High-resolution Imaging Method Research Articles

Interleaved EPI diffusion imaging using SPIRiT‐based reconstruction with virtual coil compression

To develop a novel diffusion imaging reconstruction framework based on iterative self-consistent parallel imaging reconstruction (SPIRiT) for multishot interleaved echo planar imaging (iEPI), with computation acceleration by virtual coil compression. As a general approach for autocalibrating parallel imaging, SPIRiT improves the performance of traditional generalized autocalibrating partially parallel acquisitions (GRAPPA) methods in that the formulation with self-consistency is better conditioned, suggesting SPIRiT to be a better candidate in k-space-based reconstruction. In this study, a general SPIRiT framework is adopted to incorporate both coil sensitivity and phase variation information as virtual coils and then is applied to 2D navigated iEPI diffusion imaging. To reduce the reconstruction time when using a large number of coils and shots, a novel shot-coil compression method is proposed for computation acceleration in Cartesian sampling. Simulations and in vivo experiments were conducted to evaluate the performance of the proposed method. Compared with the conventional coil compression, the shot-coil compression achieved higher compression rates with reduced errors. The simulation and in vivo experiments demonstrate that the SPIRiT-based reconstruction outperformed the existing method, realigned GRAPPA, and provided superior images with reduced artifacts. The SPIRiT-based reconstruction with virtual coil compression is a reliable method for high-resolution iEPI diffusion imaging. Magn Reson Med 79:1525-1531, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Multi-Feature Segmentation for High-Resolution Polarimetric SAR Data Based on Fractal Net Evolution Approach

Segmentation techniques play an important role in understanding high-resolution polarimetric synthetic aperture radar (PolSAR) images. PolSAR image segmentation is widely used as a preprocessing step for subsequent classification, scene interpretation and extraction of surface parameters. However, speckle noise and rich spatial features of heterogeneous regions lead to blurred boundaries of high-resolution PolSAR image segmentation. A novel segmentation algorithm is proposed in this study in order to address the problem and to obtain accurate and precise segmentation results. This method integrates statistical features into a fractal net evolution algorithm (FNEA) framework, and incorporates polarimetric features into a simple linear iterative clustering (SLIC) superpixel generation algorithm. First, spectral heterogeneity in the traditional FNEA is substituted by the G0 distribution statistical heterogeneity in order to combine the shape and statistical features of PolSAR data. The statistical heterogeneity between two adjacent image objects is measured using a log likelihood function. Second, a modified SLIC algorithm is utilized to generate compact superpixels as the initial samples for the G0 statistical model, which substitutes the polarimetric distance of the Pauli RGB composition for the CIELAB color distance. The segmentation results were obtained by weighting the G0 statistical feature and the shape features, based on the FNEA framework. The validity and applicability of the proposed method was verified with extensive experiments on simulated data and three real-world high-resolution PolSAR images from airborne multi-look ESAR, spaceborne single-look RADARSAT-2, and multi-look TerraSAR-X data sets. The experimental results indicate that the proposed method obtains more accurate and precise segmentation results than the other methods for high-resolution PolSAR images.

Dynamic phosphocreatine imaging with unlocalized pH assessment of the human lower leg muscle following exercise at 3T

To develop a high temporal resolution imaging method that measures muscle-specific phosphocreatine (PCr) resynthesis time constant (τPCr ) and pH changes in muscles of the lower leg following exercise on a clinical 3T MRI scanner. We developed a frequency-selective 3D non-Cartesian FLORET sequence to measure PCr with 17-mm nominal isotropic resolution (28 mm actual resolution) and 6-s temporal resolution to capture dynamic metabolic muscle activity. The sequence was designed to additionally collect inorganic phosphate spectra for pH quantification, which were localized using sensitivity profiles of individual coil elements. Nineteen healthy volunteers were scanned while performing a plantar flexion exercise on an in-house developed ergometer. Data were acquired with a dual-tuned multichannel coil array that enabled phosphorus imaging and proton localization for muscle segmentation. After a 90-s plantar flexion exercise at 0.66 Hz with resistance set to 40% of the maximum voluntary contraction, τPCr was estimated at 22.9 ± 8.8 s (mean ± standard deviation) with statistical coefficient of determination r2 = 0.89 ± 0.05. The corresponding pH values after exercise were in the range of 6.9-7.1 in the gastrocnemius muscle. The developed technique allows measurement of muscle-specific PCr resynthesis kinetics and pH changes following exercise, with a temporal resolution and accuracy comparable to that of single voxel 31 P-MRS sequences. Magn Reson Med 79:974-980, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Light Sheet Fluorescence Microscopy Quantifies Calcium Oscillations in Root Hairs of Arabidopsis thaliana.

Calcium oscillations play a role in the regulation of the development of tip-growing plant cells. Using optical microscopy, calcium oscillations have been observed in a few systems (e.g. pollen tubes, fungal hyphae and algal rhizoids). High-resolution, non-phototoxic and rapid imaging methods are required to study the calcium oscillation in root hairs. We show that light sheet fluorescence microscopy is optimal to image growing root hairs of Arabidopsis thaliana and to follow their oscillatory tip-focused calcium gradient. We describe a protocol for performing live imaging of root hairs in seedlings expressing the cytosol-localized ratiometric calcium indicator Yellow Cameleon 3.6. Using this protocol, we measured the calcium gradient in a large number of root hairs. We characterized their calcium oscillations and correlated them with the rate of hair growth. The method was then used to screen the effect of auxin on the properties of the growing root hairs.

Patterns in Saccharomyces cerevisiae yeast colonies via magnetic resonance imaging.

We report the use of high-resolution magnetic resonance imaging methods to observe pattern formation in colonies of Saccharomyces cerevisiae. Our results indicate substantial signal loss localized in specific regions of the colony rendering useful imaging contrast. This imaging contrast is recognizable as being due to discontinuities in magnetic susceptibility (χ) between different spatial regions. At the microscopic pixel level, the local variations in the magnetic susceptibility (Δχ) induce a loss in the NMR signal, which was quantified via T2 and T2* maps, permitting estimation of Δχ values for different regions of the colony. Interestingly the typical petal/wrinkling patterns present in the colony have a high degree of correlation with the estimated susceptibility distribution. We conclude that the presence of magnetic susceptibility inclusions, together with their spatial arrangement within the colony, may be a potential cause of the susceptibility distribution and therefore the contrast observed on the images.

Early detection of pancreatic cancer: impact of high-resolution imaging methods and biomarkers.

High-resolution imaging methods (HRIMs) and biomarkers present the second step of pancreatic cancer (PC) diagnostics in at-risk individuals. These include patients with positive risk factors, early symptoms, nonresponders to the initial antidiabetic therapy, patients older than 50 years of age with new-onset unstable diabetes requiring insulin as well as patients with long-term insulin-non-dependent diabetes and recent (up to 6 months) failure of antidiabetic therapy. The procedures should be started without delay and the co-operation between the primary and tertiary medical centers is highly desirable. An early indication of HRIMs and biomarkers is a prerequisite for the diagnosis of a resectable PC. This publication reviews the recent contribution of HRIMs and biomarkers toward an early diagnosis of PC.

Computational out-of-focus imaging increases the space–bandwidth product in lens-based coherent microscopy

The space–bandwidth product (SBP) of modern objective lenses is often significantly larger than the pixel count of opto-electronic image sensor chips, and, therefore, much of the information transmitted by the optical system cannot be adequately sampled or digitized. To resolve this mismatch, microscopes are in general designed to maintain the resolution of the optical system while significantly wasting the field of view (FOV) and SBP of the objective lens. We introduce a wide-field and high-resolution coherent imaging method that uses a stack of out-of-focus images to provide much better utilization of the SBP of an objective lens. We demonstrate our approach on a benchtop microscope by using a demagnification camera adapter to match the active area of the image sensor chip to the FOV of an objective lens. We show that the resulting spatial undersampling caused by capturing a large FOV can be mitigated through an iterative pixel super-resolution algorithm that uses e.g., ∼three to five slightly out-of-focus images, yielding an ∼8-fold increase in the SBP of the microscope. Furthermore, the same pixel super-resolution algorithm also achieves phase retrieval, revealing the optical phase information of the specimen. We compared our method against traditional off-axis and phase-shifting digital holographic microscopy modalities and demonstrated at least 3-fold reduction in the number of images required to achieve the same SBP. This technique could be used to maximize the throughput and SBP of lens-based coherent imaging and holography systems and inspire new microscopy designs that benefit from the inherent autofocusing steps of a scanning microscope to increase its SBP.

Safety assessment in macaques of light exposures for functional two-photon ophthalmoscopy in humans.

Two-photon ophthalmoscopy has potential for in vivo assessment of function of normal and diseased retina. However, light safety of the sub-100 fs laser typically used is a major concern and safety standards are not well established. To test the feasibility of safe in vivo two-photon excitation fluorescence (TPEF) imaging of photoreceptors in humans, we examined the effects of ultrashort pulsed light and the required light levels with a variety of clinical and high resolution imaging methods in macaques. The only measure that revealed a significant effect due to exposure to pulsed light within existing safety standards was infrared autofluorescence (IRAF) intensity. No other structural or functional alterations were detected by other imaging techniques for any of the exposures. Photoreceptors and retinal pigment epithelium appeared normal in adaptive optics images. No effect of repeated exposures on TPEF time course was detected, suggesting that visual cycle function was maintained. If IRAF reduction is hazardous, it is the only hurdle to applying two-photon retinal imaging in humans. To date, no harmful effects of IRAF reduction have been detected.

Imaging Subsurface Fracture and Void using Wide-Band Inversion of Fresnel Interpolated Wavepath Seismic Tomography

Studying existence of fracture, void as well as fault in subsurface are important and it has wide applications. In addition, fracture and void play important role in reservoir productivity as well as in geotechnical application. The problem in imaging fracture and void in subsurface, however, is resolution. It needs high-resolution imaging method laterally as well as vertically. The seismic velocity imaging, however, usually has poor lateral resolution. Seismic tomography provides better resolution than conventional velocity analysis methods. Conventional raypath seismic tomography, however, needs dense as well as high angle and wide measurement configuration that is high cost in field data acquisition. I propose to use Fresnel interpolated wavepath (FIW) wide-band inversion. FIW is an interpolation between imaginary part of Rhytov scattering wavepath and raypath. Then, FIW is combined with wide band inversion procedure to handle sparseness configuration of measurement. By this method, smooth constraint is implemented more naturally by based on wave's spectrum. Furthermore, it can produce more stable inversion procedure. In this paper, Wide-band inversion of FIW tomography is tested into various seismic field data in order to image void, fault and fracture. The results showed that tomography based on FIW could handle the limitation of configuration angle, sparseness configuration and resulting good image. We use many difficult cases of field data such as: subsurface tunnel imaging and also void-fracture imaging in volcanic rock

Reflector imaging using trial reflector and crosscorrelation: Application to fracture imaging for sonic data

I have developed two high-resolution imaging methods that do not require a priori information on the structural dip. The dip information is often necessary to image complex structures using Kirchhoff migration by selecting only the constructively interfering parts of waveforms, especially for data with limited acquisition geometry. However, such dip information is not generally available. The methods that I evaluated use a trial reflector, which is defined for each image point and source-receiver pair, to search for the true geologic reflector. The coincidence of these reflectors is judged by a coherency analysis of event signals for the trial reflector using the crosscorrelations, and the coherency is converted to a weight. The weight is combined with the stacking methods of waveform samples in migration. In the first method, a waveform sample summed at an image point for a source-receiver pair is obtained by the common-depth-point stack of array data for the trial reflector. In the second method, a waveform sample of a source-receiver pair at the traveltime of the reflected ray for the trial reflector is smeared in the Fresnel zone computed for the trial reflector. My methods were applied to image fractures for sonic data, whose frequency range is centered approximately 8 kHz, and they provide higher resolution images than those given by conventional Kirchhoff migration.

Optimization of Lattice Boltzmann Simulation With Graphics-Processing-Unit Parallel Computing and the Application in Reservoir Characterization

Summary Shale permeability is sufficiently low to require an unconventional scale of stimulation treatments, such as very-large-volume, high-rate, multistage hydraulic-fracturing applications. Upscaling of hydrocarbon transport processes in shales is challenging because of the low permeability and strong heterogeneity. Rock characterization with high-resolution imaging [X-ray tomography and scanning electron microscope (SEM)] is usually highly localized and contains significant uncertainties because of the small field of view. Therefore, an effective high-performance computing method is required to collect information over a larger scale to meet the ergodicity requirement in upscaling. The lattice Boltzmann (LB) method has received significant attention in computational fluid dynamics because of its capability in coping with complicated boundary conditions. A combination of high-resolution imaging and LB simulation is a powerful approach for evaluating the transport properties of a porous medium in a timely manner, on the basis of the numerical solution of the Navier-Stokes equations and Darcy's law. In this work, a graphics-processing-unit (GPU) -enhanced lattice Boltzmann simulator (GELBS) was developed, which was optimized by GPU parallel computing on the basis of the inherent parallelism of the LB method. Specifically, the LB method was used to implement the computational kernel; a sparse data structure was applied to optimize memory allocation; the OCCA (Medina et al. 2014) portability library was used, which enables the GELBS codes to use different application-programming interfaces (APIs) including open computing language (OpenCL), compute unified device architecture (CUDA), and open multiprocessing (OpenMP). OpenCL is an open standard for cross-platform parallel computing, CUDA is supported only by NVIDIA devices, and OpenMP is primarily used on central processing units (CPUs). It was found that the GPU-accelerated code was approximately 1,000 times faster than the unoptimized serial code and 10 times faster than the parallel code run on a standalone CPU. The CUDA code was slightly faster than OpenCL code on the NVIDA GPU because of the extra cost of OpenCL used to adapt to a heterogeneous platform. The GELBS was validated by comparing it with analytical solutions, laboratory measurements, and other independent numerical simulators in previous studies, and it was proved to have a second-order global accuracy. The GELBS was then used to analyze thin cuttings extracted from a sandstone reservoir and a shale-gas reservoir. The sandstone permeabilities were found relatively isotropic, whereas the shale permeabilities were strongly anisotropic because of the horizontal lamination structure. In shale cuttings, the average permeability in the horizontal direction was higher than that in the vertical direction by approximately two orders of magnitude. Correlations between porosity and permeability were observed in both rocks. The combination of GELBS and high-resolution imaging methods makes for a powerful tool for permeability evaluation when conventional laboratory measurement is impossible because of small cuttings sizes. The constitutive correlations between geometry and transport properties can be used for upscaling in different rock types. The GPU-optimized code significantly accelerates the computing speed; thus, many more samples can be analyzed given the same processing time. Consequently, the ergodicity requirement is met, which leads to a better reservoir characterization.

Effect of Spatial Inhomogeneities on the Membrane Surface on Receptor Dimerization and Signal Initiation

Important signal transduction pathways originate on the plasma membrane, where microdomains may transiently entrap diffusing receptors. This results in a non-random distribution of receptors even in the resting state, which can be visualized as “clusters” by high resolution imaging methods. Here, we explore how spatial in-homogeneities in the plasma membrane might influence the dimerization and phosphorylation status of ErbB2 and ErbB3, two receptor tyrosine kinases that preferentially heterodimerize and are often co-expressed in cancer. This theoretical study is based upon spatial stochastic simulations of the two-dimensional membrane landscape, where variables include differential distributions and overlap of transient confinement zones (“domains”) for the two receptor species. The in silico model is parameterized and validated using data from single particle tracking experiments. We report key differences in signaling output based on the degree of overlap between domains and the relative retention of receptors in such domains, expressed as escape probability. Results predict that a high overlap of domains, which favors transient co-confinement of both receptor species, will enhance the rate of hetero-interactions. Where domains do not overlap, simulations confirm expectations that homo-interactions are favored. Since ErbB3 is uniquely dependent on ErbB2 interactions for activation of its catalytic activity, variations in domain overlap or escape probability markedly alter the predicted patterns and time course of ErbB3 and ErbB2 phosphorylation. Taken together, these results implicate membrane domain organization as an important modulator of signal initiation, motivating the design of novel experimental approaches to measure these important parameters across a wider range of receptor systems.

Ozone-based Surface Conditioning Focused on an Improved Passivation for Silicon Heterojunction Solar Cells

Silicon Heterojunction (SHJ) solar cells represent a key technology to approach very high conversion efficiencies close to the theoretical limit of silicon solar cells. The main advantages of SHJ solar cells are a lean production chain with low temperature processes and the passivating hetero-structure contact which simultaneously fulfils the passivation and contacting role. For an improved passivation a smooth and low-defect concentration surface is required.This paper focuses on a new simple, cost effective and production-feasible ozone-based surface conditioning process for the controlled rounding and smoothing of textured surfaces applied in SHJ solar cells. The impact of surface conditioning on optical and morphological properties is analyzed for alkaline textured surfaces with small to medium and large size pyramids by reflection measurements and high resolution imaging methods as scanning electron microscopy (SEM) and atomic force microscopy (AFM).

Characterization of lipid-rich plaques using spectroscopic optical coherence tomography.

Intravascular optical coherence tomography (IV-OCT) is a high-resolution imaging method used to visualize the internal structures of walls of coronary arteries in vivo. However, accurate characterization of atherosclerotic plaques with gray-scale IV-OCT images is often limited by various intrinsic artifacts. In this study, we present an algorithm for characterizing lipid-rich plaques with a spectroscopic OCT technique based on a Gaussian center of mass (GCOM) metric. The GCOM metric, which reflects the absorbance properties of lipids, was validated using a lipid phantom. In addition, the proposed characterization method was successfully demonstrated in vivo using an atherosclerotic rabbit model and was found to have a sensitivity and specificity of 94.3% and 76.7% for lipid classification, respectively.

In-situ Isotopic Analysis at Nanoscale using Parallel Ion Electron Spectrometry: A Powerful New Paradigm for Correlative Microscopy.

Isotopic analysis is of paramount importance across the entire gamut of scientific research. To advance the frontiers of knowledge, a technique for nanoscale isotopic analysis is indispensable. Secondary Ion Mass Spectrometry (SIMS) is a well-established technique for analyzing isotopes, but its spatial-resolution is fundamentally limited. Transmission Electron Microscopy (TEM) is a well-known method for high-resolution imaging down to the atomic scale. However, isotopic analysis in TEM is not possible. Here, we introduce a powerful new paradigm for in-situ correlative microscopy called the Parallel Ion Electron Spectrometry by synergizing SIMS with TEM. We demonstrate this technique by distinguishing lithium carbonate nanoparticles according to the isotopic label of lithium, viz. 6Li and 7Li and imaging them at high-resolution by TEM, adding a new dimension to correlative microscopy.

Shear wave transmissivity measurement by color Doppler shear wave imaging

Shear wave elastography is a useful method for evaluating tissue stiffness. We have proposed a novel shear wave imaging method (color Doppler shear wave imaging: CD SWI), which utilizes a signal processing unit in ultrasound color flow imaging in order to detect the shear wave wavefront in real time. Shear wave velocity is adopted to characterize tissue stiffness; however, it is difficult to measure tissue stiffness with high spatial resolution because of the artifact produced by shear wave diffraction. Spatial average processing in the image reconstruction method also degrades the spatial resolution. In this paper, we propose a novel measurement method for the shear wave transmissivity of a tissue boundary. Shear wave wavefront maps are acquired by changing the displacement amplitude of the shear wave and the transmissivity of the shear wave, which gives the difference in shear wave velocity between two mediums separated by the boundary, is measured from the ratio of two threshold voltages required to form the shear wave wavefronts in the two mediums. From this method, a high-resolution shear wave amplitude imaging method that reconstructs a tissue boundary is proposed.

Color calibration and fusion of lens-free and mobile-phone microscopy images for high-resolution and accurate color reproduction.

Lens-free holographic microscopy can achieve wide-field imaging in a cost-effective and field-portable setup, making it a promising technique for point-of-care and telepathology applications. However, due to relatively narrow-band sources used in holographic microscopy, conventional colorization methods that use images reconstructed at discrete wavelengths, corresponding to e.g., red (R), green (G) and blue (B) channels, are subject to color artifacts. Furthermore, these existing RGB colorization methods do not match the chromatic perception of human vision. Here we present a high-color-fidelity and high-resolution imaging method, termed “digital color fusion microscopy” (DCFM), which fuses a holographic image acquired at a single wavelength with a color-calibrated image taken by a low-magnification lens-based microscope using a wavelet transform-based colorization method. We demonstrate accurate color reproduction of DCFM by imaging stained tissue sections. In particular we show that a lens-free holographic microscope in combination with a cost-effective mobile-phone-based microscope can generate color images of specimens, performing very close to a high numerical-aperture (NA) benchtop microscope that is corrected for color distortions and chromatic aberrations, also matching the chromatic response of human vision. This method can be useful for wide-field imaging needs in telepathology applications and in resource-limited settings, where whole-slide scanning microscopy systems are not available.

Achieve atomic resolution in in situ S/TEM experiments to examine complex interface structures in nanomaterials

Characterization methods utilizing Scanning / Transmission Electron Microscopes have become routine techniques to investigate interface structures in nanomaterials. High resolution imaging methods reveals atomic structure; while spectroscopy gives additional access to elemental distribution and chemical bonding. Focus behind these developments is the research on nanomaterial-based technologies.Current trends in S/TEM research focus on extending atomic scale characterization capabilities from static to dynamic studies to understand in more detail the link between structure and its evolution vs. unique properties directly on its characteristic length scale.Progress in recent research is briefly reviewed to highlight the potential when using latest S/TEM methodology optimized for atomic scale investigations and how this can be extended to in situ studies of interfacial effects, followed by comments on how to achieve and maintain highest possible resolution & sensitivity when keeping the effect of electron beam under control during these atomic-scale in situ experiments.

X-ray photoelectron spectroscopic analysis of rice kernels and flours: Measurement of surface chemical composition

The objectives of this study were to evaluate the ability of X-ray photoelectron spectroscopy (XPS) to differentiate rice macromolecules and to calculate the surface composition of rice kernels and flours. The uncooked kernels and flours surface composition of the two selected rice varieties, Thadokkham-11 (TDK11) and Doongara (DG) demonstrated an over-expression of lipids and proteins and an under-expression of starch compared to the bulk composition. The results of the study showed that XPS was able to differentiate rice polysaccharides (mainly starch), proteins and lipids in uncooked rice kernels and flours. Nevertheless, it was unable to distinguish components in cooked rice samples possibly due to complex interactions between gelatinized starch, denatured proteins and lipids. High resolution imaging methods (Scanning Electron Microscopy and Confocal Laser Scanning Microscopy) were employed to obtain complementary information about the properties and location of starch, proteins and lipids in rice kernels and flours.

Time-frequency tomographic imaging of a rotating object in a narrow-band radar

The backscatter from radar object carries Doppler information of scatterers on the object determined by the radial velocity of scattering points and the radar transmitted frequency. For a rotating object this information is contained in the frequency characteristics over varying aspect angle. Frequency characteristics are used to create projections for Doppler radar tomographic imaging. This paper presents a method for high resolution imaging of a rotating target using a time-frequency transform of a returned signal as tomographic projections. The resolution of a tomographic image depends not only on radar system parameters but also depends on the resolution of input projections. The reassigned spectrogram is proposed for building of tomographic projections, due to its possibility of squeezing of frequency spread. The reassigned spectrogram is sensitive to noise so the denoising procedure in the time-frequency domain must be performed before the reassignment procedure. The denoising is performed by removing Short Time Fourier Transform (STFT) noise coefficients below the appropriate threshold. The STFT is a linear time-frequency transform and coefficients, which belong to the signal and coefficients which belong to noise can be analyzed separately. The efficiency of the proposed idea of imaging is supported by results of numerical experiments.