in persistent atrial fibrillation enhance calcium release

AIMS

In atrial fibrillation (AF), abnormalities in Ca(2+) release contribute to arrhythmia generation and contractile dysfunction. We explore whether ryanodine receptor (RyR) cluster ultrastructure is altered and is associated with functional abnormalities in AF.

METHODS AND RESULTS

Using high-resolution confocal microscopy (STED), we examined RyR cluster morphology in fixed atrial myocytes from sheep with persistent AF (N = 6) and control (Ctrl; N = 6) animals. RyR clusters on average contained 15 contiguous RyRs; this did not differ between AF and Ctrl. However, the distance between clusters was significantly reduced in AF (288 ± 12 vs. 376 ± 17 nm). When RyR clusters were grouped into Ca(2+) release units (CRUs), i.e. clusters separated by <150 nm, CRUs in AF had more clusters (3.43 ± 0.10 vs. 2.95 ± 0.02 in Ctrl), which were more dispersed. Furthermore, in AF cells, more RyR clusters were found between Z lines. In parallel experiments, Ca(2+) sparks were monitored in live permeabilized myocytes. In AF, myocytes had >50% higher spark frequency with increased spark time to peak (TTP) and duration, and a higher incidence of macrosparks. A computational model of the CRU was used to simulate the morphological alterations observed in AF cells. Increasing cluster fragmentation to the level observed in AF cells caused the observed changes, i.e. higher spark frequency, increased TTP and duration; RyR clusters dispersed between Z-lines increased the occurrence of macrosparks.

CONCLUSION

In persistent AF, ultrastructural reorganization of RyR clusters within CRUs is associated with overactive Ca(2+) release, increasing the likelihood of propagating Ca(2+) release.

Generation of a vector doughnut beam from an internal mirror He-Ne laser

We demonstrate the direct generation of a vector doughnut mode from an internal mirror He-Ne laser using the spot defect method. A circular-shaped spot defect of ∼30 μm in diameter with low reflectivity created on the inner surface of a cavity mirror by laser ablation suppressed the oscillation of a Gaussian beam resulting in the oscillation of a doughnut beam. Polarization investigation showed that the generated beam was a vector hybrid mode.

The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging

Numerous methods for determining the orientation of single-molecule transition dipole moments from microscopic images of the molecular fluorescence have been developed in recent years. At the same time, techniques that rely on nanometer-level accuracy in the determination of molecular position, such as single-molecule super-resolution imaging, have proven immensely successful in their ability to access unprecedented levels of detail and resolution previously hidden by the optical diffraction limit. However, the level of accuracy in the determination of position is threatened by insufficient treatment of molecular orientation. Here we review a number of methods for measuring molecular orientation using fluorescence microscopy, focusing on approaches that are most compatible with position estimation and single-molecule super-resolution imaging. We highlight recent methods based on quadrated pupil imaging and on double-helix point spread function microscopy and apply them to the study of fluorophore mobility on immunolabeled microtubules.

Excitation polarization provides structural resolution of individual non-blinking nano-objects

We propose to combine the method of fluorescence intensity centroid localization with rotation of the plane of excitation polarization. Polarized light interacts selectively with differently oriented fluorophores; thus yielding topological information on the nanometer scale, without any need for fluorophore blinking. The method is applicable to photostable individual systems, when most of the traditional super-resolution methods fail. A theoretical study is supported by experiments on 30 nm long cyclodextrin-encapsulated single polyrotaxane conjugated polymer chains.

STED nanoscopy with time-gated detection: theoretical and experimental aspects

In a stimulated emission depletion (STED) microscope the region in which fluorescence markers can emit spontaneously shrinks with continued STED beam action after a singular excitation event. This fact has been recently used to substantially improve the effective spatial resolution in STED nanoscopy using time-gated detection, pulsed excitation and continuous wave (CW) STED beams. We present a theoretical framework and experimental data that characterize the time evolution of the effective point-spread-function of a STED microscope and illustrate the physical basis, the benefits, and the limitations of time-gated detection both for CW and pulsed STED lasers. While gating hardly improves the effective resolution in the all-pulsed modality, in the CW-STED modality gating strongly suppresses low spatial frequencies in the image. Gated CW-STED nanoscopy is in essence limited (only) by the reduction of the signal that is associated with gating. Time-gated detection also reduces/suppresses the influence of local variations of the fluorescence lifetime on STED microscopy resolution.

Strategies to maximize the performance of a STED microscope

In stimulated emission depletion (STED) microscopy, the spatial resolution scales as the inverse square root of the STED beam's intensity. However, to fully exploit the maximum effective resolution achievable for a given STED beam's intensity, several experimental precautions have to be considered. We focus our attention on the temporal alignment between the excitation and STED pulses and the polarization state of the STED beam. We present a simple theoretical framework that help to explain their influence on the performance of a STED microscope and we validate the results by imaging calibration and biological samples with a custom made STED architecture based on a supercontinuum laser source. We also highlight the advantages of using time gating detection in terms of temporal alignment.

Position and orientation estimation of fixed dipole emitters using an effective Hermite point spread function model

We introduce a method for determining the position and orientation of fixed dipole emitters based on a combination of polarimetry and spot shape detection. A key element is an effective Point Spread Function model based on Hermite functions. The model offers a good description of the shape variations with dipole orientation and polarization detection channel, and provides computational advantages over the exact vectorial description of dipole image formation. The realized localization uncertainty is comparable to the free dipole case in which spots are rotationally symmetric and can be well modeled with a Gaussian. This result holds for all dipole orientations, for all practical signal levels, and for defocus values within the depth of focus, implying that the massive localization bias for defocused emitters with tilted dipole axis found with Gaussian spot fitting is eliminated.

Light microscopy with doughnut modes: a concept to detect, characterize, and manipulate individual nanoobjects

Higher order laser modes, mainly called doughnut modes (DMs) have use in many different branches of research, such as, bio-imaging, material science, single-molecule microscopy, and spectroscopy. The main reason of their increasing importance is that recently, the techniques to generate well-defined DMs have been refined or rediscovered. Although their potential is still not fully utilized, their specifically polarized field distribution gives rise to a wide field of applications. They are contributing to complete our fundamental knowledge of the optical properties of single emitting species, such as molecules, nanoparticles, or quantum dots, offering insight into the three-dimensional dipole or particle orientation in space. The perfect zero intensity in the focus center qualifies some DMs for stimulated emission depletion (STED) microscopy. For the same reason, they have been suggested for trapping and tweezing applications.

Molecular orientation affects localization accuracy in superresolution far-field fluorescence microscopy

We investigate the cooperative effect of molecular tilt and defocus on fluorophore localization by centroid calculation in far-field superresolution microscopy based on stochastic single molecule switching. If tilt angle and defocus are unknown, the localization contains systematic errors up to about ±125 nm. When imaging rotation-impaired fluorophores of unknown random orientation, the average localization accuracy in three-dimensional samples is typically limited to about ±32 nm, restricting the attainable resolution accordingly.

Accuracy of the gaussian point spread function model in 2D localization microscopy

The gaussian function is simple and easy to implement as Point Spread Function (PSF) model for fitting the position of fluorescent emitters in localization microscopy. Despite its attractiveness the appropriateness of the gaussian is questionable as it is not based on the laws of optics. Here we study the effect of emission dipole orientation in conjunction with optical aberrations on the localization accuracy of position estimators based on a gaussian model PSF. Simulated image spots, calculated with all effects of high numerical aperture, interfaces between media, polarization, dipole orientation and aberrations taken into account, were fitted with a gaussian PSF based Maximum Likelihood Estimator. For freely rotating dipole emitters it is found that the gaussian works fine. The same, theoretically optimum, localization accuracy is found as if the true PSF were a gaussian, even for aberrations within the usual tolerance limit of high-end optical imaging systems such as microscopes (Marechal's diffraction limit). For emitters with a fixed dipole orientation this is not the case. Localization errors are found that reach up to 40 nm for typical system parameters and aberration levels at the diffraction limit. These are systematic errors that are independent of the total photon count in the image. The gaussian function is therefore inappropriate, and more sophisticated PSF models are a practical necessity.

Controlling the contribution of the electric field components to the focus of a high-aperture lens using binary phase structures

We show that the contribution of the electric field components into the focal region can be controlled using binary phase structures. We discuss differently polarized incident waves, for each case suggesting easily implemented binary phase distributions that ensure a maximum contribution of a definite electric field component on the optical axis. A decrease in the size of the central focal spot produced by a high numerical aperture (NA) focusing system comes as the result of the spatial redistribution of the contribution of different electric field components into the focal region. Using a polarization conversion matrix of a high NA lens and the numerical simulation of the focusing system in Debye's approximation, we demonstrate benefits of using asymmetric to polar angle ϕ binary phase distributions (such as arg[cos ϕ] or arg[sin 2ϕ]) for generating a subwavelength focal spot in separate electric field components. Additional binary structure variations with respect to the azimuthal angle also make possible controlling the longitudinal distribution of light. In particular, the contribution of the transverse components in the focal plane can be reduced by the use of a simple axicon-like structure that serves to enhance the NA of the lens central part, redirecting the energy from focal plane. As compared with the superimposition of a narrow annular aperture, this approach is more energy efficient, and as compared with the Toraldo filters, it is easier to control when applied to three-dimensional focal shaping.

Improved method for counting DNA molecules on biofunctionalized nanoparticles

In order to accurately determine low numbers (1-100) of immobilized ssDNA molecules at a single, silica 250 nm nanoparticle surface, we hereby propose an integrated approach combining classic single molecule confocal microscopy (SMCM), that is, stepwise photobleaching of labeled ssDNA, with modified total internal reflection fluorescence microscopy (mTIRF). We postulate that SMCM alone is unable to exactly account for all labeled ssDNA because of inherent laser polarization effects; that is, perpendicularly oriented molecules to the sample surface are not (or are only slightly) susceptible to laser excitation and thus are invisible in a classic photobleaching experiment. The SMCM method accounts for at best two-thirds (68%) of the present ssDNA molecules. The principle of the mTIRF technique, which relies on the creation of highly inclined illumination combined with part of the laser remaining in normal Kohler illumination, enables accurate counting of SMCM invisible molecules. The combined approach proposed here circumvents the polarization issue and allows a complete single molecule counting on individual nanoparticles, fully in line with bulk measurements, as will be demonstrated.

Birefringent device converts a standard scanning microscope into a STED microscope that also maps molecular orientation

Stimulated emission depletion (STED) microscopy usually employs a scanning excitation beam that is superimposed by a donut-shaped STED beam for keeping the fluorophores at the periphery of the excitation spot dark. Here, we introduce a simple birefringent device that produces a donut-shaped focal spot with suitable polarization for STED, while leaving the excitation spot virtually intact. The device instantly converts a scanning (confocal) microscope with a co-aligned STED beam into a full-blown STED microscope. The donut can be adapted to reveal, through the resulting fluorescence image, the orientation of fluorophores in the sample, thus directly providing subdiffraction resolution images of molecular orientation.

Effects of primary aberrations on the fluorescence depletion patterns of STED microscopy

Effects of primary aberrations including spherical aberration, coma and astigmatism on the three fluorescence depletion patterns mainly used in stimulated emission of depletion (STED) microscopy are investigated by using vectorial integral. The three depletion patterns are created by inserting a vortex phase plate, a central half-wavelength plate or a semi-circular half-wavelength mask within Gaussian beam respectively. Attention is given to the modification of the shape, peak intensity, the central intensity of the dark hole and the hole size of these depletion patterns in the presence of primary aberrations.

Investigation of the influence of the aberration induced by a plane interface on STED microscopy

The structure of the inhibition patterns is important to the stimulated emission depletion (STED) microscopy. Usually, Laguerre- Gaussian (LG) beam and the central zero-intensity patterns created by inserting phase masks in Gaussian beams are used as the erase beam in STED microscopy. Aberration is generated when focusing beams through an interface between the media of the mismatched refractive indices. By use of the vectorial integral, the effects of such aberration on the shape of depletion patterns and the size of fluorescence emission spot in the STED microscopy are studied. Results are presented as a comparison between the aberration-free case and the aberrated cases.

Beyond the diffraction limit: far-field fluorescence imaging with ultrahigh resolution

Fluorescence microscopy is an important and extensively utilised tool for imaging biological systems. However, the image resolution that can be obtained has a limit as defined through the laws of diffraction. Demand for improved resolution has stimulated research into developing methods to image beyond the diffraction limit based on far-field fluorescence microscopy techniques. Rapid progress is being made in this area of science with methods emerging that enable fluorescence imaging in the far-field to possess a resolution well beyond the diffraction limit. This review outlines developments in far-field fluorescence methods which enable ultrahigh resolution imaging and application of these techniques to biology. Future possible trends and directions in far-field fluorescence imaging with ultrahigh resolution are also outlined.