Multicomponent Imaging Research Articles

Elastic reverse time migration using an efficient and accurate adaptive variable grid discretization method

Abstract The conventional reverse time migration utilizes regularly sampled computational grids to simulate wave propagation. Selecting the appropriate grid sampling is important for computational accuracy and efficiency. In general, the uniform-size grid cannot represent the complexity of the geology well. The grid may appear sparse in the low-velocity zone, especially in shallow depths where dispersion may occur. Conversely, it may appear excessively dense in the high-velocity zone, such as at greater depths or within a salt body, which results in higher computational memory and time consumption. To overcome these issues, we developed an efficient and accurate adaptive variable grid discretization method that automatically selects the vertical grid size based on the velocity, depth, and dominant frequency of the wavelet in elastic medium. Then we reformulated the elastic equations based on the adaptive variable grid by introducing a mapping relationship. To test the effectiveness, accuracy, and efficiency of the equation, we implemented it to both the forward propagation and migration of elastic wavefield. Synthetic numerical examples demonstrate that our proposed method can achieve elastic wavefield separation and no significant dispersion phenomenon. The multi-component imaging accuracy of reverse time migration is nearly equivalent to the traditional method, while significantly improving computational efficiency and saving storage space.

An Optimized Multicomponent Imaging Method on a Homebuilt 0.5 T MRI System: Combing Intra- and Inter-Voxel Constraints

An Optimized Multicomponent Imaging Method on a Homebuilt 0.5 T MRI System: Combing Intra- and Inter-Voxel Constraints

Quantification of Synovial Fluid Using Magnetic Resonance Fingerprinting Multicomponent Imaging in the Articular Cartilage of the Knee

The purpose of this study was to verify the feasibility of magnetic resonance fingerprinting (MRF)-derived synovial fluid fraction (SFF) mapping for quantifying subvoxel-sized cartilage defects. MRF was performed on a 3-Tesla scanner and used to derive T2 and SFF maps. An ex vivo experiment was performed using bovine bone; different numbers of holes (4, 6, 8, 10, and 12) were drilled separately on the articular surface, and SFF values were compared among the drilled areas. In a clinical study, 16 osteoarthritis patients underwent sagittal 3D fast spinecho (FSE) and MRF scanning, and knee cartilage segmentation was performed on each image. For morphologic analysis, fluid-excluded images of the SFF (FEISFF) and T2 maps (FEIT2) were generated using the cartilage segmentations, and the whole-organ magnetic resonance imaging score (WORMS) of each FEI and 3D FSE image were compared using the kappa coefficient. For quantitative analysis, intact cartilage volumes in the SFF (VSFF) and T2 maps (VT2) were calculated, and their correlations with reference to the actual cartilage volume on 3D FSE images (V3D) were evaluated. In the ex vivo experiment, the SFF value increased as the number of holes increased. The kappa coefficients of the WORMS were 0.80 and 0.64 in the SFF and T2 maps, respectively, and substantial to almost perfect agreement was observed in the medial tibiofemoral joint. The V3D-VSFF and V3D-VT2 correlation coefficients differed by 0.03 or more in the medial tibiofemoral joint. The MRF-derived SFF map can feasibly evaluate small, invisible cartilage defects and quantify cartilage volumes.

Biochemical Analysis Leads to Improved Orthogonal Bioluminescent Tools.

Engineered luciferase-luciferin pairs have expanded the number of cellular targets that can be visualized in tandem. While light production relies on selective processing of synthetic luciferins by mutant luciferases, little is known about the origin of selectivity. The development of new and improved pairs requires a better understanding of the structure-function relationship of bioluminescent probes. In this work, we report a biochemical approach to assessing and optimizing two popular bioluminescent pairs: Cashew/d-luc and Pecan/4'-BrLuc. Single mutants derived from Cashew and Pecan revealed key residues for selectivity and thermal stability. Stability was further improved through a rational addition of beneficial residues. In addition to providing increased stability, the known stabilizing mutations surprisingly also improved selectivity. The resultant improved pair of luciferases are >100-fold selective for their respective substrates and highly thermally stable. Collectively, this work highlights the importance of mechanistic insight for improving bioluminescent pairs and provides significantly improved Cashew and Pecan enzymes which should be immediately suitable for multicomponent imaging applications.

Red-Shifted Coumarin Luciferins for Improved Bioluminescence Imaging.

Multicomponent bioluminescence imaging in vivo requires an expanded collection of tissue-penetrant probes. Toward this end, we generated a new class of near-infrared (NIR) emitting coumarin luciferin analogues (CouLuc-3s). The scaffolds were easily accessed from commercially available dyes. Complementary mutant luciferases for the CouLuc-3 analogues were also identified. The brightest probes enabled sensitive imaging in vivo. The CouLuc-3 scaffolds are also orthogonal to popular bioluminescent reporters and can be used for multicomponent imaging applications. Collectively, this work showcases a new set of bioluminescent tools that can be readily implemented for multiplexed imaging in a variety of biological settings.

Identification, Quantification, and Characterization of HIV-1 Reservoirs in the Human Brain.

The major barrier to cure HIV infection is the early generation and extended survival of HIV reservoirs in the circulation and tissues. Currently, the techniques used to detect and quantify HIV reservoirs are mostly based on blood-based assays; however, it has become evident that viral reservoirs remain in tissues. Our study describes a novel multi-component imaging method (HIV DNA, mRNA, and viral proteins in the same assay) to identify, quantify, and characterize viral reservoirs in tissues and blood products obtained from HIV-infected individuals even when systemic replication is undetectable. In the human brains of HIV-infected individuals under ART, we identified that microglia/macrophages and a small population of astrocytes are the main cells with integrated HIV DNA. Only half of the cells with integrated HIV DNA expressed viral mRNA, and one-third expressed viral proteins. Surprisingly, we identified residual HIV-p24, gp120, nef, vpr, and tat protein expression and accumulation in uninfected cells around HIV-infected cells suggesting local synthesis, secretion, and bystander uptake. In conclusion, our data show that ART reduces the size of the brain’s HIV reservoirs; however, local/chronic viral protein secretion still occurs, indicating that the brain is still a major anatomical target to cure HIV infection.

Rapid Multicomponent Bioluminescence Imaging via Substrate Unmixing.

Studies of biological function demand probes that can report on processes in real time and in physiological environments. Bioluminescent tools are uniquely suited for this purpose, as they enable sensitive imaging in cells and tissues. Bioluminescent reporters can also be monitored continuously over time without detriment, as excitation light is not required. Rather, light emission derives from luciferase-luciferin reactions. Several engineered luciferases and luciferins have expanded the scope of bioluminescence imaging in recent years. Multicomponent tracking remains challenging, though, due to a lack of streamlined methods to visualize combinations of bioluminescent reporters. Conventional approaches image one luciferase at a time. Consequently, short-term changes in cell growth or gene expression cannot be easily captured. Here, we report a strategy for rapid, multiplexed imaging with a wide range of luciferases and luciferins. Sequential addition of orthogonal luciferins, followed by substrate unmixing, enabled facile detection of multiple luciferases in vitro and in vivo. Multicomponent imaging in mice was also achieved on the minutes-to-hours time scale.

Predicting reservoir quality in the Bakken Formation, North Dakota, using petrophysics and 3C seismic data

Combining rock-property analysis with multicomponent seismic imaging can be an effective approach for reservoir quality prediction in the Bakken Formation, North Dakota. The hydrocarbon potential of shale is indicated on well logs by low density, high gamma-ray response, low compressional-wave (P-wave) and shear-wave (S-wave) velocities, and high neutron porosity. We have recognized the shale intervals by cross plotting sonic velocities versus density. Intervals with total organic carbon (TOC) content higher than 10 wt% deviate from lower TOC regions in the density domain and exhibit slightly lower velocities and densities (<2.30 g/cm3). We consider TOC to be the principal factor affecting changes in the density and P- and S-wave velocities in the Bakken shales, where VP/ VS ranges between 1.65 and 1.75. We generate the synthetic seismic data using an anisotropic version of the Zoeppritz equations, including estimated Thomsen’s parameters. For the tops of the Upper and Lower Bakken, the amplitude shows a negative intercept and a positive gradient, which corresponds to an amplitude variation with offset of class IV. The P-impedance error decreases by 14% when incorporating the converted-wave information in the inversion process. A statistical approach using multiattribute analysis and neural networks delimits the zones of interest in terms of P-impedance, density, TOC content, and brittleness. The inverted and predicted results show reasonable correlations with the original well logs. The integration of well log analysis, rock physics, seismic modeling, constrained inversions, and statistical predictions contributes to identifying the areas of highest reservoir quality within the Bakken Formation.

Multicomponent Bioluminescence Imaging with a π-Extended Luciferin.

Bioluminescence imaging with luciferase-luciferin pairs is commonly used for monitoring biological processes in cells and whole organisms. Traditional bioluminescent probes are limited in scope, though, as they cannot be easily distinguished in biological environments, precluding efforts to visualize multicellular processes. Additionally, many luciferase-luciferin pairs emit light that is poorly tissue penetrant, hindering efforts to visualize targets in deep tissues. To address these issues, we synthesized a set of π-extended luciferins that were predicted to be red-shifted luminophores. The scaffolds were designed to be rotationally labile such that they produced light only when paired with luciferases capable of enforcing planarity. A luciferin comprising an intramolecular "lock" was identified as a viable light-emitting probe. Native luciferases were unable to efficiently process the analog, but a complementary luciferase was identified via Rosetta-guided enzyme design. The unique enzyme-substrate pair is red-shifted compared to well-known bioluminescent tools. The probe set is also orthogonal to other luciferase-luciferin probes and can be used for multicomponent imaging. Four substrate-resolved luciferases were imaged in a single session. Collectively, this work provides the first example of Rosetta-guided design in engineering bioluminescent tools and expands the scope of orthogonal imaging probes.

Simultaneous Identification of Low and High Atomic Number Atoms in Monolayer 2D Materials Using 4D Scanning Transmission Electron Microscopy

Simultaneous imaging of individual low and high atomic number atoms using annular dark field scanning transmission electron microscopy (ADF-STEM) is often challenging due to substantial differences in their scattering cross sections. This often leads to contrast from only the high atomic number species when imaged using ADF-STEM such as the Mo and 2S sites in monolayer MoS2 crystals, without detection of lighter atoms such as C, O, or N. Here, we show that by capturing an array of convergent beam electron diffraction patterns using a 2D pixelated electron detector (2D-PED) in a 4D STEM geometry enables identification of individual low and high atomic number atoms in 2D materials by multicomponent imaging. We have used ptychographic phase reconstructions, combined with angular dependent ADF-STEM reconstructions, to image light elements at lateral (nanopores) and vertical interfaces (surface dopants) within 2D monolayer MoS2. Differential phase contrast imaging (Div(DPC)) using quadrant segmentation of the 2D pixelated direct electron detector data not only qualitatively matches the ptychographic phase reconstructions in both resolution and contrast but also offers the additional potential for real time display. Using 4D-STEM, we have identified surface adatoms on MoS2 monolayers and have separated atomic columns with similar total atomic number into their relative combinations of low and high atomic number elements. These results demonstrate the rich information present in the data obtained during 4D-STEM imaging of ultrathin 2D materials and the ability of this approach to extract unique insights beyond conventional imaging.

Parallel Screening for Rapid Identification of Orthogonal Bioluminescent Tools.

Bioluminescence imaging with luciferase enzymes and luciferin small molecules is a well-established technique for tracking cells and other biological features in rodent models. Despite its popularity, bioluminescence has long been hindered by a lack of distinguishable probes. Here we present a method to rapidly identify new substrate-selective luciferases for multicomponent imaging. Our strategy relies on parallel screening of luciferin analogues with panels of mutant enzymes. The compiled data set is then analyzed in silico to uncover mutually orthogonal sets. Using this approach, we screened 159 mutant enzymes with 12 luciferins. Thousands of orthogonal pairs were revealed with sufficient selectivity for use in biological environments. Over 100 pairs were validated in vitro, and three were applied in cell and animal models. The parallel screening method is both generalizable and scalable and will streamline the search for larger collections of orthogonal probes.

Orthogonal Luciferase-Luciferin Pairs for Bioluminescence Imaging.

Bioluminescence imaging with luciferase-luciferin pairs is widely used in biomedical research. Several luciferases have been identified in nature, and many have been adapted for tracking cells in whole animals. Unfortunately, the optimal luciferases for imaging in vivo utilize the same substrate and therefore cannot easily differentiate multiple cell types in a single subject. To develop a broader set of distinguishable probes, we crafted custom luciferins that can be selectively processed by engineered luciferases. Libraries of mutant enzymes were iteratively screened with sterically modified luciferins, and orthogonal enzyme-substrate "hits" were identified. These tools produced light when complementary enzyme-substrate partners interacted both in vitro and in cultured cell models. Based on their selectivity, these designer pairs will bolster multicomponent imaging and enable the direct interrogation of cell networks not currently possible with existing tools. Our screening platform is also general and will expedite the identification of more unique luciferases and luciferins, further expanding the bioluminescence toolkit.

Poster 19 In Vivo Characterization of White Matter Myelin Content After Stroke Using Multicomponent T2 Relaxation Imaging

Poster 19 In Vivo Characterization of White Matter Myelin Content After Stroke Using Multicomponent T2 Relaxation Imaging

Use of crossed dipole antennas in 3D imaging of multi-component GPR data

Crossed dipole (cross-pole) antennas are not commonly used for ground penetrating radar (GPR) measurements, but can contain valuable information about the subsurface. Recently, a multi-component imaging algorithm has been derived which combines parallel dipole (co-pole) and cross-pole antenna measurements to obtain an image of the subsurface. The performance of this multi-component imaging algorithm is investigated by imaging modelled data of a point scatterer with a conductivity (real-valued) contrast in a homogeneous halfspace. The imaging is carried out for one single frequency at the depth of the point scatterer, which results in a resolution function. The contributions of the cross-pole and co-pole antenna measurements are imaged separately. The combination of the cross-pole and co-pole antenna imaging results show a circular-symmetric real-valued resolution function, which adequately represents the point-scatterer. Experimental results show that cross-pole antenna measurements contain valuable information of objects present in the subsurface, which is shown for an oblique pipe.

Studying the Effects of Protein and Lipid Composition on Lung Surfactant Adsorption Through Confocal Microscopy

Lung surfactant (LS) is a mixture of lipids and proteins that lines the air-water interface of the alveolar walls. It modulates the surface tension in the lungs which greatly reduces the mechanical work of breathing and also prevents the collapse of the alveoli upon expiration. Although lipids are the major constituent of LS, the hydrophobic surfactant proteins SP-B and SP-C play an integral role in proper adsorption of LS to the air-water interface. Understanding the role of these proteins will allow for better design of exogenous LS therapies for the treatment of respiratory distress syndrome. Confocal microscopy's abilities to optically section a sample and simultaneously image multiple dyes provide an ideal tool to study LS adsorption in vitro. Combining three-dimensional, multi-component imaging with surface tension measurements allows us to determine whether a particular surfactant mixture can successfully transition from bilayer aggregates in the bulk to a functional monolayer on the interface. SP-B and SP-C are believed to play an integral role in both the transport of aggregates to the interface and the unfolding of surfactant bilayers into a monolayer. Confocal microscopy has allowed us to study the importance of lipid and protein composition on the transport and unfolding of LS.

Multicomponent VSP imaging of tight-gas sands

Low-porosity Bossier and Cotton Valley sands of the East Texas Basin, U. S., have only a small acoustic impedance contrast with the encasing shales but a greater relative contrast in shear-wave impedance. Vertical seismic profile (VSP) data acquired with both a near-offset and far-offset P-wave source clearly demonstrate the P-P reflectivity and P-S mode conversions within the Bossier section. We designate conventional P-wave reflectivity as P-P, shear-wave reflectivity as S-S, and P-wave/shear-wave mode conversion data as P-S. While Bossier P-P reflectivity is low, it appears to be adequate for mapping thick sandbodies such as the York Sandstone, the main exploration target in this area. However, P-P reflectivity is even lower and is inadequate for imaging the overlying Cotton Valley Sands. In contrast, the far-offset VSP data acquired with a P-wave source demonstrate a high level of P-S-mode conversion, which is used to image this interval with definition that is not provided by P-P reflectivity. This provides strong support for the use of P-S-mode conversion imaging for seismic characterization of tight sand reservoirs. Near-offset shear-wave VSP data acquired with a shearwave source show low S/N ratio and limited bandwidth for the downgoing waveform because of the depth of the target; shear-wave energy appears to have a more limited range of propagation than P-waves. Such effects may also have a strong negative impact on multicomponent imaging of these sands using surface seismic techniques. Multicomponent 3D VSP imaging provides a superior solution by placing the geophones closer to the subsurface zone of interest.

Three‐dimensional multicomponent georadar imaging of sedimentary structures

ABSTRACTMulticomponent georadar methods that involve recording data using several different antenna configurations and orientations should provide better constrained information about the subsurface than conventional single‐component techniques. We test this hypothesis using three‐dimensional (3D) multicomponent data recently acquired across braided river sediments deposited adjacent to the Alpine Fault in New Zealand. Strong reflections were observed in the two pairs of co‐ and cross‐polarized data sets. Relatively high reflection amplitudes in the cross‐polarized data were a consequence of the dip and oblique orientation of most sedimentary structures relative to the antennae. Many differences in structural information content and reflection amplitude observed in the different components could be explained on the basis of rather simple wavefield models. To obtain reliable subsurface information, a novel 3D multicomponent imaging (migration) algorithm was applied to the data. This algorithm accounted for the effects of antenna orientation, antenna offset and far‐field electromagnetic radiation patterns. In addition to correcting the dips, positions and lengths of reflections, the multicomponent imaging also adjusted their relative amplitudes according to the far‐field wavefield model. The contributions of the cross‐polarized data to the images were particularly important in our data set, because they selectively enhanced dipping reflections oriented at oblique angles to the antenna axes. Phase characteristics of reflections with certain orientations and dips were not recovered consistently, indicating a need for further investigation.

Three‐dimensional imaging of multicomponent ground‐penetrating radar data

Scalar imaging algorithms originally developed for the processing of remote sensing measurements (e.g., the synthetic‐aperture radar method) or seismic reflection data (e.g., the Gazdag phase‐shift method) are commonly used for the processing of ground‐penetrating radar (GPR) data. Unfortunately, these algorithms do not account for the radiation characteristics of GPR source and receiver antennas or the vectorial nature of radar waves. We present a new multicomponent imaging algorithm designed specifically for vector electromagnetic‐wave propagation. It accounts for all propagation effects, including the vectorial characteristics of the source and receiver antennas and the polarization of the electromagnetic wavefield. A constant‐offset source‐receiver antenna pair is assumed to overlie a dielectric medium. To assess the performance of the scalar and multicomponent imaging algorithms, we compute their spatial resolution function, which is defined as the image of a point scatterer at a fixed depth using a single frequency. Application of the new multicomponent imaging algorithm results in a circularly symmetric resolution function, demonstrating that the radiation characteristics of the source and receiver antennas do not influence the derived image. In contrast, the two tested scalar imaging algorithms return distinctly asymmetric resolution functions with incorrect phase characteristics, which could result in erroneous images of the subsurface when these algorithms are applied to GPR data. The multicomponent and two scalar imaging algorithms are tested on data acquired across numerous buried objects with various dielectric properties and different strike directions. Phase differences between the different images are similar to those observed in the synthetic examples. Of the tested algorithms, we conclude that the multicomponent approach produces the most reliable results.

Improved Three-Dimensional Image Reconstruction Technique for Multi-Component Ground Penetrating Radar Data

For electromagnetic imaging the vectorial character of the emitted field and the radiation characteristics of both source and receiver play an important role. Recently, a new imaging algorithm was presented dedicated to the electromagnetic case. The radiation characteristics of GPR source and receiver antennas and the vectorial nature of the electromagnetic waves are taken into account for a monostatic fixed offset GPR survey. This resulted in a representative image of a point scatterer. Comparison with scalar imaging algorithms shows that for a homogeneous space the SAR image has an opposite sign compared to the multi-component image, whereas the Gazdag image has a phase shift of about 90° with respect to the multi-component image. In this paper, modified scalar imaging algorithms are introduced that minimize these differences. However, between the images obtained in a homogeneous half-space phase differences of 10–20° are still present. These differences indicate the possible error in nature of the physical property contrast when it is determined with the modified scalar imaging algorithms. The multi-component imaging algorithm returns a representative image because it uses the appropriate Greens functions to eliminate the propagation effects. For practical imaging strategies, only far-field radiation characteristics can be used to compensate for the propagation effects due to the large computing time needed to evaluate the total-field expressions. Synthetic analysis of the imaging of a point scatterer calculated using total-field expressions shows that using the far-field expressions in the multi-component imaging algorithm the images better approximate the actual contrast than using the modified scalar imaging algorithms. Experimental results are presented from imaging several buried objects with different medium properties and different orientations. The phase differences in the experimental data are similar to those obtained synthetically. This likeness indicates that using the multi-component imaging algorithm, a more reliable image is obtained than with the modified scalar imaging algorithms.

In‐mine seismic delineation of mineralization and rock structure

Significant progress has been made towards the goal of generating detailed seismic images as an aid to mine planning and exploration at the Kambalda nickel mines of Western Australia. Crosshole and vertical‐seismic‐profiling instrumentation, including a slimline multi‐element hydrophone array, three‐component geophone sensors, and a multishot detonator sound source, have been developed along with special seismic imaging software to map rock structure. Seismic trials at the Hunt underground mine established that high frequency (> 1 kHz) signals can be propagated over distances of tens of meters. Tomographic as well as novel 3-D multicomponent reflection imaging procedures have been applied to the data to produce useful pictures of the ore‐stope geometry and host rock. Tomogram interpretation remains problematic because velocity changes not only relate to differing rock types and/or the presence of mineralisation, but can also be caused by alteration/weathering and other rock condition variations. Ultrasonic measurements on rock core samples help in assigning velocity values to lithology, but geological assessment of tomograms remains ambiguous. Reflection imaging is complicated by the presence of strong tube‐wave to body‐wave mode conversion events present in the records, which obscure the weak reflection signatures. Three‐dimensional reflection data processing, especially three‐component analysis, is time consuming and difficult to perform. Notwithstanding the difficulties, the seismic migrations at the Hunt mine show a striking correlation with the known geology. Combined seismic and radar surveying from available underground boreholes and mine drivages is probably needed in the future to more confidently delineate mineralisation.