Showing papers on "Resolution (electron density) published in 2000"
TL;DR: Lateral resolution that exceeds the classical diffraction limit by a factor of two is achieved by using spatially structured illumination in a wide‐field fluorescence microscope with strikingly increased clarity compared to both conventional and confocal microscopes.
Abstract: Lateral resolution that exceeds the classical diffraction limit by a factor of two is achieved by using spatially structured illumination in a wide-field fluorescence microscope. The sample is illuminated with a series of excitation light patterns, which cause normally inaccessible high-resolution information to be encoded into the observed image. The recorded images are linearly processed to extract the new information and produce a reconstruction with twice the normal resolution. Unlike confocal microscopy, the resolution improvement is achieved with no need to discard any of the emission light. The method produces images of strikingly increased clarity compared to both conventional and confocal microscopes.
3,274 citations
TL;DR: The diffraction barrier responsible for a finite focal spot size and limited resolution in far-field fluorescence microscopy has been fundamentally broken by quenching excited organic molecules at the rim of the focal spot through stimulated emission.
Abstract: The diffraction barrier responsible for a finite focal spot size and limited resolution in far-field fluorescence microscopy has been fundamentally broken. This is accomplished by quenching excited organic molecules at the rim of the focal spot through stimulated emission. Along the optic axis, the spot size was reduced by up to 6 times beyond the diffraction barrier. The simultaneous 2-fold improvement in the radial direction rendered a nearly spherical fluorescence spot with a diameter of 90–110 nm. The spot volume of down to 0.67 attoliters is 18 times smaller than that of confocal microscopy, thus making our results also relevant to three-dimensional photochemistry and single molecule spectroscopy. Images of live cells reveal greater details.
1,662 citations
Journal Article•
1,402 citations
TL;DR: In this article, the authors report on the resolution limits of EBL in the conventional polymethylmethacrylate (PMMA) organic resist and show that resolution can be pushed below 10 nm for isolated features and dense arrays of periodic structures can be fabricated at a pitch of 30 nm, leading to a density close to 700 Gbit/in2.
1,017 citations
TL;DR: Undersampled projection reconstruction (PR) is investigated as an alternative method for MRA (MR angiography), where bright, contrast‐filled vessels dominate, artifacts are often acceptable and the greater resolution per unit time provided by undersampled PR can be realized.
Abstract: Undersampled projection reconstruction (PR) is investigated as an alternative method for MRA (MR angiography). In conventional 3D Fourier transform (FT) MRA, resolution in the phase-encoding direction is proportional to acquisition time. Since the PR resolution in all directions is determined by the readout resolution, independent of the number of projections (Np), high resolution can be generated rapidly. However, artifacts increase for reduced Np. In X-ray CT, undersampling artifacts from bright objects like bone can dominate other tissue. In MRA, where bright, contrast-filled vessels dominate, artifacts are often acceptable and the greater resolution per unit time provided by undersampled PR can be realized. The resolution increase is limited by SNR reduction associated with reduced voxel size. The hybrid 3D sequence acquires fractional echo projections in the k(x)-k(y) plane and phase encodings in k(z). PR resolution and artifact characteristics are demonstrated in a phantom and in contrast-enhanced volunteer studies.
399 citations
Book•
16 Mar 2000
TL;DR: In this paper, the authors describe a line profile analysis of a powder diffraction line profile that is influenced by straining, small size, and stacking faults in the line profile, and their correction by simple empirical functions accounting for size and microstrain.
Abstract: Introduction to Defect and Microstructure Analysis or the Analysis of Real-Structure Some Applications of the Kinematical Theory of X-ray Diffraction Profile Fitting and Analytical Functions Effects of Instrument Function, Crystallite Size, and Strain on Reflection Profiles Use of Pattern Decomposition or Simulation to Study Microstructure: theoretical considerations Classical Treatment of Line Profiles Influenced by Strain, Small Size, and Stacking Faults Voigt-Function Model in Diffraction Line-Broadening Analysis X-Ray Analysis of Precipitation Related Crystals with Dislocation Substructure The Dislocation Based Model of Strain Broadening in X-Ray Line-Profile Analysis Diffraction-Line Broadening Analysis of Dislocation Configurations Diffraction-Line Broadening Analysis of Strain Fields in Crystalline Solids Paracrystallinity The Model of the Paracrystal and its Application to Polymers Effect of Planar Defects in Crystal on the Position and Profile of Powder Diffraction Line Effect of Stacking Disorder on the Profile of the Powder Diffraction Line Crystallite Statistics and Accuracy in Powder Diffraction Intensity Measurements Reciprocal Space Mapping and Ultra-High Resolution Diffraction of Polycrystalline Materials X-Ray Analysis of The Inhomogeneous Stress State Texture Analysis Texture Effects in Powder Diffraction and their Correction by Simple Empirical Functions Accounting For Size and Microstrain in Whole Powder Pattern Fitting Modelling of Texture in Whole Pattern Fitting A New Whole Powder Pattern Fitting Approach The Role of Whole-Pattern Databases in Materials Science Restoration and Preprocessing of Physical Profiles from Measured Data Towards Higher Resolution: A Mathematical Approach Use of Pattern Decomposition to Study Microstructure: Practical Aspects and Applications X-Ray Diffraction Broadening Effects in Materials Characterization Crystal Size and Distortion Parameters in Fibres using WAXS Pressure Induced Profile Change of Energy Dispersive Diffraction
346 citations
TL;DR: Three-dimensional transmission electron microscopy (3D-TEM), effectuated by multiple imaging of a sample combined with image analysis, offers a new approach in materials science to obtain 3D information as discussed by the authors.
Abstract: Three-dimensional transmission electron microscopy (3D-TEM), effectuated by multiple imaging of a sample combined with image analysis, offers a new approach in materials science to obtain 3D inform...
243 citations
TL;DR: Combining X-ray crystallographically determined atomic structures of component domains or subunits with cryo-electron microscopic three-dimensional images at around 22 A resolution can produce structural information that is accurate to about 2.2 A resolution, which helps to fit the component structures into the EM density maps.
Abstract: Combining X-ray crystallographically determined atomic structures of component domains or subunits with cryo-electron microscopic three-dimensional images at around 22 A resolution can produce structural information that is accurate to about 2.2 A resolution. In an initial step, it is necessary to determine accurately the absolute scale and absolute hand of the cryo-electron microscopy map, the former of which can be off by up to 5%. It is also necessary to determine the relative height of density by using a suitable scaling function. Difference maps can identify, for instance, sites of glycosylation, the position of which helps to fit the component structures into the EM density maps. Examples are given from the analysis of alphaviruses, rhinovirus–receptor interactions and poliovirus–receptor interactions.
196 citations
TL;DR: The charge density distribution of a protein has been refined experimentally and the resulting electron density maps of redistributed valence electrons compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide.
Abstract: The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 A) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules.
193 citations
TL;DR: This study is the first characterization of a three-dimensional crystal of a G protein-coupled receptor and may be valuable for future structural studies on related receptors of this important superfamily.
182 citations
TL;DR: Using atomic force microscopy, it is shown that the I(alpha) phase of native cellulose first proposed in 1984 and subsequently characterized by a triclinic unit cell exists over large areas of the surface of microcrystals from Valonia, one of the most highly crystalline celluloses.
02 May 2000
TL;DR: In this article, a wide field fluorescence microscopy (WFFL) was proposed to obtain spatial information that exceeds the classical resolution limit by a factor of two by illuminating the sample with spatially structured (patterned) excitation light, and then restoring this information to its proper location in reciprocal space.
Abstract: Spatial information that exceeds the classical resolution limit by a factor of two can be made visible in the widefield fluorescence microscope by illuminating the sample with spatially structured (patterned) excitation light. By computationally restoring this information to its proper location in reciprocal space, an image with twice the normal lateral resolution can be produced. The method can be applied in three dimensions, and yields an axial sectioning power equal to that of confocal microscopes. Unlike the case in confocal microscopy, however, both the lateral and axial resolution enhancements are achieved without any loss of emission light, resulting in uncompromised sensitivity. The method has been experimentally verified on both test objects and complex biological structures and performs in complete agreement with theoretical predictions. The resulting images possess a visual clarity that dramatically exceeds that of both conventional and confocal microscopes.
Journal Article•
TL;DR: If S (ST) is the minimal size of a (tree-like) refutation, it is proved that ST = exp(O(S log log S/log S)), which implies that the most commonly used automated theorem procedures, which produce tree-like resolution refutations, will perform badly on some inputs, while other simple procedures will have polynomial run-time on these very same inputs.
Abstract: We present the best known separation between tree-like and general resolution, improving on the recent exp(n∈) separation of [2]. This is done by constructing a natural family of contradictions, of size n, that have O(n)-size resolution refutations, but only exp(Ω(n/log n))- size tree-like refutations. This result implies that the most commonly used automated theorem procedures, which produce tree-like resolution refutations, will perform badly on some inputs, while other simple procedures, that produce general resolution refutations, will have polynomial run-time on these very same inputs. We show, furthermore that the gap we present is nearly optimal. Specifically, if S (ST) is the minimal size of a (tree-like) refutation, we prove that ST = exp(O(S log log S/log S)).
TL;DR: The oversampling technique thus greatly extends the specimen range of X-ray crystallography but it imposes a high radiation dose on the specimens compared with the situation in crystallography, in which it is usual for the pattern to be sampled at the (much less fine) Bragg spacing (the inverse of the size of the unit cell).
Abstract: It is known that sampling the diffraction pattern of a finite specimen, at a spacing somewhat finer than the Nyquist spacing (the inverse of the size of the diffracting specimen), corresponds to generating a no-density region surrounding the electron density of the specimen. This no-density region can then be used to retrieve the phase information. In earlier papers [Miao, Sayre & Chapman (1998). J. Opt. Soc. Am. A15, 1662-1669; Sayre, Chapman & Miao (1998). Acta Cryst. A54, 232-239], it was demonstrated, in the case of non-crystalline specimens, that this no-density region could be used to retrieve the phase information; here the same is performed for crystalline and near-crystalline specimens. By employment of an iterative algorithm, the phase information could be recovered from computer-generated oversampled diffraction patterns of small specimens that are (a) perfect or imperfect crystals, or (b) have a repeated motif without orientational regularity, or (c) are an unrepeated motif, such as an amorphous glass, a single molecule or a single biological cell. Cases (a) and (b) represent an extension over work recently published [Miao, Charalambous, Kirz & Sayre (1999). Nature (London), 400, 342-344]. Our algorithm requires an approximate envelope for the specimen. It does not require any structural knowledge concerning the specimen and does not require data to atomic resolution (although it can use such data if present). After a few hundred to a few thousand iterations, the correct phase set and image are recovered. The oversampling technique thus greatly extends the specimen range of X-ray crystallography but it imposes a high radiation dose on the specimens compared with the situation in crystallography, in which it is usual for the pattern to be sampled at the (much less fine) Bragg spacing (the inverse of the size of the unit cell). In cases where the specimen is a crystal, there are also possibilities for oversampling relative to Bragg (instead of Nyquist) sampling, thus providing a lesser degree of oversampling and the possibility of lower dosage. Damage of the specimen in consequence of the dose will in many cases seriously affect the quality and resolution of the imaging, but in at least one case [the biological cell in (c) above] the imaging obtainable with the aid of a cryogenic protective technique should surpass any other present method of whole-cell imaging. In addition, with the possible appearance in the future of free electron lasers (>10(12) photons and <200 fs per pulse), it is possible to circumvent the radiation-damage problem by recording diffraction patterns before damage manifests itself.
TL;DR: In this paper, the authors deal with the measurement of pyrocarbon anisotropy on very thin fiber coatings used to control the interfacial behavior in carbon/carbon composites.
Abstract: This work deals with the measurement of pyrocarbon anisotropy on very thin fiber coatings used to control the interfacial behavior in carbon/carbon composites. Differentiation of the various pyrocarbons was performed through computerized image analysis of the electron diffraction patterns by measuring the azimuth opening of the carbon 002 diffraction arcs. This orientation angle decreases when the texture switches from rough to smooth laminar. The relationship with the polarized light measurement technique at a lower resolution is discussed.
TL;DR: In this paper, a collection mode near-field probe for the terahertz spectral range is proposed. But the aperture size of the probe is determined by the probe aperture.
Abstract: We report on the development of a collection mode near-field probe for the terahertz spectral range. The near-field detector is based on an aperture type probe with dimensions of 30×30 μm2. The collection mode technique provides higher sensitivity and higher resolution than the similar illumination mode approach. Spatial resolution better than 40 μm is demonstrated for a broad spectrum of 300–600 μm, which equals to λ/15 for the longest wavelength. The observed resolution is determined by the size of the probe aperture.
TL;DR: It is shown that the kinematical theory of fluctuation microscopy for a disordered specimen can be reformulated in terms of an atom pair-pair correlation function, which reveals the correlation length and structure for a simple paracrystalline model.
TL;DR: It is concluded that the alignment of images is always accompanied by a correlation of the noise and that this correlation is indistinguishable from a correlation arising from a signal.
Abstract: Analytical expressions are derived and computer simulations are presented to assess the accuracy of procedures commonly used to estimate the resolution of three-dimensional (3D) structures derived from images of single protein molecules or complexes. It is shown that in the case of a low signal-to-noise ratio in the images, the Fourier ring correlation between two structures, each calculated using one half of the data, significantly overestimates the resolution when the two half data sets were aligned against the same reference structure. The overestimate arises because of a correlation between the noise components present in the images. The correlation is introduced by the alignment and becomes more serious as the signal-to-noise ratio is reduced. A reliable resolution measure is only obtained when the two half data sets are aligned against two independent reference structures. It is further shown that the noise correlation also significantly affects the spectral signal-to-noise ratio and the Q factor, making them unreliable measures of signal present in a 3D structure and in the original images, respectively. It is concluded that the alignment of images is always accompanied by a correlation of the noise and that this correlation is indistinguishable from a correlation arising from a signal.
TL;DR: In this article, a method for optical near field discrimination, leading to drastic artifact reduction in super-resolved imaging by scanning interference apertureless microscopy is presented, relying on second harmonic detection of the modulated optical signal scattered by a vibrating silicon tip.
Abstract: A method for optical near field discrimination, leading to drastic artifact reduction in superresolved imaging by scanning interference apertureless microscopy is presented. The method relies on second harmonic detection of the modulated optical signal scattered by a vibrating silicon tip. An edge resolution of 15 nm, or 7 nm Rayleigh-type resolution, with optical contrast as high as 50%, has been obtained on aluminum projection pattern samples in the constant gap width mode. Our method has been determined not to be affected by topographical artifacts by constant height mode scans.
TL;DR: In this paper, the deamidated form of bovine pancreatic ribonuclease with an isoaspartyl residue in position 67 diffracts to 0 87 A at 100 K.
TL;DR: Using a cryo scanning transmission X‐ray microscope, tomographic data‐sets of frozen hydrated mouse 3T3 fibroblasts are obtained and 100 nm lateral and 250’nm longitudinal resolution was obtained in images of unlabelled cells, with potential for substantial further gains in resolution.
Abstract: Using a cryo scanning transmission X-ray microscope (Maser, et al. (2000) Soft X-ray microscopy with a cryo scanning transmission X-ray microscope: I. Instrumentation, imaging and spectroscopy. J. Microsc. 197, 68-79), we have obtained tomographic data-sets of frozen hydrated mouse 3T3 fibroblasts. The ice thickess was several micrometres throughout the reconstruction volume, precluding cryo electron tomography. Projections were acquired within the depth of focus of the focusing optics, and the three-dimensional reconstruction was obtained using an algebraic reconstruction technique. In this first demonstration, 100 nm lateral and 250 nm longitudinal resolution was obtained in images of unlabelled cells, with potential for substantial further gains in resolution. Future efforts towards tomography of spectroscopically highlighted subcellular components in whole cells are discussed.
TL;DR: A model has been developed to compute the ion trajectories in 3D near a sharp hemispherical electrode defined at the atomic scale and the predicted order of evaporation provided by this model is in excellent agreement with experiments.
01 Apr 2000-Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms
TL;DR: In this paper, the authors present a method and an equipment for performing μm-resolved X-ray diffraction area maps, and apply it to wafer defect analysis and industrial wafer quality inspection.
Abstract: We present a method and an equipment for performing μm-resolved X-ray diffraction area maps, and apply it to wafer defect analysis and industrial wafer quality inspection. The method determines simultaneously the macroscopic warpage, the mesoscopic curvature and the microscopic defect structure of semiconductor wagers. It is based on X-ray diffraction rocking curve imaging of the whole wafer with down to 1 μm 2 resolution. The new wafer testing equipment determines the maximal and integral peak intensities, the peak position and the half width of the rocking curves with a microscopic resolution, thus imaging simultaneously the macroscopic quality parameters and the microscopic defect structure. This permits to establish a direct one-to-one correlation between the microscopic defects and the resulting macroscopic effects. As an example, wafers of different materials, fabrication technology and resulting perfection are studied. When investigating layered samples, the technique allows furthermore to determine the influence of the wafer quality on the layer properties. The method can be applied generally to characterize non-destructively the quality of all kinds of crystalline structures, like, e.g. microelectronic and optoelectronic devices.
TL;DR: The paper presents several methods to extract the Fourier coefficients needed for a 3-D reconstruction and reminds us that the problem can be treated by considering the curvature of the Ewald sphere or equivalently by considering that different layers within the structure are imaged with different amounts of defocus.
TL;DR: It is shown quantitatively that if a matrix of temporal delays is inserted between the individual foci, it is possible to solve the classical conflict between the light budget and the sectioning property in three-dimensional microscopy and to provide a virtually unlimited density of foci at best axial resolution.
Abstract: We investigate the imaging properties of high-aperture multifocal multiphoton microscopy on the basis of diffraction theory. Particular emphasis is placed on the relationship between the sectioning property and the distance between individual foci. Our results establish a relationship between the degree of parallelization and the axial resolution for both two- and three-photon excitation. In addition, we show quantitatively that if a matrix of temporal delays is inserted between the individual foci, it is, for the first time to our knowledge, possible to solve the classical conflict between the light budget and the sectioning property in three-dimensional microscopy and to provide a virtually unlimited density of foci at best axial resolution.
11 Sep 2000-Nuclear Instruments & Methods in Physics Research Section A-accelerators Spectrometers Detectors and Associated Equipment
TL;DR: In this paper, the use of charge-coupled devices (CCDs) under direct illumination of X-rays for two-dimensional position-sensitive detectors in high-resolution diffraction experiments is discussed.
Abstract: The use of charge-coupled devices (CCDs) under direct illumination of X-rays for two-dimensional position-sensitive detectors in high-resolution diffraction experiments is discussed Two detectors are compared: a standard CCD and a “deep depletion” CCD These give position resolution close to the pixel size ( ∼22 μm ), and energy resolution close to the theoretical resolution of a Si detector These detectors can be used for photon-counting and an algorithm for electronic noise suppression is presented This algorithm is useful for experiments with frequent readouts and low intensity Examples demonstrating the advantages of this algorithm for diffraction experiments are given
TL;DR: This first visualization of individual membrane proteins in live cells by fluorescence labeled ligands with 40nm 3D positional resolution opens new perspectives for the study of cellular organization and processes at the molecular level.
Abstract: High affinity binding of fluorescence labeled hongotoxin (HgTX1-Cy5) to the potassium channel KV1.3 in T-lymphocyte cell membranes was utilized for imaging single ion channels optically, employing Single Dye Tracing (SDT). Binding sites were seen as single fluorescence peaks in cross-sections through the cell. Their number matched, at conditions of saturated binding, the number of sites expected from biochemical determination. By fitting the peaks to the point-spread-function, well approximated by a Gaussian distribution, resolution of channel positions to within ±40nm was obtained in all three dimensions. Within the focal plane (x-y plane) positional resolution is given by the accuracy of determining the peak position of the Gaussian. The positional resolution along the optical axis (z-direction) was obtained from the accuracy of estimating the position of minimum defocusing for a single molecule. For this, the width of the fluorescence peaks in consecutive images, taken at different degrees of defocusing, were shown to accurately match the theoretical prediction, yielding ∼40nm accuracy of finding the z-position of the labeled channels. This first visualization of individual membrane proteins in live cells by fluorescence labeled ligands with 40nm 3D positional resolution opens new perspectives for the study of cellular organization and processes at the molecular level.
TL;DR: In this article, a simple model that demonstrates the importance of non-radiative transfer and takes into account the dependence of non radiative transfer on tip geometry is presented. But the model is not applicable to the case of apertureless near field optical microscopy.
Abstract: We report on fluorescence experiments by apertureless near-field optical microscopy. We develop a simple model that demonstrates the importance of non-radiative transfer and that takes into account the dependence of non-radiative transfer on tip geometry. This process is in competition with field enhancement and it is a key process to understand the observed fluorescence enhancement factors. The analysis of the different factors involved in the global fluorescence enhancement or quenching leads to new strategies to reach resolution down to a few nanometers by apertureless fluorescence microscopy.
TL;DR: X-ray scattering investigations of surfaces and interfaces in soft-condensed matter are reviewed in this paper, where both high-resolution structural determinations in the direct space and investigations of fluctuations with long-range correlations requiring a high resolution in the Fourier space are discussed.
Abstract: X-ray scattering investigations of surfaces and interfaces in soft-condensed matter are reviewed. Both high-resolution structural determinations in the direct space and investigations of fluctuations with long-range correlations requiring a high resolution in the Fourier space are discussed. All the scattering cross-sections for diffraction or diffuse scattering are derived within a unified frame, and the experimental aspects related to their measurement are discussed in detail. The general principles are illustrated by various examples of studies of the liquid-vapour interface, Langmuir and Langmuir-Blodgett films, wetting films, polymer films, liquid crystals and liquid-liquid interfaces.
TL;DR: An analysis of the potential of CCD-based detectors to fully replace photographic film for high-resolution electron crystallographic applications and how to bypass the slow and tedious process of processing images recorded on photographic film is presented.
Abstract: 1. Introduction 11.1 The ‘band gap’ in silicon 22. Principles of CCD detector operation 32.1 Direct detection 32.2 Electron energy conversion into light 42.3 Optical coupling: lens or fibre optics? 62.4 Readout speed and comparison with film 83. Practical considerations for electron microscopic applications 93.1 Sources of noise 93.1.1 Dark current noise 93.1.2 Readout noise 93.1.3 Spurious events due to X-rays or cosmic rays 103.2 Efficiency of detection 113.3 Spatial resolution and modulation transfer function 123.4 Interface to electron microscope 143.5 Electron diffraction applications 154. Prospects for high-resolution imaging with CCD detectors 185. Alternative technologies for electronic detection 235.1 Image plates 235.2 Hybrid pixel detectors 246. References 26During the past decade charge-coupled device (CCD) detectors have increasingly become the preferred choice of medium for recording data in the electron microscope. The CCD detector itself can be likened to a new type of television camera with superior properties, which makes it an ideal detector for recording very low exposure images. The success of CCD detectors for electron microscopy, however, also relies on a number of other factors, which include its fast response, low noise electronics, the ease of interfacing them to the electron microscope, and the improvements in computing that have made possible the storage and processing of large images.CCD detectors have already begun to be routinely used in a number of important biological applications such as tomography of cellular organelles (reviewed by Baumeister, 1999), where the resolution requirements are relatively modest. However, in most high-
resolution microscopic applications, especially where the goal of the microscopy is to obtain structural information at near-atomic resolution, photographic film has continued to remain the medium of choice. With the increasing interest and demand for high-throughput structure determination of important macromolecular assemblies, it is clearly important to have tools for electronic data collection that bypass the slow and tedious process of processing images recorded on photographic film.In this review, we present an analysis of the potential of CCD-based detectors to fully replace photographic film for high-resolution electron crystallographic applications.