Resolution Of Tomograms Research Articles

Pore‐Scale MultiResolution Rock‐Typing of Layered Sandstones via Minkowski Maps

AbstractA challenge in utilizing pore‐scale information in subsurface transport calculations is the small field‐of‐view of tomographic imaging methods resolving pore‐scale features. While low‐resolution tomography provides a larger field‐of‐view, critical connectivity information may not be resolved, or lost in the upscaling process. In this study, we present a multiscale upscaling approach utilizing regional morphological measures—Minkowski maps—at two different resolutions. The workflow consists of the definition of high‐resolution rock‐types and their characterization, followed by an image registration process to lower resolution tomograms, a projection of the high‐resolution rock‐types to low‐resolution Minkowski maps via support vector machines, and application of high‐resolution transport characteristics to the low‐resolution rock‐types, followed by upscaling. The method is applied to a complex thinly laminated reservoir sandstone. Upscaled permeability and electrical conductivity agree well with full‐resolution calculations.

Mechanisms of Confining Pressure Dependence of Resistivity Index for Tight Sandstones by Digital Core Analysis

SummaryResistivity measurements are a major input into hydrocarbon reserve estimation and are usually described by Archie’s laws. In this study, we use digital rock physics to analyze the mechanisms of non-Archie and Archie behavior of formation factor (FF) and resistivity index (RI) of low-porosity Fontainebleau (FB) sandstone for ambient conditions and under high confining pressure, respectively.FB sandstone was imaged by micro-X-ray computed tomography (micro-CT) at a resolution of 1 µm. Subresolution details of the grain contact width distribution along with their length were extracted from a set of scanning electron microscope (SEM) images. The nanoscale aperture of grain contacts, which is below tomogram resolution, is accounted for in micro-CT-based numerical calculations by assigning effective porosity and conductivity to individual voxels of the extracted grain contact network. A porosity reduction of grain contacts and open pore space as a function of applied confining pressure is introduced, capturing the pressure dependence. The concept was implemented by grain contact labeling, introducing an additional phase derived from a Euclidean distance transform (EDT). Subvoxel stress-strain effects were incorporated by attributing all compressibility effects to the pore space (open pore space and grain contacts), treating the solid phase as perfectly rigid. Voxel-scale input conductivities are assigned using Archie’s law followed by solving the Laplace equation for sample-scale rock resistivity and RI directly on the segmented image using the finite element method.For the numerical modeling of the FF and RI of low-porosity FB sandstone as a function of confining pressure, which depends on subresolution features, a set of hypotheses were tested. These are based on two segmentation scenarios incorporating the measured contact aperture distribution from SEM analysis—a homogeneous aperture-based segmentation by assuming all grain contacts as an average constant value and a heterogeneous aperture-based segmentation assigning two groups of grain contact apertures. The segmentation scenarios enable homogeneous and heterogeneous morphological change of grain contacts due to confining pressure effects. Furthermore, partial saturation of grain contacts is considered. In all cases, strong water-wetness was assumed, and discretization effects were analyzed carefully.The numerical results highlight the relative contribution of each of two conductive components of FB sandstone (open pores vs. grain contacts) over the full range of partial saturations. Of importance is the connectivity of the system, with discretization effects having a significant effect on FF, but a small effect on the RI. Grain contacts and confining pressure are found to have a significant impact on RI behavior of low-porosity FB sandstone. Both the grain contact network with homogeneous aperture and the heterogeneous grain contact network are able to describe experimental observations. However, it is not sufficient to assume a homogeneous change in contact area, and an inhomogeneous deformation of grain contact zones is required to match the experiment.

Reprojection Alignment for Trajectory Perturbation Estimation in Microtomography

For standard laboratory microtomography systems, acquired radiographs do not always adhere to the strict geometrical assumptions of the reconstruction algorithm. The consequence of this geometrical inconsistency is that the reconstructed tomogram contains motion artifacts, e.g., blurring, streaking, double-edges. To achieve a motion-artifact-free tomographic reconstruction, one must estimate, and subsequently correct for, the per-radiograph experimental geometry parameters. In this paper, we examine the use of re-projection alignment (RA) to estimate per-radiograph geometry. Our simulations evaluate how the convergence properties of RA vary with: motion-type (smooth versus random), trajectory (helical versus discrete-sampling ‘space-filling’ trajectories) and tomogram resolution. The idealized simulations demonstrate for the space-filling trajectory that RA convergence rate and accuracy is invariant with regard to the motion-type and that the per-projection motions can be estimated to less than 0.25 pixel mean absolute error by performing a single quarter-resolution RA iteration followed by a single half-resolution RA iteration. The direct impact is that, for the space-filling trajectory, one can incorporate RA in an iterative multi-grid reconstruction scheme with only a single RA iteration per multi-grid resolution step. We also find that for either trajectory, slowly varying vertical errors cannot be reliably estimated by employing the RA method alone; such errors are indistinguishable from a trajectory of different pitch. This has minimal effect in practice because RA can be combined with reference frame correction which is effective for correcting low-frequency errors.

3D radar wavefield tomography of comet interiors

Answering fundamental questions about the origin and evolution of small planetary bodies hinges on our ability to image their surface and interior structure in detail and at high resolution. The interior structure is not easily accessible without systematic imaging using, e.g., radar transmission and reflection data from multiple viewpoints, as in medical tomography. Radar tomography can be performed using methodology adapted from terrestrial exploration seismology. Our feasibility study primarily focuses on full wavefield methods that facilitate high quality imaging of small body interiors. We consider the case of a monostatic system (co-located transmitters and receivers) operated in various frequency bands between 5 and 15 MHz, from a spacecraft in slow polar orbit around a spinning comet nucleus. Using realistic numerical experiments, we demonstrate that wavefield techniques can generate high resolution tomograms of comets nuclei with arbitrary shape and complex interior properties.

Photosome membranes merge and organize tending towards rhombohedral symmetry when light is emitted.

Polynoid worm elytra emit light when mechanically or electrically stimulated. Specialized cells, the photocytes, contain light emitting machineries, the photosomes. Successive stimulations induce light intensity variations and show a coupling within and between photosomes. Here, we describe, using electron tomography of cryo-substituted elytra and freeze-fracturing, the structural transition associated to light emission: undulating tubules come closer, organize and their number forming photosomes increases. Two repeating undulating tubules in opposite phase compose the photosome. Undulations are located on three hexagonal layers that regularly repeat and are equally displaced, in x y and z. The tubule membranes within layers merge giving rise to rings that tend to obey to quasi-rhombohedral symmetry. Merging may result either from close-association, hemifusion (one leaflet fusion) or from fusion (two leaflets fusion). Although the resolution of tomograms is not sufficient to distinguish these three cases, freeze-fracturing shows that hemifusion is a frequent process that leads to an reversible anastomosed membrane complex favoring communications, appearing as a major coupling factor of photosome light emission.

In situ hard X-ray transmission microscopy for material science

Hard X-ray transmission microscopy based on refractive X-ray optics can be employed as a tool in material science to investigate buried-in microstructures in two or three dimensions with spatial resolution approaching 100 nm. Switching from monochromatic to radiation with a broader bandwidth, frame rates down to a few milliseconds can be realized, opening new possibilities for in situ studies of microstructure evolution and response to external fields at spatiotemporal resolutions that go well beyond previous benchmarks, demonstrated by ~200 nm resolution tomograms of eutectic microstructures acquired in less than 2 s. The microscope can also be operated in Zernike phase contrast mode, which expands the range of possible applications to cases which otherwise would produce only very faint contrast. A few possible application areas for the microscope are illustrated by a selection of material science test cases.

Opacificación capsular posterior en lentes intraoculares hidrofílicos en comparación con lentes intraoculares hidrofóbicos usando imágenes de Scheimpflug

PurposeTo determine the visual outcomes and posterior capsule opacification in acrylic intraocular lenses (IOL). MethodsProspective analysis of 38 eyes of 19 patients who had uneventful phacoemulsification with implantation of a IOL Akreos MI60 or a IOL Acrysof IQ from February 2013 to January 2014. Patients from a single surgeon, the protocol included the determination logMAR best corrected visual acuity, spherical equivalent, contrast sensitivity assessed by the freiburg visual acuity test and posterior capsule opacification scoring using the evaluation of posterior capsular opacification system (EPCO2000) by digital retroillumination photography and high resolution tomograms from Scheimpflug reconstructions analyzed using ImageJ freeware. ResultsThe mean follow up was 6.2 months±1.4 (SD). Contrast sensitivity and best corrected visual acuity were similar between the lenses. Mean pixel intensity value using EPCO2000 software for Akreos MI60 was 1.08U and 1.08U for Acrysof IQ (P=.785). Using ImageJ mean value in pixels for Akreos MI60 was 1.76U and for Acrysof IQ was 2.56U (P=.027). There were no significant correlationship between EPCO2000 and Scheimpflug images (r=.141, P=.412). ConclusionsThis study found that the results of visual function were comparable between both lenses. The posterior capsular opacification was seen to be lesser extent with the Akreos MI60 IOL when measured by Scheimpflug images, probably due to the very design of the lens which showed no correlation compared to the digital retroillumination photoghaphy.

Multi-scale 3D mapping of Tomography Data

Synchrotron based high-resolution tomography reveals fine structures in a porous media, which strongly determines their flow properties as well as mechanics. Measurements at higher resolution limit the field of view. Lower resolution tomograms on the other hand give a wider field of view but highly compromises the contrast of micro/nano structures in the sample. Lack of contrast in the finer details seriously reduces the image quality as well as quantitative exploitation, limiting the accuracy in the retrieved physical properties. To overcome this, the sample has to be measured at different resolutions on different instruments.

Validating vertical velocity gradients in near-surface refraction seismology

Wavepath eikonal traveltime (WET) refraction tomograms are generated with the generalised reciprocal method (GRM), a novel medium resolution common offset gather (COG) implementation of the GRM, using uniform velocities and vertical velocity gradients, and the low resolution default starting model consisting of smooth vertical velocity gradients. All tomograms have comparable misfit errors, which illustrates the ubiquity of non-uniqueness and the necessity for validating all starting models. Nevertheless, the use of even the maximum vertical velocity gradients in the weathered region does not produce any improvement in the spatial resolution of the seismic velocities in the sub-weathered region with either the default or the COG GRM starting models. Therefore, if a low resolution starting model is used, then the most likely outcome will be a low resolution WET tomogram, irrespective of whether or not vertical velocity gradients are employed. Vertical velocity gradients can be represented as part of a continuum of seismic velocities in the weathered layer, which range from uniform to hyperbolic velocities, and which are consistent with the traveltime data. Acceptable models employ seismic velocities in the weathered and sub-weathered regions computed with the same XY value. In this study, the optimum XY value is representative of uniform seismic velocities, whereas the maximum XY value, which is the average cross-over distance, is representative of default and hyperbolic velocities. Intermediate XY values indicate more moderate vertical velocity gradients and/or undetected layers. WET tomography is largely a smoothing operation which does not improve the spatial resolution of either medium resolution or detailed starting models. A limited number of iterations, usually a maximum of five, can improve the cosmetics of refraction tomograms, whereas repeated applications can result in considerable reductions in spatial resolution, and eventually, low resolution tomograms consisting of essentially featureless parallel quasi horizontal layers.

Assessing the benefits of focal pair cryo-electron tomography

Cryo electron tomography provides nanometer-scale information on biological matter preserved in a close-to native state. The resolution of tomograms and structures resolved by sub-tomogram averaging is typically limited by the contrast transfer function of the electron microscope, which is especially critical for thick samples. Here, we report a method to increase the attainable resolution by recording tomographic 'focal pairs', which are pairs of tilt series of the same object acquired in complementary defocus conditions. Low defocus imaging provides high resolution at low contrast, while high defocus imaging yields high contrast at the price of limited resolution. Quantitative assessment of the quality of lipid bilayer reconstructions in the resulting tomograms demonstrates stable resolution preservation beyond 3 nm for cells thicker than 500 nm. Further, in computational simulations on synthetic datasets we show the applicability of the method to sub-tomogram averaging, demonstrating its potential for achieving higher resolution.

Fast tomographic reconstruction on multicore computers

Tomo3D implements a multithreaded vectorized approach to tomographic reconstruction that takes full advantage of the computer power in modern multicore computers. Full resolution tomograms are generated at high speed on standard computers with no special system requirements. Tomo3D has the most common reconstruction methods implemented, namely weighted Back-projection (WBP) and simultaneous iterative reconstruction technique (SIRT). It proves to be competitive with current graphic processor unit solutions in terms of processing time, in the order of a few seconds with WBP or minutes with SIRT. The program is compatible with standard packages, which easily allows integration in the electron tomography workflow.

Vectorization with SIMD extensions speeds up reconstruction in electron tomography

Electron tomography allows structural studies of cellular structures at molecular detail. Large 3D reconstructions are needed to meet the resolution requirements. The processing time to compute these large volumes may be considerable and so, high performance computing techniques have been used traditionally. This work presents a vector approach to tomographic reconstruction that relies on the exploitation of the SIMD extensions available in modern processors in combination to other single processor optimization techniques. This approach succeeds in producing full resolution tomograms with an important reduction in processing time, as evaluated with the most common reconstruction algorithms, namely WBP and SIRT. The main advantage stems from the fact that this approach is to be run on standard computers without the need of specialized hardware, which facilitates the development, use and management of programs. Future trends in processor design open excellent opportunities for vector processing with processor's SIMD extensions in the field of 3D electron microscopy.

High-resolution surface NMR tomography of shallow aquifers based on multioffset measurements

Conventional surface nuclear magnetic resonance (NMR) surveying based on 1D inversions of data recorded using a common (coincidence) transmitter and receiver loop provides only limited or distorted water-concentration information in regions characterized by strong lateral heterogeneity. We introduce a combined field-acquisition and tomographic-inversion strategy suitable for 2D surface NMR investigations of free (i.e., unbound) water stored in hydrogeologically complex regions. Using combinations of coincident and multioffset loops, we take advantage of the range of sensitivities offered by different loop configurations to variations in subsurface free-water concentration. The new tomographic scheme can invert data acquired with diverse loop configurations. Tests of the combined acquisition and inversion strategy on complicated synthetic and observed data demonstrate the substantially higher resolution information provided by combinations of loop configurations vis-à-vis that supplied by a standard coincident loop. A combination of coincident and half-overlapping loop data sets yields tomograms rich in detail, comparable to tomograms derived from a combination of all considered loop configurations. If resources are limited, surface NMR practitioners should consider the half-overlapping loop configuration as an alternative to the standard coincident loop configuration. For a four-station data recording campaign, the half-overlapping loop configuration with 50% more measurements and equal number of loop deployments and retrievals provides significantly higher resolution tomograms than a coincident loop configuration.

Ferritin reporter used for gene expression imaging by magnetic resonance

Magnetic resonance imaging (MRI) is a minimally invasive way to provide high spatial resolution tomograms. However, MRI has been considered to be useless for gene expression imaging compared to optical imaging. In this study, we used a ferritin reporter, binding with biogenic iron, to make it a powerful tool for gene expression imaging in MRI studies. GL261 mouse glioma cells were over-expressed with dual-reporter ferritin–DsRed under β-actin promoter, then gene expression was observed by optical imaging and MRI in a brain tumor model. GL261 cells expressing ferritin–DsRed fusion protein showed enhanced visualizing effect by reducing T2-weighted signal intensity for in vitro and in vivo MRI studies, as well as DsRed fluorescence for optical imaging. Furthermore, a higher contrast was achieved on T2-weighted images when permeating the plasma membrane of ferritin–DsRed-expressing GL261. Thus, a ferritin expression vector can be used as an MRI reporter to monitor in vivo gene expression.

Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution

Transmission electron microscopy has provided most of what is known about the ultrastructural organization of tissues, cells, and organelles. Due to tremendous advances in crystallography and magnetic resonance imaging, almost any protein can now be modeled at atomic resolution. To fully understand the workings of biological "nanomachines" it is necessary to obtain images of intact macromolecular assemblies in situ. Although the resolution power of electron microscopes is on the atomic scale, in biological samples artifacts introduced by aldehyde fixation, dehydration and staining, but also section thickness reduces it to some nanometers. Cryofixation by high pressure freezing circumvents many of the artifacts since it allows vitrifying biological samples of about 200 mum in thickness and immobilizes complex macromolecular assemblies in their native state in situ. To exploit the perfect structural preservation of frozen hydrated sections, sophisticated instruments are needed, e.g., high voltage electron microscopes equipped with precise goniometers that work at low temperature and digital cameras of high sensitivity and pixel number. With them, it is possible to generate high resolution tomograms, i.e., 3D views of subcellular structures. This review describes theory and applications of the high pressure cryofixation methodology and compares its results with those of conventional procedures. Moreover, recent findings will be discussed showing that molecular models of proteins can be fitted into depicted organellar ultrastructure of images of frozen hydrated sections. High pressure freezing of tissue is the base which may lead to precise models of macromolecular assemblies in situ, and thus to a better understanding of the function of complex cellular structures.

Ultrasonic travel-time tomography in core plugs

This paper applies ultrasonic travel-time tomography in order to investigate the resolution (i.e. definition of dimension and shape) of velocity heterogeneities in tomograms from core plugs. Designing the tomographic algorithm involves two main steps, namely, modelling and inversion. In the modelling step, we use straight and curved ray-tracing schemes to calculate raypaths and travel times corresponding to the source–receiver configuration. The inversion step then submits a predefined norm of the residuals between calculated and measured travel times to a minimization process. The conjugate gradient method works to iteratively minimize the � 1 norm of travel-time residuals. Numerical experiments show that, in addition to the dominant frequency of the probing ultrasonic pulse, the resolution of tomograms from core plugs with high-contrast heterogeneities depends on the chosen ray-tracing scheme. In summary, if the rock sample exhibits low to moderate velocity contrasts, the tomographic algorithm using straight rays in the modelling step yields tomograms with good resolution. However, in the presence of high velocity contrasts, plausibly resolved tomograms can be obtained only by adopting a curved ray-tracing scheme. The application of ultrasonic tomography using travel-time data from real core plugs corroborates the results obtained with numerical data.

Tomographic estimation of seismic velocity on an interactive workstation

Tomographic estimation of seismic velocity from directly transmitted arrivals in offset VSP or crosshole data requires the following processing operations: (a) statics estimation and corrections; (b) stacking to enhance arrivals of interest and to remove coherent noise; (c) deconvolution and time picking; (d) iteration between tomographic inversion of picked source-receiver delay times and ray tracing. Velocity tomography with reflection data may also require migration to estimate the position of reflectors for picking two-way travel times. A workstation based software system has been developed which permits interactive tomographic velocity estimation from shallow crosshole and offset VSP data. The flexibility gained by performing velocity tomography interactively has many advantages, such as easy comparisons of intermediate results and the ability to update filtering sequences to accommodate the results of interactive analyses of signal and noise characteristics. We illustrate this for shallow crosshole velocity tomography with examples of (a) interactive tau-p filtering for arrival enhancement and coherent noise removal; (b) the dependence of tomogram resolution on raypath coverage; (c) interactive smoothing to compensate for resolution artifacts related to incomplete tomographic raypath coverage. The use of interactive smoothing to cater for different types of geological prior information in tomography is discussed.

Cerebral blood flow tomography with xenon-133

Cerebral blood flow (CBF) can be measured tomographically by inhalation of Xenon-133. The calculation is based on taking a sequence of tomograms during the wash-in and wash-out phase of the tracer. Due to the dynamic nature of the process, a highly sensitive and fast moving single photon emission computed tomograph (SPECT) is required. Two brain-dedicated SPECT systems designed for this purpose are mentioned, and the method is described with special reference to the limitations inherent in the soft energy of the 133Xe primary photons. CBF tomography can be used for a multitude of clinical and investigative purposes. This article discusses in particular its use for the selection of patients with carotid occlusion for extracranial/intracranial bypass surgery, for detection of severe arterial spasm after aneurysm bleeding, and for detection of low flow areas during severe migraine attacks. The use of other tracers for CBF tomography using SPECT is summarized with emphasis on the 99mTc chelates that freely pass the intact blood-brain barrier. The highly sensitive brain-dedicated SPECT systems described are a prerequisite for achieving high resolution tomograms with such tracers.