Ultrabright photoactivatable fluorophores created by reductive caging

Quantifying and optimizing single-molecule switching nanoscopy at high speeds

Single-molecule switching nanoscopy overcomes the diffraction limit of light by stochastically switching single fluorescent molecules on and off, and then localizing their positions individually. Recent advances in this technique have greatly accelerated the data acquisition speed and improved the temporal resolution of super-resolution imaging. However, it has not been quantified whether this speed increase comes at the cost of compromised image quality. The spatial and temporal resolution depends on many factors, among which laser intensity and camera speed are the two most critical parameters. Here we quantitatively compare the image quality achieved when imaging Alexa Fluor 647-immunolabeled microtubules over an extended range of laser intensities and camera speeds using three criteria - localization precision, density of localized molecules, and resolution of reconstructed images based on Fourier Ring Correlation. We found that, with optimized parameters, single-molecule switching nanoscopy at high speeds can achieve the same image quality as imaging at conventional speeds in a 5-25 times shorter time period. Furthermore, we measured the photoswitching kinetics of Alexa Fluor 647 from single-molecule experiments, and, based on this kinetic data, we developed algorithms to simulate single-molecule switching nanoscopy images. We used this software tool to demonstrate how laser intensity and camera speed affect the density of active fluorophores and influence the achievable resolution. Our study provides guidelines for choosing appropriate laser intensities for imaging Alexa Fluor 647 at different speeds and a quantification protocol for future evaluations of other probes and imaging parameters.

Sequential superresolution imaging of multiple targets using a single fluorophore

Fluorescence superresolution (SR) microscopy, or fluorescence nanoscopy, provides nanometer scale detail of cellular structures and allows for imaging of biological processes at the molecular level. Specific SR imaging methods, such as localization-based imaging, rely on stochastic transitions between on (fluorescent) and off (dark) states of fluorophores. Imaging multiple cellular structures using multi-color imaging is complicated and limited by the differing properties of various organic dyes including their fluorescent state duty cycle, photons per switching event, number of fluorescent cycles before irreversible photobleaching, and overall sensitivity to buffer conditions. In addition, multiple color imaging requires consideration of multiple optical paths or chromatic aberration that can lead to differential aberrations that are important at the nanometer scale. Here, we report a method for sequential labeling and imaging that allows for SR imaging of multiple targets using a single fluorophore with negligible cross-talk between images. Using brightfield image correlation to register and overlay multiple image acquisitions with ~10 nm overlay precision in the x-y imaging plane, we have exploited the optimal properties of AlexaFluor647 for dSTORM to image four distinct cellular proteins. We also visualize the changes in co-localization of the epidermal growth factor (EGF) receptor and clathrin upon EGF addition that are consistent with clathrin-mediated endocytosis. These results are the first to demonstrate sequential SR (s-SR) imaging using direct stochastic reconstruction microscopy (dSTORM), and this method for sequential imaging can be applied to any superresolution technique.

Magnetic-field-enabled resolution enhancement in super-resolution imaging

A novel strategy for modulating the photophysics of organic dyes in super-resolution fluorescence imaging using an external magnetic field was reported. The magnetic field induced increase in fluorescence intensity, localization number of probe molecules, and the number of photons emitted per molecule as compared to those acquired without a magnetic field were experimentally confirmed. Improved dSTORM localization precision and imaging resolution were consequently achieved.

Emerging methods to study bacteriophage infection at the single-cell level

Bacteria and their viruses (phages) are abundant across diverse ecosystems and their interactions influence global biogeochemical cycles and incidence of disease. Problematically, both classical and metagenomic methods insufficiently assess the host specificity of phages and phage–host infection dynamics in nature. Here we review emerging methods to study phage–host interaction and infection dynamics with a focus on those that offer resolution at the single-cell level. These methods leverage ever-increasing sequence data to identify virus signals from single-cell amplified genome datasets or to produce primers/probes to target particular phage–bacteria pairs (digital PCR and phageFISH), even in complex communities. All three methods enable study of phage infection of uncultured bacteria from environmental samples, while the latter also discriminates between phage–host interaction outcomes (e.g., lytic, chronic, lysogenic) in model systems. Together these techniques enable quantitative, spatiotemporal studies of phage–bacteria interactions from environmental samples of any ecosystem, which will help elucidate and predict the ecological and evolutionary impacts of specific phage–host pairings in nature.

Azimuthal polarization filtering for accurate, precise, and robust single-molecule localization microscopy

Many single nanoemitters such as fluorescent molecules produce dipole radiation that leads to systematic position errors in both particle tracking and super-resolution microscopy. Via vectorial diffraction equations and simulations, we show that imaging only azimuthally polarized light in the microscope naturally avoids emission from the z-component of the transition dipole moment, resulting in negligible localization errors for all emitter orientations and degrees of objective lens misfocus. Furthermore, localization accuracy is maintained even in the presence of aberrations resulting from imaging in mismatched media.

Cryogenic colocalization microscopy for nanometer-distance measurements

The main limiting factor in spatial resolution of localization microscopy is the number of detected photons. Recently we showed that cryogenic measurements improve the photostability of fluorophores, giving access to Angstrom precision in localization of single molecules. Here, we extend this method to colocalize two fluorophores attached to well-defined positions of a double-stranded DNA. By measuring the separations of the fluorophore pairs prepared at different design positions, we verify the feasibility of cryogenic distance measurement with sub-nanometer accuracy. We discuss the important challenges of our method as well as its potential for further improvement and various applications.

Polarization-controlled TIRFM with focal drift and spatial field intensity correction

Total internal reflection fluorescence microscopy (TIRFM) is becoming an increasingly common methodology to narrow the illumination excitation thickness to study cellular process such as exocytosis, endocytosis, and membrane dynamics. It is also frequently used as a method to improve signal/noise in other techniques such as in vitro single-molecule imaging, stochastic optical reconstruction microscopy/photoactivated localization microscopy imaging, and fluorescence resonance energy transfer imaging. The unique illumination geometry of TIRFM also enables a distinct method to create an excitation field for selectively exciting fluorophores that are aligned either parallel or perpendicular to the optical axis. This selectivity has been used to study orientation of cell membranes and cellular proteins. Unfortunately, the coherent nature of laser light, the typical excitation source in TIRFM, often creates spatial interference fringes across the illuminated area. These fringes are particularly problematic when imaging large cellular areas or when accurate quantification is necessary. Methods have been developed to minimize these fringes by modulating the TIRFM field during a frame capture period; however, these approaches eliminate the possibility to simultaneously excite with a specific polarization. A new, to our knowledge, technique is presented, which compensates for spatial fringes while simultaneously permitting rapid image acquisition of both parallel and perpendicular excitation directions in ~25 ms. In addition, a back reflection detection scheme was developed that enables quick and accurate alignment of the excitation laser. The detector also facilitates focus drift compensation, a common problem in TIRFM due to the narrow excitation depth, particularly when imaging over long time courses or when using a perfusion flow chamber. The capabilities of this instrument were demonstrated by imaging membrane orientation using DiO on live cells and on lipid bilayers that were supported on a glass slide (supported lipid bilayer). The use of the approach to biological problems was illustrated by examining the temporal and spatial dynamics of exocytic vesicles.

Twinkle, twinkle little star: photoswitchable fluorophores for super-resolution imaging

Photoswitchable fluorescent probes are key elements of newly developed super-resolution fluorescence microscopy techniques that enable far-field interrogation of biological systems with a resolution of 50 nm or better. In contrast to most conventional fluorescence imaging techniques, the performance achievable by most super-resolution techniques is critically impacted by the photoswitching properties of the fluorophores. Here we review photoswitchable fluorophores for super-resolution imaging with discussion of the fundamental principles involved, a focus on practical implementation with available tools, and an outlook on future directions.

Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm

Highly accurate sample drift correction is essential in super-resolution localization microscopy to guarantee a high spatial resolution, especially when the technique is used to visualize small cell organelle. Here we present a localization events-based drift correction method using a redundant cross-correlation algorithm originally developed to correct beam-induced motion in cryo-electron microscopy. With simulated, synthesized as well as experimental data, we have demonstrated its superior precision compared to previously published localization events-based drift correction methods. The major advantage of this method is the robustness when the number of localization events is low, either because a short correction time step is required or because the imaged structure is small and sparse. This method has allowed us to improve the effective resolution when imaging Golgi apparatus in mammalian cells.

Three-dimensional super-resolution and localization of dense clusters of single molecules

When a single molecule is detected in a wide-field microscope, the image approximates the point spread function of the system. However, as the distribution of molecules becomes denser and their images begin to overlap, existing solutions to determine the number of molecules present and their precise three-dimensional locations can tolerate little to no overlap. We propose a localization scheme that can identify several overlapping molecule images while maintaining high localization precision. A solution to this problem involving matched optical and digital techniques, as here proposed, can substantially increase the allowable labeling density and accelerate the data collection time of single-molecule localization microscopy by more than one order of magnitude.

Localization microscopy coming of age: from concepts to biological impact

Super-resolution fluorescence imaging by single-molecule photoactivation or photoswitching and position determination (localization microscopy) has the potential to fundamentally revolutionize our understanding of how cellular function is encoded at the molecular level. Among all powerful, high-resolution imaging techniques introduced in recent years, localization microscopy excels because it delivers single-molecule information about molecular distributions, even giving absolute numbers of proteins present in subcellular compartments. This provides insight into biological systems at a molecular level that can yield direct experimental feedback for modeling the complexity of biological interactions. In addition, efficient new labeling methods and strategies to improve localization are emerging that promise to achieve true molecular resolution. This raises localization microscopy as a powerful complementary method for correlative light and electron microscopy experiments.

Super-resolution molecular and functional imaging of nanoscale architectures in life and materials science

Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.

Fluorescence microscopy with 6 nm resolution on DNA origami

Resolution of emerging superresolution microscopy is commonly characterized by the width of a point-spread-function or by the localization accuracy of single molecules. In contrast, resolution is defined as the ability to separate two objects. Recently, DNA origamis have been proven as valuable scaffold for self-assembled nanorulers in superresolution microscopy. Here, we use DNA origami nanorulers to overcome the discrepancy of localizing single objects and separating two objects by resolving two docking sites at distances of 18, 12, and 6 nm by using the superresolution technique DNA PAINT(point accumulation for imaging in nanoscale topography). For the smallest distances, we reveal the influence of localization noise on the yield of resolvable structures that we rationalize by Monte Carlo simulations.

Sample preparation for single molecule localization microscopy

Single molecule localization-based optical nanoscopy was introduced in 2006, surpassing traditional diffraction-limited resolutions by an order of magnitude. Seven years later, this superresolution technique is continuing to follow a trend of increasing popularity and pervasiveness, with the proof-of-concept work long finished and commercial implementations now available. However one important aspect that tends to become lost in translation is the importance of proper sample preparation, with very few resources addressing the considerations that must be made when preparing samples for imaging with single molecule level sensitivity. Presented here is a an in-depth analysis of all aspects of sample preparation for single molecule superresolution, including both live and fixed cell preparation, choice of fluorophore, fixation and staining techniques, and imaging buffer considerations.

Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging

Photoactivatable fluorescent proteins (PAFPs) have been widely used for superresolution imaging based on the switching and localization of single molecules. Several properties of PAFPs strongly influence the quality of the superresolution images. These properties include (i) the number of photons emitted per switching cycle, which affects the localization precision of individual molecules; (ii) the ratio of the on- and off-switching rate constants, which limits the achievable localization density; (iii) the dimerization tendency, which could cause undesired aggregation of target proteins; and (iv) the signaling efficiency, which determines the fraction of target-PAFP fusion proteins that is detectable in a cell. Here, we evaluated these properties for 12 commonly used PAFPs fused to both bacterial target proteins, H-NS, HU, and Tar, and mammalian target proteins, Zyxin and Vimentin. Notably, none of the existing PAFPs provided optimal performance in all four criteria, particularly in the signaling efficiency and dimerization tendency. The PAFPs with low dimerization tendencies exhibited low signaling efficiencies, whereas mMaple showed the highest signaling efficiency but also a high dimerization tendency. To address this limitation, we engineered two new PAFPs based on mMaple, which we termed mMaple2 and mMaple3. These proteins exhibited substantially reduced or undetectable dimerization tendencies compared with mMaple but maintained the high signaling efficiency of mMaple. In the meantime, these proteins provided photon numbers and on-off switching rate ratios that are comparable to the best achieved values among PAFPs.

Superresolution microscope image reconstruction by spatiotemporal object decomposition and association: application in resolving t-tubule structure in skeletal muscle

One key factor that limits resolution of single-molecule superresolution microscopy relates to the localization accuracy of the activated emitters, which is usually deteriorated by two factors. One originates from the background noise due to out-of-focus signals, sample auto-fluorescence, and camera acquisition noise; and the other is due to the low photon count of emitters at a single frame. With fast acquisition rate, the activated emitters can last multiple frames before they transiently switch off or permanently bleach. Effectively incorporating the temporal information of these emitters is critical to improve the spatial resolution. However, majority of the existing reconstruction algorithms locate the emitters frame by frame, discarding or underusing the temporal information. Here we present a new image reconstruction algorithm based on tracklets, short trajectories of the same objects. We improve the localization accuracy by associating the same emitters from multiple frames to form tracklets and by aggregating signals to enhance the signal to noise ratio. We also introduce a weighted mean-shift algorithm (WMS) to automatically detect the number of modes (emitters) in overlapping regions of tracklets so that not only well-separated single emitters but also individual emitters within multi-emitter groups can be identified and tracked. In combination with a maximum likelihood estimator method (MLE), we are able to resolve low to medium density of overlapping emitters with improved localization accuracy. We evaluate the performance of our method with both synthetic and experimental data, and show that the tracklet-based reconstruction is superior in localization accuracy, particularly for weak signals embedded in a strong background. Using this method, for the first time, we resolve the transverse tubule structure of the mammalian skeletal muscle.

Faster fluorescence microscopy: advances in high speed biological imaging

The past decade has seen explosive growth in new high speed imaging methods. These can broadly be classified as either point-scanning (which offer better depth penetration) or parallelized systems (which offer higher speed). We discuss each class generally, and cover specific advances in diffraction-limited microscopes (laser-scanning confocal, spinning-disk, and light-sheet) and superresolution microscopes (single-molecule imaging, stimulated emission-depletion, and structured illumination). A theme of our review is that there is no free lunch: each technique has strengths and weaknesses, and an advance in speed usually comes at the expense of either spatial resolution or depth penetration.

Structurally distinct Ca(2+) signaling domains of sperm flagella orchestrate tyrosine phosphorylation and motility

Spermatozoa must leave one organism, navigate long distances, and deliver their paternal DNA into a mature egg. For successful navigation and delivery, a sperm-specific calcium channel is activated in the mammalian flagellum. The genes encoding this channel (CatSpers) appear first in ancient uniflagellates, suggesting that sperm use adaptive strategies developed long ago for single-cell navigation. Here, using genetics, super-resolution fluorescence microscopy, and phosphoproteomics, we investigate the CatSper-dependent mechanisms underlying this flagellar switch. We find that the CatSper channel is required for four linear calcium domains that organize signaling proteins along the flagella. This unique structure focuses tyrosine phosphorylation in time and space as sperm acquire the capacity to fertilize. In heterogeneous sperm populations, we find unique molecular phenotypes, but only sperm with intact CatSper domains that organize time-dependent and spatially specific protein tyrosine phosphorylation successfully migrate. These findings illuminate flagellar adaptation, signal transduction cascade organization, and fertility.

Quantitative super-resolution microscopy: pitfalls and strategies for image analysis

Super-resolution microscopy is an enabling technology that allows biologists to visualize cellular structures at nanometer length scales using far-field optics. To break the diffraction barrier, it is necessary to leverage the distinct molecular states of fluorescent probes. At the same time, the existence of these different molecular states and the photophysical properties of the fluorescent probes can complicate data quantification and interpretation. Here, we review the pitfalls in super-resolution data analysis that must be avoided for proper interpretation of images.

Meeting report--Visualizing signaling nanoplatforms at a higher spatiotemporal resolution

The International Symposium entitled ‘Visualizing signaling nanoplatforms at a higher spatiotemporal resolution’ sponsored by the Institució Catalana de Recerca i Estudis Avançats (ICREA) was held on 29–31 May 2013 at the ICFO-Institute of Photonic Sciences, in Barcelona, Spain. The meeting brought together a multidisciplinary group of international leaders in the fields of super-resolution imaging (nanoscopy) and cell membrane biology, and served as a forum to further our understanding of the fundamental mechanisms that govern nanostructures and protein–function relationships at the cell membrane.

Introduction to super-resolution microscopy

In this review, we introduce the principles of spatial resolution improvement in super-resolution microscopies that were recently developed. These super-resolution techniques utilize the interaction of light and fluorescent probes in order to break the diffraction barrier that limits spatial resolution. The imaging property of each super-resolution technique is also compared with the corresponding conventional one. Typical applications of the super-resolution techniques in biological research are also introduced.

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

Super-resolution fluorescence microscopy is a powerful tool for biological research, but obtaining multiplexed images for a large number of distinct target species remains challenging. Here we use the transient binding of short fluorescently labeled oligonucleotides (DNA-PAINT, a variation of point accumulation for imaging in nanoscale topography) for simple and easy-to-implement multiplexed super-resolution imaging that achieves sub-10-nm spatial resolution in vitro on synthetic DNA structures. We also report a multiplexing approach (Exchange-PAINT) that allows sequential imaging of multiple targets using only a single dye and a single laser source. We experimentally demonstrate ten-color super-resolution imaging in vitro on synthetic DNA structures as well as four-color two-dimensional (2D) imaging and three-color 3D imaging of proteins in fixed cells.

Super-resolution localization microscopy with photoactivatable fluorescent marker proteins

Fluorescent proteins (FPs) have become popular imaging tools because of their high specificity, minimal invasive labeling and allowing visualization of proteins and structures inside living organisms. FPs are genetically encoded and expressed in living cells, therefore, labeling involves minimal effort in comparison to approaches involving synthetic dyes. Photoactivatable FPs (paFPs) comprise a subclass of FPs that can change their absorption/emission properties such as brightness and color upon irradiation. This methodology has found a broad range of applications in the life sciences, especially in localization-based super-resolution microscopy of cells, tissues and even entire organisms. In this review, we discuss recent developments and applications of paFPs in super-resolution localization imaging.

Reduced dyes enhance single-molecule localization density for live superresolution imaging

Cell-permeable rhodamine dyes are reductively quenched by NaBH4 into a non-fluorescent leuco-rhodamine form. Quenching is reversible, and their fluorescence is recovered when the dyes are oxidized. In living cells, oxidation occurs spontaneously, and can result in up to ten-fold higher densities of single molecule localizations, and more photons per localization as compared with unmodified dyes. These two parameters directly impact the achievable resolution, and we see a significant improvement in the quality of live-cell point-localization super-resolution images taken with reduced dyes. These improvements carry over to increase the density of trajectories for single-molecule tracking experiments.

Fixed pattern noise in localization microscopy

Localization microscopy vastly improves the resolution achieved by fluorescence microscopy by fitting the positions of individual fluorophores. We examine the reconstructions produced by different fitting algorithms for instances of fixed pattern noise--systematic tendencies to alter estimated emitter positions according to their subpixel location in a way that does not reflect the ground truth structure. We show that while not readily visible at standard empirical signal strengths, fixed pattern noise can occur when performing sub-pixel fitting, and that its degree varies according to the algorithm used and the relative size of the pixels compared to the point spread function. For pixel sizes in the range 80-170 nm, this results in variations in accuracy of the order of 2-4 nm-comparatively small for many applications, but non-negligible in scenarios where very high accuracy is sought.

Isotropic 3D Super-resolution Imaging with a Self-bending Point Spread Function

Airy beams maintain their intensity profiles over a large propagation distance without substantial diffraction and exhibit lateral bending during propagation^1-5. This unique property has been exploited for micromanipulation of particles⁶, generation of plasma channels⁷ and guidance of plasmonic waves⁸, but has not been explored for high-resolution optical microscopy. Here, we introduce a self-bending point spread function (SB-PSF) based on Airy beams for three-dimensional (3D) super-resolution fluorescence imaging. We designed a side-lobe-free SB-PSF and implemented a two-channel detection scheme to enable unambiguous 3D localization of fluorescent molecules. The lack of diffraction and the propagation-dependent lateral bending make the SB-PSF well suited for precise 3D localization of molecules over a large imaging depth. Using this method, we obtained super-resolution imaging with isotropic 3D localization precision of 10-15 nm over a 3 μm imaging depth from ∼2000 photons per localization.

Imaging cellular ultrastructure by PALM, iPALM, and correlative iPALM-EM

Many biomolecules in cells can be visualized with high sensitivity and specificity by fluorescence microscopy. However, the resolution of conventional light microscopy is limited by diffraction to ~200-250 nm laterally and >500 nm axially. Here, we describe superresolution methods based on single-molecule localization analysis of photoswitchable fluorophores (PALM: photoactivated localization microscopy) as well as our recent three-dimensional (3D) method (iPALM: interferometric PALM) that allows imaging with a resolution better than 20 nm in all three dimensions. Considerations for their implementations, applications to multicolor imaging, and a recent development that extend the imaging depth of iPALM to ~750 nm are discussed. As the spatial resolution of superresolution fluorescence microscopy converges with that of electron microscopy (EM), direct imaging of the same specimen using both approaches becomes feasible. This could be particularly useful for cross validation of experiments, and thus, we also describe recent methods that were developed for correlative superresolution fluorescence and EM.

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.

Super-resolution fluorescence imaging with single molecules

The ability to detect, image and localize single molecules optically with high spatial precision by their fluorescence enables an emergent class of super-resolution microscopy methods which have overcome the longstanding diffraction barrier for far-field light-focusing optics. Achieving spatial resolutions of 20-40nm or better in both fixed and living cells, these methods are currently being established as powerful tools for minimally-invasive spatiotemporal analysis of structural details in cellular processes which benefit from enhanced resolution. Briefly covering the basic principles, this short review then summarizes key recent developments and application examples of two-dimensional and three-dimensional (3D) multi-color techniques and faster time-lapse schemes. The prospects for quantitative imaging - in terms of improved ability to correct for dipole-emission-induced systematic localization errors and to provide accurate counts of molecular copy numbers within nanoscale cellular domains - are discussed.

Approach to multiparticle parallel tracking in thick samples with three-dimensional nanoresolution

This Letter proposes a method referred to as distorted grating (DG) and double-helix point spread function (DH-PSF) combination microscopy (DDCM), which is capable of multiparticle parallel localization and tracking in a transparent sample thicker than 10 μm, the thickness of cells. A special phase mask, combining the field depth extension capabilities of DG with the three-dimensional (3D) nanolocalization capabilities of the DH-PSF, is designed for multiparticle parallel localization. Time-lapse tracking of one particle moving along the z axis and parallel tracking of two particles are simulated. Results demonstrate that, with only a single snapshot, particles can be localized, tracking with 3D nanoresolution wherever they are. The theoretical localization precisions of DDCM, DH-PSF, and multifocus microscopy are compared. DDCM results in almost constant localization precisions in all three dimensions for a depth of field larger than 10 μm. DDCM is expected to become a tool in investigations of important dynamic events in living cells.

Rotational mobility of single molecules affects localization accuracy in super-resolution fluorescence microscopy

The asymmetric nature of single-molecule (SM) dipole emission patterns limits the accuracy of position determination in localization-based super-resolution fluorescence microscopy. The degree of mislocalization depends highly on the rotational mobility of SMs; only for SMs rotating within a cone half angle α > 60° can mislocalization errors be bounded to ≤10 nm. Simulations demonstrate how low or high rotational mobility can cause resolution degradation or distortion in super-resolution reconstructions.

Imaging the invisible: resolving cellular microcompartments by superresolution microscopy techniques

Unraveling the spatio-temporal organization of dynamic cellular microcompartments requires live cell imaging techniques capable of resolving submicroscopic structures. While the resolution of traditional far-field fluorescence imaging techniques is limited by the diffraction barrier, several fluorescence-based microscopy techniques providing sub-100 nm resolution have become available during the past decade. Here, we briefly introduce the optical principles of these techniques and compare their capabilities and limitations with respect to spatial and temporal resolution as well as live cell capabilities. Moreover, we summarize how these techniques contributed to a better understanding of plasma membrane microdomains, the dynamic nanoscale organization of neuronal synapses and the sub-compartmentation of microorganisms. Based on these applications, we highlight complementarity of these techniques and their potential to address specific challenges in the context of dynamic cellular microcompartments, as well as the perspectives to overcome current limitations of these methods.

Resolution doubling in 3D-STORM imaging through improved buffers

Super-resolution imaging methods have revolutionized fluorescence microscopy by revealing the nanoscale organization of labeled proteins. In particular, single-molecule methods such as Stochastic Optical Reconstruction Microscopy (STORM) provide resolutions down to a few tens of nanometers by exploiting the cycling of dyes between fluorescent and non-fluorescent states to obtain a sparse population of emitters and precisely localizing them individually. This cycling of dyes is commonly induced by adding different chemicals, which are combined to create a STORM buffer. Despite their importance, the composition of these buffers has scarcely evolved since they were first introduced, fundamentally limiting what can be resolved with STORM. By identifying a new chemical suitable for STORM and optimizing the buffer composition for Alexa-647, we significantly increased the number of photons emitted per cycle by each dye, providing a simple means to enhance the resolution of STORM independently of the optical setup used. Using this buffer to perform 3D-STORM on biological samples, we obtained images with better than 10 nanometer lateral and 30 nanometer axial resolution.

Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms

Newly developed scientific complementary metal–oxide–semiconductor (sCMOS) cameras have the potential to dramatically accelerate data acquisition in single-molecule switching nanoscopy (SMSN) while simultaneously increasing the effective quantum efficiency. However, sCMOS-intrinsic pixel-dependent readout noise substantially reduces the localization precision and introduces localization artifacts. Here we present algorithms that overcome these limitations and provide unbiased, precise localization of single molecules at the theoretical limit. In combination with a multi-emitter fitting algorithm, we demonstrate single-molecule localization super-resolution imaging at up to 32 reconstructed images/second (recorded at 1,600–3,200 camera frames/second) in both fixed and living cells.

Application of advanced fluorescence microscopy to the structure of meiotic chromosomes

Chromosomes undergoing meiosis are defined by a macromolecular protein assembly called the synaptonemal complex which holds homologs together and carries out important meiotic functions. By retaining the molecular specificity, multiplexing ability, and in situ imaging capabilities of fluorescence microscopy, but with vastly increased resolution, 3D-SIM and other superresolution techniques are poised to make significant discoveries about the structure and function of the synaptonemal complex. This review discusses recent developments in this field and poses questions approachable with current and future technology.