Showing papers on "Resolution (electron density) published in 2016"
TL;DR: A modified time-of-flight three-dimensional imaging system, which can use compressed sensing techniques to reduce acquisition times, whilst distributing the optical illumination over the full field of view, is shown.
Abstract: A three-dimensional imaging system which distributes the optical illumination over the full field-of-view is sought after. Here, the authors demonstrate the capability of reconstructing 128 × 128 pixel resolution three-dimensional scenes to an accuracy of 3 mm as well as real-time video with a frame-rate up to 12 Hz.
409 citations
TL;DR: It is anticipated that the combination of lightwave electronics and the atomic resolution of the approach will open the door to visualizing ultrafast photochemistry and the operation of molecular electronics on the single-orbital scale.
Abstract: Watching a single molecule move on its intrinsic timescale has been one of the central goals of modern nanoscience, and calls for measurements that combine ultrafast temporal resolution with atomic spatial resolution. Steady-state experiments access the requisite spatial scales, as illustrated by direct imaging of individual molecular orbitals using scanning tunnelling microscopy or the acquisition of tip-enhanced Raman and luminescence spectra with sub-molecular resolution. But tracking the intrinsic dynamics of a single molecule directly in the time domain faces the challenge that interactions with the molecule must be confined to a femtosecond time window. For individual nanoparticles, such ultrafast temporal confinement has been demonstrated by combining scanning tunnelling microscopy with so-called lightwave electronics, which uses the oscillating carrier wave of tailored light pulses to directly manipulate electronic motion on timescales faster even than a single cycle of light. Here we build on ultrafast terahertz scanning tunnelling microscopy to access a state-selective tunnelling regime, where the peak of a terahertz electric-field waveform transiently opens an otherwise forbidden tunnelling channel through a single molecular state. It thereby removes a single electron from an individual pentacene molecule's highest occupied molecular orbital within a time window shorter than one oscillation cycle of the terahertz wave. We exploit this effect to record approximately 100-femtosecond snapshot images of the orbital structure with sub-angstrom spatial resolution, and to reveal, through pump/probe measurements, coherent molecular vibrations at terahertz frequencies directly in the time domain. We anticipate that the combination of lightwave electronics and the atomic resolution of our approach will open the door to visualizing ultrafast photochemistry and the operation of molecular electronics on the single-orbital scale.
361 citations
331 citations
TL;DR: The mathematical theory of super resolution developed recently by Candes and Fernandes-Granda states that a continuous, sparse frequency spectrum can be recovered with infinite precision via super-resolution as discussed by the authors.
Abstract: The mathematical theory of super-resolution developed recently by Candes and Fernandes-Granda states that a continuous, sparse frequency spectrum can be recovered with infinite precision via...
186 citations
TL;DR: This paper proposes time-efficient non-invasive microsphere-based scanning superlens microscopy that enables the large-area observation of live-cell morphology or sub-membrane structures with sub-diffraction-limited resolution and is demonstrated by observing biological and non-biological objects.
Abstract: Nanoscale correlation of structural information acquisition with specific-molecule identification provides new insight for studying rare subcellular events. To achieve this correlation, scanning electron microscopy has been combined with super-resolution fluorescent microscopy, despite its destructivity when acquiring biological structure information. Here we propose time-efficient non-invasive microsphere-based scanning superlens microscopy that enables the large-area observation of live-cell morphology or sub-membrane structures with sub-diffraction-limited resolution and is demonstrated by observing biological and non-biological objects. This microscopy operates in both non-invasive and contact modes with ∼200 times the acquisition efficiency of atomic force microscopy, which is achieved by replacing the point of an atomic force microscope tip with an imaging area of microspheres and stitching the areas recorded during scanning, enabling sub-diffraction-limited resolution. Our method marks a possible path to non-invasive cell imaging and simultaneous tracking of specific molecules with nanoscale resolution, facilitating the study of subcellular events over a total cell period.
140 citations
TL;DR: In this article, the authors overcome the resolution limit of Fourier transform spectrometry and measure line-shape-free broadband molecular spectra with lines narrower than the optical path-limited resolution.
Abstract: We overcome the resolution limit of Fourier-transform spectrometry and measure instrumental line-shape-free broadband molecular spectra with lines narrower than the optical path-limited resolution
128 citations
TL;DR: This work advocates the use of a standard spoke-pattern imaging target and the mandatory inclusion of information about underlying a priori assumptions in the reporting of spatial resolution for coherent imaging methods.
Abstract: The definition and reporting of spatial resolution for coherent imaging methods varies widely in the imaging community. We advocate the use of a standard spoke-pattern imaging target and the mandatory inclusion of information about underlying a priori assumptions.
113 citations
TL;DR: In this article, the hierarchical structures of the polyamide (PA) active layer of the SW30HR RO membrane were examined in 3D using scanning electron microscopy combined with focused ion beam milling (FIB-SEM).
110 citations
TL;DR: Dark field electron holography, the geometrical phase analysis of high angle annular dark field scanning transmission electron microscopy images, nanobeam diffraction and precession diffraction, all performed at the state-of-the-art to five different types of semiconductor samples.
109 citations
TL;DR: A newly developed C_{c/C{s}/C_{s} corrector is introduced that is capable of correcting both the chromatic and the spherical aberration in the range of accelerating voltages from 20 to 80 kV, showing unprecedented contrast and resolution that matches image calculations.
Abstract: Atomic resolution in transmission electron microscopy of thin and light-atom materials requires a rigorous reduction of the beam energy to reduce knockon damage. However, at the same time, the chromatic aberration deteriorates the resolution of the TEM image dramatically. Within the framework of the SALVE project, we introduce a newly developed ${C}_{c}/{C}_{s}$ corrector that is capable of correcting both the chromatic and the spherical aberration in the range of accelerating voltages from 20 to 80 kV. The corrector allows correcting axial aberrations up to fifth order as well as the dominating off-axial aberrations. Over the entire voltage range, optimum phase-contrast imaging conditions for weak signals from light atoms can be adjusted for an optical aperture of at least 55 mrad. The information transfer within this aperture is no longer limited by chromatic aberrations. We demonstrate the performance of the microscope using the examples of 30 kV phase-contrast TEM images of graphene and molybdenum disulfide, showing unprecedented contrast and resolution that matches image calculations.
107 citations
TL;DR: Four structures of the amyloid core of the Sup35 prion protein are shown that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction.
Abstract: Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.
TL;DR: By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution.
Abstract: How electronic charge is distributed over a molecule determines to a large extent its chemical properties. Here, we demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with submolecular resolution. We exploit the fact that distortions typically observed in high-resolution atomic force microscopy images are for a significant part caused by the electrostatic force acting between charges of the tip and the molecule of interest. By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution.
TL;DR: A major obstacle of cryo‐CLEM currently hindering many biological applications is the large resolution gap betweenCryo‐FM (typically in the range of ∼400 nm) and cryo-EM (single nanometre to the Ångstrom range).
TL;DR: A quantitative resolution measure of the ab initio shapes restored from small-angle scattering data is introduced based on the variability of multiple reconstructions and its efficiency has been demonstrated in applications to experimental data.
TL;DR: Piezoresponse force microscopy (PFM) has been used to probe electromechanical functionality in a wide range of piezoelectric materials including organic and biological systems.
Abstract: Piezoresponse force microscopy (PFM) probes the mechanical deformation of a sample in response to an electric field applied with the tip of an atomic force microscope. Originally developed more than two decades ago to study ferroelectric materials, this technique has since been used to probe electromechanical functionality in a wide range of piezoelectric materials including organic and biological systems. Piezoresponse force microscopy has also been demonstrated as a useful tool to detect mechanical strain originating from electrical phenomena in non-piezoelectric materials. Parallelling advances in analytical and numerical modelling, many technical improvements have been made in the last decade: switching spectroscopy PFM allows the polarisation switching properties of ferroelectrics to be resolved in real space with nanometric resolution, while dual ac resonance tracking and band excitation PFM have been used to improve the signal-to-noise ratio. In turn, these advances have led to increasingly large m...
TL;DR: Based on observations that the electron beam induces doming of the thin vitreous ice layer, an algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images is developed.
Abstract: Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution breakthroughs in cryo-electron microscopy. Improving the accuracy and efficiency of motion correction can lead to further resolution improvement. Based on observations that the electron beam induces doming of the thin vitreous ice layer, we developed an algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. The multi-GPU accelerated program, MotionCor2, is sufficiently fast to keep up with automated data collection. The result is an exceptionally robust strategy that can work on a wide range of data sets, including those very close to focus or with very short integration times, obviating the need for particle polishing. Application significantly improves Thon ring quality and 3D reconstruction resolution.
TL;DR: In this paper, in-situ superresolution microscopy of dye-labeled submicron sized pNIPAM microgels revealing the internal density profile during swelling and collapse of individual particles.
TL;DR: The mirror-assisted excitation confinement enhanced the axial resolution six-fold and the lateral resolution two-fold for STED, which together achieved 19-nm resolution to resolve the inner rim of a nuclear pore complex and to discriminate the contents of 120 nm viral filaments.
Abstract: Axial excitation confinement beyond the diffraction limit is crucial to the development of next-generation, super-resolution microscopy. STimulated Emission Depletion (STED) nanoscopy offers lateral super-resolution using a donut-beam depletion, but its axial resolution is still over 500 nm. Total internal reflection fluorescence microscopy is widely used for single-molecule localization, but its ability to detect molecules is limited to within the evanescent field of ~ 100 nm from the cell attachment surface. We find here that the axial thickness of the point spread function (PSF) during confocal excitation can be easily improved to 110 nm by replacing the microscopy slide with a mirror. The interference of the local electromagnetic field confined the confocal PSF to a 110-nm spot axially, which enables axial super-resolution with all laser-scanning microscopes. Axial sectioning can be obtained with wavelength modulation or by controlling the spacer between the mirror and the specimen. With no additional complexity, the mirror-assisted excitation confinement enhanced the axial resolution six-fold and the lateral resolution two-fold for STED, which together achieved 19-nm resolution to resolve the inner rim of a nuclear pore complex and to discriminate the contents of 120 nm viral filaments. The ability to increase the lateral resolution and decrease the thickness of an axial section using mirror-enhanced STED without increasing the laser power is of great importance for imaging biological specimens, which cannot tolerate high laser power.
TL;DR: A 2-photon random access mesoscope that allows high-resolution imaging anywhere within a volume spanning multiple brain areas and a fast threedimensional scanning system allows efficient sampling of neural activity in arbitrary regions of interest across the entire imaging volume is developed.
Abstract: Imaging is used to map activity across populations of neurons. Microscopes with cellular resolution have small (
TL;DR: Close-packed virus particles were shown not only to be useful for high-resolution 3D reconstructions but also to allow data collection at significantly improved throughput for near-atomic resolution reconstructions.
TL;DR: It is found that the Volta phase plate provides a significant contrast enhancement that permits individual NCPs and DNA to be clearly identified in amorphous ice and proves that phase-plate cryo-EM promises to become an important method to determine novel near-atomic resolution structures of small and challenging samples.
Abstract: The Volta phase plate is a recently developed electron cryo-microscopy (cryo-EM) device that enables contrast enhancement of biological samples. Here we have evaluated the potential of combining phase-plate imaging and single particle analysis to determine the structure of a small protein-DNA complex. To test the method, we made use of a 200 kDa Nucleosome Core Particle (NCP) reconstituted with 601 DNA for which a high-resolution X-ray crystal structure is known. We find that the phase plate provides a significant contrast enhancement that permits individual NCPs and DNA to be clearly identified in amorphous ice. The refined structure from 26,060 particles has an overall resolution of 3.9 A and the density map exhibits structural features consistent with the estimated resolution, including clear density for amino acid side chains and DNA features such as the phosphate backbone. Our results demonstrate that phase-plate cryo-EM promises to become an important method to determine novel near-atomic resolution structures of small and challenging samples, such as nucleosomes in complex with nucleosome-binding factors.
TL;DR: In this article, a deconvolution method was proposed to determine the lattice-site positions of single atoms in an optical lattice with high reliability, even for limited acquisition time or optical resolution.
Abstract: We report on image processing techniques and experimental procedures to determine the lattice-site positions of single atoms in an optical lattice with high reliability, even for limited acquisition time or optical resolution. Determining the positions of atoms beyond the diffraction limit relies on parametric deconvolution in close analogy to methods employed in super-resolution microscopy. We develop a deconvolution method that makes effective use of the prior knowledge of the optical transfer function, noise properties, and discreteness of the optical lattice. We show that accurate knowledge of the image formation process enables a dramatic improvement on the localization reliability. This allows us to demonstrate super-resolution of the atoms' position in closely packed ensembles where the separation between particles cannot be directly optically resolved. Furthermore, we demonstrate experimental methods to precisely reconstruct the point spread function with sub-pixel resolution from fluorescence images of single atoms, and we give a mathematical foundation thereof. We also discuss discretized image sampling in pixel detectors and provide a quantitative model of noise sources in electron multiplying CCD cameras. The techniques developed here are not only beneficial to neutral atom experiments, but could also be employed to improve the localization precision of trapped ions for ultra precise force sensing.
01 Jan 2016-Nuclear Instruments & Methods in Physics Research Section A-accelerators Spectrometers Detectors and Associated Equipment
TL;DR: In this article, the influence of Landau fluctuations and the scattering of secondary electrons (δ-rays) on intrinsic resolution of scintillation detectors is pointed out, and a study on undoped NaI and CsI at liquid nitrogen temperature with a light readout by avalanche photodiodes strongly suggests that the non-proportionality of many crystals is not their intrinsic property and may be improved by selective co-doping.
Abstract: According to current knowledge, the non-proportionality of the light yield of scintillators appears to be a fundamental limitation of energy resolution. A good energy resolution is of great importance for most applications of scintillation detectors. Thus, its limitations are discussed below; which arise from the non-proportional response of scintillators to gamma rays and electrons, being of crucial importance to the intrinsic energy resolution of crystals. The important influence of Landau fluctuations and the scattering of secondary electrons (δ-rays) on intrinsic resolution is pointed out here. The study on undoped NaI and CsI at liquid nitrogen temperature with a light readout by avalanche photodiodes strongly suggests that the non-proportionality of many crystals is not their intrinsic property and may be improved by selective co-doping. Finally, several observations that have been collected in the last 15 years on the influence of the slow components of light pulses on energy resolution suggest that more complex processes are taking place in the scintillators. This was observed with CsI(Tl), CsI(Na), ZnSe(Te), and undoped NaI at liquid nitrogen temperature and, finally, for NaI(Tl) at temperatures reduced below 0 °C. A common conclusion of these observations is that the highest energy resolution, and particularly intrinsic resolution measured with the scintillators, characterized by two or more components of the light pulse decay, is obtainable when the spectrometry equipment integrates the whole light of the components. In contrast, the slow components observed in many other crystals degrade the intrinsic resolution. In the limiting case, afterglow could also be considered as a very slow component that spoils the energy resolution. The aim of this work is to summarize all of the above observations by looking for their origin.
TL;DR: This work demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets and found the structure to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit.
Abstract: Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-A resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.
TL;DR: A new configuration of the IMic is proposed by placing the lens array not at the image plane, but at the pupil (or Fourier) plane of the microscope objective, where the spatial resolution is increased by factor 1.4, and the depth of field is substantially enlarged.
Abstract: Integral microscopes (IMic) have been recently developed in order to capture the spatial and the angular information of 3D microscopic samples with a single exposure. Computational post-processing of this information permits to carry out a 3D reconstruction of the sample. By applying conventional algorithms, both depth and also view reconstructions are possible. However, the main drawback of IMic is that the resolution of the reconstructed images is low and axially heterogeneous. In this paper, we propose a new configuration of the IMic by placing the lens array not at the image plane, but at the pupil (or Fourier) plane of the microscope objective. With this novel system, the spatial resolution is increased by factor 1.4, and the depth of field is substantially enlarged. Our experiments show the feasibility of the proposed method.
TL;DR: The state of the art of ultrafast transient absorption microscopy has been reviewed in this article, where current experimental concepts and highlights future challenges are discussed, together with different setup modifications and approaches towards transient absorption spectroscopy with spatial resolution below the diffraction limit.
Abstract: This article reviews the state of the art of ultrafast transient absorption microscopy, discusses current experimental concepts and highlights future challenges. The advantages of transient absorption microscopy over other micro-spectroscopic techniques are its high optical resolution combined with high temporal resolution as well as its ability to study non-fluorescent and weakly fluorescent molecular species and to probe excited-state processes. In conventional transient absorption spectroscopy the spectroscopic information usually presents a spatial average over the focal spot of the typically weakly focused probe beam. Transient absorption microscopy, however, enables investigations of the excited state dynamics in individual microscopic areas of a sample. Hence, the technique does not only yield detailed morphological information based on a label-free molecular contrast, but also gives insight into the ultrafast morphology-dependent photoinduced processes in heterogeneous samples. Different variations of transient absorption microscopy have found a number of applications ranging from material sciences to biology, which are discussed in this review together with different setup modifications and approaches towards transient absorption spectroscopy with spatial resolution below the diffraction limit.
TL;DR: This paper presents a method to simultaneously acquire an aberration-corrected, wide field-of-view fluorescence image and a high-resolution coherent bright-field image using a computational microscopy method.
Abstract: This paper presents a method to simultaneously acquire an aberration-corrected, wide field-of-view fluorescence image and a high-resolution coherent bright-field image using a computational microscopy method. First, the procedure applies Fourier ptychographic microscopy (FPM) to retrieve the amplitude and phase of a sample, at a resolution that significantly exceeds the cutoff spatial frequency of the microscope objective lens. At the same time, redundancy within the set of acquired FPM bright-field images offers a means to estimate microscope aberrations. Second, the procedure acquires an aberrated fluorescence image, and computationally improves its resolution through deconvolution with the estimated aberration map. An experimental demonstration successfully improves the bright-field resolution of fixed, stained and fluorescently tagged HeLa cells by a factor of 4.9, and reduces the error caused by aberrations in a fluorescence image by up to 31%, over a field of view of 6.2 mm by 9.3 mm. For optimal deconvolution, we show the fluorescence image needs to have a signal-to-noise ratio of at least ~18.
TL;DR: A new configuration was devised in which the scintillator is located underneath the thin foil on the optical axis of the microscope, and the light is reflected towards the camera by a mirror, and can be potentially used for collecting maps of relatively high spatial resolution.
TL;DR: This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
Abstract: Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 A resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX. Serial femtosecond crystallography using X-ray free-electron lasers has huge potential for time-resolved structural experiments. Here, the authors present a structure of the light-driven proton pump bacteriorhodopsin using these techniques.