Sub-second, super-resolved imaging of biological systems using parallel EO-STED (original) (raw)
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Nature Communications
Imaging of nuclear structures within intact eukaryotic nuclei is imperative to understand the effect of chromatin folding on genome function. Recent developments of super-resolution fluorescence microscopy techniques combine high specificity, sensitivity, and less-invasive sample preparation procedures with the sub-diffraction spatial resolution required to image chromatin at the nanoscale. Here, we present a method to enhance the spatial resolution of a stimulated-emission depletion (STED) microscope based only on the modulation of the STED intensity during the acquisition of a STED image. This modulation induces spatially encoded variations of the fluorescence emission that can be visualized in the phasor plot and used to improve and quantify the effective spatial resolution of the STED image. We show that the method can be used to remove direct excitation by the STED beam and perform dual color imaging. We apply this method to the visualization of transcription and replication foci within intact nuclei of eukaryotic cells.
Nanodiamond Landmarks for Subcellular Multimodal Optical and Electron Imaging
Scientific Reports, 2013
There is a growing need for biolabels that can be used in both optical and electron microscopies, are non-cytotoxic, and do not photobleach. Such biolabels could enable targeted nanoscale imaging of sub-cellular structures, and help to establish correlations between conjugation-delivered biomolecules and function. Here we demonstrate a subcellular multi-modal imaging methodology that enables localization of inert particulate probes, consisting of nanodiamonds having fluorescent nitrogen-vacancy centers. These are functionalized to target specific structures, and are observable by both optical and electron microscopies. Nanodiamonds targeted to the nuclear pore complex are rapidly localized in electron-microscopy diffraction mode to enable "zooming-in" to regions of interest for detailed structural investigations. Optical microscopies reveal nanodiamonds for in-vitro tracking or uptake-confirmation. The approach is general, works down to the single nanodiamond level, and can leverage the unique capabilities of nanodiamonds, such as biocompatibility, sensitive magnetometry, and gene and drug delivery. Nanoparticles have emerged in recent years as a promising approach to particulate labeling probes for multimodal imaging, and also for targeted drug or gene delivery. They can also be used for tracking at the single-molecule level. 1 In general, little is known about the immediate environment of targeted nanoparticles due to a lack of suitable visualization protocols. Knowledge of the local environment would enable clear delineation of relationships between the activity of a labeled agent and the local biological environment. One would like to know, for example, the nature and proximity to adjacent macromolecular assemblies. Despite considerable investigation, the identification and optimization of such a cross-platform biomarker has remained elusive. Optical microscopy offers versatility, specificity, and sensitivity in fixed and live cell settings. 2 The development of super-resolution techniques has improved spatial resolution to tens of nanometers, but these techniques are restricted to a subset of cellular processes. 3-5 Transmission electron microscopy (TEM) offers higher spatial resolution. 6 But, it lacks reliable multimodal markers to align the field-of-view with a desired subcellular region. This is particularly true if multiple iterations between imaging techniques is desired. Routine multimodal correlated imaging, which could enable the study of live cells with concurrent visualization of ultra-structural details, 7 would require the development of inert biomarkers and protocols for correlating optical and electron microscopies.
Journal of biomedical optics, 2014
Stimulated emission depletion (STED) microscopy is one type of far-field optical technique demonstrated to provide subdiffraction resolution. STED microscopy utilizes a donut-shaped depletion beam to limit the probe volume to be much smaller than a diffraction-limited spot. Resolutions as small as a few tens of nanometers laterally are reported for cell analysis. The different versions of STED microscopes are described and contrasted in terms of their applicability for biological imaging. Finally, we suggest likely avenues for improving the performance and increasing the utility of STED microscopy.
Nanoscopic resolution within a single imaging frame
Mean-Shift Super Resolution (MSSR) is a principle based on the Mean Shift theory that improves the spatial resolution in fluorescence images beyond the diffraction limit. MSSR works on low- and high-density fluorophore images, is not limited by the architecture of the detector (EM-CCD, sCMOS, or photomultiplier-based laser scanning systems) and is applicable to single images as well as temporal series. The theoretical limit of spatial resolution, based on optimized real-world imaging conditions and analysis of temporal image series, has been measured to be 40 nm. Furthermore, MSSR has denoising capabilities that outperform other analytical super resolution image approaches. Altogether, MSSR is a powerful, flexible, and generic tool for multidimensional and live cell imaging applications.
Large parallelization of STED nanoscopy using optical lattices
Optics Express, 2014
As a scanning microscope, STimulated Emission Depletion (STED) nanoscopy needs parallelization for fast wide-field imaging. Using well-designed optical lattices for depletion together with wide-field excitation and a fast camera for detection, we achieve large parallelization of STED nanoscopy. Wide field of view super-resolved images are acquired by scanning over a single unit cell of the optical lattice, which can be as small as 290nm * 290nm. Optical Lattice STED (OL-STED) imaging is demonstrated with a resolution down to 70 nm at 12.5 frames per second.
Gated CW-STED microscopy: A versatile tool for biological nanometer scale investigation
Methods (San Diego, Calif.), 2013
Stimulation emission depletion (STED) microscopy breaks the spatial resolution limit of conventional light microscopy while retaining its major advantages, such as working under physiological conditions. These properties make STED microscopy a perfect tool for investigating dynamic sub-cellular processes in living organisms. However, up to now, the massive dissemination of STED microscopy has been hindered by the complexity and cost of its implementation. Gated CW-STED (gCW-STED) substantially helps solve this problem without sacrificing spatial resolution. Here, we describe a versatile gCW-STED microscope able to speedily image the specimen, at a resolution below 50 nm, with light intensities comparable to the more complicated all-pulsed STED system. We show this ability on calibration samples as well as on biological samples.
SPIE Proceedings, 2015
Our aim is to develop quantitative single-molecule assays to study when and where molecules are interacting inside living cells and where enzymes are active. To this end we present a three-camera imaging microscope for fast tracking of multiple interacting molecules simultaneously, with high spatiotemporal resolution. The system was designed around an ASI RAMM frame using three separate tube lenses and custom multi-band dichroics to allow for enhanced detection efficiency. The frame times of the three Andor iXon Ultra EMCCD cameras are hardware synchronized to the laser excitation pulses of the three excitation lasers, such that the fluorophores are effectively immobilized during frame acquisitions and do not yield detections that are motion-blurred. Stroboscopic illumination allows robust detection from even rapidly moving molecules while minimizing bleaching, and since snapshots can be spaced out with varying time intervals, stroboscopic illumination enables a direct comparison to be made between fast and slow molecules under identical light dosage. We have developed algorithms that accurately track and co-localize multiple interacting biomolecules. The three-color microscope combined with our co-movement algorithms have made it possible for instance to simultaneously image and track how the chromosome environment affects diffusion kinetics or determine how mRNAs diffuse during translation. Such multiplexed single-molecule measurements at a high spatiotemporal resolution inside living cells will provide a major tool for testing models relating molecular architecture and biological dynamics.
Homogeneous multifocal excitation for high-throughput super-resolution imaging
2020
Super-resolution microscopies, which allow features below the diffraction limit to be resolved, have become an established tool in biological research. However, imaging throughput remains a major bottleneck in using them for quantitative biology, which requires large datasets to overcome the noise of the imaging itself and to capture the variability inherent to biological processes. Here, we develop a multi-focal flat illumination for field independent imaging (mfFIFI) module, and integrate it into an instant structured illumination microscope (iSIM). Our instrument extends the field of view (FOV) to >100×100 µm2 without compromising image quality, and maintains high-speed (100 Hz), multi-color, volumetric imaging at double the diffraction-limited resolution. We further extend the effective FOV by stitching multiple adjacent images together to perform fast live-cell super-resolution imaging of dozens of cells. Finally, we combine our flat-fielded iSIM setup with ultrastructure ex...
Nanoparticle-Assisted Stimulated- Emission-Depletion Nanoscopy
We show that metal nanoparticles can be used to improve the performance of super-resolution fluorescence nanoscopes based on stimulated-emission-depletion (STED). Compared with a standard STED nanoscope, we show theoretically a resolution improvement by more than an order of magnitude, or equivalently, depletion intensity reductions by more than 2 orders of magnitude and an even stronger photostabilization. Our scheme may allow improvement of existing STED nanoscopes and assist in the development of low-power, low-cost nanoscopes.
Nature Communications
Non-uniform illumination limits quantitative analyses of fluorescence imaging techniques. In particular, single molecule localization microscopy (SMLM) relies on high irradiances, but conventional Gaussian-shaped laser illumination restricts the usable field of view to around 40 µm × 40 µm. We present Adaptable Scanning for Tunable Excitation Regions (ASTER), a versatile illumination technique that generates uniform and adaptable illumination. ASTER is also highly compatible with optical sectioning techniques such as total internal reflection fluorescence (TIRF). For SMLM, ASTER delivers homogeneous blinking kinetics at reasonable laser power over fields-of-view up to 200 µm × 200 µm. We demonstrate that ASTER improves clustering analysis and nanoscopic size measurements by imaging nanorulers, microtubules and clathrin-coated pits in COS-7 cells, and β2-spectrin in neurons. ASTER’s sharp and quantitative illumination paves the way for high-throughput quantification of biological str...