3D-spectral domain computational imaging
NASA Astrophysics Data System (ADS)
Anderson, Trevor; Segref, Armin; Frisken, Grant; Ferra, Herman; Lorenser, Dirk; Frisken, Steven
2016-03-01
We present a proof-of-concept experiment utilizing a novel "snap-shot" spectral domain OCT technique that captures a phase coherent volume in a single frame. The sample is illuminated with a collimated beam of 75 μm diameter and the back-reflected light is analyzed by a 2-D matrix of spectral interferograms. A key challenge that is addressed is simultaneously maintaining lateral and spectral phase coherence over the imaged volume in the presence of sample motion. Digital focusing is demonstrated for 5.0 μm lateral resolution over an 800 μm axial range.
Volumetric (3D) compressive sensing spectral domain optical coherence tomography
Xu, Daguang; Huang, Yong; Kang, Jin U.
2014-01-01
In this work, we proposed a novel three-dimensional compressive sensing (CS) approach for spectral domain optical coherence tomography (SD OCT) volumetric image acquisition and reconstruction. Instead of taking a spectral volume whose size is the same as that of the volumetric image, our method uses a sub set of the original spectral volume that is under-sampled in all three dimensions, which reduces the amount of spectral measurements to less than 20% of that required by the Shan-non/Nyquist theory. The 3D image is recovered from the under-sampled spectral data dimension-by-dimension using the proposed three-step CS reconstruction strategy. Experimental results show that our method can significantly reduce the sampling rate required for a volumetric SD OCT image while preserving the image quality. PMID:25426320
NASA Astrophysics Data System (ADS)
Hu, Zhihong; Wu, Xiaodong; Hariri, Amirhossein; Sadda, SriniVas R.
2013-03-01
Spectral-domain optical coherence tomography (SD-OCT) is a 3-D imaging technique, allowing direct visualization of retinal morphology and architecture. The various layers of the retina may be affected differentially by various diseases. In this study, an automated graph-based multilayer approach was developed to sequentially segment eleven retinal surfaces including the inner retinal bands to the outer retinal bands in normal SD-OCT volume scans at three different stages. For stage 1, the four most detectable and/or distinct surfaces were identified in the four-times-downsampled images and were used as a priori positional information to limit the graph search for other surfaces at stage 2. Eleven surfaces were then detected in the two-times-downsampled images at stage 2, and refined in the original image space at stage 3 using the graph search integrating the estimated morphological shape models. Twenty macular SD-OCT (Heidelberg Spectralis) volume scans from 20 normal subjects (one eye per subject) were used in this study. The overall mean and absolute mean differences in border positions between the automated and manual segmentation for all 11 segmented surfaces were -0.20 +/- 0.53 voxels (-0.76 +/- 2.06 μm) and 0.82 +/- 0.64 voxels (3.19 +/- 2.46 μm). Intensity and thickness properties in the resultant retinal layers were investigated. This investigation in normal subjects may provide a comparative reference for subsequent investigations in eyes with disease.
3-D segmentation of retinal blood vessels in spectral-domain OCT volumes of the optic nerve head
NASA Astrophysics Data System (ADS)
Lee, Kyungmoo; Abràmoff, Michael D.; Niemeijer, Meindert; Garvin, Mona K.; Sonka, Milan
2010-03-01
Segmentation of retinal blood vessels can provide important information for detecting and tracking retinal vascular diseases including diabetic retinopathy, arterial hypertension, arteriosclerosis and retinopathy of prematurity (ROP). Many studies on 2-D segmentation of retinal blood vessels from a variety of medical images have been performed. However, 3-D segmentation of retinal blood vessels from spectral-domain optical coherence tomography (OCT) volumes, which is capable of providing geometrically accurate vessel models, to the best of our knowledge, has not been previously studied. The purpose of this study is to develop and evaluate a method that can automatically detect 3-D retinal blood vessels from spectral-domain OCT scans centered on the optic nerve head (ONH). The proposed method utilized a fast multiscale 3-D graph search to segment retinal surfaces as well as a triangular mesh-based 3-D graph search to detect retinal blood vessels. An experiment on 30 ONH-centered OCT scans (15 right eye scans and 15 left eye scans) from 15 subjects was performed, and the mean unsigned error in 3-D of the computer segmentations compared with the independent standard obtained from a retinal specialist was 3.4 +/- 2.5 voxels (0.10 +/- 0.07 mm).
Belghith, Akram; Bowd, Christopher; Weinreb, Robert N.; Zangwill, Linda M.
2014-01-01
Glaucoma is an ocular disease characterized by distinctive changes in the optic nerve head (ONH) and visual field. Glaucoma can strike without symptoms and causes blindness if it remains without treatment. Therefore, early disease detection is important so that treatment can be initiated and blindness prevented. In this context, important advances in technology for non-invasive imaging of the eye have been made providing quantitative tools to measure structural changes in ONH topography, an essential element for glaucoma detection and monitoring. 3D spectral domain optical coherence tomography (SD-OCT), an optical imaging technique, has been commonly used to discriminate glaucomatous from healthy subjects. In this paper, we present a new framework for detection of glaucoma progression using 3D SD-OCT images. In contrast to previous works that the retinal nerve fiber layer (RNFL) thickness measurement provided by commercially available spectral-domain optical coherence tomograph, we consider the whole 3D volume for change detection. To integrate a priori knowledge and in particular the spatial voxel dependency in the change detection map, we propose the use of the Markov Random Field to handle a such dependency. To accommodate the presence of false positive detection, the estimated change detection map is then used to classify a 3D SDOCT image into the “non-progressing” and “progressing” glaucoma classes, based on a fuzzy logic classifier. We compared the diagnostic performance of the proposed framework to existing methods of progression detection. PMID:25606299
NASA Astrophysics Data System (ADS)
Belghith, Akram; Bowd, Christopher; Weinreb, Robert N.; Zangwill, Linda M.
2014-03-01
Glaucoma is an ocular disease characterized by distinctive changes in the optic nerve head (ONH) and visual field. Glaucoma can strike without symptoms and causes blindness if it remains without treatment. Therefore, early disease detection is important so that treatment can be initiated and blindness prevented. In this context, important advances in technology for non-invasive imaging of the eye have been made providing quantitative tools to measure structural changes in ONH topography, an essential element for glaucoma detection and monitoring. 3D spectral domain optical coherence tomography (SD-OCT), an optical imaging technique, has been commonly used to discriminate glaucomatous from healthy subjects. In this paper, we present a new framework for detection of glaucoma progression using 3D SD-OCT images. In contrast to previous works that the retinal nerve fiber layer (RNFL) thickness measurement provided by commercially available spectral-domain optical coherence tomograph, we consider the whole 3D volume for change detection. To integrate a priori knowledge and in particular the spatial voxel dependency in the change detection map, we propose the use of the Markov Random Field to handle a such dependency. To accommodate the presence of false positive detection, the estimated change detection map is then used to classify a 3D SDOCT image into the "non-progressing" and "progressing" glaucoma classes, based on a fuzzy logic classifier. We compared the diagnostic performance of the proposed framework to existing methods of progression detection.
NASA Astrophysics Data System (ADS)
Bagnaninchi, P. O.
2010-02-01
Monitoring non-invasively the cellular events in three dimensional carriers is a major challenge for tissue engineering and regenerative medicine that prevents time-lapsed studies over large population of sample. The potential of optical coherence tomography has been demonstrated to assess tissue formation within porous matrices. In this study we explore the combination of dielectric spectroscopy (DS) and spectral domain optical coherence tomography (SDOCT) to quality assess ADSCs loaded in three dimensional carriers. A SDOCT (930nm, FWHM 90nm) was combined to an open ended coaxial probe connected to material analyser, and broadband measurements between 20MHz and 1GHz were synchronized with Labview. Both ADSCs maintained in undifferentiated state within 3D carrier and induced towards osteoblasts were monitored with this multimodality technique and their DS spectra were acquired at high cell concentration simultaneously to 3D imaging. This multimodality technique will be instrumental to assess non-invasively cell loaded carriers for cell therapy.
3D fluorescence spectral data interpolation by using IDW.
He, Qinghang; Zhang, Zhenxi; Yi, Chao
2008-12-01
Because measured precision of some spectral instruments such as fluorescence spectrometer HITACHI F-4500 cannot reach the requirement of spectral analytical technique, and measured data is finite, which causes some three-dimensional (3D) fluorescence spectral data missed. The fact of missing data can result in errors in interpretations of 3D fluorescence spectral data. This paper takes ethanol solution (volume percentage phi(beta)=0.400) 3D fluorescence spectral data for example, applies inverse distance weighting (IDW) to 3D fluorescence spectral data interpolation. The results prove that the more details of 3D fluorescence spectra are expressed well by using IDW in contrast to that of original 3D fluorescence spectra. To evaluate the effectiveness of interpolation by using IDW, this paper compares standard deviation, coefficient of variation, and the mean, median, maximum and minimum values of original ethanol solution (phi(beta)=0.400) 3D fluorescence spectral data and that of the interpolated, whose results suggest that the interpolation of the 3D fluorescence spectra data by using IDW is exact. PMID:18550425
3D spatial resolution and spectral resolution of interferometric 3D imaging spectrometry.
Obara, Masaki; Yoshimori, Kyu
2016-04-01
Recently developed interferometric 3D imaging spectrometry (J. Opt. Soc. Am A18, 765 [2001]1084-7529JOAOD610.1364/JOSAA.18.000765) enables obtainment of the spectral information and 3D spatial information for incoherently illuminated or self-luminous object simultaneously. Using this method, we can obtain multispectral components of complex holograms, which correspond directly to the phase distribution of the wavefronts propagated from the polychromatic object. This paper focuses on the analysis of spectral resolution and 3D spatial resolution in interferometric 3D imaging spectrometry. Our analysis is based on a novel analytical impulse response function defined over four-dimensional space. We found that the experimental results agree well with the theoretical prediction. This work also suggests a new criterion and estimate method regarding 3D spatial resolution of digital holography. PMID:27139648
Spectral ladar: towards active 3D multispectral imaging
NASA Astrophysics Data System (ADS)
Powers, Michael A.; Davis, Christopher C.
2010-04-01
In this paper we present our Spectral LADAR concept, an augmented implementation of traditional LADAR. This sensor uses a polychromatic source to obtain range-resolved 3D spectral images which are used to identify objects based on combined spatial and spectral features, resolving positions in three dimensions and up to hundreds of meters in distance. We report on a proof-of-concept Spectral LADAR demonstrator that generates spectral point clouds from static scenes. The demonstrator transmits nanosecond supercontinuum pulses generated in a photonic crystal fiber. Currently we use a rapidly tuned receiver with a high-speed InGaAs APD for 25 spectral bands with the future expectation of implementing a linear APD array spectrograph. Each spectral band is independently range resolved with multiple return pulse recognition. This is a critical feature, enabling simultaneous spectral and spatial unmixing of partially obscured objects when not achievable using image fusion of monochromatic LADAR and passive spectral imagers. This enables higher identification confidence in highly cluttered environments such as forested or urban areas (e.g. vehicles behind camouflage or foliage). These environments present challenges for situational awareness and robotic perception which can benefit from the unique attributes of Spectral LADAR. Results from this demonstrator unit are presented for scenes typical of military operations and characterize the operation of the device. The results are discussed here in the context of autonomous vehicle navigation and target recognition.
Registration of 3D spectral OCT volumes using 3D SIFT feature point matching
NASA Astrophysics Data System (ADS)
Niemeijer, Meindert; Garvin, Mona K.; Lee, Kyungmoo; van Ginneken, Bram; Abràmoff, Michael D.; Sonka, Milan
2009-02-01
The recent introduction of next generation spectral OCT scanners has enabled routine acquisition of high resolution, 3D cross-sectional volumetric images of the retina. 3D OCT is used in the detection and management of serious eye diseases such as glaucoma and age-related macular degeneration. For follow-up studies, image registration is a vital tool to enable more precise, quantitative comparison of disease states. This work presents a registration method based on a recently introduced extension of the 2D Scale-Invariant Feature Transform (SIFT) framework1 to 3D.2 The SIFT feature extractor locates minima and maxima in the difference of Gaussian scale space to find salient feature points. It then uses histograms of the local gradient directions around each found extremum in 3D to characterize them in a 4096 element feature vector. Matching points are found by comparing the distance between feature vectors. We apply this method to the rigid registration of optic nerve head- (ONH) and macula-centered 3D OCT scans of the same patient that have only limited overlap. Three OCT data set pairs with known deformation were used for quantitative assessment of the method's robustness and accuracy when deformations of rotation and scaling were considered. Three-dimensional registration accuracy of 2.0+/-3.3 voxels was observed. The accuracy was assessed as average voxel distance error in N=1572 matched locations. The registration method was applied to 12 3D OCT scans (200 x 200 x 1024 voxels) of 6 normal eyes imaged in vivo to demonstrate the clinical utility and robustness of the method in a real-world environment.
Coverage Assessment and Target Tracking in 3D Domains
Boudriga, Noureddine; Hamdi, Mohamed; Iyengar, Sitharama
2011-01-01
Recent advances in integrated electronic devices motivated the use of Wireless Sensor Networks (WSNs) in many applications including domain surveillance and mobile target tracking, where a number of sensors are scattered within a sensitive region to detect the presence of intruders and forward related events to some analysis center(s). Obviously, sensor deployment should guarantee an optimal event detection rate and should reduce coverage holes. Most of the coverage control approaches proposed in the literature deal with two-dimensional zones and do not develop strategies to handle coverage in three-dimensional domains, which is becoming a requirement for many applications including water monitoring, indoor surveillance, and projectile tracking. This paper proposes efficient techniques to detect coverage holes in a 3D domain using a finite set of sensors, repair the holes, and track hostile targets. To this end, we use the concepts of Voronoi tessellation, Vietoris complex, and retract by deformation. We show in particular that, through a set of iterative transformations of the Vietoris complex corresponding to the deployed sensors, the number of coverage holes can be computed with a low complexity. Mobility strategies are also proposed to repair holes by moving appropriately sensors towards the uncovered zones. The tracking objective is to set a non-uniform WSN coverage within the monitored domain to allow detecting the target(s) by the set of sensors. We show, in particular, how the proposed algorithms adapt to cope with obstacles. Simulation experiments are carried out to analyze the efficiency of the proposed models. To our knowledge, repairing and tracking is addressed for the first time in 3D spaces with different sensor coverage schemes. PMID:22163733
3D spectral imaging system for anterior chamber metrology
NASA Astrophysics Data System (ADS)
Anderson, Trevor; Segref, Armin; Frisken, Grant; Frisken, Steven
2015-03-01
Accurate metrology of the anterior chamber of the eye is useful for a number of diagnostic and clinical applications. In particular, accurate corneal topography and corneal thickness data is desirable for fitting contact lenses, screening for diseases and monitoring corneal changes. Anterior OCT systems can be used to measure anterior chamber surfaces, however accurate curvature measurements for single point scanning systems are known to be very sensitive to patient movement. To overcome this problem we have developed a parallel 3D spectral metrology system that captures simultaneous A-scans on a 2D lateral grid. This approach enables estimates of the elevation and curvature of anterior and posterior corneal surfaces that are robust to sample movement. Furthermore, multiple simultaneous surface measurements greatly improve the ability to register consecutive frames and enable aggregate measurements over a finer lateral grid. A key element of our approach has been to exploit standard low cost optical components including lenslet arrays and a 2D sensor to provide a path towards low cost implementation. We demonstrate first prototypes based on 6 Mpixel sensor using a 250 μm pitch lenslet array with 300 sample beams to achieve an RMS elevation accuracy of 1μm with 95 dB sensitivity and a 7.0 mm range. Initial tests on Porcine eyes, model eyes and calibration spheres demonstrate the validity of the concept. With the next iteration of designs we expect to be able to achieve over 1000 simultaneous A-scans in excess of 75 frames per second.
3D Vectorial Time Domain Computational Integrated Photonics
Kallman, J S; Bond, T C; Koning, J M; Stowell, M L
2007-02-16
The design of integrated photonic structures poses considerable challenges. 3D-Time-Domain design tools are fundamental in enabling technologies such as all-optical logic, photonic bandgap sensors, THz imaging, and fast radiation diagnostics. Such technologies are essential to LLNL and WFO sponsors for a broad range of applications: encryption for communications and surveillance sensors (NSA, NAI and IDIV/PAT); high density optical interconnects for high-performance computing (ASCI); high-bandwidth instrumentation for NIF diagnostics; micro-sensor development for weapon miniaturization within the Stockpile Stewardship and DNT programs; and applications within HSO for CBNP detection devices. While there exist a number of photonics simulation tools on the market, they primarily model devices of interest to the communications industry. We saw the need to extend our previous software to match the Laboratory's unique emerging needs. These include modeling novel material effects (such as those of radiation induced carrier concentrations on refractive index) and device configurations (RadTracker bulk optics with radiation induced details, Optical Logic edge emitting lasers with lateral optical inputs). In addition we foresaw significant advantages to expanding our own internal simulation codes: parallel supercomputing could be incorporated from the start, and the simulation source code would be accessible for modification and extension. This work addressed Engineering's Simulation Technology Focus Area, specifically photonics. Problems addressed from the Engineering roadmap of the time included modeling the Auston switch (an important THz source/receiver), modeling Vertical Cavity Surface Emitting Lasers (VCSELs, which had been envisioned as part of fast radiation sensors), and multi-scale modeling of optical systems (for a variety of applications). We proposed to develop novel techniques to numerically solve the 3D multi-scale propagation problem for both the microchip
Spectral Element Modeling of 3D Site Effects in the Alpine Valley of Grenoble, France.
NASA Astrophysics Data System (ADS)
Chaljub, E.; Cornou, C.; Gueguen, P.; Causse, M.; Komatitsch, D.
2004-12-01
Sitting on top of a 3D Y-shaped basin filled mostly with late quaternary deposits, the city of Grenoble (French Alps) is subject to strong amplification of seismic motion (see the SISMOVALP web site). In order to assess the magnitude and 3D complexity of these site effects, we propose a spectral element modeling approach previously applied to the prediction of strong ground motion in the Los Angeles sedimentary basin (Komatitstch et al., 2004). The spectral element method naturally accounts for depth variations of the free surface and of internal interfaces, such as the contact between the sediments and the bedrock. It is also well suited to model the propagation of surface waves generated at the basin edges. The 3D spectral element mesh honors the stiff surface topography of the mountains surrounding the city, as well as the bedrock depth obtained from extensive gravimetric measurements. In the basin, we use a generic 1D velocity model derived from geophysical measurements performed in a deep borehole that reached the substratum at 550 m depth in 1999. Results and comparison to data are shown in the time and frequency domain for small-size (Mw=2.5 and Mw=3.5) local events recorded in the past years. Then, a Mw=5.5 strike-slip event is simulated on the eastern border of the basin along the Belledonne fault, and the results are compared to those obtained by the method of Empirical Green Functions. References: http://www-lgit.obs.ujf-grenoble.fr/sismovalp/ Simulations of ground motion in the Los Angeles basin based upon the spectral- element method, Dimitri Komatitsch, Qinya Liu, Jeroen Tromp, Peter Süss, Christiane Stidham and John H. Shaw, Bulletin of the Seismological Society of America, vol. 94, p 187-206 (2004).
3D Spectral Element Method Simulations Of The Seismic Response of Caracas (Venezuela) Basin
NASA Astrophysics Data System (ADS)
Delavaud, E.; Vilotte, J.; Festa, G.; Cupillard, P.
2007-12-01
We present here 3D numerical simulations of the response of the Caracas (Venezuela) valley up to 5 Hz for different scenarios of plane wave excitation based on the regional seismicity. Attention is focused on the effects of the 3D basin geometry and of the adjacent regional topography. The simulations are performed using Spectral Element method (SEM) together with an unstructured hexahedral mesh discretization and perfectly matched layers (PML). These simulations show 3D amplification phenomena associated with complex wave reflexion, diffraction and focalisation patterns linked to the geometry of the basin. Time and frequency analysis reveal some interesting features both in terms of amplification and energy residence in the basin. The low frequency amplification pattern is mainly controlled by the early response of the basin to the incident plane wave while the high frequency amplification patterns result mainly from late arrivals where complex 3D wave diffraction phenomena are dominating and the memory of the initial excitation is lost. Interestingly enough, it is shown that H/V method correctly predict the low frequency amplification pattern when apply to the late part of the recorded seismograms. The complex high frequency amplification pattern is shown to be associated with surface wave generation at, and propagation from, sharp edges of the basin. Importance of 3D phenomena is assessed by comparison with simple 2D simulations. Significant differences in terms of time of residence, energy and amplification levels point out the interest of complete 3D modeling. In conclusions some of the limitations associated with the use of unstructured hexahedral meshes will be adressed. Despite the use of unstructured meshing tool, modeling the geometry of geological basins remain a complex and time consuming task. Possible extensions using more elaborate techniques like non conforming domain decomposition will be also discussed in conclusion.
Simulation domain size requirements for elastic response of 3D polycrystalline materials
NASA Astrophysics Data System (ADS)
Ozturk, Tugce; Stein, Clayton; Pokharel, Reeju; Hefferan, Christopher; Tucker, Harris; Jha, Sushant; John, Reji; Lebensohn, Ricardo A.; Kenesei, Peter; Suter, Robert M.; Rollett, Anthony D.
2016-01-01
A fast Fourier transform (FFT) based spectral algorithm is used to compute the full field mechanical response of polycrystalline microstructures. The field distributions in a specific region are used to determine the sensitivity of the method to the number of surrounding grains through quantification of the divergence of the field values from the largest simulation domain, as successively smaller surrounding volumes are included in the simulation. The analysis considers a mapped 3D structure where the location of interest is taken to be a particular pair of surface grains that enclose a small fatigue crack, and synthetically created statistically representative microstructures to further investigate the effect of anisotropy, loading condition, loading direction, and texture. The synthetic structures are generated via DREAM3D and the measured material is a cyclically loaded, Ni-based, low solvus high refractory (LSHR) superalloy that was characterized via 3D high energy x-ray diffraction microscopy (HEDM). Point-wise comparison of distributions in the grain pairs shows that, in order to obtain a Pearson correlation coefficient larger than 99%, the domain must extend to at least the third nearest neighbor. For an elastic FFT calculation, the stress-strain distributions are not sensitive to the shape of the domain. The main result is that convergence can be specified in terms of the number of grains surrounding a region of interest.
Spectral fusing Gabor domain optical coherence microscopy.
Meemon, Panomsak; Widjaja, Joewono; Rolland, Jannick P
2016-02-01
Gabor domain optical coherence microscopy (GD-OCM) is one of many variations of optical coherence tomography (OCT) techniques that aims for invariant high resolution across a 3D field of view by utilizing the ability to dynamically refocus the imaging optics in the sample arm. GD-OCM acquires multiple cross-sectional images at different focus positions of the objective lens, and then fuses them to obtain an invariant high-resolution 3D image of the sample, which comes with the intrinsic drawback of a longer processing time as compared to conventional Fourier domain OCT. Here, we report on an alternative Gabor fusing algorithm, the spectral-fusion technique, which directly processes each acquired spectrum and combines them prior to the Fourier transformation to obtain a depth profile. The implementation of the spectral-fusion algorithm is presented and its performance is compared to that of the prior GD-OCM spatial-fusion approach. The spectral-fusion approach shows twice the speed of the spatial-fusion approach for a spectrum size of less than 2000 point sampling, which is a commonly used spectrum size in OCT imaging, including GD-OCM. PMID:26907410
Time domain topology optimization of 3D nanophotonic devices
NASA Astrophysics Data System (ADS)
Elesin, Y.; Lazarov, B. S.; Jensen, J. S.; Sigmund, O.
2014-02-01
We present an efficient parallel topology optimization framework for design of large scale 3D nanophotonic devices. The code shows excellent scalability and is demonstrated for optimization of broadband frequency splitter, waveguide intersection, photonic crystal-based waveguide and nanowire-based waveguide. The obtained results are compared to simplified 2D studies and we demonstrate that 3D topology optimization may lead to significant performance improvements.
Registration of 3D spectral OCT volumes combining ICP with a graph-based approach
NASA Astrophysics Data System (ADS)
Niemeijer, Meindert; Lee, Kyungmoo; Garvin, Mona K.; Abràmoff, Michael D.; Sonka, Milan
2012-02-01
The introduction of spectral Optical Coherence Tomography (OCT) scanners has enabled acquisition of high resolution, 3D cross-sectional volumetric images of the retina. 3D-OCT is used to detect and manage eye diseases such as glaucoma and age-related macular degeneration. To follow-up patients over time, image registration is a vital tool to enable more precise, quantitative comparison of disease states. In this work we present a 3D registrationmethod based on a two-step approach. In the first step we register both scans in the XY domain using an Iterative Closest Point (ICP) based algorithm. This algorithm is applied to vessel segmentations obtained from the projection image of each scan. The distance minimized in the ICP algorithm includes measurements of the vessel orientation and vessel width to allow for a more robust match. In the second step, a graph-based method is applied to find the optimal translation along the depth axis of the individual A-scans in the volume to match both scans. The cost image used to construct the graph is based on the mean squared error (MSE) between matching A-scans in both images at different translations. We have applied this method to the registration of Optic Nerve Head (ONH) centered 3D-OCT scans of the same patient. First, 10 3D-OCT scans of 5 eyes with glaucoma imaged in vivo were registered for a qualitative evaluation of the algorithm performance. Then, 17 OCT data set pairs of 17 eyes with known deformation were used for quantitative assessment of the method's robustness.
3D printed miniaturized spectral system for tissue fluorescence lifetime measurements
NASA Astrophysics Data System (ADS)
Zou, Luwei; Mahmoud, Mohamad; Fahs, Mehdi; Liu, Rui; Lo, Joe F.
2016-04-01
Various types of collagens, e.g. type I and III, represent the main load-bearing components in biological tissues. Their composition changes during processes like wound healing and fibrosis. Collagens exhibit autofluorescence when excited by ultra-violet light, distinguishable by their unique fluorescent lifetimes across a range of emission wavelengths. Therefore, we designed a miniaturized spectral-lifetime detection system for collagens as a non-invasive probe for monitoring tissue in wound healing and scarring applications. A sine modulated LED illumination was applied to enable frequency domain (FD) fluorescence lifetime measurements under different wavelengths bands, separated via a series of longpass dichroics at 387nm, 409nm and 435nm. To achieve the minute scale of optomechanics, we employed a stereolithography based 3D printer with <50 μm resolution to create a custom designed optical mount in a hand-held form factor. We examined the characteristics of the 3D printed optical system with finite element modeling to simulate the effect of thermal (LED) and mechanical (handling) strain on the optical system. Using this device, the phase shift and demodulation of collagen types were measured, where the separate spectral bands enhanced the differentiation of their lifetimes.
Multivariate statistical analysis as a tool for the segmentation of 3D spectral data.
Lucas, G; Burdet, P; Cantoni, M; Hébert, C
2013-01-01
Acquisition of three-dimensional (3D) spectral data is nowadays common using many different microanalytical techniques. In order to proceed to the 3D reconstruction, data processing is necessary not only to deal with noisy acquisitions but also to segment the data in term of chemical composition. In this article, we demonstrate the value of multivariate statistical analysis (MSA) methods for this purpose, allowing fast and reliable results. Using scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX) coupled with a focused ion beam (FIB), a stack of spectrum images have been acquired on a sample produced by laser welding of a nickel-titanium wire and a stainless steel wire presenting a complex microstructure. These data have been analyzed using principal component analysis (PCA) and factor rotations. PCA allows to significantly improve the overall quality of the data, but produces abstract components. Here it is shown that rotated components can be used without prior knowledge of the sample to help the interpretation of the data, obtaining quickly qualitative mappings representative of elements or compounds found in the material. Such abundance maps can then be used to plot scatter diagrams and interactively identify the different domains in presence by defining clusters of voxels having similar compositions. Identified voxels are advantageously overlaid on secondary electron (SE) images with higher resolution in order to refine the segmentation. The 3D reconstruction can then be performed using available commercial softwares on the basis of the provided segmentation. To asses the quality of the segmentation, the results have been compared to an EDX quantification performed on the same data. PMID:24035679
Segmented Domain Decomposition Multigrid For 3-D Turbomachinery Flows
NASA Technical Reports Server (NTRS)
Celestina, M. L.; Adamczyk, J. J.; Rubin, S. G.
2001-01-01
A Segmented Domain Decomposition Multigrid (SDDMG) procedure was developed for three-dimensional viscous flow problems as they apply to turbomachinery flows. The procedure divides the computational domain into a coarse mesh comprised of uniformly spaced cells. To resolve smaller length scales such as the viscous layer near a surface, segments of the coarse mesh are subdivided into a finer mesh. This is repeated until adequate resolution of the smallest relevant length scale is obtained. Multigrid is used to communicate information between the different grid levels. To test the procedure, simulation results will be presented for a compressor and turbine cascade. These simulations are intended to show the ability of the present method to generate grid independent solutions. Comparisons with data will also be presented. These comparisons will further demonstrate the usefulness of the present work for they allow an estimate of the accuracy of the flow modeling equations independent of error attributed to numerical discretization.
Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA
NASA Technical Reports Server (NTRS)
Lietzke, Susan E; Barnes, Cindy L.
1998-01-01
3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.
Oxygen spectral line synthesis: 3D non-LTE with CO5BOLD hydrodynamical model atmospheres.
NASA Astrophysics Data System (ADS)
Prakapavičius, D.; Steffen, M.; Kučinskas, A.; Ludwig, H.-G.; Freytag, B.; Caffau, E.; Cayrel, R.
In this work we present first results of our current project aimed at combining the 3D hydrodynamical stellar atmosphere approach with non-LTE (NLTE) spectral line synthesis for a number of key chemical species. We carried out a full 3D-NLTE spectrum synthesis of the oxygen IR 777 nm triplet, using a modified and improved version of our NLTE3D package to calculate departure coefficients for the atomic levels of oxygen in a CO5BOLD 3D hydrodynamical solar model atmosphere. Spectral line synthesis was subsequently performed with the Linfor3D code. In agreement with previous studies, we find that the lines of the oxygen triplet produce deeper cores under NLTE conditions, due to the diminished line source function in the line forming region. This means that the solar oxygen IR 777 nm lines should be stronger in NLTE, leading to negative 3D NLTE-LTE abundance corrections. Qualitatively this result would support previous claims for a relatively low solar oxygen abundance. Finally, we outline several further steps that need to be taken in order to improve the physical realism and numerical accuracy of our current 3D-NLTE calculations.
NASA Astrophysics Data System (ADS)
Molcard, A. J.; Pinardi, N.; Ansaloni, R.
A new numerical model, SEOM (Spectral Element Ocean Model, (Iskandarani et al, 1994)), has been implemented in the Mediterranean Sea. Spectral element methods combine the geometric flexibility of finite element techniques with the rapid convergence rate of spectral schemes. The current version solves the shallow water equations with a fifth (or sixth) order accuracy spectral scheme and about 50.000 nodes. The domain decomposition philosophy makes it possible to exploit the power of parallel machines. The original MIMD master/slave version of SEOM, written in F90 and PVM, has been ported to the Cray T3D. When critical for performance, Cray specific high-performance one-sided communication routines (SHMEM) have been adopted to fully exploit the Cray T3D interprocessor network. Tests performed with highly unstructured and irregular grid, on up to 128 processors, show an almost linear scalability even with unoptimized domain decomposition techniques. Results from various case studies on the Mediterranean Sea are shown, involving realistic coastline geometry, and monthly mean 1000mb winds from the ECMWF's atmospheric model operational analysis from the period January 1987 to December 1994. The simulation results show that variability in the wind forcing considerably affect the circulation dynamics of the Mediterranean Sea.
3D high spectral and spatial resolution imaging of ex vivo mouse brain
Foxley, Sean Karczmar, Gregory S.; Domowicz, Miriam; Schwartz, Nancy
2015-03-15
Purpose: Widely used MRI methods show brain morphology both in vivo and ex vivo at very high resolution. Many of these methods (e.g., T{sub 2}{sup *}-weighted imaging, phase-sensitive imaging, or susceptibility-weighted imaging) are sensitive to local magnetic susceptibility gradients produced by subtle variations in tissue composition. However, the spectral resolution of commonly used methods is limited to maintain reasonable run-time combined with very high spatial resolution. Here, the authors report on data acquisition at increased spectral resolution, with 3-dimensional high spectral and spatial resolution MRI, in order to analyze subtle variations in water proton resonance frequency and lineshape that reflect local anatomy. The resulting information compliments previous studies based on T{sub 2}{sup *} and resonance frequency. Methods: The proton free induction decay was sampled at high resolution and Fourier transformed to produce a high-resolution water spectrum for each image voxel in a 3D volume. Data were acquired using a multigradient echo pulse sequence (i.e., echo-planar spectroscopic imaging) with a spatial resolution of 50 × 50 × 70 μm{sup 3} and spectral resolution of 3.5 Hz. Data were analyzed in the spectral domain, and images were produced from the various Fourier components of the water resonance. This allowed precise measurement of local variations in water resonance frequency and lineshape, at the expense of significantly increased run time (16–24 h). Results: High contrast T{sub 2}{sup *}-weighted images were produced from the peak of the water resonance (peak height image), revealing a high degree of anatomical detail, specifically in the hippocampus and cerebellum. In images produced from Fourier components of the water resonance at −7.0 Hz from the peak, the contrast between deep white matter tracts and the surrounding tissue is the reverse of the contrast in water peak height images. This indicates the presence of a shoulder in
Spectral/Fourier Domain Optical Coherence Tomography
NASA Astrophysics Data System (ADS)
de Boer, Johannes F.
Optical coherence tomography is a low-coherence interferometric method for imaging of biological tissue [1, 2]. For more than a decade after its inception between 1988 and 1991, the dominant implementation has been time domain OCT (TD-OCT), in which the length of a reference arm is rapidly scanned. The first spectral or Fourier domain OCT (SD/FD-OCT) implementation was reported in 1995 [3]. In SD-OCT the reference arm is kept stationary, and the depth information is obtained by a Fourier transform of the spectrally resolved interference fringes in the detection arm of a Michelson interferometer. This approach has provided a significant advantage in signal-to-noise ratio (SNR), which despite reports as early as 1997 [4, 5] has taken about half a decade to be recognized fully by the OCT community in 2003 [6-8]. The first demonstration of SD-OCT for in vivo retinal imaging in 2002 [9] was followed by a full realization of the sensitivity advantage by video rate in vivo retinal imaging [10], including high-speed 3-D volumetric imaging [11], ultrahigh-resolution video rate imaging [12, 13], and Doppler blood flow determination in the human retina [14, 15]. The superior sensitivity of SD-OCT, combined with the lack of need for a fast mechanical scanning mechanism, has opened up the possibility of much faster scanning without loss of image quality and provided a paradigm shift from point sampling to volumetric mapping of biological tissue in vivo. The technology has been particularly promising for ophthalmology [16, 17]. In this chapter, the principles and system design considerations of SD-OCT will be discussed in more detail.
From pixel to voxel: a deeper view of biological tissue by 3D mass spectral imaging
Ye, Hui; Greer, Tyler; Li, Lingjun
2011-01-01
Three dimensional mass spectral imaging (3D MSI) is an exciting field that grants the ability to study a broad mass range of molecular species ranging from small molecules to large proteins by creating lateral and vertical distribution maps of select compounds. Although the general premise behind 3D MSI is simple, factors such as choice of ionization method, sample handling, software considerations and many others must be taken into account for the successful design of a 3D MSI experiment. This review provides a brief overview of ionization methods, sample preparation, software types and technological advancements driving 3D MSI research of a wide range of low- to high-mass analytes. Future perspectives in this field are also provided to conclude that the positive and promises ever-growing applications in the biomedical field with continuous developments of this powerful analytical tool. PMID:21320052
3D parallel computations of turbofan noise propagation using a spectral element method
NASA Astrophysics Data System (ADS)
Taghaddosi, Farzad
2006-12-01
A three-dimensional code has been developed for the simulation of tone noise generated by turbofan engine inlets using computational aeroacoustics. The governing equations are the linearized Euler equations, which are further simplified to a set of equations in terms of acoustic potential, using the irrotational flow assumption, and subsequently solved in the frequency domain. Due to the special nature of acoustic wave propagation, the spatial discretization is performed using a spectral element method, where a tensor product of the nth-degree polynomials based on Chebyshev orthogonal functions is used to approximate variations within hexahedral elements. Non-reflecting boundary conditions are imposed at the far-field using a damping layer concept. This is done by augmenting the continuity equation with an additional term without modifying the governing equations as in PML methods. Solution of the linear system of equations for the acoustic problem is based on the Schur complement method, which is a nonoverlapping domain decomposition technique. The Schur matrix is first solved using a matrix-free iterative method, whose convergence is accelerated with a novel local preconditioner. The solution in the entire domain is then obtained by finding solutions in smaller subdomains. The 3D code also contains a mean flow solver based on the full potential equation in order to take into account the effects of flow variations around the nacelle on the scattering of the radiated sound field. All aspects of numerical simulations, including building and assembling the coefficient matrices, implementation of the Schur complement method, and solution of the system of equations for both the acoustic and mean flow problems are performed on multiprocessors in parallel using the resources of the CLUMEQ Supercomputer Center. A large number of test cases are presented, ranging in size from 100 000-2 000 000 unknowns for which, depending on the size of the problem, between 8-48 CPU's are
Reconstructing photorealistic 3D models from image sequence using domain decomposition method
NASA Astrophysics Data System (ADS)
Xiong, Hanwei; Pan, Ming; Zhang, Xiangwei
2009-11-01
In the fields of industrial design, artistic design and heritage conservation, physical objects are usually digitalized by reverse engineering through some 3D scanning methods. Structured light and photogrammetry are two main methods to acquire 3D information, and both are expensive. Even if these expensive instruments are used, photorealistic 3D models are seldom available. In this paper, a new method to reconstruction photorealistic 3D models using a single camera is proposed. A square plate glued with coded marks is used to place the objects, and a sequence of about 20 images is taken. From the coded marks, the images are calibrated, and a snake algorithm is used to segment object from the background. A rough 3d model is obtained using shape from silhouettes algorithm. The silhouettes are decomposed into a combination of convex curves, which are used to partition the rough 3d model into some convex mesh patches. For each patch, the multi-view photo consistency constraints and smooth regulations are expressed as a finite element formulation, which can be resolved locally, and the information can be exchanged along the patches boundaries. The rough model is deformed into a fine 3d model through such a domain decomposition finite element method. The textures are assigned to each element mesh, and a photorealistic 3D model is got finally. A toy pig is used to verify the algorithm, and the result is exciting.
Vessel segmentation in 3D spectral OCT scans of the retina
NASA Astrophysics Data System (ADS)
Niemeijer, Meindert; Garvin, Mona K.; van Ginneken, Bram; Sonka, Milan; Abràmoff, Michael D.
2008-03-01
The latest generation of spectral optical coherence tomography (OCT) scanners is able to image 3D cross-sectional volumes of the retina at a high resolution and high speed. These scans offer a detailed view of the structure of the retina. Automated segmentation of the vessels in these volumes may lead to more objective diagnosis of retinal vascular disease including hypertensive retinopathy, retinopathy of prematurity. Additionally, vessel segmentation can allow color fundus images to be registered to these 3D volumes, possibly leading to a better understanding of the structure and localization of retinal structures and lesions. In this paper we present a method for automatically segmenting the vessels in a 3D OCT volume. First, the retina is automatically segmented into multiple layers, using simultaneous segmentation of their boundary surfaces in 3D. Next, a 2D projection of the vessels is produced by only using information from certain segmented layers. Finally, a supervised, pixel classification based vessel segmentation approach is applied to the projection image. We compared the influence of two methods for the projection on the performance of the vessel segmentation on 10 optic nerve head centered 3D OCT scans. The method was trained on 5 independent scans. Using ROC analysis, our proposed vessel segmentation system obtains an area under the curve of 0.970 when compared with the segmentation of a human observer.
Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation
Mourad, Raphaël; Cuvier, Olivier
2016-01-01
Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the identification of genomic features that influence domain borders. Using Drosophila Hi-C data at a very high resolution of 1 kb, our model suggests that, among architectural proteins, BEAF-32 and CP190 are the main positive drivers of 3D domain borders. In humans, our model identifies well-known architectural proteins CTCF and cohesin, as well as ZNF143 and Polycomb group proteins as positive drivers of domain borders. The model also reveals the existence of several negative drivers that counteract the presence of domain borders including P300, RXRA, BCL11A and ELK1. PMID:27203237
Tomographic Spectral Imaging with Multivariate Statistical Analysis: Comprehensive 3D Microanalysis.
Kotula, Paul G; Keenan, Michael R; Michael, Joseph R
2006-02-01
A comprehensive three-dimensional (3D) microanalysis procedure using a combined scanning electron microscope (SEM)/focused ion beam (FIB) system equipped with an energy-dispersive X-ray spectrometer (EDS) has been developed. The FIB system was used first to prepare a site-specific region for X-ray microanalysis followed by the acquisition of an electron-beam generated X-ray spectral image. A small section of material was then removed by the FIB, followed by the acquisition of another X-ray spectral image. This serial sectioning procedure was repeated 10-12 times to sample a volume of material. The series of two-spatial-dimension spectral images were then concatenated into a single data set consisting of a series of volume elements or voxels each with an entire X-ray spectrum. This four-dimensional (three real space and one spectral dimension) spectral image was then comprehensively analyzed with Sandia's automated X-ray spectral image analysis software. This technique was applied to a simple Cu-Ag eutectic and a more complicated localized corrosion study where the powerful site-specific comprehensive analysis capability of tomographic spectral imaging (TSI) combined with multivariate statistical analysis is demonstrated. PMID:17481340
Laplace-domain waveform modeling and inversion for the 3D acoustic-elastic coupled media
NASA Astrophysics Data System (ADS)
Shin, Jungkyun; Shin, Changsoo; Calandra, Henri
2016-06-01
Laplace-domain waveform inversion reconstructs long-wavelength subsurface models by using the zero-frequency component of damped seismic signals. Despite the computational advantages of Laplace-domain waveform inversion over conventional frequency-domain waveform inversion, an acoustic assumption and an iterative matrix solver have been used to invert 3D marine datasets to mitigate the intensive computing cost. In this study, we develop a Laplace-domain waveform modeling and inversion algorithm for 3D acoustic-elastic coupled media by using a parallel sparse direct solver library (MUltifrontal Massively Parallel Solver, MUMPS). We precisely simulate a real marine environment by coupling the 3D acoustic and elastic wave equations with the proper boundary condition at the fluid-solid interface. In addition, we can extract the elastic properties of the Earth below the sea bottom from the recorded acoustic pressure datasets. As a matrix solver, the parallel sparse direct solver is used to factorize the non-symmetric impedance matrix in a distributed memory architecture and rapidly solve the wave field for a number of shots by using the lower and upper matrix factors. Using both synthetic datasets and real datasets obtained by a 3D wide azimuth survey, the long-wavelength component of the P-wave and S-wave velocity models is reconstructed and the proposed modeling and inversion algorithm are verified. A cluster of 80 CPU cores is used for this study.
Global regular solutions for the 3D Kawahara equation posed on unbounded domains
NASA Astrophysics Data System (ADS)
Larkin, Nikolai A.; Simões, Márcio Hiran
2016-08-01
An initial boundary value problem for the 3D Kawahara equation posed on a channel-type domain was considered. The existence and uniqueness results for global regular solutions as well as exponential decay of small solutions in the H 2-norm were established.
Global regular solutions for the 3D Zakharov-Kuznetsov equation posed on unbounded domains
NASA Astrophysics Data System (ADS)
Larkin, N. A.
2015-09-01
An initial-boundary value problem for the 3D Zakharov-Kuznetsov equation posed on unbounded domains is considered. Existence and uniqueness of a global regular solution as well as exponential decay of the H2-norm for small initial data are proven.
In Vivo 3D Meibography of the Human Eyelid Using Real Time Imaging Fourier-Domain OCT
Hwang, Ho Sik; Shin, Jun Geun; Lee, Byeong Ha; Eom, Tae Joong; Joo, Choun-Ki
2013-01-01
Recently, we reported obtaining tomograms of meibomian glands from healthy volunteers using commercial anterior segment optical coherence tomography (AS-OCT), which is widely employed in clinics for examination of the anterior segment. However, we could not create 3D images of the meibomian glands, because the commercial OCT does not have a 3D reconstruction function. In this study we report the creation of 3D images of the meibomian glands by reconstructing the tomograms of these glands using high speed Fourier-Domain OCT (FD-OCT) developed in our laboratory. This research was jointly undertaken at the Department of Ophthalmology, Seoul St. Mary's Hospital (Seoul, Korea) and the Advanced Photonics Research Institute of Gwangju Institute of Science and Technology (Gwangju, Korea) with two healthy volunteers and seven patients with meibomian gland dysfunction. A real time imaging FD-OCT system based on a high-speed wavelength swept laser was developed that had a spectral bandwidth of 100 nm at the 1310 nm center wavelength. The axial resolution was 5 µm and the lateral resolution was 13 µm in air. Using this device, the meibomian glands of nine subjects were examined. A series of tomograms from the upper eyelid measuring 5 mm (from left to right, B-scan) × 2 mm (from upper part to lower part, C-scan) were collected. Three-D images of the meibomian glands were then reconstructed using 3D “data visualization, analysis, and modeling software”. Established infrared meibography was also performed for comparison. The 3D images of healthy subjects clearly showed the meibomian glands, which looked similar to bunches of grapes. These results were consistent with previous infrared meibography results. The meibomian glands were parallel to each other, and the saccular acini were clearly visible. Here we report the successful production of 3D images of human meibomian glands by reconstructing tomograms of these glands with high speed FD-OCT. PMID:23805297
Spectral triangulation: a 3D method for locating single-walled carbon nanotubes in vivo.
Lin, Ching-Wei; Bachilo, Sergei M; Vu, Michael; Beckingham, Kathleen M; Bruce Weisman, R
2016-05-21
Nanomaterials with luminescence in the short-wave infrared (SWIR) region are of special interest for biological research and medical diagnostics because of favorable tissue transparency and low autofluorescence backgrounds in that region. Single-walled carbon nanotubes (SWCNTs) show well-known sharp SWIR spectral signatures and therefore have potential for noninvasive detection and imaging of cancer tumours, when linked to selective targeting agents such as antibodies. However, such applications face the challenge of sensitively detecting and localizing the source of SWIR emission from inside tissues. A new method, called spectral triangulation, is presented for three dimensional (3D) localization using sparse optical measurements made at the specimen surface. Structurally unsorted SWCNT samples emitting over a range of wavelengths are excited inside tissue phantoms by an LED matrix. The resulting SWIR emission is sampled at points on the surface by a scanning fibre optic probe leading to an InGaAs spectrometer or a spectrally filtered InGaAs avalanche photodiode detector. Because of water absorption, attenuation of the SWCNT fluorescence in tissues is strongly wavelength-dependent. We therefore gauge the SWCNT-probe distance by analysing differential changes in the measured SWCNT emission spectra. SWCNT fluorescence can be clearly detected through at least 20 mm of tissue phantom, and the 3D locations of embedded SWCNT test samples are found with sub-millimeter accuracy at depths up to 10 mm. Our method can also distinguish and locate two embedded SWCNT sources at distinct positions. PMID:27140495
3D modeling of satellite spectral images, radiation budget and energy budget of urban landscapes
NASA Astrophysics Data System (ADS)
Gastellu-Etchegorry, J. P.
2008-12-01
DART EB is a model that is being developed for simulating the 3D (3 dimensional) energy budget of urban and natural scenes, possibly with topography and atmosphere. It simulates all non radiative energy mechanisms (heat conduction, turbulent momentum and heat fluxes, water reservoir evolution, etc.). It uses DART model (Discrete Anisotropic Radiative Transfer) for simulating radiative mechanisms: 3D radiative budget of 3D scenes and their remote sensing images expressed in terms of reflectance or brightness temperature values, for any atmosphere, wavelength, sun/view direction, altitude and spatial resolution. It uses an innovative multispectral approach (ray tracing, exact kernel, discrete ordinate techniques) over the whole optical domain. This paper presents two major and recent improvements of DART for adapting it to urban canopies. (1) Simulation of the geometry and optical characteristics of urban elements (houses, etc.). (2) Modeling of thermal infrared emission by vegetation and urban elements. The new DART version was used in the context of the CAPITOUL project. For that, districts of the Toulouse urban data base (Autocad format) were translated into DART scenes. This allowed us to simulate visible, near infrared and thermal infrared satellite images of Toulouse districts. Moreover, the 3D radiation budget was used by DARTEB for simulating the time evolution of a number of geophysical quantities of various surface elements (roads, walls, roofs). Results were successfully compared with ground measurements of the CAPITOUL project.
3D topology and arrangement of proteins inside ceramide-rich domains
NASA Astrophysics Data System (ADS)
Imhäuser, Christian; Gulbins, Heike; Gulbins, Erich; Lipinski, Hans-Gerd
2010-04-01
Clustering of receptor and signalling molecules (such as CD95 or CD40) within ceramide-enriched membrane domains results in a very high density of these proteins facilitating activation of associated enzymes, the exclusion of inhibitory molecules and/or the recruitment of further signalling molecules to transmit the signal into the cells. However, at present the mechanisms of receptor clustering and the exact distribution of proteins within the ceramide-enriched domains are unknown. Therefore, we generated digital images from anti-CD95 stimulated JYcells that were stained with FITC-coupled anti-ceramide and Cy3-labelled anti-CD95 antibodies. We developed image processing methods to determine the spatial distribution of proteins in ceramide-enriched membrane domains and visualized them by volume rendering and surface models. After image preprocessing with appropriate filters for contrast enhancement, noise reduction and logarithmic scaling, 3D models were generated using adapted volume and surface reconstruction. To detect the colocalization of CD95 and ceramide molecules we developed several different methods rasterizing 3D data of each channel into cells and counting intensity values above a specified colour threshold value. The colocalization voxel was set either by normalized product of totals (product intensity) or depending on binarization. In addition, a cross-covariance function to quantify the colocalization was determined and embedded as a 3D object. These computerized techniques allowed for a quantitative analysis of the spatial arrangement of proteins in ceramide-rich domains of living cells.
3D versus 2D domain wall interaction in ideal and rough nanowires
NASA Astrophysics Data System (ADS)
Pivano, A.; Dolocan, Voicu O.
2015-11-01
The interaction between transverse magnetic domain walls (TDWs) in planar (2D) and cylindrical (3D) nanowires is examined using micromagnetic simulations. We show that in perfect and surface deformed wires the free TDWs behave differently, as the 3D TDWs combine into metastable states with average lifetimes of 300 ns depending on roughness, while the 2D TDWs do not due to 2D shape anisotropy. When the 2D and 3D TDWs are pinned at artificial constrictions, they behave similarly as they interact mainly through the dipolar field. This magnetostatic interaction is well described by the point charge model with multipole expansion. In surface deformed wires with artificial constrictions, the interaction becomes more complex as the depinning field decreases and dynamical pinning can lead to local resonances. This can strongly influence the control of TDWs in DW-based devices.
3D time-domain airborne EM modeling for an arbitrarily anisotropic earth
NASA Astrophysics Data System (ADS)
Yin, Changchun; Qi, Yanfu; Liu, Yunhe
2016-08-01
Time-domain airborne EM data is currently interpreted based on an isotropic model. Sometimes, it can be problematic when working in the region with distinct dipping stratifications. In this paper, we simulate the 3D time-domain airborne EM responses over an arbitrarily anisotropic earth with topography by edge-based finite-element method. Tetrahedral meshes are used to describe the abnormal bodies with complicated shapes. We further adopt the Backward Euler scheme to discretize the time-domain diffusion equation for electric field, obtaining an unconditionally stable linear equations system. We verify the accuracy of our 3D algorithm by comparing with 1D solutions for an anisotropic half-space. Then, we switch attentions to effects of anisotropic media on the strengths and the diffusion patterns of time-domain airborne EM responses. For numerical experiments, we adopt three typical anisotropic models: 1) an anisotropic anomalous body embedded in an isotropic half-space; 2) an isotropic anomalous body embedded in an anisotropic half-space; 3) an anisotropic half-space with topography. The modeling results show that the electric anisotropy of the subsurface media has big effects on both the strengths and the distribution patterns of time-domain airborne EM responses; this effect needs to be taken into account when interpreting ATEM data in areas with distinct anisotropy.
SOFIA: a flexible source finder for 3D spectral line data
NASA Astrophysics Data System (ADS)
Serra, Paolo; Westmeier, Tobias; Giese, Nadine; Jurek, Russell; Flöer, Lars; Popping, Attila; Winkel, Benjamin; van der Hulst, Thijs; Meyer, Martin; Koribalski, Bärbel S.; Staveley-Smith, Lister; Courtois, Hélène
2015-04-01
We introduce SOFIA, a flexible software application for the detection and parametrization of sources in 3D spectral line data sets. SOFIA combines for the first time in a single piece of software a set of new source-finding and parametrization algorithms developed on the way to future H I surveys with ASKAP (WALLABY, DINGO) and APERTIF. It is designed to enable the general use of these new algorithms by the community on a broad range of data sets. The key advantages of SOFIA are the ability to: search for line emission on multiple scales to detect 3D sources in a complete and reliable way, taking into account noise level variations and the presence of artefacts in a data cube; estimate the reliability of individual detections; look for signal in arbitrarily large data cubes using a catalogue of 3D coordinates as a prior; provide a wide range of source parameters and output products which facilitate further analysis by the user. We highlight the modularity of SOFIA, which makes it a flexible package allowing users to select and apply only the algorithms useful for their data and science questions. This modularity makes it also possible to easily expand SOFIA in order to include additional methods as they become available. The full SOFIA distribution, including a dedicated graphical user interface, is publicly available for download.
Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model
NASA Astrophysics Data System (ADS)
Qin, W.; Yang, L.
2004-05-01
Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study
Recasting the 3D Wigner-Liouville equation with spectral components of the force
NASA Astrophysics Data System (ADS)
van de Put, Maarten; Sorée, Bart; Magnus, Wim
The phasespace approach to many-body quantum mechanics, by means of the Wigner-function is interesting through its connection to classical mechanics. Time-evolution of any statistical distribution of states under influence of a (time-dependent) Hamiltonian is obtained through use of the Wigner-Liouville equation. The standard form of this equation contains two 3D integrals, over the entire phase space. As a result, this form emphasizes the non-locality of the interaction of the potential, but lacks simplicity and ease of understanding. Furthermore, the integrals make numerical solution of the Wigner-Liouville equation challenging. We present an alternative form to the Wigner-Liouville equation based on the force rather than the potential, in alignment with the classical Boltzmann equation. Decomposition of the force in its spectral components yields a simpler form of the Wigner-Liouville equation. This new form has only one 3D integral over the spectral force components, and is local in position, simplifying both interpretation and numerical implementation. Because of its use of the force, it straightforwardly reduces to the Boltzmann equation under classical conditions.
Spectral triangulation: a 3D method for locating single-walled carbon nanotubes in vivo
NASA Astrophysics Data System (ADS)
Lin, Ching-Wei; Bachilo, Sergei M.; Vu, Michael; Beckingham, Kathleen M.; Bruce Weisman, R.
2016-05-01
Nanomaterials with luminescence in the short-wave infrared (SWIR) region are of special interest for biological research and medical diagnostics because of favorable tissue transparency and low autofluorescence backgrounds in that region. Single-walled carbon nanotubes (SWCNTs) show well-known sharp SWIR spectral signatures and therefore have potential for noninvasive detection and imaging of cancer tumours, when linked to selective targeting agents such as antibodies. However, such applications face the challenge of sensitively detecting and localizing the source of SWIR emission from inside tissues. A new method, called spectral triangulation, is presented for three dimensional (3D) localization using sparse optical measurements made at the specimen surface. Structurally unsorted SWCNT samples emitting over a range of wavelengths are excited inside tissue phantoms by an LED matrix. The resulting SWIR emission is sampled at points on the surface by a scanning fibre optic probe leading to an InGaAs spectrometer or a spectrally filtered InGaAs avalanche photodiode detector. Because of water absorption, attenuation of the SWCNT fluorescence in tissues is strongly wavelength-dependent. We therefore gauge the SWCNT-probe distance by analysing differential changes in the measured SWCNT emission spectra. SWCNT fluorescence can be clearly detected through at least 20 mm of tissue phantom, and the 3D locations of embedded SWCNT test samples are found with sub-millimeter accuracy at depths up to 10 mm. Our method can also distinguish and locate two embedded SWCNT sources at distinct positions.Nanomaterials with luminescence in the short-wave infrared (SWIR) region are of special interest for biological research and medical diagnostics because of favorable tissue transparency and low autofluorescence backgrounds in that region. Single-walled carbon nanotubes (SWCNTs) show well-known sharp SWIR spectral signatures and therefore have potential for noninvasive detection and
Early detection of skin cancer via terahertz spectral profiling and 3D imaging.
Rahman, Anis; Rahman, Aunik K; Rao, Babar
2016-08-15
Terahertz scanning reflectometry, terahertz 3D imaging and terahertz time-domain spectroscopy have been used to identify features in human skin biopsy samples diagnosed for basal cell carcinoma (BCC) and compared with healthy skin samples. It was found from the 3D images that the healthy skin samples exhibit regular cellular pattern while the BCC skin samples indicate lack of regular cell pattern. The skin is a highly layered structure organ; this is evident from the thickness profile via a scan through the thickness of the healthy skin samples, where, the reflected intensity of the terahertz beam exhibits fluctuations originating from different skin layers. Compared to the healthy skin samples, the BCC samples' profiles exhibit significantly diminished layer definition; thus indicating a lack of cellular order. In addition, terahertz time-domain spectroscopy reveals significant and quantifiable differences between the healthy and BCC skin samples. Thus, a combination of three different terahertz techniques constitutes a conclusive route for detecting the BCC condition on a cellular level compared to the healthy skin. PMID:27040943
3D frequency-domain finite-difference modeling of acoustic wave propagation
NASA Astrophysics Data System (ADS)
Operto, S.; Virieux, J.
2006-12-01
We present a 3D frequency-domain finite-difference method for acoustic wave propagation modeling. This method is developed as a tool to perform 3D frequency-domain full-waveform inversion of wide-angle seismic data. For wide-angle data, frequency-domain full-waveform inversion can be applied only to few discrete frequencies to develop reliable velocity model. Frequency-domain finite-difference (FD) modeling of wave propagation requires resolution of a huge sparse system of linear equations. If this system can be solved with a direct method, solutions for multiple sources can be computed efficiently once the underlying matrix has been factorized. The drawback of the direct method is the memory requirement resulting from the fill-in of the matrix during factorization. We assess in this study whether representative problems can be addressed in 3D geometry with such approach. We start from the velocity-stress formulation of the 3D acoustic wave equation. The spatial derivatives are discretized with second-order accurate staggered-grid stencil on different coordinate systems such that the axis span over as many directions as possible. Once the discrete equations were developed on each coordinate system, the particle velocity fields are eliminated from the first-order hyperbolic system (following the so-called parsimonious staggered-grid method) leading to second-order elliptic wave equations in pressure. The second-order wave equations discretized on each coordinate system are combined linearly to mitigate the numerical anisotropy. Secondly, grid dispersion is minimized by replacing the mass term at the collocation point by its weighted averaging over all the grid points of the stencil. Use of second-order accurate staggered- grid stencil allows to reduce the bandwidth of the matrix to be factorized. The final stencil incorporates 27 points. Absorbing conditions are PML. The system is solved using the parallel direct solver MUMPS developed for distributed
3D homogeneity study in PMMA layers using a Fourier domain OCT system
NASA Astrophysics Data System (ADS)
Briones-R., Manuel de J.; Torre-Ibarra, Manuel H. De La; Tavera, Cesar G.; Luna H., Juan M.; Mendoza-Santoyo, Fernando
2016-11-01
Micro-metallic particles embedded in polymers are now widely used in several industrial applications in order to modify the mechanical properties of the bulk. A uniform distribution of these particles inside the polymers is highly desired for instance, when a biological backscattering is simulated or a bio-framework is designed. A 3D Fourier domain optical coherence tomography system to detect the polymer's internal homogeneity is proposed. This optical system has a 2D camera sensor array that records a fringe pattern used to reconstruct with a single shot the tomographic image of the sample. The system gathers the full 3D tomographic and optical phase information during a controlled deformation by means of a motion linear stage. This stage avoids the use of expensive tilting stages, which in addition are commonly controlled by piezo drivers. As proof of principle, a series of different deformations were proposed to detect the uniform or non-uniform internal deposition of copper micro particles. The results are presented as images coming from the 3D tomographic micro reconstruction of the samples, and the 3D optical phase information that identifies the in-homogeneity regions within the Poly methyl methacrylate (PMMA) volume.
NASA Astrophysics Data System (ADS)
Galvez, P.; Ampuero, J.-P.; Dalguer, L. A.; Somala, S. N.; Nissen-Meyer, T.
2014-08-01
An important goal of computational seismology is to simulate dynamic earthquake rupture and strong ground motion in realistic models that include crustal heterogeneities and complex fault geometries. To accomplish this, we incorporate dynamic rupture modelling capabilities in a spectral element solver on unstructured meshes, the 3-D open source code SPECFEM3D, and employ state-of-the-art software for the generation of unstructured meshes of hexahedral elements. These tools provide high flexibility in representing fault systems with complex geometries, including faults with branches and non-planar faults. The domain size is extended with progressive mesh coarsening to maintain an accurate resolution of the static field. Our implementation of dynamic rupture does not affect the parallel scalability of the code. We verify our implementation by comparing our results to those of two finite element codes on benchmark problems including branched faults. Finally, we present a preliminary dynamic rupture model of the 2011 Mw 9.0 Tohoku earthquake including a non-planar plate interface with heterogeneous frictional properties and initial stresses. Our simulation reproduces qualitatively the depth-dependent frequency content of the source and the large slip close to the trench observed for this earthquake.
3D optical phase reconstruction within PMMA samples using a spectral OCT system
NASA Astrophysics Data System (ADS)
Briones-R., Manuel d. J.; De La Torre-Ibarra, Manuel H.; Mendoza Santoyo, Fernando
2015-08-01
The optical coherence tomography (OCT) technique has proved to be a useful method in biomedical areas such as ophthalmology, dentistry, dermatology, among many others. In all these applications the main target is to reconstruct the internal structure of the samples from which the physician's expertise may recognize and diagnose the existence of a disease. Nowadays OCT has been applied one step further and is used to study the mechanics of some particular type of materials, where the resulting information involves more than just their internal structure and the measurement of parameters such as displacements, stress and strain. Here we report on a spectral OCT system used to image the internal 3D microstructure and displacement maps from a PMMA (Poly-methyl-methacrylate) sample, subjected to a deformation by a controlled three point bending and tilting. The internal mechanical response of the polymer is shown as consecutive 2D images.
3D Multi-spectral Image-guided Near-infrared Spectroscopy using Boundary Element Method
Srinivasan, Subhadra; Pogue, Brian W.; Paulsen, Keith D.
2010-01-01
Image guided (IG) Near-Infrared spectroscopy (NIRS) has the ability to provide high-resolution metabolic and vascular characterization of tissue, with clinical applications in diagnosis of breast cancer. This method is specific to multimodality imaging where tissue boundaries obtained from alternate modalities such as MRI/CT, are used for NIRS recovery. IG-NIRS is severely limited in 3D by challenges such as volumetric meshing of arbitrary anatomical shapes and computational burden encountered by existing models which use finite element method (FEM). We present an efficient and feasible alternative to FEM using boundary element method (BEM). The main advantage is the use of surface discretization which is reliable and more easily generated than volume grids in 3D and enables automation for large number of clinical data-sets. The BEM has been implemented for the diffusion equation to model light propagation in tissue. Image reconstruction based on BEM has been tested in a multi-threading environment using four processors which provides 60% improvement in computational time compared to a single processor. Spectral priors have been implemented in this framework and applied to a three-region problem with mean error of 6% in recovery of NIRS parameters. PMID:21179380
Large-scale 3D inversion of frequency domain controlled-source electromagnetic data
NASA Astrophysics Data System (ADS)
Miller, C. R.; Routh, P. S.; Donaldson, P.; Oldenburg, D. W.
2005-05-01
Controlled Source Audio-Frequency Magnetotellurics (CSAMT) is a frequency domain EM sounding technique. The CSAMT source is a grounded horizontal electric dipole approximately one to two kilometers in length. This dipole source generates both inductive and galvanic currents so that the observed electric field arises due to both the static the vector potentials. At low frequencies, the behavior of the fields is similar to that observed in a geometric sounding such as a direct current experiment. At higher frequencies, the inductive character of the source modifies the behavior of the fields so that the experiment becomes more like a frequency sounding. Higher frequency data are useful for imaging near-surface features and lower frequency data are sensitive to deeper structure. Inversion of controlled source EM data provides a means to image the subsurface electrical conductivity structure. We consider a 3D CSAMT data set acquired over a known geothermal resource area in Western Idaho. The data are amplitudes and phases of the electric and magnetic fields acquired at 25 frequencies. The conductivity contrast between the geothermal fluid conduits and the resistive host material allows us to relate the inverted conductivity image to the distribution of fluid flow pathways in the geothermal system. Our 1D CSAMT inversion of the 3D data set indicates regions of conductive fluid pathways in the subsurface. Our next step is to invert these data using the full Maxwell's equations in 3D. Inversion of a single frequency data set at 2 Hz using the 3D frequency domain inversion algorithm (Haber et. al, 2004) shows regions of fluid circulation indicated by zones of higher conductivity. Comparing the images from different single frequency inversions allows us to identify persistent features in the conductivity image that adequately satisfy the data. With the aid of synthetic modeling we are investigating what frequencies? and what geometries? are appropriate to better resolve
3D Laplace-domain full waveform inversion using a single GPU card
NASA Astrophysics Data System (ADS)
Shin, Jungkyun; Ha, Wansoo; Jun, Hyunggu; Min, Dong-Joo; Shin, Changsoo
2014-06-01
The Laplace-domain full waveform inversion is an efficient long-wavelength velocity estimation method for seismic datasets lacking low-frequency components. However, to invert a 3D velocity model, a large cluster of CPU cores have commonly been required to overcome the extremely long computing time caused by a large impedance matrix and a number of source positions. In this study, a workstation with a single GPU card (NVIDIA GTX 580) is successfully used for the 3D Laplace-domain full waveform inversion rather than a large cluster of CPU cores. To exploit a GPU for our inversion algorithm, the routine for the iterative matrix solver is ported to the CUDA programming language for forward and backward modeling parts with minimized modification of the remaining parts, which were originally written in Fortran 90. Using a uniformly structured grid set, nonzero values in the sparse impedance matrix can be arranged according to certain rules, which efficiently parallelize the preconditioned conjugate gradient method for a number of threads contained in the GPU card. We perform a numerical experiment to verify the accuracy of a floating point operation performed by a GPU to calculate the Laplace-domain wavefield. We also measure the efficiencies of the original CPU and modified GPU programs using a cluster of CPU cores and a workstation with a GPU card, respectively. Through the analysis, the parallelized inversion code for a GPU achieves the speedup of 14.7-24.6x compared to a CPU-based serial code depending on the degrees of freedom of the impedance matrix. Finally, the practicality of the proposed algorithm is examined by inverting a 3D long-wavelength velocity model using wide azimuth real datasets in 3.7 days.
3D domain swapping in a chimeric c-Src SH3 domain takes place through two hinge loops.
Cámara-Artigas, Ana; Martínez-Rodríguez, Sergio; Ortiz-Salmerón, Emilia; Martín-García, José M
2014-04-01
In the Src Homology 3 domain (SH3) the RT and n-Src loops form a pocket that accounts for the specificity and affinity in binding of proline rich motifs (PRMs), while the distal and diverging turns play a key role in the folding of the protein. We have solved the structure of a chimeric mutant c-Src-SH3 domain where specific residues at the RT- and n-Src-loops have been replaced by those present in the corresponding Abl-SH3 domain. Crystals of the chimeric protein show a single molecule in the asymmetric unit, which appears in an unfolded-like structure that upon generation of the symmetry related molecules reveals the presence of a domain swapped dimer where both, RT- and n-Src loops, act as hinge loops. In contrast, the fold of the diverging type II β-turn and the distal loop are well conserved. Our results are the first evidence for the presence of a structured diverging type II β-turn in an unfolded-like intermediate of the c-Src-SH3 domain, which can be stabilized by interactions from the β-strands of the same polypeptide chain or from a neighboring one. Futhermore, this crystallographic structure opens a unique opportunity to study the effect of the amino acid sequence of the hinge loops on the 3D domain swapping process of c-Src-SH3. PMID:24556574
NASA Astrophysics Data System (ADS)
Chen, R.; Zhao, X.; Yao, H.; He, X.; Zeng, P.; Chang, F.; Yang, Y.; Zhang, X.; Xi, X.; He, L.
2015-12-01
Induced polarization (IP) is a powerful tool in metalliferous ore exploration. However, there are many sources, such as clay and graphite, which can generate IP anomaly. Spectral induced polarization (SIP) measures IP response on a wide frequency range. This method provides a way to discriminate IP response generated by metalliferous ore or other objects. The best way to explore metalliferous ore is 3D SIP exploration. However, if we consider the exploration cost and efficiency, we can use SIP profiling to find an anomaly, and then use 2D/3D SIP sounding to characterize the anomaly. Based on above idea, we used a large-scale distributed SIP measurement system which can realize 800 sounding sites in one direction at the same time. This system can be used for SIP profiling, 2D/3D SIP sounding with high efficiency, high resolution, and large depth of investigation (> 1000 m). Qiushuwan copper - molybdenum deposit is located in Nanyang city, Henan province, China. It is only a middle-size deposit although over 100 holes were drilled and over 40 years of exploration were spent because of very complex geological setting. We made SIP measurement over 100 rock and ore samples to discriminate IP responses of ore and rock containing graphite. Then we carried out 7 lines of 2D SIP exploration with the depth of investigation great than 1000 m. The minimum electode spacing for potential difference is only 20 m. And we increase the spacing of current electodes at linear scale. This acquisition setting ensures high density data acquired and high quality data acquisition. Modeling and inversion result proves that we can get underground information with high resolution by our method. Our result shows that there exists a strong SIP response related to ore body in depth > 300 m. Pseudo-3D inversion of five 2D SIP sounding lines shows the location and size of IP anomaly. The new drillings based our result found a big copper-molybdenum ore body in new position with depth > 300 m and
3D simulation of seismic wave propagation around a tunnel using the spectral element method
NASA Astrophysics Data System (ADS)
Lambrecht, L.; Friederich, W.
2010-05-01
We model seismic wave propagation in the environment of a tunnel for later application to reconnaissance. Elastic wave propagation can be simulated by different numerical techniques such as finite differences and pseudospectral methods. Their disadvantage is the lack of accuracy on free surfaces, numerical dispersion and inflexibility of the mesh. Here we use the software package SPECFEM3D_SESAME in an svn development version, which is based on the spectral element method (SEM) and can handle complex mesh geometries. A weak form of the elastic wave equation leads to a linear system of equations with a diagonal mass matrix, where the free surface boundary of the tunnel can be treated under realistic conditions and can be effectively implemented in parallel. We have designed a 3D external mesh including a tunnel and realistic features such as layers and holes to simulate elastic wave propagation in the zone around the tunnel. The source is acting at the tunnel surface so that we excite Rayleigh waves which propagate to the front face of the tunnel. A conversion takes place and a high amplitude S-wave is radiated in the direction of the tunnel axis. Reflections from perturbations in front of the tunnel can be measured by receivers implemented on the tunnel face. For a shallow tunnel the land surface has high influence on the wave propagation. By implementing additional receivers at this surface we intent to improve the prediction. It shows that the SEM is very capable to handle the complex geometry of the model and especially incorporates the free surfaces of the model.
Morgan, F. Dale; Sogade, John
2004-12-14
This project was designed as a broad foundational study of spectral induced polarization (SIP) for characterization of contaminated sites. It encompassed laboratory studies of the effects of chemistry on induced polarization, development of 3D forward modeling and inversion codes, and investigations of inductive and capacitive coupling problems. In the laboratory part of the project a physico-chemical model developed in this project was used to invert laboratory IP spectra for the grain size and the effective grain size distribution of the sedimentary rocks as well as the formation factor, porosity, specific surface area, and the apparent fractal dimension. Furthermore, it was established that the IP response changed with the solution chemistry, the concentration of a given solution chemistry, valence of the constituent ions, and ionic radius. In the field part of the project, a 3D complex forward and inverse model was developed. It was used to process data acquired at two frequencies (1/16 Hz and 1/ 4Hz) in a cross-borehole configuration at the A-14 outfall area of the Savannah River Site (SRS) during March 2003 and June 2004. The chosen SRS site was contaminated with Tetrachloroethylene (TCE) and Trichloroethylene (PCE) that were disposed in this area for several decades till the 1980s. The imaginary conductivity produced from the inverted 2003 data correlated very well with the log10 (PCE) concentration derived from point sampling at 1 ft spacing in five ground-truth boreholes drilled after the data acquisition. The equivalent result for the 2004 data revealed that there were significant contaminant movements during the period March 2003 and June 2004, probably related to ground-truth activities and nearby remediation activities. Therefore SIP was successfully used to develop conceptual models of volume distributions of PCE/TCE contamination. In addition, the project developed non-polarizing electrodes that can be deployed in boreholes for years. A total of 28
3D seismic data reconstruction based on complex-valued curvelet transform in frequency domain
NASA Astrophysics Data System (ADS)
Zhang, Hua; Chen, Xiaohong; Li, Hongxing
2015-02-01
Traditional seismic data sampling must follow the Nyquist Sampling Theorem. However, the field data acquisition may not meet the sampling criteria due to missing traces or limits in exploration cost, causing a prestack data reconstruction problem. Recently researchers have proposed many useful methods to regularize the seismic data. In this paper, a 3D seismic data reconstruction method based on the Projections Onto Convex Sets (POCS) algorithm and a complex-valued curvelet transform (CCT) has been introduced in the frequency domain. In order to improve reconstruction efficiency and reduce the computation time, the seismic data are transformed from the t-x-y domain to the f-x-y domain and the data reconstruction is processed for every frequency slice during the reconstruction process. The selection threshold parameter is important for reconstruction efficiency for each iteration, therefore an exponential square root decreased (ESRD) threshold is proposed. The experimental results show that the ESRD threshold can greatly reduce iterations and improve reconstruction efficiency compared to the other thresholds for the same reconstruction result. We also analyze the antinoise ability of the CCT-based POCS reconstruction method. The example studies on synthetic and real marine seismic data showed that our proposed method is more efficient and applicable.
Robust and Blind 3D Mesh Watermarking in Spatial Domain Based on Faces Categorization and Sorting
NASA Astrophysics Data System (ADS)
Molaei, Amir Masoud; Ebrahimnezhad, Hossein; Sedaaghi, Mohammad Hossein
2016-06-01
In this paper, a 3D watermarking algorithm in spatial domain is presented with blind detection. In the proposed method, a negligible visual distortion is observed in host model. Initially, a preprocessing is applied on the 3D model to make it robust against geometric transformation attacks. Then, a number of triangle faces are determined as mark triangles using a novel systematic approach in which faces are categorized and sorted robustly. In order to enhance the capability of information retrieval by attacks, block watermarks are encoded using Reed-Solomon block error-correcting code before embedding into the mark triangles. Next, the encoded watermarks are embedded in spherical coordinates. The proposed method is robust against additive noise, mesh smoothing and quantization attacks. Also, it is stout next to geometric transformation, vertices and faces reordering attacks. Moreover, the proposed algorithm is designed so that it is robust against the cropping attack. Simulation results confirm that the watermarked models confront very low distortion if the control parameters are selected properly. Comparison with other methods demonstrates that the proposed method has good performance against the mesh smoothing attacks.
Domain Decomposition PN Solutions to the 3D Transport Benchmark over a Range in Parameter Space
NASA Astrophysics Data System (ADS)
Van Criekingen, S.
2014-06-01
The objectives of this contribution are twofold. First, the Domain Decomposition (DD) method used in the parafish parallel transport solver is re-interpreted as a Generalized Schwarz Splitting as defined by Tang [SIAM J Sci Stat Comput, vol.13 (2), pp. 573-595, 1992]. Second, parafish provides spherical harmonic (i.e., PN) solutions to the NEA benchmark suite for 3D transport methods and codes over a range in parameter space. To the best of the author's knowledge, these are the first spherical harmonic solutions provided for this demanding benchmark suite. They have been obtained using 512 CPU cores of the JuRoPa machine installed at the Jülich Computing Center (Germany).
An Automatic 3D Mesh Generation Method for Domains with Multiple Materials.
Zhang, Yongjie; Hughes, Thomas J R; Bajaj, Chandrajit L
2010-01-01
This paper describes an automatic and efficient approach to construct unstructured tetrahedral and hexahedral meshes for a composite domain made up of heterogeneous materials. The boundaries of these material regions form non-manifold surfaces. In earlier papers, we developed an octree-based isocontouring method to construct unstructured 3D meshes for a single-material (homogeneous) domain with manifold boundary. In this paper, we introduce the notion of a material change edge and use it to identify the interface between two or several different materials. A novel method to calculate the minimizer point for a cell shared by more than two materials is provided, which forms a non-manifold node on the boundary. We then mesh all the material regions simultaneously and automatically while conforming to their boundaries directly from volumetric data. Both material change edges and interior edges are analyzed to construct tetrahedral meshes, and interior grid points are analyzed for proper hexahedral mesh construction. Finally, edge-contraction and smoothing methods are used to improve the quality of tetrahedral meshes, and a combination of pillowing, geometric flow and optimization techniques is used for hexahedral mesh quality improvement. The shrink set of pillowing schemes is defined automatically as the boundary of each material region. Several application results of our multi-material mesh generation method are also provided. PMID:20161555
FDFD: A 3D Finite-Difference Frequency-Domain Code for Electromagnetic Induction Tomography
NASA Astrophysics Data System (ADS)
Champagne, Nathan J.; Berryman, James G.; Buettner, H. Michael
2001-07-01
A new 3D code for electromagnetic induction tomography with intended applications to environmental imaging problems has been developed. The approach consists of calculating the fields within a volume using an implicit finite-difference frequency-domain formulation. The volume is terminated by an anisotropic perfectly matched layer region that simulates an infinite domain by absorbing outgoing waves. Extensive validation of this code has been done using analytical and semianalytical results from other codes, and some of those results are presented in this paper. The new code is written in Fortran 90 and is designed to be easily parallelized. Finally, an adjoint field method of data inversion, developed in parallel for solving the fully nonlinear inverse problem for electrical conductivity imaging (e.g., for mapping underground conducting plumes), uses this code to provide solvers for both forward and adjoint fields. Results obtained from this inversion method for high-contrast media are encouraging and provide a significant improvement over those obtained from linearized inversion methods.
Validating 3D Seismic Velocity Models Using the Spectral Element Method
NASA Astrophysics Data System (ADS)
Maceira, M.; Rowe, C. A.; Allen, R. M.; Obrebski, M. J.
2010-12-01
As seismic instrumentation, data storage and dissemination and computational power improve, seismic velocity models attempt to resolve smaller structures and cover larger areas. However, it is unclear how accurate these velocity models are and, while the best models available are used for event determination, it is difficult to put uncertainties on seismic event parameters. Model validation is typically done using resolution tests that assume the imaging theory used is accurate and thus only considers the impact of the data coverage on resolution. We present the results of a more rigorous approach to model validation via full three-dimensional waveform propagation using Spectral Element Methods (SEM). This approach makes no assumptions about the theory used to generate the models but require substantial computational resources. We first validate 3D tomographic models for the Western USA generated using both ray-theoretical and finite-frequency methods. The Dynamic North America (DNA) Models of P- and S- velocity structure (DNA09-P and DNA09-S) use teleseismic body-wave traveltime residuals recorded at over 800 seismic stations provided by the Earthscope USArray and regional seismic networks. We performed systematic computations of synthetics for the dataset used to generate the DNA models. Direct comparison of these synthetic seismograms to the actual observations allows us to accurately assess and validate the models. Implementation of the method for a densely instrumented region such as that covered by the DNA model provides a useful testbed for the validation methods that we will subsequently apply to other, more challenging study areas.
3D micro profile measurement with the method of spatial frequency domain analysis
NASA Astrophysics Data System (ADS)
Xu, Yongxiang
2015-10-01
3D micro profiles are often needed for measurement in many fields, e.g., binary optics, electronic industry, mechanical manufacturing, aeronautic and space industry, etc. In the case where height difference between two neighboring points of a test profile is equal to or greater than λ / 4, microscopic interferometry based on laser source will no longer be applicable because of the uncertainty in phase unwrapping. As white light possesses the characteristic of interference length approximate to zero, applying it for micro profilometry can avoid the trouble and can yield accurate results. Using self-developed Mirau-type scanning interference microscope, a step-like sample was tested twice, with 128 scanning interferograms recorded for each test. To process each set of the interferograms, the method of spatial frequency domain analysis was adopted. That is, for each point, by use of Furrier transform, white-light interference intensities were decomposed in spatial frequency domain, thus obtaining phase values corresponding to different wavenumbers; by using least square fitting on phases and wave numbers, a group-velocity OPD was gained for the very point; and finally in terms of the relation between relative height and the group-velocity OPD, the profile of the test sample was obtained. Two tests yielded same profile result for the sample, and step heights obtained were 50.88 nm and 50.94 nm, respectively. Meantime, the sample was also measured with a Zygo Newview 7200 topography instrument, with same profile result obtained and step height differing by 0.9 nm. In addition, data processing results indicate that chromatic dispersion equal to and higher than 2nd order is negligible when applying spatial frequency domain analysis method.
Signatures of small-scale heating events in EUV spectral lines as modeled from 3D MHD simulations
NASA Astrophysics Data System (ADS)
Guerreiro, Nuno; Haberreiter, Margit; Hansteen, Viggo; Curdt, Werner; Schmutz, Werner
2014-05-01
We aim at understanding the implications of small scale heating events in the solar atmosphere for the variations of the solar spectral irradiance. We present a technique for identification and characterization of these events in 3D simulations of the solar atmosphere. An accurate property determination of these events in time and space will help us to understand how spectral lines, in particular in the EUV, respond to them and which kind of spectral signatures one would expect to find in observations as from SOHO/SUMER and eventually from future space missions, as for example observations by SPICE on board Solar Orbiter.
Alexander Marshak; Warren Wiscombe; Yuri Knyazikhin; Christine Chiu
2011-05-24
We proposed a variety of tasks centered on the following question: what can we learn about 3D cloud-radiation processes and aerosol-cloud interaction from rapid-sampling ARM measurements of spectral zenith radiance? These ARM measurements offer spectacular new and largely unexploited capabilities in both the temporal and spectral domains. Unlike most other ARM instruments, which average over many seconds or take samples many seconds apart, the new spectral zenith radiance measurements are fast enough to resolve natural time scales of cloud change and cloud boundaries as well as the transition zone between cloudy and clear areas. In the case of the shortwave spectrometer, the measurements offer high time resolution and high spectral resolution, allowing new discovery-oriented science which we intend to pursue vigorously. Research objectives are, for convenience, grouped under three themes: â¢ Understand radiative signature of the transition zone between cloud-free and cloudy areas using data from ARM shortwave radiometers, which has major climatic consequences in both aerosol direct and indirect effect studies. â¢ Provide cloud property retrievals from the ARM sites and the ARM Mobile Facility for studies of aerosol-cloud interactions. â¢ Assess impact of 3D cloud structures on aerosol properties using passive and active remote sensing techniques from both ARM and satellite measurements.
Westerhof, Lotte B; Wilbers, Ruud H P; Roosien, Jan; van de Velde, Jan; Goverse, Aska; Bakker, Jaap; Schots, Arjen
2012-01-01
Heterologous expression platforms of biopharmaceutical proteins have been significantly improved over the last decade. Further improvement can be established by examining the intrinsic properties of proteins. Interleukin-10 (IL-10) is an anti-inflammatory cytokine with a short half-life that plays an important role in re-establishing immune homeostasis. This homodimeric protein of 36 kDa has significant therapeutic potential to treat inflammatory and autoimmune diseases. In this study we show that the major production bottleneck of human IL-10 is not protein instability as previously suggested, but extensive multimerisation due to its intrinsic 3D domain swapping characteristic. Extensive multimerisation of human IL-10 could be visualised as granules in planta. On the other hand, mouse IL-10 hardly multimerised, which could be largely attributed to its glycosylation. By introducing a short glycine-serine-linker between the fourth and fifth alpha helix of human IL-10 a stable monomeric form of IL-10 (hIL-10(mono)) was created that no longer multimerised and increased yield up to 20-fold. However, hIL-10(mono) no longer had the ability to reduce pro-inflammatory cytokine secretion from lipopolysaccharide-stimulated macrophages. Forcing dimerisation restored biological activity. This was achieved by fusing human IL-10(mono) to the C-terminal end of constant domains 2 and 3 of human immunoglobulin A (Fcα), a natural dimer. Stable dimeric forms of IL-10, like Fcα-IL-10, may not only be a better format for improved production, but also a more suitable format for medical applications. PMID:23049703
Modified block-matching 3-D filter in Laplacian pyramid domain for speckle reduction
NASA Astrophysics Data System (ADS)
Wen, Donghai; Jiang, Yuesong; Zhang, Yanzhong; He, Yuntao; Hua, Houqiang; Yu, Rong; Wu, Xiaofang; Gao, Qian
2014-07-01
The Laplacian pyramid-based block-matching 3-D filtering (BM3D) is proposed (LPBM3D) for despeckling the speckle image. For BM3D in each pyramid layer, the criterion used to collect blocks in the 3-D groups to the actual data statistics is devised. An adaptive wavelet thresholding operator that depends on both noise level and signal characteristics is proposed. The performance of the proposed LPBM3D method has been compared with the state-of-the-art methods, including the recently proposed nonlocal mean (NLM) and BM3D method. Experimental results show that the visual quality and evaluation indexes outperform the other methods with no edge preservation. The proposed algorithm effectively realizes both despeckling and edge preservation.
Improvements to the ICRH antenna time-domain 3D plasma simulation model
NASA Astrophysics Data System (ADS)
Smithe, David N.; Jenkins, Thomas G.; King, J. R.
2015-12-01
We present a summary of ongoing improvements to the 3D time-domain plasma modeling software that has been used to look at ICRH antennas on Alcator C-Mod, NSTX, and ITER [1]. Our past investigations have shown that in low density cases where the slow wave is propagating, strong amplitude lower hybrid resonant fields can occur. Such a scenario could result in significant parasitic power loss in the SOL. The primary resonance broadening in this case is likely collisions with neutral gas, and thus we are upgrading the model to include realistic neutral gas in the SOL, in order to provide a better understanding of energy balance in these situations. Related to this, we are adding a temporal variation capability to the local plasma density in front of the antenna in order to investigate whether the near fields of the antenna could modify the local density sufficiently to initiate a low density situation. We will start with a simple scalar ponderomotive potential density expulsion model [2] for the density evolution, but are also looking to eventually couple to a more complex fluid treatment that would include tensor pressures and convective physics and sources of neutrals and ionization. We also review continued benchmarking efforts, and ongoing and planned improvements to the computational algorithms, resulting from experience gained during our recent supercomputing runs on the Titan supercomputer, including GPU operations.
Two-dimensional angular filter array for angular domain imaging with 3D printed angular filters
NASA Astrophysics Data System (ADS)
Ng, Eldon; Carson, Jeffrey J. L.
2013-02-01
Angular Domain Imaging (ADI) is a technique that is capable of generating two dimensional shadowgrams of attenuating targets embedded in a scattering medium. In ADI, an angular filter array (AFA) is positioned between the sample and the detector to distinguish between quasi-ballistic photons and scattered photons. An AFA is a series of micro-channels with a high aspect ratio. Previous AFAs from our group were constructed by micro-machining the micro-channels into a silicon wafer, limiting the imaging area to a one dimensional line. Two dimensional images were acquired via scanning. The objective of this work was to extend the AFA design to two dimensions to allow for two dimensional imaging with minimal scanning. The second objective of this work was to perform an initial characterization of the imaging capabilities of the 2D AFA. Our approach was to use rapid 3D prototyping techniques to generate an array of micro-channels. The imaging capabilities were then evaluated by imaging a 0.9 mm graphite rod submerged in a scattering media. Contrast was observed to improve when a second angular filter array was placed in front of the sample to mask the incoming light.
Real Time Gabor-Domain Optical Coherence Microscopy for 3D Imaging.
Rolland, Jannick P; Canavesi, Cristina; Tankam, Patrice; Cogliati, Andrea; Lanis, Mara; Santhanam, Anand P
2016-01-01
Fast, robust, nondestructive 3D imaging is needed for the characterization of microscopic tissue structures across various clinical applications. A custom microelectromechanical system (MEMS)-based 2D scanner was developed to achieve, together with a multi-level GPU architecture, 55 kHz fast-axis A-scan acquisition in a Gabor-domain optical coherence microscopy (GD-OCM) custom instrument. GD-OCM yields high-definition micrometer-class volumetric images. A dynamic depth of focusing capability through a bio-inspired liquid lens-based microscope design, as in whales' eyes, was developed to enable the high definition instrument throughout a large field of view of 1 mm3 volume of imaging. Developing this technology is prime to enable integration within the workflow of clinical environments. Imaging at an invariant resolution of 2 μm has been achieved throughout a volume of 1 × 1 × 0.6 mm3, acquired in less than 2 minutes. Volumetric scans of human skin in vivo and an excised human cornea are presented. PMID:27046601
3D imaging of dental hard tissues with Fourier domain optical coherence tomography
NASA Astrophysics Data System (ADS)
Chen, Yueli L.; Yang, Yi; Ma, Jing; Yan, Jun; Shou, Yuanxin; Wang, Tianheng; Ramesh, Aruna; Zhao, Jing; Zhu, Quing
2011-03-01
A fiber optical coherence tomography (OCT) probe is used for three dimensional dental imaging. The probe has a lightweight miniaturized design with a size of a pen to facilitate clinic in vivo diagnostics. The probe is interfaced with a swept-source / Fourier domain optical coherence tomography at 20K axial scanning rate. The tooth samples were scanned from occlusal, buccal, lingual, mesial, and distal orientations. Three dimensional imaging covers tooth surface area up to 10 mm x 10 mm with a depth about 5 mm, where a majority of caries affection occurs. OCT image provides better resolution and contrast compared to gold standard dental radiography (X-ray). In particular, the technology is well suited for occlusal caries detection. This is complementary to X-ray as occlusal caries affection is difficult to be detected due to the X-ray projectile scan geometry. The 3D topology of occlusal surface as well as the dentin-enamel junction (DEJ) surface inside the tooth can be visualized. The lesion area appears with much stronger back scattering signal intensity.
Verification and validation of ShipMo3D ship motion predictions in the time and frequency domains
NASA Astrophysics Data System (ADS)
McTaggart, Kevin A.
2011-03-01
This paper compares frequency domain and time domain predictions from the ShipMo3D ship motion library with observed motions from model tests and sea trials. ShipMo3D evaluates hull radiation and diffraction forces using the frequency domain Green function for zero forward speed, which is a suitable approach for ships travelling at moderate speed (e.g., Froude numbers up to 0.4). Numerical predictions give generally good agreement with experiments. Frequency domain and linear time domain predictions are almost identical. Evaluation of nonlinear buoyancy and incident wave forces using the instantaneous wetted hull surface gives no improvement in numerical predictions. Consistent prediction of roll motions remains a challenge for seakeeping codes due to the associated viscous effects.
NASA Astrophysics Data System (ADS)
Hu, Zhihong; Abràmoff, Michael D.; Niemeijer, Meindert; Garvin, Mona K.
2011-03-01
Segmenting vessels in spectral-domain optical coherence tomography (SD-OCT) volumes is particularly challenging in the region near and inside the neural canal opening (NCO). Furthermore, accurately segmenting them in color fundus photographs also presents a challenge near the projected NCO. However, both modalities also provide complementary information to help indicate vessels, such as a better NCO contrast from the NCO-aimed OCT projection image and a better vessel contrast inside the NCO from fundus photographs. We thus present a novel multimodal automated classification approach for simultaneously segmenting vessels in SD-OCT volumes and fundus photographs, with a particular focus on better segmenting vessels near and inside the NCO by using a combination of their complementary features. In particular, in each SD-OCT volume, the algorithm pre-segments the NCO using a graph-theoretic approach and then applies oriented Gabor wavelets with oriented NCO-based templates to generate OCT image features. After fundus-to-OCT registration, the fundus image features are computed using Gaussian filter banks and combined with OCT image features. A k-NN classifier is trained on 5 and tested on 10 randomly chosen independent image pairs of SD-OCT volumes and fundus images from 15 subjects with glaucoma. Using ROC analysis, we demonstrate an improvement over two closest previous works performed in single modal SD-OCT volumes with an area under the curve (AUC) of 0.87 (0.81 for our and 0.72 for Niemeijer's single modal approach) in the region around the NCO and 0.90 outside the NCO (0.84 for our and 0.81 for Niemeijer's single modal approach).
Spectral mapping of 3D multi-cellular tumor spheroids: time-resolved confocal microscopy.
Mohapatra, Saswat; Nandi, Somen; Chowdhury, Rajdeep; Das, Gaurav; Ghosh, Surajit; Bhattacharyya, Kankan
2016-07-21
A tumor-like multi-cellular spheroid (3D) differs from a 2D cell in a number of ways. This is demonstrated using time resolved confocal microscopy. Two different tumor spheroids - HeLa (cervical cancer) and A549 (lung cancer) - are studied using 3 different fluorescent dyes - C153 (non-covalent), CPM (covalent) and doxorubicin (non-covalent, anti-cancer drug). The pattern of localization of these three fluorescent probes in the 3D tumor cell exhibits significant differences from that in the conventional 2D cells. For both the cells (HeLa and A549), the total uptake of doxorubicin in the 3D cell is much lower than that in the 2D cell. The uptake of doxorubicin molecules in the A549 spheroid is significantly different compared to the HeLa spheroid. The local polarity (i.e. emission maxima) and solvation dynamics in the 3D tumor cell differ from those in 2D cells. The covalent probe CPM exhibits intermittent fluorescence oscillations in the 1-2 s time scale. This is attributed to redox processes. These results may provide new insights into 3D tumors. PMID:27336201
NASA Technical Reports Server (NTRS)
Wiscombe, Warren J.
2012-01-01
The main theme for our research is the understanding and closure of the surface spectral shortwave radiation problem in fully 3D cloud situations by combining the new ARM scanning radars, shortwave spectrometers, and microwave radiometers with the arsenal of radiative transfer tools developed by our group. In particular, we define first a large number of cloudy test cases spanning all 3D possibilities not just the customary uniform-overcast ones. Second, for each case, we define a "Best Estimate of Clouds That Affect Shortwave Radiation" using all relevant ARM instruments, notably the new scanning radars, and contribute this to the ARM Archive. Third, we test the ASR-signature radiative transfer model RRTMG_SW for those cases, focusing on the near-IR because of long-standing problems in this spectral region, and work with the developers to improve RRTMG_SW in order to increase its penetration into the modeling community.
NASA Astrophysics Data System (ADS)
Greenhalgh, Stewart; Zhou, Bing; Maurer, Hansruedi
2010-05-01
We have developed a modified version of the spectral element method (SEM), called the Gaussian Quadrature Grid (GQG) approach, for frequency domain 3D seismic modelling in arbitrary heterogeneous, anisotropic media. The model may incorporate an arbitrary free-surface topography and irregular subsurface interfaces. Unlike the SEM ,it does not require a powerful mesh generator such as the Delauney Triangular or TetGen. Rather, the GQG approach replaces the element mesh with Gaussian quadrature abscissae to directly sample the physical properties of the model parameters and compute the weighted residual or variational integral. This renders the model discretisation simple and easily matched to the model topography, as well as direct control of the model paramterisation for subsequent inversion. In addition, it offers high accuracy in numerical modelling provided that an appropriate density of the Gaussian quadrature abscissae is employed. The second innovation of the GQG is the incorporation of a new implementation of perfectly matched layers to suppress artificial reflections from the domain margins. We employ PML model parameters (specified complex valued density and elastic moduli) rather than explicitly solving the governing wave equation with a complex co-ordinate system as in conventional approaches. Such an implementation is simple, general, effective and easily extendable to any class of anisotropy and other numerical modelling methods. The accuracy of the GQG approach is controlled by the number of Gaussian quadrature points per minimum wavelength, the so-called sampling density. The optimal sampling density should be the one which enables high definition of geological characteristics and high precision of the variational integral evaluation and spatial differentiation. Our experiments show that satisfactory results can be obtained using sampling densities of 5 points per minimum wavelength. Efficiency of the GQG approach mainly depends on the linear
Waveform prediction with travel time model LLNL-G3D assessed by Spectral-Element simulation
NASA Astrophysics Data System (ADS)
Morency, C.; Simmons, N. A.; Myers, S. C.; Johannesson, G.; Matzel, E.
2013-12-01
Seismic monitoring requires accurate prediction of travel times, amplitudes, and whole waveforms. As a first step towards developing a model that is suited to seismic monitoring, LLNL developed the LLNL-G3D P-wave travel time model (Simmons et al., 2012, JGR) to improve seismic event location accuracy. LLNL-G3D fulfills the need to predict travel times from events occurring anywhere in the globe to stations ranging from local to teleseismic distances. Prediction over this distance range requires explicit inclusion of detailed 3-dimensional structure from Earths surface to the core. An open question is how well a model optimized to fit P-wave travel time data can predict waveforms? We begin to address this question by using the P-wave velocities in LLNL-G3D as a proxy for S-wave velocity and density, then performing waveform simulations via the SPECFEM3D_GLOBE spectral-element code. We assess the ability of LLNL-G3D to predict waveforms and draw comparisons to other 3D models available in SPECFEM3D_GLOBE package and widely used in the scientific community. Although we do not expect the P-wave model to perform as well as waveform based models, we view our effort as a first step towards accurate prediction of time times, amplitudes and full waveforms based on a single model. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
An iterative KP1 method for solving the transport equation in 3D domains on unstructured grids
NASA Astrophysics Data System (ADS)
Kokonkov, N. I.; Nikolaeva, O. V.
2015-10-01
A two-step iterative KP1 method for solving systems of grid equations that approximate the integro-differential transport equation in 3D domains on unstructured grids using nodal SN methods is described. Results of testing the efficiency of the proposed method in solving benchmark problems of reactor protection on tetrahedral grids are presented.
On line contribution functions and examining spectral line formation in 3D model stellar atmospheres
NASA Astrophysics Data System (ADS)
Amarsi, A. M.
2015-09-01
Line contribution functions are useful diagnostics for studying spectral line formation in stellar atmospheres. I derive an expression for the contribution function to the absolute flux depression that emerges from three-dimensional `box-in-a-star' model stellar atmospheres. I illustrate the result by comparing the local thermodynamic equilibrium (LTE) spectral line formation of the high-excitation permitted OI 777 nm lines with the non-LTE case.
Chiu, Jui-Yuan
2015-09-14
ARM set out 20 years ago to “close” the radiation problem, that is, to improve radiation models to the point where they could routinely predict the observed spectral radiation fluxes knowing the optical properties of the surface and of gases, clouds and aerosols in the atmosphere. Only then could such radiation models form a proper springboard for global climate model (GCM) parameterizations of spectral radiation. Sustained efforts have more or less achieved that goal with regard to longwave radiation; ASR models now routinely predict ARM spectral longwave radiances to 1–2%. Similar efforts in the shortwave have achieved far less; the successes are mainly for carefully selected 1D stratiform cloud cases. Such cases amount, even with the most optimistic interpretation, to no more than 30% of all cases at SGP. The problem has not been lack of effort but lack of appropriate instruments.The new ARM stimulus-funded instruments, with their new capabilities, will dramatically improve this situation and once again make progress possible on the shortwave problem. The new shortwave spectrometers will provide a reliable, calibrated record including the near infrared – and for other climatic regimes than SGP. The new scanning radars will provide the 3D cloud view, making it possible to tackle fully 3D situations. Thus, our main theme for the project is the understanding and closure of the surface spectral shortwave radiation problem in fully 3D cloud situations by combining the new ARM scanning radars and shortwave spectrometers with the arsenal of radiative transfer tools.
Jacassi, Andrea; Bozzola, Angelo; Zilio, Pierfrancesco; Tantussi, Francesco; De Angelis, Francesco
2016-01-01
We fabricated and investigated a new configuration of 3D coaxial metallic antennas working in the infrared which combines the strong lateral light scattering of vertical plasmonic structures with the selective spectral transmission of 2D arrays of coaxial apertures. The coaxial structures are fabricated with a top-down method based on a template of hollow 3D antennas. Each antenna has a multilayer radial structure consisting of dielectric and metallic materials not achievable in a 2D configuration. A planar metallic layer is inserted normally to the antennas. The outer dielectric shell of the antenna defines a nanometric gap between the horizontal plane and the vertical walls. Thanks to this aperture, light can tunnel to the other side of the plane, and be transmitted to the far field in a set of resonances. These are investigated with finite-elements electromagnetic calculations and with Fourier-transform infrared spectroscopy measurements. The spectral position of the resonances can be tuned by changing the lattice period and/or the antenna length. Thanks to the strong scattering provided by the 3D geometry, the transmission peaks possess a high signal-to-noise ratio even when the illuminated area is less than 2 × 2 times the operation wavelength. This opens new possibilities for multispectral imaging in the IR with wavelength-scale spatial resolution. PMID:27345517
NASA Astrophysics Data System (ADS)
Jacassi, Andrea; Bozzola, Angelo; Zilio, Pierfrancesco; Tantussi, Francesco; de Angelis, Francesco
2016-06-01
We fabricated and investigated a new configuration of 3D coaxial metallic antennas working in the infrared which combines the strong lateral light scattering of vertical plasmonic structures with the selective spectral transmission of 2D arrays of coaxial apertures. The coaxial structures are fabricated with a top-down method based on a template of hollow 3D antennas. Each antenna has a multilayer radial structure consisting of dielectric and metallic materials not achievable in a 2D configuration. A planar metallic layer is inserted normally to the antennas. The outer dielectric shell of the antenna defines a nanometric gap between the horizontal plane and the vertical walls. Thanks to this aperture, light can tunnel to the other side of the plane, and be transmitted to the far field in a set of resonances. These are investigated with finite-elements electromagnetic calculations and with Fourier-transform infrared spectroscopy measurements. The spectral position of the resonances can be tuned by changing the lattice period and/or the antenna length. Thanks to the strong scattering provided by the 3D geometry, the transmission peaks possess a high signal-to-noise ratio even when the illuminated area is less than 2 × 2 times the operation wavelength. This opens new possibilities for multispectral imaging in the IR with wavelength-scale spatial resolution.
Jacassi, Andrea; Bozzola, Angelo; Zilio, Pierfrancesco; Tantussi, Francesco; De Angelis, Francesco
2016-01-01
We fabricated and investigated a new configuration of 3D coaxial metallic antennas working in the infrared which combines the strong lateral light scattering of vertical plasmonic structures with the selective spectral transmission of 2D arrays of coaxial apertures. The coaxial structures are fabricated with a top-down method based on a template of hollow 3D antennas. Each antenna has a multilayer radial structure consisting of dielectric and metallic materials not achievable in a 2D configuration. A planar metallic layer is inserted normally to the antennas. The outer dielectric shell of the antenna defines a nanometric gap between the horizontal plane and the vertical walls. Thanks to this aperture, light can tunnel to the other side of the plane, and be transmitted to the far field in a set of resonances. These are investigated with finite-elements electromagnetic calculations and with Fourier-transform infrared spectroscopy measurements. The spectral position of the resonances can be tuned by changing the lattice period and/or the antenna length. Thanks to the strong scattering provided by the 3D geometry, the transmission peaks possess a high signal-to-noise ratio even when the illuminated area is less than 2 × 2 times the operation wavelength. This opens new possibilities for multispectral imaging in the IR with wavelength-scale spatial resolution. PMID:27345517
NASA Astrophysics Data System (ADS)
Tong, Ping; Komatitsch, Dimitri; Tseng, Tai-Lin; Hung, Shu-Huei; Chen, Chin-Wu; Basini, Piero; Liu, Qinya
2014-10-01
We present a three-dimensional (3-D) hybrid method that interfaces the spectral-element method (SEM) with the frequency-wave number (FK) technique to model the propagation of teleseismic plane waves beneath seismic arrays. The accuracy of the resulting 3-D SEM-FK hybrid method is benchmarked against semianalytical FK solutions for 1-D models. The accuracy of 2.5-D modeling based on 2-D SEM-FK hybrid method is also investigated through comparisons to this 3-D hybrid method. Synthetic examples for structural models of the Alaska subduction zone and the central Tibet crust show that this method is capable of accurately capturing interactions between incident plane waves and local heterogeneities. This hybrid method presents an essential tool for the receiver function and scattering imaging community to verify and further improve their techniques. These numerical examples also show the promising future of the 3-D SEM-FK hybrid method in high-resolution regional seismic imaging based on waveform inversions of converted/scattered waves recorded by seismic array.
On the construction of a new 3d atlas of stellar spectral energy distributions
NASA Astrophysics Data System (ADS)
Mironov, A. V.; Zakharov, A. I.; Moshkalev, V. G.; Malkov, O. Yu.; Kilpio, E. Yu.
Modern spectrophotometric atlases are burdened with significant systematic errors. In particular, the problems of spectrum calibration in the ultraviolet region are not solved; different parts of the spectrum are not thoroughly fit to each other; spectra of (even bright) stars, obtained by different authors, display large discrepancies. Here we discuss a possibility to construct a new atlas of spectral energy distributions (SEDs) for a large set of stars by comparison of empirical stellar spectra in dozens of modern spectrophotometric atlases, as well as the comparison of synthetic and observed color indices in different multicolor photometric systems. In this way we suppose to exclude most of systematic errors and construct a new three-dimensional (spectral class, luminosity class, metallicity) atlas of empirical stellar spectra for several thousand stars. After exclusion of interstellar reddenings, a semi-empirical atlas of average SEDs can be constructed for about 150--200 spectral subtypes. This would allow us to make calibrations of spectrophotometric and photometric parameters in terms of spectral types and physical parameters (Teff, log g, [m/H]) and to verify the accuracy of model stellar atmospheres.
3-D SPECTRAL IP IMAGING: NON-INVASIVE CHARACTERIZATION OF CONTAMINANT PLUMES
The objective of this study is to develop a noninvasive tomographic imaging technique,based on the spectral induced-polarization method, to characterize the in-situ distribution of organic and inorganic groundwater contaminants. Recent advances in tomographic imaging, applied to ...
NASA Astrophysics Data System (ADS)
Bognet, B.; Leygue, A.; Chinesta, F.; Poitou, A.
2011-01-01
In this paper, we focus on the simulation of linear elastic behaviour of plates using a 3D approach which numerical cost only scales like a 2D one. In the case of plates, the kinematic hypothesis introduced in plate theories to go from 3D to 2D is usually unsatisfactory where one cannot rely on St Venant's principle (usually close to the plate edges). We propose to apply the PGD (Proper Generalized Decomposition) method [1] to the simulation of the linear elastic behavior of plates. This method allows us to separately search for the in-plane and the out-of plane contributions to the 3D solution, yielding significant savings in computational cost. The method is validated on a simple case and its full potential is then presented for the simulation of the behavior of laminated composite plates.
Three-dimensional tracker for spectral domain optical coherence tomography
NASA Astrophysics Data System (ADS)
Hammer, Daniel X.; Iftimia, Nicusor V.; Bigelow, Chad E.; Ustun, Teoman E.; Bloom, Benjamin; Ferguson, R. Daniel; Milner, Thomas E.
2007-02-01
Spectral domain optical coherence tomography (SDOCT) is a relatively new imaging technique that allows high-speed cross-sectional scanning of retinal structures with little motion artifact. However, instrumentation for these systems is not yet fast enough to collect high-density three-dimensional retinal maps free of the adverse effects of lateral eye movements. Low coherence interferometry instruments must also contend with axial motion primarily from head movements that shift the target tissue out of the coherence detection range. Traditional SDOCT instruments suffer from inherent deficiencies that exacerbate the effect of depth motion, including limited range, depth-dependent signal attenuation, and complex conjugate overlap. We present initial results on extension of our transverse retinal tracking system to three-dimensions especially for SDOCT imagers. The design and principle of operation of two depth tracking techniques, adaptive ranging (AR) and Doppler velocity (DV) tracking, are presented. We have integrated the threedimensional tracking hardware into a hybrid line scanning laser ophthalmoscope (LSLO)/SDOCT imaging system. Imaging and tracking performance was characterized by tests involving a limited number of human subjects. The hybrid imager could switch between wide-field en-face confocal LSLO images, high-resolution cross-sectional OCT images, and an interleaved mode of sequential LSLO and OCT images. With 3-D tracking, the RMS error for axial motion decreased to <50 Âµm and for lateral motion decreased to <10 Âµm. The development of real-time tracking and SDOCT image processing hardware is also discussed. Future implementation of 3-D tracking should increase the yield of usable images and decrease the patient measurement time for clinical SDOCT systems.
Towards using spectral domain optical coherence tomography for dental wear monitoring
NASA Astrophysics Data System (ADS)
Mǎrcǎuteanu, Corina; Bradu, Adrian; Sinescu, Cosmin; Topalǎ, Florin I.; Negrutiu, Meda Lavinia; Podoleanu, Adrian G.
2014-03-01
In this paper we demonstrate that fast spectral domain optical coherence tomography imaging systems have the potential to monitor the evolution of pathological dental wear. On 10 caries free teeth, four levels of artificially defects similar to those observed in the clinic were created. After every level of induced defect, OCT scanning was performed. B-scans were acquired and 3D reconstructions were generated.
STEMS3D: An X-ray spectral model for magnetar persistent radiations
NASA Astrophysics Data System (ADS)
Gogus, Ersin; Weng, Shan-Shan
2016-07-01
Anomalous X-ray pulsars and soft gamma-ray repeaters are recognized as the most promising magnetar candidates, as indicated by their energetic bursts and rapid spin-downs. It is expected that the strong magnetic field leaves distinctive imprints on the emergent radiation both by affecting the radiative processes in atmospheres of magnetars and by scattering in the upper magnetospheres. We construct a self-consistent physical model that incorporates emission from the magnetar surface and its reprocessing in the three-dimensional twisted magnetosphere using a Monte Carlo technique. The synthetic spectra are characterized by four parameters: surface temperature kT, surface magnetic field strength B, magnetospheric twist angle Δφ, and the normalized electron velocity β. We also create a tabular model (STEMS3D) and apply it to X-ray spectra of magnetars.
Spectral domain optical coherence tomography with dual-balanced detection
NASA Astrophysics Data System (ADS)
Bo, En; Liu, Xinyu; Chen, Si; Luo, Yuemei; Wang, Nanshuo; Wang, Xianghong; Liu, Linbo
2016-03-01
We developed a spectral domain optical coherence tomography (SD-OCT) system employing dual-balanced detection (DBD) for direct current term suppression and SNR enhancement, especially for auto-autocorrelation artifacts reduction. The DBD was achieved by using a beam splitter to building a free-space Michelson interferometer, which generated two interferometric spectra with a phase difference of π. These two phase-opposed spectra were guided to the spectrometer through two single mode fibers of the 8 fiber v-groove array and acquired by ultizing the upper two lines of a three-line CCD camera. We rotated this fiber v-groove array by 1.35 degrees to focus two spectra onto the first and second line of the CCD camera. Two spectra were aligned by optimum spectrum matching algorithm. By subtracting one spectrum from the other, this dual-balanced detection system achieved a direct current term suppression of ~30 dB, SNR enhancement of ~3 dB, and auto-autocorrelation artifacts reduction of ~10 dB experimentally. Finally we respectively validated the feasibility and performance of dual-balanced detection by imaging a glass plate and swine corneal tissue ex vivo. The quality of images obtained using dual-balanced detection was significantly improved with regard to the conventional single-detection (SD) images.
Determination and validation of mTOR kinase-domain 3D structure by homology modeling
Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine
2015-01-01
The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site. PMID:26257525
JP3D compressed-domain watermarking of volumetric medical data sets
NASA Astrophysics Data System (ADS)
Ouled Zaid, Azza; Makhloufi, Achraf; Olivier, Christian
2010-01-01
Increasing transmission of medical data across multiple user systems raises concerns for medical image watermarking. Additionaly, the use of volumetric images triggers the need for efficient compression techniques in picture archiving and communication systems (PACS), or telemedicine applications. This paper describes an hybrid data hiding/compression system, adapted to volumetric medical imaging. The central contribution is to integrate blind watermarking, based on turbo trellis-coded quantization (TCQ), to JP3D encoder. Results of our method applied to Magnetic Resonance (MR) and Computed Tomography (CT) medical images have shown that our watermarking scheme is robust to JP3D compression attacks and can provide relative high data embedding rate whereas keep a relative lower distortion.
Modulated Magnetic Nanowires for Controlling Domain Wall Motion: Toward 3D Magnetic Memories.
Ivanov, Yurii P; Chuvilin, Andrey; Lopatin, Sergei; Kosel, Jurgen
2016-05-24
Cylindrical magnetic nanowires are attractive materials for next generation data storage devices owing to the theoretically achievable high domain wall velocity and their efficient fabrication in highly dense arrays. In order to obtain control over domain wall motion, reliable and well-defined pinning sites are required. Here, we show that modulated nanowires consisting of alternating nickel and cobalt sections facilitate efficient domain wall pinning at the interfaces of those sections. By combining electron holography with micromagnetic simulations, the pinning effect can be explained by the interaction of the stray fields generated at the interface and the domain wall. Utilizing a modified differential phase contrast imaging, we visualized the pinned domain wall with a high resolution, revealing its three-dimensional vortex structure with the previously predicted Bloch point at its center. These findings suggest the potential of modulated nanowires for the development of high-density, three-dimensional data storage devices. PMID:27138460
Michaelsen, Kelly E.; Krishnaswamy, Venkataramanan; Shi, Linxi; Vedantham, Srinivasan; Poplack, Steven P.; Karellas, Andrew; Pogue, Brian W.; Paulsen, Keith D.
2015-01-01
Calibration of a three-dimensional multimodal digital breast tomosynthesis (DBT) x-ray and non-fiber based near infrared spectral tomography (NIRST) system is challenging but essential for clinical studies. Phantom imaging results yielded linear contrast recovery of total hemoglobin (HbT) concentration for cylindrical inclusions of 15 mm, 10 mm and 7 mm with a 3.5% decrease in the HbT estimate for each 1 cm increase in inclusion depth. A clinical exam of a patient’s breast containing both benign and malignant lesions was successfully imaged, with greater HbT was found in the malignancy relative to the benign abnormality and fibroglandular regions (11 μM vs. 9.5 μM). Tools developed improved imaging system characterization and optimization of signal quality, which will ultimately improve patient selection and subsequent clinical trial results. PMID:26713210
Michaelsen, Kelly E; Krishnaswamy, Venkataramanan; Shi, Linxi; Vedantham, Srinivasan; Poplack, Steven P; Karellas, Andrew; Pogue, Brian W; Paulsen, Keith D
2015-12-01
Calibration of a three-dimensional multimodal digital breast tomosynthesis (DBT) x-ray and non-fiber based near infrared spectral tomography (NIRST) system is challenging but essential for clinical studies. Phantom imaging results yielded linear contrast recovery of total hemoglobin (HbT) concentration for cylindrical inclusions of 15 mm, 10 mm and 7 mm with a 3.5% decrease in the HbT estimate for each 1 cm increase in inclusion depth. A clinical exam of a patient's breast containing both benign and malignant lesions was successfully imaged, with greater HbT was found in the malignancy relative to the benign abnormality and fibroglandular regions (11 μM vs. 9.5 μM). Tools developed improved imaging system characterization and optimization of signal quality, which will ultimately improve patient selection and subsequent clinical trial results. PMID:26713210
Upadhyay, Atul Kumar; Sowdhamini, Ramanathan
2016-01-01
3D-domain swapping is one of the mechanisms of protein oligomerization and the proteins exhibiting this phenomenon have many biological functions. These proteins, which undergo domain swapping, have acquired much attention owing to their involvement in human diseases, such as conformational diseases, amyloidosis, serpinopathies, proteionopathies etc. Early realisation of proteins in the whole human genome that retain tendency to domain swap will enable many aspects of disease control management. Predictive models were developed by using machine learning approaches with an average accuracy of 78% (85.6% of sensitivity, 87.5% of specificity and an MCC value of 0.72) to predict putative domain swapping in protein sequences. These models were applied to many complete genomes with special emphasis on the human genome. Nearly 44% of the protein sequences in the human genome were predicted positive for domain swapping. Enrichment analysis was performed on the positively predicted sequences from human genome for their domain distribution, disease association and functional importance based on Gene Ontology (GO). Enrichment analysis was also performed to infer a better understanding of the functional importance of these sequences. Finally, we developed hinge region prediction, in the given putative domain swapped sequence, by using important physicochemical properties of amino acids. PMID:27467780
Propagation of 3D nonlinear waves over complex bathymetry using a High-Order Spectral method
NASA Astrophysics Data System (ADS)
Gouin, Maïté; Ducrozet, Guillaume; Ferrant, Pierre
2016-04-01
Scattering of regular and irregular surface gravity waves propagating over a region of arbitrary three-dimensional varying bathymetry is considered here. The three-dimensional High-Order Spectral method (HOS) with an extension to account for a variable bathymetry is used. The efficiency of the model has been proved to be conserved even with this extension. The method is first applied to a bathymetry consisting of an elliptical lens, as used in the Vincent and Briggs (1989) experiment. Incident waves passing across the lens are transformed and a strong convergence region is observed after the elliptical mound. The wave amplification depends on the incident wave. Numerical results for regular and irregular waves are analysed and compared with other methods and experimental data demonstrating the efficiency and practical applicability of the present approach. Then the method is used to model waves propagating over a real bathymetry: the canyons of Scripps/La Jolla in California. The implementation of this complex bathymetry in the model is presented, as well as the first results achieved. They will be compared to the ones obtained with another numerical model.
NASA Astrophysics Data System (ADS)
Korneev, V. G.
2012-09-01
BPS is a well known an efficient and rather general domain decomposition Dirichlet-Dirichlet type preconditioner, suggested in the famous series of papers Bramble, Pasciak and Schatz (1986-1989). Since then, it has been serving as the origin for the whole family of domain decomposition Dirichlet-Dirichlet type preconditioners-solvers as for h so hp discretizations of elliptic problems. For its original version, designed for h discretizations, the named authors proved the bound O(1 + log2 H/ h) for the relative condition number under some restricting conditions on the domain decomposition and finite element discretization. Here H/ h is the maximal relation of the characteristic size H of a decomposition subdomain to the mesh parameter h of its discretization. It was assumed that subdomains are images of the reference unite cube by trilinear mappings. Later similar bounds related to h discretizations were proved for more general domain decompositions, defined by means of coarse tetrahedral meshes. These results, accompanied by the development of some special tools of analysis aimed at such type of decompositions, were summarized in the book of Toselli and Widlund (2005). This paper is also confined to h discretizations. We further expand the range of admissible domain decompositions for constructing BPS preconditioners, in which decomposition subdomains can be convex polyhedrons, satisfying some conditions of shape regularity. We prove the bound for the relative condition number with the same dependence on H/ h as in the bound given above. Along the way to this result, we simplify the proof of the so called abstract bound for the relative condition number of the domain decomposition preconditioner. In the part, related to the analysis of the interface sub-problem preconditioning, our technical tools are generalization of those used by Bramble, Pasciak and Schatz.
Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization
Ea, Vuthy; Baudement, Marie-Odile; Lesne, Annick; Forné, Thierry
2015-01-01
Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and extremely dynamic. This review presents the most recent advances in topological domains’ organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. CTCF protein appears as a central factor of these two organization levels having either a strong insulating role at TAD borders, or a weaker architectural role in chromatin loop formation. TAD borders directly impact on chromatin dynamics by restricting contacts within specific genomic portions thus confining chromatin loop formation within TADs. We discuss how sub-TAD chromatin dynamics, constrained into a recently described statistical helix conformation, can produce functional interactions by contact stabilization. PMID:26226004
Restoration of 3D medical images with total variation scheme on wavelet domains (TVW)
NASA Astrophysics Data System (ADS)
Ogier, Arnaud; Hellier, Pierre; Barillot, Christian
2006-03-01
The multiplicity of sensors used in medical imaging leads to different noises. Non informative noise can damage the image interpretation process and the performance of automatic analysis. The method proposed in this paper allows compensating highly noisy image data from non informative noise without sophisticated modeling of the noise statistics. This generic approach uses jointly a wavelet decomposition scheme and a non-isotropic Total Variation filtering of the transform coefficients. This framework benefits from both the hierarchical capabilities of the wavelet transform and the well-posed regularization scheme of the Total Variation. This algorithm has been tested and validated on test-bed data, as well as different clinical MR and 3D ultrasound images, enhancing the capabilities of the proposed method to cope with different noise models.
Real-time 3D Fourier-domain optical coherence tomography guided microvascular anastomosis
NASA Astrophysics Data System (ADS)
Huang, Yong; Ibrahim, Zuhaib; Lee, W. P. A.; Brandacher, Gerald; Kang, Jin U.
2013-03-01
Vascular and microvascular anastomosis is considered to be the foundation of plastic and reconstructive surgery, hand surgery, transplant surgery, vascular surgery and cardiac surgery. In the last two decades innovative techniques, such as vascular coupling devices, thermo-reversible poloxamers and suture-less cuff have been introduced. Intra-operative surgical guidance using a surgical imaging modality that provides in-depth view and 3D imaging can improve outcome following both conventional and innovative anastomosis techniques. Optical coherence tomography (OCT) is a noninvasive high-resolution (micron level), high-speed, 3D imaging modality that has been adopted widely in biomedical and clinical applications. In this work we performed a proof-of-concept evaluation study of OCT as an assisted intraoperative and post-operative imaging modality for microvascular anastomosis of rodent femoral vessels. The OCT imaging modality provided lateral resolution of 12 μm and 3.0 μm axial resolution in air and 0.27 volume/s imaging speed, which could provide the surgeon with clearly visualized vessel lumen wall and suture needle position relative to the vessel during intraoperative imaging. Graphics processing unit (GPU) accelerated phase-resolved Doppler OCT (PRDOCT) imaging of the surgical site was performed as a post-operative evaluation of the anastomosed vessels and to visualize the blood flow and thrombus formation. This information could help surgeons improve surgical precision in this highly challenging anastomosis of rodent vessels with diameter less than 0.5 mm. Our imaging modality could not only detect accidental suture through the back wall of lumen but also promptly diagnose and predict thrombosis immediately after reperfusion. Hence, real-time OCT can assist in decision-making process intra-operatively and avoid post-operative complications.
Implicit scheme for Maxwell equations solution in case of flat 3D domains
NASA Astrophysics Data System (ADS)
Boronina, Marina; Vshivkov, Vitaly
2016-02-01
We present a new finite-difference scheme for Maxwell's equations solution for three-dimensional domains with different scales in different directions. The stability condition of the standard leap-frog scheme requires decreasing of the time-step with decreasing of the minimal spatial step, which depends on the minimal domain size. We overcome the conditional stability by modifying the standard scheme adding implicitness in the direction of the smallest size. The new scheme satisfies the Gauss law for the electric and magnetic fields in the final- differences. The approximation order, the maintenance of the wave amplitude and propagation speed, the invariance of the wave propagation on angle with the coordinate axes are analyzed.
High speed 3D endoscopic optical frequency domain imaging probe for lung cancer diagnosis
NASA Astrophysics Data System (ADS)
Li, Jianan; Feroldi, Fabio; Mo, Jianhua; Helderman, Frank; de Groot, Mattijs; de Boer, Johannes F.
2013-06-01
We present a miniature motorized endoscopic probe for Optical Frequency Domain Imaging with an outer diameter of 1.65 mm and a rotation speed of 3,000 - 12,500 rpm. The probe has a motorized distal end which provides a significant advantage over proximally driven probes since it does not require a drive shaft to transfer the rotational torque to the distal end of the probe and functions without a fiber rotary junction. The probe has a focal Full Width at Half Maximum of 9.6 μm and a working distance of 0.47 mm. We analyzed the non-uniform rotation distortion and found a location fluctuation of only 1.87° in repeated measurements of the same object. The probe was integrated in a high-speed Optical Frequency Domain Imaging setup at 1310 nm. We demonstrated its performance with imaging ex vivo pig bronchial and in vivo goat lung.
NASA Astrophysics Data System (ADS)
Gumerov, Nail A.; Karavaev, Alexey V.; Surjalal Sharma, A.; Shao, Xi; Papadopoulos, Konstantinos D.
2011-04-01
Efficient spectral and pseudospectral algorithms for simulation of linear and nonlinear 3D whistler waves in a cold electron plasma are developed. These algorithms are applied to the simulation of whistler waves generated by loop antennas and spheromak-like stationary waves of considerable amplitude. The algorithms are linearly stable and show good stability properties for computations of nonlinear waves over tens of thousands of time steps. Additional speedups by factors of 10-20 (comparing single core CPU and one GPU) are achieved by using graphics processors (GPUs), which enable efficient numerical simulation of the wave propagation on relatively high resolution meshes (tens of millions nodes) in personal computing environment. Comparisons of the numerical results with analytical solutions and experiments show good agreement. The limitations of the codes and the performance of the GPU computing are discussed.
Ultrahigh speed spectral/Fourier domain ophthalmic OCT imaging
NASA Astrophysics Data System (ADS)
Potsaid, Benjamin; Gorczynska, Iwona; Srinivasan, Vivek J.; Chen, Yueli; Liu, Jonathan; Jiang, James; Cable, Alex; Duker, Jay S.; Fujimoto, James G.
2009-02-01
Ultrahigh speed spectral / Fourier domain optical coherence tomography (OCT) imaging using a CMOS line scan camera with acquisition rates of 70,000 - 312,500 axial scans per second is investigated. Several design configurations are presented to illustrate trade-offs between acquisition speed, sensitivity, resolution and sensitivity roll-off performance. We demonstrate: extended imaging range and improved sensitivity roll-off at 70,000 axial scans per second , high speed and ultrahigh resolution imaging at 106,382 axial scans per second, and ultrahigh speed imaging at 250,000-312,500 axial scans per second. Each configuration is characterized through optical testing and the trade-offs demonstrated with in vivo imaging of the fovea and optic disk in the human retina. OCT fundus images constructed from 3D-OCT data acquired at 250,000 axial scans per second have no noticeable discontinuity of retinal features and show that there are minimal motion artifacts. The fine structures of the lamina cribrosa can be seen. Long cross sectional scans are acquired at 70,000 axial scans per second for imaging large areas of the retina, including the fovea and optic disk. Rapid repeated imaging of a small volume (4D-OCT) enables time resolved visualization of the capillary network surrounding the INL and may show individual red blood cells. The results of this study suggest that high speed CMOS cameras can achieve a significant improvement in performance for ophthalmic imaging. This promises to have a powerful impact in clinical applications by improving early diagnosis, reproducibility of measurements and enabling more sensitive assessment of disease progression or response to therapy.
NASA Astrophysics Data System (ADS)
Schultz, A.
2010-12-01
3D forward solvers lie at the core of inverse formulations used to image the variation of electrical conductivity within the Earth's interior. This property is associated with variations in temperature, composition, phase, presence of volatiles, and in specific settings, the presence of groundwater, geothermal resources, oil/gas or minerals. The high cost of 3D solutions has been a stumbling block to wider adoption of 3D methods. Parallel algorithms for modeling frequency domain 3D EM problems have not achieved wide scale adoption, with emphasis on fairly coarse grained parallelism using MPI and similar approaches. The communications bandwidth as well as the latency required to send and receive network communication packets is a limiting factor in implementing fine grained parallel strategies, inhibiting wide adoption of these algorithms. Leading Graphics Processor Unit (GPU) companies now produce GPUs with hundreds of GPU processor cores per die. The footprint, in silicon, of the GPU's restricted instruction set is much smaller than the general purpose instruction set required of a CPU. Consequently, the density of processor cores on a GPU can be much greater than on a CPU. GPUs also have local memory, registers and high speed communication with host CPUs, usually through PCIe type interconnects. The extremely low cost and high computational power of GPUs provides the EM geophysics community with an opportunity to achieve fine grained (i.e. massive) parallelization of codes on low cost hardware. The current generation of GPUs (e.g. NVidia Fermi) provides 3 billion transistors per chip die, with nearly 500 processor cores and up to 6 GB of fast (DDR5) GPU memory. This latest generation of GPU supports fast hardware double precision (64 bit) floating point operations of the type required for frequency domain EM forward solutions. Each Fermi GPU board can sustain nearly 1 TFLOP in double precision, and multiple boards can be installed in the host computer system. We
Efficient 3D Acoustic Numerical modeling in the Logarithmic-grid using the Expanding Domain Method
NASA Astrophysics Data System (ADS)
Hong, B. R.; Chung, W.; Ko, H.; Bae, H. S.
2015-12-01
In the numerical modeling of seismic wave propagation by the use of a discrete computing domain, dispersion analysis is preceded by the determination of the spatial grid spacings in order to ensure accurate modeling results. Grid spacing is a function of wavelength, and the wavelength depends on the minimum velocity and maximum source frequency. Therefore, as the frequency increases, the number of grids increase and this leads to computational overburden. In order to reduce the computing complexity, coordinate transformation techniques such as Riemannian coordinates and logarithmic grid sets are proposed. Riemannian wave-field extrapolation is a way to reformulate the wave-field by expressing it in Riemannian coordinates. In the logarithmic grid, grid spacing changes logarithmically, so this enables us to reduce the number of grids compared to a conventional grid set. Furthermore, this could completely remove boundary reflections by extending the model dimensions. However, numerical modeling in the logarithmic grid is still inefficient because it is performed for whole model at every individual time step. In this study we applied the expanding domain method to the logarithmic modeling in order to improve computational efficiency. This method, based on amplitude comparison, excludes computations for zero wave-fields by considering a non-zero domain boundary. Numerical examples demonstrated that our new modeling method enhances computational efficiency maintaining accuracy compared with conventional modeling methods. In wider and higher-order dimensions, particularly, the efficiency of our modeling method increased. Our new modeling technique could also be applied to the generation of underwater target echo signals requiring high frequency analysis.
High speed miniature motorized endoscopic probe for 3D optical frequency domain imaging
NASA Astrophysics Data System (ADS)
Li, Jianan; Feroldi, Fabio; Mo, Jianhua; Helderman, Frank; de Groot, Mattijs; de Boer, Johannes F.
2013-03-01
We present a miniature motorized endoscopic probe for Optical Frequency Domain Imaging with an outer diameter of 1.65 mm and a rotation speed of 3,000 - 12,500 rpm. This is the smallest motorized high speed OCT probe to our knowledge. The probe has a motorized distal end which provides a significant advantage over proximally driven probes since it does not require a drive shaft to transfer the rotational torque to the distal end of the probe and functions without a fiber rotary junction. The probe has a focal Full Width at Half Maximum of 9.6 μm and a working distance of 0.47 mm. We analyzed the non-uniform rotation distortion and found a location fluctuation of only 1.87° in repeated measurements of the same object. The probe was integrated in a high-speed Optical Frequency Domain Imaging setup at 1310 nm We demonstrated its performance with imaging ex vivo pig bronchial and in vivo goat lung.
NASA Astrophysics Data System (ADS)
Devaux, Fabrice; Lantz, Eric; Chauvet, Mathieu
2016-04-01
We report an application of the tri-dimensional pseudo-spectral time domain algorithm, that solves with accuracy the nonlinear Maxwell's equations, to predict second harmonic generation in lithium niobate ridge-type waveguides with high index contrast. Characteristics of the nonlinear process such as conversion efficiency as well as impact of the multimode character of the waveguide are investigated as a function of the waveguide geometry in uniformly and periodically poled medium.
Sonka, Milan; Abramoff, Michael D.
2013-01-01
In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR. PMID:24222760
NASA Astrophysics Data System (ADS)
Huang, Qinghua; Li, Zhanhui; Wang, Yanbin
2010-12-01
We presented a parallel 3-D staggered grid pseudospectral time domain (PSTD) method for simulating ground-penetrating radar (GPR) wave propagation. We took the staggered grid method to weaken the global effect in PSTD and developed a modified fast Fourier transform (FFT) spatial derivative operator to eliminate the wraparound effect due to the implicit periodical boundary condition in FFT operator. After the above improvements, we achieved the parallel PSTD computation based on an overlap domain decomposition method without any absorbing condition for each subdomain, which can significantly reduce the required grids in each overlap subdomain comparing with other proposed algorithms. We test our parallel technique for some numerical models and obtained consistent results with the analytical ones and/or those of the nonparallel PSTD method. The above numerical tests showed that our parallel PSTD algorithm is effective in simulating 3-D GPR wave propagation, with merits of saving computation time, as well as more flexibility in dealing with complicated models without losing the accuracy. The application of our parallel PSTD method in applied geophysics and paleoseismology based on GPR data confirmed the efficiency of our algorithm and its potential applications in various subdisciplines of solid earth geophysics. This study would also provide a useful parallel PSTD approach to the simulation of other geophysical problems on distributed memory PC cluster.
Martino, Mikaël M.; Mochizuki, Mayumi; Rothenfluh, Dominique A.; Rempel, Sandra A.; Hubbell, Jeffrey A.; Barker, Thomas H.
2009-01-01
The extracellular matrix (ECM) exerts powerful control over many cellular phenomena, including stem cell differentiation. As such, design and modulation of ECM analogs to ligate specific integrin is a promising approach to control cellular processes in vitro and in vivo for regenerative medicine strategies. Although fibronectin (FN), a crucial ECM protein in tissue development and repair, and its RGD peptide are widely used for cell adhesion, the promiscuity with which they engage integrins leads to difficulty in control of receptor-specific interactions. Recent simulations of force-mediated unfolding of FN domains and sequences analysis of human versus mouse FN suggest that the structural stability of the FN’s central cell-binding domains (FN III9-10) affects its integrin specificity. Through production of FN III9-10 variants with variable stabilities, we obtained ligands that present different specificities for the integrin α5β1 and that can be covalently linked into fibrin matrices. Here, we demonstrate the capacity of α5β1 integrin-specific engagement to influence human mesenchymal stem cell (MSC) behavior in 2D and 3D environments. Our data indicate that α5β1 has an important role in the control of MSC osteogenic differentiation. FN fragments with increased specificity for α5β1 versus αvβ3 results in significantly enhanced osteogenic differentiation of MSCs in 2D and in a clinically relevant 3D fibrin matrix system, although attachment/spreading and proliferation were comparable with that on full-length FN. This work shows how integrin-dependant cellular interactions with the ECM can be engineered to control stem cell fate, within a system appropriate for both 3D cell culture and tissue engineering. PMID:19027948
NASA Astrophysics Data System (ADS)
Ryu, Dongok; Kim, Sug-Whan; Kim, Dae Wook; Lee, Jae-Min; Lee, Hanshin; Park, Won Hyun; Seong, Sehyun; Ham, Sun-Jeong
2010-09-01
Understanding the Earth spectral bio-signatures provides an important reference datum for accurate de-convolution of collapsed spectral signals from potential earth-like planets of other star systems. This study presents a new ray tracing computation method including an improved 3D optical earth model constructed with the coastal line and vegetation distribution data from the Global Ecological Zone (GEZ) map. Using non-Lambertian bidirectional scattering distribution function (BSDF) models, the input earth surface model is characterized with three different scattering properties and their annual variations depending on monthly changes in vegetation distribution, sea ice coverage and illumination angle. The input atmosphere model consists of one layer with Rayleigh scattering model from the sea level to 100 km in altitude and its radiative transfer characteristics is computed for four seasons using the SMART codes. The ocean scattering model is a combination of sun-glint scattering and Lambertian scattering models. The land surface scattering is defined with the semi empirical parametric kernel method used for MODIS and POLDER missions. These three component models were integrated into the final Earth model that was then incorporated into the in-house built integrated ray tracing (IRT) model capable of computing both spectral imaging and radiative transfer performance of a hypothetical space instrument as it observes the Earth from its designated orbit. The IRT model simulation inputs include variation in earth orientation, illuminated phases, and seasonal sea ice and vegetation distribution. The trial simulation runs result in the annual variations in phase dependent disk averaged spectra (DAS) and its associated bio-signatures such as NDVI. The full computational details are presented together with the resulting annual variation in DAS and its associated bio-signatures.
Dialog-Based 3D-Image Recognition Using a Domain Ontology
NASA Astrophysics Data System (ADS)
Hois, Joana; Wünstel, Michael; Bateman, John A.; Röfer, Thomas
The combination of vision and speech, together with the resulting necessity for formal representations, builds a central component of an autonomous system. A robot that is supposed to navigate autonomously through space must be able to perceive its environment as automatically as possible. But each recognition system has its own inherent limits. Especially a robot whose task is to navigate through unknown terrain has to deal with unidentified or even unknown objects, thus compounding the recognition problem still further. The system described in this paper takes this into account by trying to identify objects based on their functionality where possible. To handle cases where recognition is insufficient, we examine here two further strategies: on the one hand, the linguistic reference and labeling of the unidentified objects and, on the other hand, ontological deduction. This approach then connects the probabilistic area of object recognition with the logical area of formal reasoning. In order to support formal reasoning, additional relational scene information has to be supplied by the recognition system. Moreover, for a sound ontological basis for these reasoning tasks, it is necessary to define a domain ontology that provides for the representation of real-world objects and their corresponding spatial relations in linguistic and physical respects. Physical spatial relations and objects are measured by the visual system, whereas linguistic spatial relations and objects are required for interactions with a user.
3D Polarized Radiative Transfer for Solar System Applications Using the public-domain HYPERION Code
NASA Astrophysics Data System (ADS)
Wolff, M. J.; Robitaille, T.; Whitney, B. A.
2012-12-01
We present a public-domain radiative transfer tool that will allow researchers to examine a wide-range of interesting solar system applications. Hyperion is a new three-dimensional continuum Monte-Carlo radiative transfer code that is designed to be as general as possible, allowing radiative transfer to be computed through a variety of three-dimensional grids (Robitaille, 2011, Astronomy & Astrophysics 536 A79). The main part of the code is problem-independent, and only requires the user to define the three-dimensional density structure, and the opacity and the illumination properties (as well as a few parameters that control execution and output of the code). Hyperion is written in Fortran 90 and parallelized using the MPI-2 standard. It is bundled with Python libraries that enable very flexible pre- and post-processing options (arbitrary shapes, multiple aerosol components, etc.). These routines are very amenable to user-extensibility. The package is currently distributed at www.hyperion-rt.org. Our presentation will feature 1) a brief overview of the code, including a description of the solar system-specific modifications that we have made beyond the capabilities in the original release; 2) Several solar system applications (i.e., Deep Impact Plume, Martian atmosphere, etc.); 3) discussion of availability and distribution of code components via www.hyperion-rt.org.
Spectral-domain interferometry for quantitative DIC microscopy
NASA Astrophysics Data System (ADS)
Li, Chengshuai; Zhu, Yizheng
2014-03-01
A spectral-domain differential interference contrast (SD-DIC) microscopy system is presented for quantitative imaging of both reflective and transparent samples. The spectral-domain interferometry, combined with the common-path DIC geometry, provides a shot noise-limited sensitivity of 14.3pm in optical pathlength gradient measurement. The optical resolution of the system was characterized using images of a USAF resolution target. Fused silica microspheres were imaged to demonstrate the reconstruction of two-dimensional optical pathlength topography from measured gradient fields. The exquisite sensitivity of the system showed potential in quantitative imaging of sub-diffraction limit objects such as gold nanoparticles.
NASA Astrophysics Data System (ADS)
Parent, Francois; Kanti Mandal, Koushik; Loranger, Sebastien; Watanabe Fernandes, Eric Hideki; Kashyap, Raman; Kadoury, Samuel
2016-03-01
We propose here a new alternative to provide real-time device tracking during minimally invasive interventions using a truly-distributed strain sensor based on optical frequency domain reflectometry (OFDR) in optical fibers. The guidance of minimally invasive medical instruments such as needles or catheters (ex. by adding a piezoelectric coating) has been the focus of extensive research in the past decades. Real-time tracking of instruments in medical interventions facilitates image guidance and helps the user to reach a pre-localized target more precisely. Image-guided systems using ultrasound imaging and shape sensors based on fiber Bragg gratings (FBG)-embedded optical fibers can provide retroactive feedback to the user in order to reach the targeted areas with even more precision. However, ultrasound imaging with electro-magnetic tracking cannot be used in the magnetic resonance imaging (MRI) suite, while shape sensors based on FBG embedded in optical fibers provides discrete values of the instrument position, which requires approximations to be made to evaluate its global shape. This is why a truly-distributed strain sensor based on OFDR could enhance the tracking accuracy. In both cases, since the strain is proportional to the radius of curvature of the fiber, a strain sensor can provide the three-dimensional shape of medical instruments by simply inserting fibers inside the devices. To faithfully follow the shape of the needle in the tracking frame, 3 fibers glued in a specific geometry are used, providing 3 degrees of freedom along the fiber. Near real-time tracking of medical instruments is thus obtained offering clear advantages for clinical monitoring in remotely controlled catheter or needle guidance. We present results demonstrating the promising aspects of this approach as well the limitations of using the OFDR technique.
The 3D structure of Kaposi sarcoma herpesvirus LANA C-terminal domain bound to DNA
Hellert, Jan; Weidner-Glunde, Magdalena; Krausze, Joern; Lünsdorf, Heinrich; Ritter, Christiane; Schulz, Thomas F.; Lührs, Thorsten
2015-01-01
Kaposi sarcoma herpesvirus (KSHV) persists as a latent nuclear episome in dividing host cells. This episome is tethered to host chromatin to ensure proper segregation during mitosis. For duplication of the latent genome, the cellular replication machinery is recruited. Both of these functions rely on the constitutively expressed latency-associated nuclear antigen (LANA) of the virus. Here, we report the crystal structure of the KSHV LANA DNA-binding domain (DBD) in complex with its high-affinity viral target DNA, LANA binding site 1 (LBS1), at 2.9 Å resolution. In contrast to homologous proteins such as Epstein-Barr virus nuclear antigen 1 (EBNA-1) of the related γ-herpesvirus Epstein-Barr virus, specific DNA recognition by LANA is highly asymmetric. In addition to solving the crystal structure, we found that apart from the two known LANA binding sites, LBS1 and LBS2, LANA also binds to a novel site, denoted LBS3. All three sites are located in a region of the KSHV terminal repeat subunit previously recognized as a minimal replicator. Moreover, we show that the LANA DBD can coat DNA of arbitrary sequence by virtue of a characteristic lysine patch, which is absent in EBNA-1 of the Epstein-Barr virus. Likely, these higher-order assemblies involve the self-association of LANA into supermolecular spirals. One such spiral assembly was solved as a crystal structure of 3.7 Å resolution in the absence of DNA. On the basis of our data, we propose a model for the controlled nucleation of higher-order LANA oligomers that might contribute to the characteristic subnuclear KSHV microdomains (“LANA speckles”), a hallmark of KSHV latency. PMID:25947153
Bi-planar 2D-to-3D registration in Fourier domain for stereoscopic x-ray motion tracking
NASA Astrophysics Data System (ADS)
Zosso, Dominique; Le Callennec, Benoît; Bach Cuadra, Meritxell; Aminian, Kamiar; Jolles, Brigitte M.; Thiran, Jean-Philippe
2008-03-01
In this paper we present a new method to track bone movements in stereoscopic X-ray image series of the knee joint. The method is based on two different X-ray image sets: a rotational series of acquisitions of the still subject knee that allows the tomographic reconstruction of the three-dimensional volume (model), and a stereoscopic image series of orthogonal projections as the subject performs movements. Tracking the movements of bones throughout the stereoscopic image series means to determine, for each frame, the best pose of every moving element (bone) previously identified in the 3D reconstructed model. The quality of a pose is reflected in the similarity between its theoretical projections and the actual radiographs. We use direct Fourier reconstruction to approximate the three-dimensional volume of the knee joint. Then, to avoid the expensive computation of digitally rendered radiographs (DRR) for pose recovery, we develop a corollary to the 3-dimensional central-slice theorem and reformulate the tracking problem in the Fourier domain. Under the hypothesis of parallel X-ray beams, the heavy 2D-to-3D registration of projections in the signal domain is replaced by efficient slice-to-volume registration in the Fourier domain. Focusing on rotational movements, the translation-relevant phase information can be discarded and we only consider scalar Fourier amplitudes. The core of our motion tracking algorithm can be implemented as a classical frame-wise slice-to-volume registration task. Results on both synthetic and real images confirm the validity of our approach.
NASA Astrophysics Data System (ADS)
Galvez, P.; Ampuero, J. P.; Dalguer, L. A.; Nissen-Meyer, T.
2011-12-01
On March 11th 2011, a Mw 9 earthquake stroke Japan causing 28000 victims and triggering a devastating tsunami that caused severe damage along the Japanese coast. The exceptional amount of data recorded by this earthquake, with thousands of sensors located all over Japan, provides a great opportunity for seismologist and engineers to investigate in detail the rupture process in order to better understand the physics of this type of earthquakes and their associated effects, like tsunamis. Here we investigate, by means of dynamic rupture simulations, a plausible mechanism to explain key observations about the rupture process of the 2011 M9 Tohoku earthquake, including the spatial complementarity between high and low frequency aspects of slip (e.g, Simons et al, Science 2011, Meng et al, GRL 2011). To model the dynamic rupture of this event, we use a realistic non-planar fault geometry of the megathrust interface, using the unstructured 3D spectral element open source code SPECFEM3D-SESAME, in which we recently implemented the dynamic fault boundary conditions. This implementation follows the principles introduced by Ampuero (2002) and Kaneko et al. (2008) and involves encapsulated modules plugged into the code. Our current implementation provides the possibility of modeling dynamic rupture for multiple, non-planar faults governed by slip-weakening friction. We successfully verified the code in several SCEC benchmarks, including a 3D problem with branched faults, as well as modeling the rupture of subduction megathrust with a splay fault, finding results comparable to published results. Our first set of simulations is aimed at testing if the diversity of rupture phenomena during the 2011 M9 Tohoku earthquake (see Ampuero et al in this session) can be overall reproduced by assuming the most basic friction law, linear slip-weakening friction, but prescribing a spatially heterogeneous distribution of the critical slip weakening distance Dc and initial fault stresses. Our
Separation Surfaces in the Spectral TV Domain for Texture Decomposition
NASA Astrophysics Data System (ADS)
Horesh, Dikla; Gilboa, Guy
2016-09-01
In this paper we introduce a novel notion of separation surfaces for image decomposition. A surface is embedded in the spectral total-variation (TV) three dimensional domain and encodes a spatially-varying separation scale. The method allows good separation of textures with gradually varying pattern-size, pattern-contrast or illumination. The recently proposed total variation spectral framework is used to decompose the image into a continuum of textural scales. A desired texture, within a scale range, is found by fitting a surface to the local maximal responses in the spectral domain. A band above and below the surface, referred to as the \\textit{Texture Stratum}, defines for each pixel the adaptive scale-range of the texture. Based on the decomposition an application is proposed which can attenuate or enhance textures in the image in a very natural and visually convincing manner.
Spectral domain detection in low-coherence spectroscopy
Bosschaart, Nienke; Aalders, Maurice C. G.; van Leeuwen, Ton G.; Faber, Dirk J.
2012-01-01
Low-coherence spectroscopy (LCS) offers the valuable possibility to measure quantitative and wavelength resolved optical property spectra within a tissue volume of choice that is controllable both in size and in depth. Until now, only time domain detection was investigated for LCS (tdLCS), but spectral domain detection offers a theoretical speed/sensitivity advantage over tdLCS. In this article, we introduce a method for spectral domain detection in LCS (sdLCS), with optimal sensitivity as a function of measurement depth. We validate our method computationally in a simulation and experimentally on a phantom with known optical properties. The attenuation, absorption and scattering coefficient spectra from the phantom that were measured by sdLCS agree well with the expected optical properties and the measured optical properties by tdLCS. PMID:23024918
NASA Astrophysics Data System (ADS)
Bower, Bradley A.; Chiu, Stephanie J.; Davies, Emily; Davis, Anjul M.; Zawadzki, Robert J.; Fuller, Alfred R.; Wiley, David F.; Izatt, Joseph A.; Toth, Cynthia A.
2007-02-01
We report on the development of quantitative, reproducible diagnostic observables for age-related macular degeneration (AMD) based on high speed spectral domain optical coherence tomography (SDOCT). 3D SDOCT volumetric data sets (512 x 1000 x 100 voxels) were collected (5.7 seconds acquisition time) in over 50 patients with age-related macular degeneration and geographic atrophy using a state-of-the-art SDOCT scanner. Commercial and custom software utilities were used for manual and semi-automated segmentation of photoreceptor layer thickness, total drusen volume, and geographic atrophy cross-sectional area. In a preliminary test of reproducibility in segmentation of total drusen volume and geographic atrophy surface area, inter-observer error was less than 5%. Extracted volume and surface area of AMD-related drusen and geographic atrophy, respectively, may serve as useful observables for tracking disease state that were not accessible without the rapid 3D volumetric imaging capability unique to retinal SDOCT.
Hartman, Olga; Zhang, Chu; Adams, Elizabeth L.; Farach-Carson, Mary C.; Petrelli, Nicholas J.; Chase, Bruce D.; Rabolt, John F.
2010-01-01
Because prostate cancer cells metastasize to bone and exhibit osteoblastic features (osteomimicry), the interrelationships between bone-specific microenvironment and prostate cancer cells at sites of bone metastasis are critical to disease progression. In this work the bone marrow microenvironment in vitro was recreated both by tailoring scaffolds physical properties and by functionalizing electrospun polymer fibers with a bioactive peptide derived from domain IV of perlecan heparan sulfate proteoglycan. Electrospun poly (ε-caprolactone) (PCL) fibers and PCL/gelatin composite scaffolds were modified covalently with perlecan domain IV (PlnDIV) peptide. The expression of tight junction protein (E-cadherin) and focal adhesion kinase (FAK) phosphorylation on tyrosine 397 also were investigated. The described bioactive motif significantly enhanced adherence and infiltration of the metastatic prostate cancer cells on all modified electrospun substrates by day 5 post-seeding. Cells cultured on PlnDIV-modified matrices organized stress fibers and increased proliferation at statistically significant rates. Additional findings suggest that presence of PlnDIV peptide in the matrix reduced expression of tight junction protein and binding to PlnDIV peptide was accompanied by increased focal adhesion kinase (FAK) phosphorylation on tyrosine 397. We conclude that PlnDIV peptide supports key signaling events leading to proliferation, survival, and migration of C4-2B cancer cells; hence its incorporation into electrospun matrix is a key improvement to create a successful three-dimensional (3-D) pharmacokinetic cancer model. PMID:20417554
NASA Astrophysics Data System (ADS)
Li, Y.; Han, B.; Métivier, L.; Brossier, R.
2016-09-01
We investigate an optimal fourth-order staggered-grid finite-difference scheme for 3D frequency-domain viscoelastic wave modeling. An anti-lumped mass strategy is incorporated to minimize the numerical dispersion. The optimal finite-difference coefficients and the mass weighting coefficients are obtained by minimizing the misfit between the normalized phase velocities and the unity. An iterative damped least-squares method, the Levenberg-Marquardt algorithm, is utilized for the optimization. Dispersion analysis shows that the optimal fourth-order scheme presents less grid dispersion and anisotropy than the conventional fourth-order scheme with respect to different Poisson's ratios. Moreover, only 3.7 grid-points per minimum shear wavelength are required to keep the error of the group velocities below 1%. The memory cost is then greatly reduced due to a coarser sampling. A parallel iterative method named CARP-CG is used to solve the large ill-conditioned linear system for the frequency-domain modeling. Validations are conducted with respect to both the analytic viscoacoustic and viscoelastic solutions. Compared with the conventional fourth-order scheme, the optimal scheme generates wavefields having smaller error under the same discretization setups. Profiles of the wavefields are presented to confirm better agreement between the optimal results and the analytic solutions.
Orlikowska, Marta; Jankowska, Elżbieta; Kołodziejczyk, Robert; Jaskólski, Mariusz; Szymańska, Aneta
2011-02-01
Cystatins are natural inhibitors of cysteine proteases, enzymes that are widely distributed in animals, plants, and microorganisms. Human cystatin C (hCC) has been also recognized as an aggregating protein directly involved in the formation of pathological amyloid fibrils, and these amyloidogenic properties greatly increase in a naturally occurring L68Q hCC variant. For a long time only dimeric structure of wild-type hCC has been known. The dimer is created through 3D domain swapping process, in which two parts of the cystatin structure become separated from each other and next exchanged between two molecules. Important role in the domain swapping plays the L1 loop, which connects the exchanging segments and, upon dimerization, transforms from a β-turn into a part of a long β-strand. In the very recently published first monomeric structure of human cystatin C (hCC-stab1), dimerization was abrogated due to clasping of the β-strands from the swapping domains by an engineered disulfide bridge. We have designed and constructed another mutated cystatin C with the smallest possible structural intervention, that is a single-point mutation replacing hydrophobic V57 from the L1 loop by polar asparagine, known as a stabilizer of a β-turn motif. V57N hCC mutant occurred to be stable in its monomeric form and crystallized as a monomer, revealing typical cystatin fold with a five-stranded antiparallel β-sheet wrapped around an α-helix. Here we report a 2.04 Å resolution crystal structure of V57N hCC and discuss the architecture of the protein in comparison to chicken cystatin, hCC-stab1 and dimeric hCC. PMID:21074623
Peterson, Alexis W.; Caldwell, David J.; Stegemann, Jan P.; Deng, Cheri X.
2014-01-01
Non-destructive monitoring of engineered tissues is needed for translation of these products from the lab to the clinic. In this study, non-invasive, high resolution spectral ultrasound imaging (SUSI) was used to monitor the differentiation of MC3T3 pre-osteoblasts seeded within collagen hydrogels. SUSI was used to measure the diameter, concentration and acoustic attenuation of scatterers within such constructs cultured in either control or osteogenic medium over 21 days. Conventional biochemical assays were used on parallel samples to determine DNA content and calcium deposition. Construct volume and morphology were accurately imaged using ultrasound. Cell diameter was estimated to be approximately 12.5–15.5 µm using SUSI, which corresponded well to measurements of fluorescently stained cells. The total number of cells per construct assessed by quantitation of DNA content decreased from 5.6±2.4×104 at day 1 to 0.9±0.2×104 at day 21. SUSI estimation of the equivalent number of acoustic scatters showed a similar decreasing trend, except at day 21 in the osteogenic samples, which showed a marked increase in both scatterer number and acoustic impedance, suggestive of mineral deposition by the differentiating MC3T3 cells. Estimation of calcium content by SUSI was 41.7±11.4 µg/ml, which agreed well with the biochemical measurement of 38.7±16.7 µg/ml. Color coded maps of parameter values were overlaid on B-mode images to show spatiotemporal changes in cell diameter and calcium deposition. This study demonstrates the use of non-destructive ultrasound imaging to provide quantitative information on the number and differentiated state of cells embedded within 3D engineered constructs, and therefore presents a valuable tool for longitudinal monitoring of engineered tissue development. PMID:24465680
Spectral element modeling of 3D wave propagation in the Earth: the graver part of the spectrum
NASA Astrophysics Data System (ADS)
Chaljub, E.; Valette, B.
2003-04-01
The Spectral Element Method (SEM) has been recently established as a new reference to compute synthetic seismograms in 3D models of the Earth. So far, all the studies involving the SEM have been performed within the Cowling approximation, i. e. neglecting the variations of the gravity field during wave propagation. For low-frequency studies (typically less than 5 mHz) the previous assumption fails and the complete treatment of self-gravitation has to be considered. This requires the introduction of the mass redistribution potential (MRP) which has to satisfy Poisson's equation everywhere in space. Unlike spherical harmonics approaches, the use of a grid based method does not provide a natural framework for the resolution of the exterior problem. However, we show that a Dirichlet-to-Neumann operator at the surface of the Earth provides a simple and efficient solution to this problem. A special attention is needed for the fluid parts to avoid spurious oscillations. To this end, we introduce a general two-potentials formulation which allows to take any density stratification into account. Contrary to other studies that considered the velocity potential, our decomposition is applied to the displacement field in order to obtain natural solid-fluid boundary conditions for the MRP. At each time step, the MRP is computed from the displacement field through a preconditioned conjugate gradient algorithm. This procedure has to be accurate enough in order to ensure a stable calculation on long time series. Some examples of synthetic seismograms computed in spherical Earth models illustrate the accuracy of our approach.
Gudur, Madhu Sudhan Reddy; Rao, Rameshwar R; Peterson, Alexis W; Caldwell, David J; Stegemann, Jan P; Deng, Cheri X
2014-01-01
Non-destructive monitoring of engineered tissues is needed for translation of these products from the lab to the clinic. In this study, non-invasive, high resolution spectral ultrasound imaging (SUSI) was used to monitor the differentiation of MC3T3 pre-osteoblasts seeded within collagen hydrogels. SUSI was used to measure the diameter, concentration and acoustic attenuation of scatterers within such constructs cultured in either control or osteogenic medium over 21 days. Conventional biochemical assays were used on parallel samples to determine DNA content and calcium deposition. Construct volume and morphology were accurately imaged using ultrasound. Cell diameter was estimated to be approximately 12.5-15.5 µm using SUSI, which corresponded well to measurements of fluorescently stained cells. The total number of cells per construct assessed by quantitation of DNA content decreased from 5.6±2.4×10(4) at day 1 to 0.9±0.2×10(4) at day 21. SUSI estimation of the equivalent number of acoustic scatters showed a similar decreasing trend, except at day 21 in the osteogenic samples, which showed a marked increase in both scatterer number and acoustic impedance, suggestive of mineral deposition by the differentiating MC3T3 cells. Estimation of calcium content by SUSI was 41.7±11.4 µg/ml, which agreed well with the biochemical measurement of 38.7±16.7 µg/ml. Color coded maps of parameter values were overlaid on B-mode images to show spatiotemporal changes in cell diameter and calcium deposition. This study demonstrates the use of non-destructive ultrasound imaging to provide quantitative information on the number and differentiated state of cells embedded within 3D engineered constructs, and therefore presents a valuable tool for longitudinal monitoring of engineered tissue development. PMID:24465680
NASA Technical Reports Server (NTRS)
Steinthorsson, E.; Shih, T. I-P.; Roelke, R. J.
1991-01-01
In order to generate good quality systems for complicated three-dimensional spatial domains, the grid-generation method used must be able to exert rather precise controls over grid-point distributions. Several techniques are presented that enhance control of grid-point distribution for a class of algebraic grid-generation methods known as the two-, four-, and six-boundary methods. These techniques include variable stretching functions from bilinear interpolation, interpolating functions based on tension splines, and normalized K-factors. The techniques developed in this study were incorporated into a new version of GRID3D called GRID3D-v2. The usefulness of GRID3D-v2 was demonstrated by using it to generate a three-dimensional grid system in the coolent passage of a radial turbine blade with serpentine channels and pin fins.
Dynamic spectral-domain optical coherence elastography for tissue characterization.
Liang, Xing; Adie, Steven G; John, Renu; Boppart, Stephen A
2010-06-21
A dynamic spectral-domain optical coherence elastography (OCE) imaging technique is reported. In this technique, audio-frequency compressive vibrations are generated by a piezoelectric stack as external excitation, and strain rates in the sample are calculated and mapped quantitatively using phase-sensitive spectral-domain optical coherence tomography. At different driving frequencies, this technique provides contrast between sample regions with different mechanical properties, and thus is used to mechanically characterize tissue. We present images of a three-layer silicone tissue phantom and rat tumor tissue ex vivo, based on quantitative strain rate. Both acquisition speed and processing speed are improved dramatically compared with previous OCE imaging techniques. With high resolution, high acquisition speed, and the ability to characterize the mechanical properties of tissue, this OCE technique has potential use in non-destructive volumetric imaging and clinical applications. PMID:20588552
Dynamic spectral-domain optical coherence elastography for tissue characterization
Liang, Xing; Adie, Steven G.; John, Renu; Boppart, Stephen A.
2010-01-01
A dynamic spectral-domain optical coherence elastography (OCE) imaging technique is reported. In this technique, audio-frequency compressive vibrations are generated by a piezoelectric stack as external excitation, and strain rates in the sample are calculated and mapped quantitatively using phase-sensitive spectral-domain optical coherence tomography. At different driving frequencies, this technique provides contrast between sample regions with different mechanical properties, and thus is used to mechanically characterize tissue. We present images of a three-layer silicone tissue phantom and rat tumor tissue ex vivo, based on quantitative strain rate. Both acquisition speed and processing speed are improved dramatically compared with previous OCE imaging techniques. With high resolution, high acquisition speed, and the ability to characterize the mechanical properties of tissue, this OCE technique has potential use in non-destructive volumetric imaging and clinical applications. PMID:20588552
NASA Technical Reports Server (NTRS)
Shih, T. I.-P.; Bailey, R. T.; Nguyen, H. L.; Roelke, R. J.
1990-01-01
An efficient computer program, called GRID2D/3D was developed to generate single and composite grid systems within geometrically complex two- and three-dimensional (2- and 3-D) spatial domains that can deform with time. GRID2D/3D generates single grid systems by using algebraic grid generation methods based on transfinite interpolation in which the distribution of grid points within the spatial domain is controlled by stretching functions. All single grid systems generated by GRID2D/3D can have grid lines that are continuous and differentiable everywhere up to the second-order. Also, grid lines can intersect boundaries of the spatial domain orthogonally. GRID2D/3D generates composite grid systems by patching together two or more single grid systems. The patching can be discontinuous or continuous. For continuous composite grid systems, the grid lines are continuous and differentiable everywhere up to the second-order except at interfaces where different single grid systems meet. At interfaces where different single grid systems meet, the grid lines are only differentiable up to the first-order. For 2-D spatial domains, the boundary curves are described by using either cubic or tension spline interpolation. For 3-D spatial domains, the boundary surfaces are described by using either linear Coon's interpolation, bi-hyperbolic spline interpolation, or a new technique referred to as 3-D bi-directional Hermite interpolation. Since grid systems generated by algebraic methods can have grid lines that overlap one another, GRID2D/3D contains a graphics package for evaluating the grid systems generated. With the graphics package, the user can generate grid systems in an interactive manner with the grid generation part of GRID2D/3D. GRID2D/3D is written in FORTRAN 77 and can be run on any IBM PC, XT, or AT compatible computer. In order to use GRID2D/3D on workstations or mainframe computers, some minor modifications must be made in the graphics part of the program; no
Imaging tamoxifen retinopathy using spectral-domain optical coherence tomography
Caramoy, Albert; Scholz, Paula; Fauser, Sascha; Kirchhof, Bernd
2011-01-01
A case of tamoxifen retinopathy examined with spectral-domain optical coherence tomography (SD-OCT) is presented. The typical refractile deposits are located between ganglion cell layer and inner plexiform layer in SD-OCT. A defect on the outer retinal layer with disruption of the photoreceptor layer with sharp edges is seen. The still attached posterior hyaloids gives evidence of other pathomechanism involved in the outer retinal defect than that of macular hole, as suggested in the literature.
NASA Astrophysics Data System (ADS)
Palka, N.; Panowicz, R.; Ospald, F.; Beigang, R.
2015-08-01
An ultra-high molecular weight polyethylene composite sample totally punctured by a projectile was examined by THz TDS raster scanning method in reflection configuration. The scanning results correctly match the distribution of delaminations inside the sample, which was proven with cross-sectional and frontal views after waterjet cutting. For further analysis, a signal-processing algorithm based on the deconvolution method was developed and the modified reference signal was used to reduce disturbances. The complex refractive index of the sample was determined by transmission TDS technique and was later used for the simulation of pulse propagation by the finite difference time domain method. These simulations verified the correctness of the proposed method and showed its constraints. Using the proposed algorithm, the ambiguous raw THz image was converted into a binary 3D image of the sample, which consists only of two areas: sample—polyethylene and delamination—air. As a result, a clear image of the distribution of delaminations with their spatial extent was obtained which can be used for further comparative analysis. The limitation of the proposed method is that parts of the central area of the puncture cannot be analyzed because tilted layers deflect the incident signal.
NASA Astrophysics Data System (ADS)
Canavesi, Cristina; Cogliati, Andrea; Hayes, Adam; Santhanam, Anand P.; Tankam, Patrice; Rolland, Jannick P.
2015-10-01
Fast, robust, nondestructive 3D imaging is needed for characterization of microscopic structures in industrial and clinical applications. A custom micro-electromechanical system (MEMS)-based 2D scanner system was developed to achieve 55 kHz A-scan acquisition in a Gabor-domain optical coherence microscopy (GD-OCM) instrument with a novel multilevel GPU architecture for high-speed imaging. GD-OCM yields high-definition volumetric imaging with dynamic depth of focusing through a bio-inspired liquid lens-based microscope design, which has no moving parts and is suitable for use in a manufacturing setting or in a medical environment. A dual-axis MEMS mirror was chosen to replace two single-axis galvanometer mirrors; as a result, the astigmatism caused by the mismatch between the optical pupil and the scanning location was eliminated and a 12x reduction in volume of the scanning system was achieved. Imaging at an invariant resolution of 2 μm was demonstrated throughout a volume of 1 × 1 × 0.6 mm3, acquired in less than 2 minutes. The MEMS-based scanner resulted in improved image quality, increased robustness and lighter weight of the system - all factors that are critical for on-field deployment. A custom integrated feedback system consisting of a laser diode and a position-sensing detector was developed to investigate the impact of the resonant frequency of the MEMS and the driving signal of the scanner on the movement of the mirror. Results on the metrology of manufactured materials and characterization of tissue samples with GD-OCM are presented.
NASA Astrophysics Data System (ADS)
Ge, Liang; Sotiropoulos, Fotis
2007-08-01
A novel numerical method is developed that integrates boundary-conforming grids with a sharp interface, immersed boundary methodology. The method is intended for simulating internal flows containing complex, moving immersed boundaries such as those encountered in several cardiovascular applications. The background domain (e.g. the empty aorta) is discretized efficiently with a curvilinear boundary-fitted mesh while the complex moving immersed boundary (say a prosthetic heart valve) is treated with the sharp-interface, hybrid Cartesian/immersed-boundary approach of Gilmanov and Sotiropoulos [A. Gilmanov, F. Sotiropoulos, A hybrid cartesian/immersed boundary method for simulating flows with 3d, geometrically complex, moving bodies, Journal of Computational Physics 207 (2005) 457-492.]. To facilitate the implementation of this novel modeling paradigm in complex flow simulations, an accurate and efficient numerical method is developed for solving the unsteady, incompressible Navier-Stokes equations in generalized curvilinear coordinates. The method employs a novel, fully-curvilinear staggered grid discretization approach, which does not require either the explicit evaluation of the Christoffel symbols or the discretization of all three momentum equations at cell interfaces as done in previous formulations. The equations are integrated in time using an efficient, second-order accurate fractional step methodology coupled with a Jacobian-free, Newton-Krylov solver for the momentum equations and a GMRES solver enhanced with multigrid as preconditioner for the Poisson equation. Several numerical experiments are carried out on fine computational meshes to demonstrate the accuracy and efficiency of the proposed method for standard benchmark problems as well as for unsteady, pulsatile flow through a curved, pipe bend. To demonstrate the ability of the method to simulate flows with complex, moving immersed boundaries we apply it to calculate pulsatile, physiological flow
NASA Astrophysics Data System (ADS)
Petrov, P.; Newman, G. A.
2010-12-01
-Fourier domain we had developed 3D code for full-wave field simulation in the elastic media which take into account nonlinearity introduced by free-surface effects. Our approach is based on the velocity-stress formulation. In the contrast to conventional formulation we defined the material properties such as density and Lame constants not at nodal points but within cells. This second order finite differences method formulated in the cell-based grid, generate numerical solutions compatible with analytical ones within the range errors determinate by dispersion analysis. Our simulator will be embedded in an inversion scheme for joint seismic- electromagnetic imaging. It also offers possibilities for preconditioning the seismic wave propagation problems in the frequency domain. References. Shin, C. & Cha, Y. (2009), Waveform inversion in the Laplace-Fourier domain, Geophys. J. Int. 177(3), 1067- 1079. Shin, C. & Cha, Y. H. (2008), Waveform inversion in the Laplace domain, Geophys. J. Int. 173(3), 922-931. Commer, M. & Newman, G. (2008), New advances in three-dimensional controlled-source electromagnetic inversion, Geophys. J. Int. 172(2), 513-535. Newman, G. A., Commer, M. & Carazzone, J. J. (2010), Imaging CSEM data in the presence of electrical anisotropy, Geophysics, in press.
Compressive sensing spectral domain optical coherence tomography with dispersion compensation
NASA Astrophysics Data System (ADS)
Xu, Daguang; Huang, Yong; Kang, Jin U.
2014-03-01
In this paper, we describe a novel CS method that incorporates dispersion compensation into the CS reconstruction of spectral domain OCT (SD OCT) signal. We show that A-scans with dispersion compensation can be obtained by multiplying the dispersion correcting term to the undersampled linear-in-wavenumber spectral data before the CS reconstruction. We also implemented fast CS reconstruction by taking the advantage of fast Fourier transform (FFT). The matrix-vector multiplication commonly used in the CS reconstruction is implemented by a two-step procedure. Compared to the CS reconstruction with matrix multiplication, our method can obtain dispersion compensated A-scan at least 5 times faster. Experimental results show that the proposed method can achieve high quality image with dispersion compensation.
Spectral and lifetime domain measurements of rat brain tumours
NASA Astrophysics Data System (ADS)
Abi Haidar, D.; Leh, B.; Allaoua, K.; Genoux, A.; Siebert, R.; Steffenhagen, M.; Peyrot, D.; Sandeau, N.; Vever-Bizet, C.; Bourg-Heckly, G.; Chebbi, I.; Collado-Hilly, M.
2012-02-01
During glioblastoma surgery, delineation of the brain tumour margins remains difficult especially since infiltrated and normal tissues have the same visual appearance. This problematic constitutes our research interest. We developed a fibre-optical fluorescence probe for spectroscopic and time domain measurements. First measurements of endogenous tissue fluorescence were performed on fresh and fixed rat tumour brain slices. Spectral characteristics, fluorescence redox ratios and fluorescence lifetime measurements were analysed. Fluorescence information collected from both, lifetime and spectroscopic experiments, appeared promising for tumour tissue discrimination. Two photon measurements were performed on the same fixed tissue. Different wavelengths are used to acquire two-photon excitation-fluorescence of tumorous and healthy sites.
NASA Astrophysics Data System (ADS)
Wang, Dong; Zhang, Jian; Xia, Yang; Wang, Hao
2012-10-01
An improved multiple independent iterative plane algorithm, based on a projection optimization idea, is proposed for the independent and arbitrary generation of one spot or multiple spots in a speckle-suppressed 3D work-area. Details of the mathematical expressions of the algorithm are given to theoretically show how it is improved for 3D spot generation. Both simulations and experiments are conducted to investigate the performance of the algorithm for independent and arbitrary 3D spot generation in several different cases. Simulation results agree well with experimental results, which validates the effectiveness of the algorithm proposed. Several additional experiments are demonstrated for fast and independent generation of four or more spots in the 3D space domain, which confirms the capabilities and practicalities of the algorithm further.
NASA Astrophysics Data System (ADS)
Pletinckx, D.
2011-09-01
The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.
Automated method for RNFL segmentation in spectral domain OCT
NASA Astrophysics Data System (ADS)
Paranjape, Amit S.; Elmaanaoui, Badr; Dewelle, Jordan; Rylander, H. Grady; Milner, Thomas E.
2008-02-01
We introduce a method based on optical reflectivity changes to segment the retinal nerve fiber layer (RNFL) in images recorded using swept source spectral domain optical coherence tomography (OCT). The segmented image is used to determine the RNFL thickness. Simple filtering followed by edge detecting techniques can successfully be applied to segment the RNFL from recorded images and estimate RNFL thickness. The method is computationally more efficient than previously reported approaches. Higher computational efficiency allows faster segmentation and provides the ophthalmologist segmented retinal images that better utilize advantages of spectral domain OCT instrumentation. OCT B-scan and fundus images of the retina are recorded for 5 patients. The segmentation method is applied on B-scan images recorded from all patients. An expert ophthalmologist separately demarcates the RNFL layer in the OCT images from the same patients in each B-scan image. Results from automated image processing software are compared to the boundary demarcated by the expert ophthalmologist. The absolute error between the boundaries demarcated by the expert and the algorithm is expressed in terms of area and is used as an error metric. Ability of the algorithm to accurately segment the RNFL in comparison with an expert ophthalmologist is reported.
CHOROIDAL IMAGING USING SPECTRAL-DOMAIN OPTICAL COHERENCE TOMOGRAPHY
Regatieri, Caio V.; Branchini, Lauren; Fujimoto, James G.; Duker, Jay S.
2012-01-01
Background A structurally and functionally normal choroidal vasculature is essential for retinal function. Therefore, a precise clinical understanding of choroidal morphology should be important for understanding many retinal and choroidal diseases. Methods PUBMED (http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed) was used for most of the literature search for this article. The criterion for inclusion of an article in the references for this review was that it included materials about both the clinical and the basic properties of choroidal imaging using spectral-domain optical coherence tomography. Results Recent reports show successful examination and accurate measurement of choroidal thickness in normal and pathologic states using spectral-domain optical coherence tomography systems. This review focuses on the principles of the new technology that make choroidal imaging using optical coherence tomography possible and on the changes that subsequently have been documented to occur in the choroid in various diseases. Additionally, it outlines future directions in choroidal imaging. Conclusion Optical coherence tomography is now proven to be an effective noninvasive tool to evaluate the choroid and to detect choroidal changes in pathologic states. Additionally, choroidal evaluation using optical coherence tomography can be used as a parameter for diagnosis and follow-up. PMID:22487582
Adaptive compressed sensing for spectral-domain optical coherence tomography
NASA Astrophysics Data System (ADS)
Wang, Yi; Chen, Xiaodong; Wang, Ting; Li, Hongxiao; Yu, Daoyin
2014-03-01
Spectral-domain optical coherence tomography (SD-OCT) is a non-contact and non-invasive method for measuring the change of biological tissues caused by pathological changes of body. CCD with huge number of pixels is usually used in SD-OCT to increase the detecting depth, thus enhancing the hardness of data transmission and storage. The usage of compressed sensing (CS) in SD-OCT is able to reduce the trouble of large data transfer and storage, thus eliminating the complexity of processing system. The traditional CS uses the same sampling model for SD-OCT images of different tissue, leading to reconstruction images with different quality. We proposed a CS with adaptive sampling model. The new model is based on uniform sampling model, and the interference spectral of SD-OCT is considered to adjust the local sampling ratio. Compared with traditional CS, adaptive CS can modify the sampling model for images of different tissue according to different interference spectral, getting reconstruction images with high quality without changing sampling model.
NASA Astrophysics Data System (ADS)
Amarsi, A. M.; Asplund, M.; Collet, R.; Leenaarts, J.
2015-11-01
We revisit the Galactic chemical evolution of oxygen, addressing the systematic errors inherent in classical determinations of the oxygen abundance that arise from the use of one-dimensional (1D) hydrostatic model atmospheres and from the assumption of local thermodynamic equilibrium (LTE). We perform detailed 3D non-LTE radiative-transfer calculations for atomic oxygen lines across a grid of 3D hydrodynamic STAGGER model atmospheres for dwarfs and subgiants. We apply our grid of predicted line strengths of the [O I] 630 nm and O I 777 nm lines using accurate stellar parameters from the literature. We infer a steep decay in [O/Fe] for [Fe/H] ≳ -1.0, a plateau [O/Fe] ≈ 0.5 down to [Fe/H] ≈ -2.5, and an increasing trend for [Fe/H] ≲ -2.5. Our 3D non-LTE calculations yield overall concordant results from the two oxygen abundance diagnostics.
Automated detection of Schlemm's canal in spectral-domain optical coherence tomography
NASA Astrophysics Data System (ADS)
Tom, Manu; Ramakrishnan, Vignesh; van Oterendorp, Christian; Deserno, Thomas M.
2015-03-01
Recent advances in optical coherence tomography (OCT) technology allow in vivo imaging of the complex network of intra-scleral aqueous veins in the anterior segment of the eye. Pathological changes in this network, draining the aqueous humor from the eye, are considered to play a role in intraocular pressure elevation, which can lead to glaucoma, one of the major causes of blindness in the world. Through acquisition of OCT volume scans of the anterior eye segment, we aim at reconstructing the three dimensional network of aqueous veins in healthy and glaucomatous subjects. A novel algorithm for segmentation of the three-dimensional (3D) vessel system in human Schlemms canal is presented analyzing frames of spectral domain OCT (SD-OCT) of the eyes surface in either horizontal or vertical orientation. Distortions such as vertical stripes are caused by the superficial blood vessels in the conjunctiva and the episclera. They are removed in the discrete Fourier domain (DFT) masking particular frequencies. Feature-based rigid registration of these noise-filtered images is then performed using the scale invariant feature transform (SIFT). Segmentation of the vessels deep in the sclera originating at or in the vicinity of or having indirect connection to the Schlemm's canal is then performed with 3D region growing technique. The segmented vessels are visualized in 3D providing diagnostically relevant information to the physicians. A proof-of-concept study was performed on a healthy volunteer before and after a pharmaceutical narrowing of Schlemm's canal. A relative decreases 17% was measured based on manual ground truth and the image processing method.
Delvaux, Bertrand; Howard, David
2014-01-01
The piriform fossae are the 2 pear-shaped cavities lateral to the laryngeal vestibule at the lower end of the vocal tract. They act acoustically as side-branches to the main tract, resulting in a spectral zero in the output of the human voice. This study investigates their spectral role by comparing numerical and experimental results of MRI-based 3D printed Vocal Tracts, for which a new experimental method (based on room acoustics) is introduced. The findings support results in the literature: the piriform fossae create a spectral trough in the region 4–5 kHz and act as formants repellents. Moreover, this study extends those results by demonstrating numerically and perceptually the impact of having large piriform fossae on the sung output. PMID:25048199
Delvaux, Bertrand; Howard, David
2014-01-01
The piriform fossae are the 2 pear-shaped cavities lateral to the laryngeal vestibule at the lower end of the vocal tract. They act acoustically as side-branches to the main tract, resulting in a spectral zero in the output of the human voice. This study investigates their spectral role by comparing numerical and experimental results of MRI-based 3D printed Vocal Tracts, for which a new experimental method (based on room acoustics) is introduced. The findings support results in the literature: the piriform fossae create a spectral trough in the region 4-5 kHz and act as formants repellents. Moreover, this study extends those results by demonstrating numerically and perceptually the impact of having large piriform fossae on the sung output. PMID:25048199
NASA Astrophysics Data System (ADS)
Wu, Jing; Gerendas, Bianca S.; Waldstein, Sebastian M.; Simader, Christian; Schmidt-Erfurth, Ursula
2014-03-01
Spectral-domain Optical Coherence Tomography (SD-OCT) is a non-invasive modality for acquiring high reso- lution, three-dimensional (3D) cross sectional volumetric images of the retina and the subretinal layers. SD-OCT also allows the detailed imaging of retinal pathology, aiding clinicians in the diagnosis of sight degrading diseases such as age-related macular degeneration (AMD) and glaucoma.1 Disease diagnosis, assessment, and treatment requires a patient to undergo multiple OCT scans, possibly using different scanning devices, to accurately and precisely gauge disease activity, progression and treatment success. However, the use of OCT imaging devices from different vendors, combined with patient movement may result in poor scan spatial correlation, potentially leading to incorrect patient diagnosis or treatment analysis. Image registration can be used to precisely compare disease states by registering differing 3D scans to one another. In order to align 3D scans from different time- points and vendors using registration, landmarks are required, the most obvious being the retinal vasculature. Presented here is a fully automated cross-vendor method to acquire retina vessel locations for OCT registration from fovea centred 3D SD-OCT scans based on vessel shadows. Noise filtered OCT scans are flattened based on vendor retinal layer segmentation, to extract the retinal pigment epithelium (RPE) layer of the retina. Voxel based layer profile analysis and k-means clustering is used to extract candidate vessel shadow regions from the RPE layer. In conjunction, the extracted RPE layers are combined to generate a projection image featuring all candidate vessel shadows. Image processing methods for vessel segmentation of the OCT constructed projection image are then applied to optimize the accuracy of OCT vessel shadow segmentation through the removal of false positive shadow regions such as those caused by exudates and cysts. Validation of segmented vessel shadows uses
Spectrally balanced detection for optical frequency domain imaging.
Chen, Yueli; de Bruin, Daniel M; Kerbage, Charles; de Boer, Johannes F
2007-12-10
In optical frequency domain imaging (OFDI) or swept-source optical coherence tomography, balanced detection is required to suppress relative intensity noise (RIN). A regular implementation of balanced detection by combining reference and sample arm signal in a 50/50 coupler and detecting the differential output with a balanced receiver is however, not perfect. Since the splitting ratio of the 50/50 coupler is wavelength dependent, RIN is not optimally canceled at the edges of the wavelength sweep. The splitting ratio has a nearly linear shift of 0.4% per nanometer. This brings as much as +/-12% deviation at the margins of wavelength-swept range centered at 1060nm. We demonstrate a RIN suppression of 33dB by spectrally corrected balanced detection, 11dB more that regular balanced detection. PMID:19550929
ERIC Educational Resources Information Center
Zhong, Ying
2013-01-01
Virtual worlds are well-suited for building virtual laboratories for educational purposes to complement hands-on physical laboratories. However, educators may face technical challenges because developing virtual worlds requires skills in programming and 3D design. Current virtual world building tools are developed for users who have programming…
Shift-multiplexing complex spectral-domain optical coherence tomography
NASA Astrophysics Data System (ADS)
Huang, Haochong; Jiang, Zhuqing; Wang, Dayong; Cai, Wenyuan; Man, Tianlong; Wang, Zhe; Panezai, Spozmai
2014-01-01
We propose and experimentally demonstrate a shift-multiplexing complex spectral-domain optical coherence tomography (shift-multiplexing CSD-OCT) method, in which the maximum detection depth of SD-OCT can be greatly extended by incorporating the shift-multiplexing of detection positions with CSD-OCT. The tomographic imaging with twofold or threefold microscopic slides as the target sample is performed. The experimental results show that the tomographic imaging with more uniform brightness and clarity for the different depth regions in a thick sample can be achieved by the shift-multiplexing CSD-OCT system. In particular, even while the sample's depth is beyond the maximum imaging depth of CSD-OCT system, the tomographic imaging of this sample can still be realized by using the shift-multiplexing CSD-OCT method without the need for any replacement of the equipment, such as high spectral capacity grating or high resolution of CCD. The shift-multiplexing CSD-OCT system can perform the imaging with the optimization and less reduction of sensitivity for the deeper detection position in the sample.
Yan, Yangzhi; Ding, Zhihua; Shen, Yi; Chen, Zhiyan; Zhao, Chen; Ni, Yang
2013-11-01
Spectral domain phase microscopy for high-sensitive and broad-dynamic-range quantitative phase imaging is presented. The phase retrieval is realized in the depth domain to maintain a high sensitivity, while the phase information obtained in the spectral domain is exploited to extend the dynamic range of optical path difference. Sensitivity advantage of phase retrieved in the depth domain over that in the spectral domain is thoroughly investigated. The performance of the proposed depth domain phase based approach is illustrated by phase imaging of a resolution target and an onion skin. PMID:24216799
Wang, Jia; Davis, Scott C; Srinivasan, Subhadra; Jiang, Shudong; Pogue, Brian W; Paulsen, Keith D
2008-01-01
Near-infrared (NIR) region-based spectroscopy is examined for accuracy with spectral recovery using frequency domain data at a discrete number of wavelengths, as compared to that with broadband continuous wave data. Data with more wavelengths in the frequency domain always produce superior quantitative spectroscopy results with reduced noise and error in the chromophore concentrations. Performance of the algorithm in the situation of doing region-guided spectroscopy within the MRI is also considered, and the issue of false positive prior regions being identified is examined to see the effect of added wavelengths. The results indicate that broadband frequency domain data are required for maximal accuracy. A broadband frequency domain experimental system was used to validate the predictions, using a mode-locked Ti:sapphire laser for the source between 690- and 850-nm wavelengths. The 80-MHz pulsed signal is heterodyned with photomultiplier tube detection, to lower frequency for data acquisition. Tissue-phantom experiments with known hemoglobin absorption and tissue-like scatter values are used to validate the system, using measurements every 10 nm. More wavelengths clearly provide superior quantification of total hemoglobin values. The system and algorithms developed here should provide an optimal way to quantify regions with the goal of image-guided breast tissue spectroscopy within the MRI. PMID:19021313
Frye, K.M.; Lesmes, D.P.; Morgan, F.D.; Rodi, W.; Shi, W.; Sturrock, J.
1997-12-01
'The objective of this project is to develop the scientific basis for characterizing contaminant plumes in the earth''s subsurface using field measurements of induced polarization (IP) effects. The first-year accomplishments are (1) laboratory experiments on fluid-saturated sandstones quantifying the dependence of spectral IP responses on solution chemistry and rock micro-geometry; (2) library research on the current understanding of electromagnetic coupling effects on IP data acquired in the field: and (3) development of prototype forward modeling and inversion algorithms for interpreting IP data in terms of 3-D models of complex resistivity.'
Three-beam spectral-domain optical coherence tomography for retinal imaging
NASA Astrophysics Data System (ADS)
Suehira, Nobuhito; Ooto, Sotaro; Hangai, Masanori; Matsumoto, Kazuhiro; Tomatsu, Nobuhiro; Yuasa, Takashi; Yamada, Kazuro; Yoshimura, Nagahisa
2012-10-01
A three-beam spectral domain optical coherence tomography system (OCT) whose center wavelength is 840 nm was developed. The three beams focus on fundus 3.1 mm apart from each other and are detected by a single line sensor. The distance between the beams is fixed and the beams scan a total area of 10×10 mm2 while keeping this separation during three-dimensional (3-D) measurement. The line rate of the sensor is 70 kHz, therefore the total speed is equivalent to 210k A-scans per second in this system. A 1000(x)×500(z)×250(y) voxel volumetric 3D OCT data set can be acquired within 2 s. Images of a model eye, a healthy human eye and a diseased eye taken by this system are shown and evaluated. The image quality of one B-Scan is as good as an image from a single-beam OCT. Adjustment among the beams is solved by additional signal processing using a model eye. A multi-beam OCT has the potential not only for high speed imaging but also functional imaging although problems such as compensation among the beams and motion artifacts must be solved.
NASA Astrophysics Data System (ADS)
Auyeung, Kris; Auyeung, Kelsey; Kono, Rei; Chen, Chieh-Li; Zhang, Qinqin; Wang, Ruikang K.
2015-03-01
In ophthalmology, a reliable means of diagnosing glaucoma in its early stages is still an open issue. Past efforts, including forays into fluorescent angiography (FA) and early optical coherence tomography (OCT) systems, to develop a potential biomarker for the disease have been explored. However, this development has been hindered by the inability of the current techniques to provide useful depth and microvasculature information of the optic nerve head (ONH), which have been debated as possible hallmarks of glaucoma progression. We reasoned that a system incorporating a spectral-domain OCT (SD-OCT) based Optical Microangiography (OMAG) system, could allow an effective, non-invasive methodology to evaluate effects on microvasculature by glaucoma. SD-OCT follows the principle of light reflection and interference to produce detailed cross-sectional and 3D images of the eye. OMAG produces imaging contrasts via endogenous light scattering from moving particles, allowing for 3D image productions of dynamic blood perfusion at capillary-level resolution. The purpose of this study was to investigate the optic cup perfusion (flow) differences in glaucomatous and normal eyes. Images from three normal and five glaucomatous subjects were analyzed our OCT based OMAG system for blood perfusion and structural images, allowing for comparisons. Preliminary results from blood flow analysis revealed reduced blood perfusion within the whole-depth region encompassing the Lamina Cribrosa in glaucomatous cases as compared to normal ones. We conclude that our OCT-OMAG system may provide promise and viability for glaucoma screening.
NASA Astrophysics Data System (ADS)
Wahbeh, W.; Nebiker, S.; Fangi, G.
2016-06-01
This paper exploits the potential of dense multi-image 3d reconstruction of destroyed cultural heritage monuments by either using public domain touristic imagery only or by combining the public domain imagery with professional panoramic imagery. The focus of our work is placed on the reconstruction of the temple of Bel, one of the Syrian heritage monuments, which was destroyed in September 2015 by the so called "Islamic State". The great temple of Bel is considered as one of the most important religious buildings of the 1st century AD in the East with a unique design. The investigations and the reconstruction were carried out using two types of imagery. The first are freely available generic touristic photos collected from the web. The second are panoramic images captured in 2010 for documenting those monuments. In the paper we present a 3d reconstruction workflow for both types of imagery using state-of-the art dense image matching software, addressing the non-trivial challenges of combining uncalibrated public domain imagery with panoramic images with very wide base-lines. We subsequently investigate the aspects of accuracy and completeness obtainable from the public domain touristic images alone and from the combination with spherical panoramas. We furthermore discuss the challenges of co-registering the weakly connected 3d point cloud fragments resulting from the limited coverage of the touristic photos. We then describe an approach using spherical photogrammetry as a virtual topographic survey allowing the co-registration of a detailed and accurate single 3d model of the temple interior and exterior.
Kuppusamy, P; Shankar, R A; Zweier, J L
1998-07-01
Electron paramagnetic resonance imaging (EPRI) instrumentation, enabling the performance of three-dimensional spectral-spatial images of free radicals, has been developed to study spatially defined differences in tissue metabolism and oxygenation. Using this instrumentation 3D images of nitroxides in rat tail were obtained. The images visualize the arterial and venous vasculature in the tail segment. Based on the exchange broadening influence of oxygen on the EPR linewidth of nitroxides, we performed localized oxygen measurements in the in vivo rat. An oxygen concentration of 300+/-30 microM was measured in the arteries and 50+/-20 microM in the veins. These results demonstrate the feasibility of performing in vivo, non-invasive measurements and mapping of localized oxygenation in small animals using spectral-spatial EPR imaging techniques. PMID:9703045
Dharmaraj, Christopher D.; Thadikonda, Kishan; Fletcher, Anthony R.; Doan, Phuc N.; Devasahayam, Nallathamby; Matsumoto, Shingo; Johnson, Calvin A.; Cook, John A.; Mitchell, James B.; Subramanian, Sankaran; Krishna, Murali C.
2009-01-01
Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23 × 23 × 23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time. PMID:19672315
Dharmaraj, Christopher D; Thadikonda, Kishan; Fletcher, Anthony R; Doan, Phuc N; Devasahayam, Nallathamby; Matsumoto, Shingo; Johnson, Calvin A; Cook, John A; Mitchell, James B; Subramanian, Sankaran; Krishna, Murali C
2009-01-01
Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23 x 23 x 23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time. PMID:19672315
Dekemper, Emmanuel; Loodts, Nicolas; Van Opstal, Bert; Maes, Jeroen; Vanhellemont, Filip; Mateshvili, Nina; Franssens, Ghislain; Pieroux, Didier; Bingen, Christine; Robert, Charles; De Vos, Lieve; Aballea, Ludovic; Fussen, Didier
2012-09-01
We describe a new spectral imaging instrument using a TeO(2) acousto-optical tunable filter (AOTF) operating in the visible domain (450-900 nm). It allows for fast (~1 second), monochromatic (FWHM ranges from 0.6 nm at 450 nm to 3.5 nm at 800 nm) picture acquisition with good spatial resolution. This instrument was designed as a breadboard of the visible channel of a new satellite-borne atmospheric limb spectral imager, named the Atmospheric Limb Tracker for the Investigation of the Upcoming Stratosphere (ALTIUS), that is currently being developed. We tested its remote sensing capabilities by observing the dense, turbulent plume exhausted by a waste incinerator stack at two wavelengths sensitive to NO(2). An average value of 6.0±0.4×10(17) molecules cm(-2) has been obtained for the NO(2) slant column density within the plume, close to the stack outlet. Although this result was obtained with a rather low accuracy, it demonstrates the potential of spectral imaging by using AOTFs in remote sensing. PMID:22945175
NASA Astrophysics Data System (ADS)
Fechtig, Daniel J.; Ginner, Laurin; Kumar, Abhishek; Pircher, Michael; Schmoll, Tilman; Wurster, Lara M.; Drexler, Wolfgang; Leitgeb, Rainer A.
2016-03-01
We present retinal photoreceptor imaging with a line-field parallel spectral domain OCT modality, utilizing a commercially available 2D CMOS detector array operating at and imaging speed of 500 B-scans/s. Our results demonstrate for the first time in vivo structural and functional retinal assessment with a line-field OCT setup providing sufficient sensitivity, lateral and axial resolution and 3D acquisition rates in order to resolve individual photoreceptor cells. The phase stability of the system is manifested by the high phase-correlation across the lateral FOV on the level of individual photoreceptors. The setup comprises a Michelson interferometer illuminated by a broadband light source, where a line-focus is formed via a cylindrical lens and the back-propagated light from sample and reference arm is detected by a 2D array after passing a diffraction grating. The spot size of the line-focus on the retina is 5μm, which corresponds to a PSF of 50μm and an oversampling factor of 3.6 at the detector plane, respectively. A full 3D stack was recorded in only 0.8 s. We show representative enface images, tomograms and phase-difference maps of cone photoreceptors with a lateral FOV close to 2°. The high-speed capability and the phase stability due to parallel illumination and detection may potentially lead to novel structural and functional diagnostic tools on a cellular and microvascular imaging level. Furthermore, the presented system enables competitive imaging results as compared to respective point scanning modalities and facilitates utilizing software based digital aberration correction algorithms for achieving 3D isotropic resolution across the full FOV.
NASA Astrophysics Data System (ADS)
Ginner, Laurin; Fechtig, Daniel J.; Schmoll, Tilman; Wurster, Lara M.; Pircher, Michael; Leitgeb, Rainer A.; Drexler, Wolfgang
2016-03-01
We present retinal photoreceptor imaging with a line-field parallel spectral domain OCT modality, utilizing a commercially available 2D CMOS detector array operating at and imaging speed of 500 B-scans/s. Our results demonstrate for the first time in vivo structural and functional retinal assessment with a line-field OCT setup providing sufficient sensitivity, lateral and axial resolution and 3D acquisition rates in order to resolve individual photoreceptor cells. The setup comprises a Michelson interferometer illuminated by a broadband light source, where a line-focus is formed via a cylindrical lens and the back-propagated light from sample and reference arm is detected by a 2D array after passing a diffraction grating. The spot size of the line-focus on the retina is 5μm, which corresponds to a PSF of 50μm and an oversampling factor of 3.6 at the detector plane, respectively. A full 3D stack was recorded in only 0.8 s. We show representative enface images, tomograms and phase-difference maps of cone photoreceptors with a lateral FOV close to 2°. The high-speed capability and the phase stability due to parallel illumination and detection may potentially lead to novel structural and functional diagnostic tools on a cellular and microvascular imaging level. Furthermore, the presented system enables competitive imaging results as compared to respective point scanning modalities and facilitates utilizing software based digital aberration correction algorithms for achieving 3D isotropic resolution across the full FOV.
Three-Dimensional Spectral-Domain Optical Coherence Tomography Data Analysis for Glaucoma Detection
Wollstein, Gadi; Bilonick, Richard A.; Folio, Lindsey S.; Nadler, Zach; Kagemann, Larry; Schuman, Joel S.
2013-01-01
Purpose To develop a new three-dimensional (3D) spectral-domain optical coherence tomography (SD-OCT) data analysis method using a machine learning technique based on variable-size super pixel segmentation that efficiently utilizes full 3D dataset to improve the discrimination between early glaucomatous and healthy eyes. Methods 192 eyes of 96 subjects (44 healthy, 59 glaucoma suspect and 89 glaucomatous eyes) were scanned with SD-OCT. Each SD-OCT cube dataset was first converted into 2D feature map based on retinal nerve fiber layer (RNFL) segmentation and then divided into various number of super pixels. Unlike the conventional super pixel having a fixed number of points, this newly developed variable-size super pixel is defined as a cluster of homogeneous adjacent pixels with variable size, shape and number. Features of super pixel map were extracted and used as inputs to machine classifier (LogitBoost adaptive boosting) to automatically identify diseased eyes. For discriminating performance assessment, area under the curve (AUC) of the receiver operating characteristics of the machine classifier outputs were compared with the conventional circumpapillary RNFL (cpRNFL) thickness measurements. Results The super pixel analysis showed statistically significantly higher AUC than the cpRNFL (0.855 vs. 0.707, respectively, p = 0.031, Jackknife test) when glaucoma suspects were discriminated from healthy, while no significant difference was found when confirmed glaucoma eyes were discriminated from healthy eyes. Conclusions A novel 3D OCT analysis technique performed at least as well as the cpRNFL in glaucoma discrimination and even better at glaucoma suspect discrimination. This new method has the potential to improve early detection of glaucomatous damage. PMID:23408988
NASA Astrophysics Data System (ADS)
Wu, Jing; Waldstein, Sebastian M.; Gerendas, Bianca S.; Langs, Georg; Simader, Christian; Schmidt-Erfurth, Ursula
2015-03-01
Spectral-domain Optical Coherence Tomography (SD-OCT) is a non-invasive modality for acquiring high- resolution, three-dimensional (3D) cross-sectional volumetric images of the retina and the subretinal layers. SD-OCT also allows the detailed imaging of retinal pathology, aiding clinicians in the diagnosis of sight degrading diseases such as age-related macular degeneration (AMD), glaucoma and retinal vein occlusion (RVO). Disease diagnosis, assessment, and treatment will require a patient to undergo multiple OCT scans, possibly using multiple scanners, to accurately and precisely gauge disease activity, progression and treatment success. However, cross-vendor imaging and patient movement may result in poor scan spatial correlation potentially leading to incorrect diagnosis or treatment analysis. The retinal fovea is the location of the highest visual acuity and is present in all patients, thus it is critical to vision and highly suitable for use as a primary landmark for cross-vendor/cross-patient registration for precise comparison of disease states. However, the location of the fovea in diseased eyes is extremely challenging to locate due to varying appearance and the presence of retinal layer destroying pathology. Thus categorising and detecting the fovea type is an important prior stage to automatically computing the fovea position. Presented here is an automated cross-vendor method for fovea distinction in 3D SD-OCT scans of patients suffering from RVO, categorising scans into three distinct types. OCT scans are preprocessed by motion correction and noise filing followed by segmentation using a kernel graph-cut approach. A statistically derived mask is applied to the resulting scan creating an ROI around the probable fovea location from which the uppermost retinal surface is delineated. For a normal appearance retina, minimisation to zero thickness is computed using the top two retinal surfaces. 3D local minima detection and layer thickness analysis are used
NASA Astrophysics Data System (ADS)
Lauinger, Norbert
1999-08-01
Diffractive 3D phase gratings of spherical scatterers dense in hexagonal packing geometry represent adaptively tunable 4D-spatiotemporal filters with trichromatic resonance in visible spectrum. They are described in the (lambda) - chromatic and the reciprocal (nu) -aspects by reciprocal geometric translations of the lightlike Pythagoras theorem, and by the direction cosine for double cones. The most elementary resonance condition in the lightlike Pythagoras theorem is given by the transformation of the grating constants gx, gy, gz of the hexagonal 3D grating to (lambda) h1h2h3 equals (lambda) 111 with cos (alpha) equals 0.5. Through normalization of the chromaticity in the von Laue-interferences to (lambda) 111, the (nu) (lambda) equals (lambda) h1h2h3/(lambda) 111-factor of phase velocity becomes the crucial resonance factor, the 'regulating device' of the spatiotemporal interaction between 3D grating and light, space and time. In the reciprocal space equal/unequal weights and times in spectral metrics result at positions of interference maxima defined by hyperbolas and circles. A database becomes built up by optical interference for trichromatic image preprocessing, motion detection in vector space, multiple range data analysis, patchwide multiple correlations in the spatial frequency spectrum, etc.
Imaging the eye fundus with real-time en-face spectral domain optical coherence tomography.
Bradu, Adrian; Podoleanu, Adrian Gh
2014-04-01
Real-time display of processed en-face spectral domain optical coherence tomography (SD-OCT) images is important for diagnosis. However, due to many steps of data processing requirements, such as Fast Fourier transformation (FFT), data re-sampling, spectral shaping, apodization, zero padding, followed by software cut of the 3D volume acquired to produce an en-face slice, conventional high-speed SD-OCT cannot render an en-face OCT image in real time. Recently we demonstrated a Master/Slave (MS)-OCT method that is highly parallelizable, as it provides reflectivity values of points at depth within an A-scan in parallel. This allows direct production of en-face images. In addition, the MS-OCT method does not require data linearization, which further simplifies the processing. The computation in our previous paper was however time consuming. In this paper we present an optimized algorithm that can be used to provide en-face MS-OCT images much quicker. Using such an algorithm we demonstrate around 10 times faster production of sets of en-face OCT images than previously obtained as well as simultaneous real-time display of up to 4 en-face OCT images of 200 × 200 pixels(2) from the fovea and the optic nerve of a volunteer. We also demonstrate 3D and B-scan OCT images obtained from sets of MS-OCT C-scans, i.e. with no FFT and no intermediate step of generation of A-scans. PMID:24761303
Cheng, Candong; Lee, Joon-Ho; Lim, Kim Hwa; Massoud, Hisham Z.; Liu, Qing Huo
2007-01-01
A 3-D quantum transport solver based on the spectral element method (SEM) and perfectly matched layer (PML) is introduced to solve the 3-D Schrödinger equation with a tensor effective mass. In this solver, the influence of the environment is replaced with the artificial PML open boundary extended beyond the contact regions of the device. These contact regions are treated as waveguides with known incident waves from waveguide mode solutions. As the transmitted wave function is treated as a total wave, there is no need to decompose it into waveguide modes, thus significantly simplifying the problem in comparison with conventional open boundary conditions. The spectral element method leads to an exponentially improving accuracy with the increase in the polynomial order and sampling points. The PML region can be designed such that less than −100 dB outgoing waves are reflected by this artificial material. The computational efficiency of the SEM solver is demonstrated by comparing the numerical and analytical results from waveguide and plane-wave examples, and its utility is illustrated by multiple-terminal devices and semiconductor nanotube devices. PMID:18037971
Spectral Domain Optical Coherence Tomography for Glaucoma (An AOS Thesis)
Schuman, Joel S.
2008-01-01
Purpose Optical coherence tomography (OCT) is a rapidly evolving, robust technology that has profoundly changed the practice of ophthalmology. Spectral domain OCT (SD-OCT) increases axial resolution 2- to 3-fold and scan speed 60- to 110-fold vs time domain OCT (TD-OCT). SD-OCT enables novel scanning, denser sampling, and 3-dimensional imaging. This thesis tests my hypothesis that SD-OCT improves reproducibility, sensitivity, and specificity for glaucoma detection. Methods OCT progress is reviewed from invention onward, and future development is discussed. To test the hypothesis, TD-OCT and SD-OCT reproducibility and glaucoma discrimination are evaluated. Forty-one eyes of 21 subjects (SD-OCT) and 21 eyes of 21 subjects (TD-OCT) are studied to test retinal nerve fiber layer (RNFL) thickness measurement reproducibility. Forty eyes of 20 subjects (SD-OCT) and 21 eyes of 21 subjects (TD-OCT) are investigated to test macular parameter reproducibility. For both TD-OCT and SD-OCT, 83 eyes of 83 subjects are assessed to evaluate RNFL thickness and 74 eyes of 74 subjects to evaluate macular glaucoma discrimination. Results Compared to conventional TD-OCT, SD-OCT had statistically significantly better reproducibility in most sectoral macular thickness and peripapillary RNFL sectoral measurements. There was no statistically significant difference in overall mean macular or RNFL reproducibility, or between TD-OCT and SD-OCT glaucoma discrimination. Surprisingly, TD-OCT macular RNFL thickness showed glaucoma discrimination superior to SD-OCT. Conclusions At its current development state, SD-OCT shows better reproducibility than TD-OCT, but glaucoma discrimination is similar for TD-OCT and SD-OCT. Technological improvements are likely to enhance SD-OCT reproducibility, sensitivity, specificity, and utility, but these will require additional development. PMID:19277249
Quality assessment for spectral domain optical coherence tomography (OCT) images
NASA Astrophysics Data System (ADS)
Liu, Shuang; Paranjape, Amit S.; Elmaanaoui, Badr; Dewelle, Jordan; Rylander, H. Grady, III; Markey, Mia K.; Milner, Thomas E.
2009-02-01
Retinal nerve fiber layer (RNFL) thickness, a measure of glaucoma progression, can be measured in images acquired by spectral domain optical coherence tomography (OCT). The accuracy of RNFL thickness estimation, however, is affected by the quality of the OCT images. In this paper, a new parameter, signal deviation (SD), which is based on the standard deviation of the intensities in OCT images, is introduced for objective assessment of OCT image quality. Two other objective assessment parameters, signal to noise ratio (SNR) and signal strength (SS), are also calculated for each OCT image. The results of the objective assessment are compared with subjective assessment. In the subjective assessment, one OCT expert graded the image quality according to a three-level scale (good, fair, and poor). The OCT B-scan images of the retina from six subjects are evaluated by both objective and subjective assessment. From the comparison, we demonstrate that the objective assessment successfully differentiates between the acceptable quality images (good and fair images) and poor quality OCT images as graded by OCT experts. We evaluate the performance of the objective assessment under different quality assessment parameters and demonstrate that SD is the best at distinguishing between fair and good quality images. The accuracy of RNFL thickness estimation is improved significantly after poor quality OCT images are rejected by automated objective assessment using the SD, SNR, and SS.
Characterization of PET preforms using spectral domain optical coherence tomography
NASA Astrophysics Data System (ADS)
Hosseiny, Hamid; Ferreira, Manuel João.; Martins, Teresa; Carmelo Rosa, Carla
2013-11-01
Polyethylene terephthalate (PET) preforms are massively produced nowadays with the purpose of producing food and beverages packaging and liquid containers. Some varieties of these preforms are produced as multilayer structures, where very thin inner film(s) act as a barrier for nutrients leakage. The knowledge of the thickness of this thin inner layer is important in the production line. The quality control of preforms production requires a fast approach and normally the thickness control is performed by destructive means out of the production line. A spectral domain optical coherence tomography (SD-OCT) method was proposed to examine the thin layers in real time. This paper describes a nondestructive approach and all required signal processing steps to characterize the thin inner layers and also to improve the imaging speed and the signal to noise ratio. The algorithm was developed by using graphics processing unit (GPU) with computer unified device architecture (CUDA). This GPU-accelerated white light interferometry technique nondestructively assesses the samples and has high imaging speed advantage, overcoming the bottlenecks in PET performs quality control.
Spectral-Domain Optical Coherence Tomography Findings in Lipemia Retinalis.
Özturk, Banu Turgut; Bozkurt, Banu; Meşen, Ali; Gonul, Saban; İpekci, Süleyman Hilmi
2016-06-01
Severe hypertriglyceridemia can give rise to a fundus appearance with whitish-colored retinal vessels called lipemia retinalis. A 52-year-old man with hypertriglyceridemia presented with a best-corrected visual acuity of 20/20 in both eyes and creamy-white retinal vessels on fundus. Spectral-domain optical coherence tomography (SD-OCT) revealed hyperreflective and engorged retinal vessels and white dots mainly accumulated in the inner nuclear and ganglion cell layer. Follow-up fundus examination after plasmapheresis sessions revealed normal retinal vessels. The hyperreflective appearance of the retinal vessels in OCT reversed rapidly 5 days after the treatment, whereas hyperreflective dots in retina disappeared slowly in 3 months. OCT is useful in demonstrating inner retinal changes associated with lipemia retinalis at histopathological level. The hyperreflective dots in inner retina associated with leakage from superficial retinal capillaries attested the correlation of their location with their origin. [Ophthalmic Surg Lasers Imaging Retina. 2016;47:589-592.]. PMID:27327291
Retinal Imaging of Infants on Spectral Domain Optical Coherence Tomography
Vinekar, Anand; Mangalesh, Shwetha; Jayadev, Chaitra; Maldonado, Ramiro S.; Bauer, Noel; Toth, Cynthia A.
2015-01-01
Spectral domain coherence tomography (SD OCT) has become an important tool in the management of pediatric retinal diseases. It is a noncontact imaging device that provides detailed assessment of the microanatomy and pathology of the infant retina with a short acquisition time allowing office examination without the requirement of anesthesia. Our understanding of the development and maturation of the infant fovea has been enhanced by SD OCT allowing an in vivo assessment that correlates with histopathology. This has helped us understand the critical correlation of foveal development with visual potential in the first year of life and beyond. In this review, we summarize the recent literature on the clinical applications of SD OCT in studying the pathoanatomy of the infant macula, its ability to detect subclinical features, and its correlation with disease and vision. Retinopathy of prematurity and macular edema have been discussed in detail. The review also summarizes the current status of SD OCT in other infant retinal conditions, imaging the optic nerve, the choroid, and the retinal nerve fibre in infants and children, and suggests future areas of research. PMID:26221606
NASA Astrophysics Data System (ADS)
Jiao, Shuliang; Ruggeri, Marco; Wehbe, Hassan; Gregory, Giovanni; Jockovich, Maria E.; Hackam, Abigail; Puliafito, Carmen A.
2007-02-01
Noninvasive in vivo examination of the rodent retina without sacrificing the animal is the key to being able to perform longitudinal studies. This allows the monitoring of disease progression and the response to therapies through its entire course in individual animal. A high-speed high resolution three-dimensional spectral-domain OCT is built for non-contact in vivo imaging of rodent retina. The system is able to acquire high quality 3D images of the rodent retina in 2.7 seconds (total imaging time is ~5 minutes). The system was tested on mice with normal retina (B6/SJLF2), mouse model for photoreceptor degeneration (Rho -/-), and mouse model for retinoblastoma (LH BETAT AG). For the first time to our knowledge, 3D image of the tumor in retinoblastoma mouse model was successfully imaged in vivo. By segmenting the tumor boundaries in each frame of the OCT image the volume of the tumor was successfully calculated.
Socoteanu, Radu; Manda, Gina; Boscencu, Rica; Vasiliu, Georgiana; Oliveira, Anabela Sousa
2015-01-01
In this paper, two tetrapyrrolic complexes, Zn(II)-5-(3-hydroxyphenyl)-10,15,20-tris-(4-acetoxy-3-methoxyphenyl)porphyrin and Cu(II)-5-(3-hydroxyphenyl)-10,15,20-tris-(4-acetoxy-3-methoxyphenyl)porphyrin were synthesized, and characterized from a spectral and biological point of view. The study provided data concerning the behavior of identical external substituents vs. two different core insertions. Some of the properties of the proposed tetrapyrrolic structures were highlighted, having photodynamic therapy of cancer as a targeted biomedical application. Elemental analysis, NMR, FTIR and UV-Vis data in various solvents were provided. A preliminary in vitro study on normal and cancer cultured cells was carried out for biocompatibility assessment in dark conditions. The preliminary in vitro study performed on human peripheral mononuclear cells exposed to tetrapyrrolic compounds (2 µM) showed that the proposed compounds had a convenient cytotoxic profile on human normal peripheral blood mononuclear cells under dark conditions. Meanwhile, the investigated compounds reduced the number of metabolically active breast tumor MCF-7 cells, with the exception of Zn(II) complex-containing a symmetrical ligand. Accordingly, preliminary in vitro data suggest that the proposed tetrapyrrolic compounds are good candidates for PDT, as they limit tumor expansion even under dark conditions, whilst sparing normal cells. PMID:26343614
Visbal, Eli; Loeb, Abraham E-mail: aloeb@cfa.harvard.edu
2010-11-01
We discuss a method for detecting the emission from high redshift galaxies by cross correlating flux fluctuations from multiple spectral lines. If one can fit and subtract away the continuum emission with a smooth function of frequency, the remaining signal contains fluctuations of flux with frequency and angle from line emitting galaxies. Over a particular small range of observed frequencies, these fluctuations will originate from sources corresponding to a series of different redshifts, one for each emission line. It is possible to statistically isolate the fluctuations at a particular redshift by cross correlating emission originating from the same redshift, but in different emission lines. This technique will allow detection of clustering fluctuations from the faintest galaxies which individually cannot be detected, but which contribute substantially to the total signal due to their large numbers. We describe these fluctuations quantitatively through the line cross power spectrum. As an example of a particular application of this technique, we calculate the signal-to-noise ratio for a measurement of the cross power spectrum of the OI(63 μm) and OIII(52 μm) fine structure lines with the proposed Space Infrared Telescope for Cosmology and Astrophysics (SPICA). We find that the cross power spectrum can be measured beyond a redshift of z = 8. Such observations could constrain the evolution of the metallicity, bias, and duty cycle of faint galaxies at high redshifts and may also be sensitive to the reionization history through its effect on the minimum mass of galaxies. As another example of this technique, we calculate the signal-to-noise ratio for the cross power spectrum of CO line emission measured with a large ground based telescope like the Cornell Caltech Atacama Telescope (CCAT) and 21-cm radiation originating from hydrogen in galaxies after reionization with an interferometer similar in scale to the Murchison Widefield Array (MWA), but optimized for post
Liu, L.; Li, Z; Guo, Y; VanVranken, S; Mourad, W; Li, H
2010-01-01
Mycoplasma arthritidis-derived mitogen (MAM) is a superantigen that can activate large fractions of T cells bearing particular V{beta} elements of T cell receptor. Here, we report the crystal structure of a MAM mutant K201A in apo form (unliganded) at 2.8-{angstrom} resolutions. We also partially refined the crystal structures of the MAM wild type and another MAM mutant L50A in apo forms at low resolutions. Unexpectedly, the structures of these apo MAM molecules display a three-dimensional domain-swapped dimer. The entire C-terminal domains of these MAM molecules are involved in the domain swapping. Functional analyses demonstrated that the K201A and L50A mutants do not show altered ability to bind to their host receptors and that they stimulate the activation of T cells as efficiently as does the wild type. Structural comparisons indicated that the 'reconstituted' MAM monomer from the domain-swapped dimer displays large differences at the hinge regions from the MAM{sub wt} molecule in the receptor-bound form. Further comparison indicated that MAM has a flexible N-terminal loop, implying that conformational changes could occur upon receptor binding.
Fischer, D C; Haubeck, H D; Eich, K; Kolbe-Busch, S; Stöcker, G; Stuhlsatz, H W; Greiling, H
1996-01-01
Monoclonal antibodies (mAbs) were prepared against aggrecan which has been isolated from human articular cartilage and purified by several chromatographic steps. One of these mAbs, the aggrecan-specific mAb 3D12/H7, was selected for further characterization. The data presented indicate that this mAb recognizes a novel domain of keratan sulphate chains from aggrecan: (1) immunochemical staining of aggrecan is abolished by treatment with keratanase/keratanase II, but not with keratanase or chondroitin sulphate lyase AC/ABC; (2) after chemical deglycosylation of aggrecan no staining of the core-protein was observed; (3) different immunochemical reactivity was observed against keratan sulphates from articular cartilage, intervertebral disc and cornea for the mAbs 3D12/H7 and 5D4. For further characterization of the epitope, reduced and 3H-labelled keratan sulphate chains were prepared. In an IEF-gel-shift assay it was shown that the 3H-labelled oligosaccharides obtained after keratanase digestion of reduced and 3H-labelled keratan sulphate chains were recognized by the mAb 3D12/H7. Thus it can be concluded that the mAb 3D12/H7 recognizes an epitope in the linkage region present in, at least some, keratan sulphate chains of the large aggregating proteoglycan from human articular cartilage. Moreover, this domain seems to be expressed preferentially on those keratan sulphate chains which occur in the chondroitin sulphate-rich region of aggrecan, since the antibody does not recognize the keratan sulphate-rich region obtained after combined chondroitinase AC/ABC and trypsin digestion of aggrecan. PMID:8836155
Fischer, D C; Haubeck, H D; Eich, K; Kolbe-Busch, S; Stöcker, G; Stuhlsatz, H W; Greiling, H
1996-09-15
Monoclonal antibodies (mAbs) were prepared against aggrecan which has been isolated from human articular cartilage and purified by several chromatographic steps. One of these mAbs, the aggrecan-specific mAb 3D12/H7, was selected for further characterization. The data presented indicate that this mAb recognizes a novel domain of keratan sulphate chains from aggrecan: (1) immunochemical staining of aggrecan is abolished by treatment with keratanase/keratanase II, but not with keratanase or chondroitin sulphate lyase AC/ABC; (2) after chemical deglycosylation of aggrecan no staining of the core-protein was observed; (3) different immunochemical reactivity was observed against keratan sulphates from articular cartilage, intervertebral disc and cornea for the mAbs 3D12/H7 and 5D4. For further characterization of the epitope, reduced and 3H-labelled keratan sulphate chains were prepared. In an IEF-gel-shift assay it was shown that the 3H-labelled oligosaccharides obtained after keratanase digestion of reduced and 3H-labelled keratan sulphate chains were recognized by the mAb 3D12/H7. Thus it can be concluded that the mAb 3D12/H7 recognizes an epitope in the linkage region present in, at least some, keratan sulphate chains of the large aggregating proteoglycan from human articular cartilage. Moreover, this domain seems to be expressed preferentially on those keratan sulphate chains which occur in the chondroitin sulphate-rich region of aggrecan, since the antibody does not recognize the keratan sulphate-rich region obtained after combined chondroitinase AC/ABC and trypsin digestion of aggrecan. PMID:8836155
NASA Astrophysics Data System (ADS)
An, Lin
-OMAG). Unlike conventional OMAG, UHS-OMAG applied the OMAG algorithm onto the slow direction of FDOCT scan (Y-direction). Because the time interval between adjacent B-frames is much longer than that between adjacent A-lines, UHS-OMAG can achieve much higher flow sensitivity compared to the conventional OMAG. In addition, the UHS-OMAG usually employed high frame rate (typically 300 frames per second) to achieve 3D scan, it cost much less time to finish one 3D scan compared to the traditional OMAG. However, when it was applied to visualize vasculature map of human tissue, the motion artifacts caused by the inevitable movements is still the biggest challenge. Based on the phase difference calculated from two adjacent B-frames, a new phase compensation algorithm was developed. Aim 4: Developing ultrahigh speed Spectral Domain OCT system through sequentially controlling two high speed line scan CMOS cameras. Two identical high speed line cameras were employed to build two home build high speed spectrometers. Through sequentially controlling the reading time period of two cameras, the imaging speed of the whole system could reach twice higher than the single camera system. The newly built 800 nm SDOCT system which can work at 500, 000 Hz A-lines capturing speed was then used to achieve in vivo 3D imaging in both high speed and large field of view mode. In addition, through combining with the OMAG algorithm, the newly developed system is capable of providing detailed micro-vasculature imaging of human retina and optic nerve head. (Abstract shortened by UMI.)
Ho, Joseph; Sull, Alan C.; Vuong, Laurel N.; Chen, Yueli; Liu, Jonathan; Fujimoto, James G.; Schuman, Joel S.; Duker, Jay S.
2009-01-01
PURPOSE To report the frequency of optical coherence tomography (OCT) scan artifacts and compare macular thickness measurements, inter-scan reproducibility and inter-device agreeability across three spectral / Fourier domain (SD) OCTs (Cirrus HD-OCT, RTVue-100 and Topcon 3D-OCT 1000) and one time domain (TD) OCT (Stratus OCT). DESIGN Prospective, non-comparative, non-interventional case series. PARTICIPANTS 52 patients seen at New England Eye Center, Tufts Medical Center retina service between February and August 2008. METHODS Two scans were performed for each of the SD-OCT protocols: Cirrus macular cube 512×128, RTVue (E)MM5 and MM6, Topcon 3D macular and radial, in addition to one TD-OCT scan via Stratus macular thickness protocol. Scans were inspected for six types of OCT scan artifacts and analyzed. Inter-scan reproducibility and inter-device agreeability were assessed by intraclass correlation coefficients (ICCs) and Bland-Altman plots, respectively. MAIN OUTCOME MEASURE OCT image artifacts, Macular thickness, Reproducibility, Agreeability. RESULTS TD-OCT scans contained a significantly higher percentage of clinically significant improper central foveal thickness (IFT) post-manual correction (greater than or equal to 11 μm change) compared to SD-OCT scans. Cirrus HD-OCT had a significantly lower percentage of clinically significant IFT (11.1%) compared to the other SD-OCT devices (Topcon 3D: 20.4%, Topcon Radial: 29.6%, RTVue (E)MM5: 42.6%, RTVue MM6: 24.1%; p= 0.001). All three SD-OCT had central foveal subfield thicknesses significantly greater than TD-OCT post manual correction (p< 0.0001). All 3 SD-OCT demonstrated a high degree of reproducibility in the central foveal region (ICC= 0.92 to 0.97). Bland-Altman plots showed low agreeability between TD- and SD-OCT scans. CONCLUSIONS Cirrus HD-OCT scans exhibited the lowest occurrence of any artifacts (68.5%), IFT (40.7%) and clinically significant IFT (11.1%) compared to all other OCT devices examined
Spectral-domain optical coherence tomography of macula in myopia.
Choovuthayakorn, Janejit; Laowong, Taksaorn; Watanachai, Nawat; Patikulsila, Direk; Chaikitmongkol, Voraporn
2016-06-01
The aim of this study is to determine the associations between regional macular thickness and gender, age, axial length, and degree of myopia in young and middle-aged healthy myopic eyes. One hundred and seventy-one subjects with -0.5 diopters of myopia or worse underwent prospective macular thickness measurement by Spectralis spectral-domain optical coherence tomography. Subjects' mean age was 32.40 ± 8.25 years (range 18 to 49 years), with 45 % being male. The mean degree of myopia was -4.57 ± 3.52 diopters, with a mean axial length of 25.09 ± 1.67 mm. Multivariate regression analysis demonstrated significantly thicker central (mean 9.13 µm thicker) and inner subfields (mean 8.55 µm thicker) in males (P values were <0.001 and 0.002, respectively). In addition, in both genders, for each millimeter of increased axial length, the central subfield thickness increased by 2.11 µm, the inner subfield decreased by 2.25 µm, and the outer subfield decreased by 3.62 µm (P values were 0.010, <0.001, and <0.001, respectively). Factors including gender and axial length affect baseline regional macular thickness in young and middle-age myopic subjects. The central subfield and inner subfield were affected by both gender and axial length, while the outer subfield was affected only by axial length. The macular thickness of myopic subjects with macular disease should be interpreted in light of these factors. PMID:26290135
Macular Surgery Using Intraoperative Spectral Domain Optical Coherence Tomography
Riazi-Esfahani, Mohammad; Khademi, Mohammad Reza; Mazloumi, Mehdi; Khodabandeh, Alireza; Riazi-Esfahani, Hamid
2015-01-01
Purpose: To report the use of intraoperative spectral domain optical coherence tomography (SD-OCT) for detecting anatomical changes during macular surgery. Methods: In a consecutive case series, 32 eyes of 32 patients undergoing concurrent pars plana vitrectomy and intraoperative SD-OCT for macular hole (MH), epiretinal membrane (ERM) and vitreomacular traction (VMT) were enrolled. Intraoperative changes in retinal thickness and dimensions of the macular hole were measured in patients with ERM and VMT following surgical manipulation using a hand-held SD-OCT device (iVue, Optovue Inc., Fremont, CA, USA). Results: SD-OCT images of sixteen eyes with macular hole were subjected to quantitative and qualitative analysis. All MH dimensions remained stable during consecutive stages of surgery except for MH apex diameter, which showed a significant decrease after internal limiting membrane (ILM) peeling (P=0.025). Quantitative analysis of ten patients with ERM showed a significant decrease in retinal thickness after membrane removal (P=0.018) which did not remain significant until the end of the procedure (P=0.8). In three cases, subretinal fluid was formed after ILM peeling. Quantitative analysis of five patients with VMT showed a decrease in retinal thickness during consecutive steps of the surgery, although these changes were not significant. In two cases, subretinal fluid was formed after ILM peeling. Conclusion: Intraoperative SD-OCT is a useful imaging technique which provides vitreoretinal surgeons with rapid awareness of changes in macular anatomy during surgery and may therefore result in better anatomical and visual outcomes. PMID:26730318
Comparison of spectral-domain and time-domain optical coherence tomography in solar retinopathy.
Cho, Han Joo; Yoo, Eun Seok; Kim, Chul Gu; Kim, Jong Woo
2011-08-01
The purpose of this article is to compare spectral-domain (SD) and time-domain (TD) optical coherence tomography (OCT) findings in patients with solar retinopathy. Complete ocular examinations and OCT were performed in two patients presenting with acute solar retinopathy soon after observation of an eclipse. Both patients were evaluated with SD-OCT and TD-OCT at the same time. SD-OCT demonstrated characteristic defects at the level of the inner and outer segment junction of the photoreceptors in all the affected eyes and decreased reflectiveness of the retinal pigment epithelium layer. TD-OCT images showed unremarkable findings in two eyes with deteriorated visual acuity. SD-OCT improves diagnosis and assessment of the degree and nature of foveal damage in patients with solar retinopathy and may be an important tool for use in identifying foveal damage not detected by TD-OCT. SD-OCT may be preferable to TD-OCT for confirmation or assessment of the degree of foveal damage in patients with solar retinopathy. PMID:21860577
Ford-Green, Jason; Isayev, Olexandr; Gorb, Leonid; Perkins, Edward J; Leszczynski, Jerzy
2012-04-01
Overactivation of the N-methyl-D-aspartate receptor (NMDAR) in postsynaptic neurons leads to glutamate-related excitotoxicity in the central nervous system of mammals. We have built 3-D models of each domain for the universal screening of potential toxicants and their binding mechanisms. Our docking results show that the calculated pK (i) values of glycine and L: -glutamate significantly increase (>1) when the NR1 and NR2A S1S2 domains are closing, respectively. Inversely, D: -cycloserine (DCS) and 5,7-dichlorokynurenic acid (5,7-DCKA) do not show such a dependence on domain closure. Replica exchange molecular dynamics (REMD) confirmed 5 different conformational states of the S1S2 domain along the 308.2 K temperature trajectory. Analysis of residue fluctuations during this temperature trajectory showed that residues in loop 1, loop 2, the amino terminal domain (ATD), and the area linked to ion channel α-helices are involved in this movement. This further implicates the notion that efficacious ligands act through S1S2 lobe movement which can culminate in the opening or closing of the ion channel. We further tested this by docking hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) to the S1S2 domain. Our results predict that these nitramines are not efficacious and thus do not produce excitoxicity when they bind to the S1S2 domain of the NMDAR. PMID:21735122
NASA Astrophysics Data System (ADS)
Liu, Yang; Sen, Mrinal K.
2011-09-01
Most conventional finite-difference methods adopt second-order temporal and (2M)th-order spatial finite-difference stencils to solve the 3D acoustic wave equation. When spatial finite-difference stencils devised from the time-space domain dispersion relation are used to replace these conventional spatial finite-difference stencils devised from the space domain dispersion relation, the accuracy of modelling can be increased from second-order along any directions to (2M)th-order along 48 directions. In addition, the conventional high-order spatial finite-difference modelling accuracy can be improved by using a truncated finite-difference scheme. In this paper, we combine the time-space domain dispersion-relation-based finite difference scheme and the truncated finite-difference scheme to obtain optimised spatial finite-difference coefficients and thus to significantly improve the modelling accuracy without increasing computational cost, compared with the conventional space domain dispersion-relation-based finite difference scheme. We developed absorbing boundary conditions for the 3D acoustic wave equation, based on predicting wavefield values in a transition area by weighing wavefield values from wave equations and one-way wave equations. Dispersion analyses demonstrate that high-order spatial finite-difference stencils have greater accuracy than low-order spatial finite-difference stencils for high frequency components of wavefields, and spatial finite-difference stencils devised in the time-space domain have greater precision than those devised in the space domain under the same discretisation. The modelling accuracy can be improved further by using the truncated spatial finite-difference stencils. Stability analyses show that spatial finite-difference stencils devised in the time-space domain have better stability condition. Numerical modelling experiments for homogeneous, horizontally layered and Society of Exploration Geophysicists/European Association of
NASA Astrophysics Data System (ADS)
DeJong, Andrew
Numerical models of fluid-structure interaction have grown in importance due to increasing interest in environmental energy harvesting, airfoil-gust interactions, and bio-inspired formation flying. Powered by increasingly powerful parallel computers, such models seek to explain the fundamental physics behind the complex, unsteady fluid-structure phenomena. To this end, a high-fidelity computational model based on the high-order spectral difference method on 3D unstructured, dynamic meshes has been developed. The spectral difference method constructs continuous solution fields within each element with a Riemann solver to compute the inviscid fluxes at the element interfaces and an averaging mechanism to compute the viscous fluxes. This method has shown promise in the past as a highly accurate, yet sufficiently fast method for solving unsteady viscous compressible flows. The solver is monolithically coupled to the equations of motion of an elastically mounted 3-degree of freedom rigid bluff body undergoing flow-induced lift, drag, and torque. The mesh is deformed using 4 methods: an analytic function, Laplace equation, biharmonic equation, and a bi-elliptic equation with variable diffusivity. This single system of equations -- fluid and structure -- is advanced through time using a 5-stage, 4th-order Runge-Kutta scheme. Message Passing Interface is used to run the coupled system in parallel on up to 240 processors. The solver is validated against previously published numerical and experimental data for an elastically mounted cylinder. The effect of adding an upstream body and inducing wake galloping is observed.
NASA Astrophysics Data System (ADS)
Avrin, Joel
2014-11-01
In a bounded region in 3-D the velocity field u for the Navier-Stokes system satisfies in the no-slip case the familiar condition u = 0 on the boundary. We show further that if the boundary and the forcing data satisfy reasonably general smoothness assumptions then Au = 0 on the boundary as well where A is the Stokes operator (i.e. Au is the divergence-free part of -∇2 u). We apply this result to subgrid-scale modeling by noting that in a number of computational turbulence experiments hyperviscosity has been added to the NS system as an approximation to spectral eddy viscosity, but a rigorous definition of this technique and a qualitative theory for it has been restricted to the idealized case of box regions with periodic boundary conditions imposed on each face. But under the above smoothness assumptions the fact that Au = 0 on the boundary now allows us in the no-slip case to rigorously define adding hyperviscosity to the Navier-Stokes system on otherwise general bounded regions. We can also obtain a foundational qualitative theory for this system as well as for spectral hyperviscosity, which adds hyperviscosity only to the high frequencies past a cutoff wavenumber.
3D Lithospheric Imaging by Time-Domain Full-Waveform Inversion of Teleseismic Body-Waves
NASA Astrophysics Data System (ADS)
Beller, S.; Monteiller, V.; Operto, S.; Nolet, G.; Combe, L.; Metivier, L.; Virieux, J.; Nissen-Meyer, T.; Paul, A.
2014-12-01
With the deployment of dense seismic arrays and the continuous growth of computing facilities, full-waveform inversion (FWI) of teleseismic data has become a method of choice for high-resolution lithospheric imaging. FWI can be recast as a local optimization problem that seeks to estimate Earth's elastic properties by iteratively minimizing the misfit function between observed and modeled seismograms.In passive teleseismic configurations, the seismic source no longer corresponds to a point source embedded in the targeted medium but rather corresponds to a wavefront incoming from the outside of the model. We develop a 3-dimensional time-domain full-waveform inversion program that is more designed for this configuration. The gradient of the misfit function is efficiently computed with the adjoint-state method. A velocity-stress finite-difference time-domain modeling engine, which is interfaced with the so-called total-field/scattered-field method, is used to propagate in the targeted medium the incident wavefield inferred from a global Earth simulation (AxiSEM). Such interfacing is required to account for the multiple arrivals in the incoming wavefield and the sphericity of the Earth. Despite the limited number of nearly plane-wave sources, the interaction of the incident wavefield with the topography (P-Sv conversions and P-P reflections acting as secondary sources) provides a suitable framework to record both transmitted wavefields and reflected wavefields from lithospheric reflectors. These recordings of both transmitted and reflected waves makes FWI amenable to a broadband-wavenumber (i.e., high resolution) reconstruction of the lithosphere.Feasibility of the method is assessed with a realistic synthetic model representative of the Western Alps. One key issue is the estimation of the temporal source excitation, as there might be some trade-off between the source estimation and the subsurface update. To avoid being trapped in a local minimum, we follow a
In vivo volumetric imaging of the human corneo-scleral limbus with spectral domain OCT
Bizheva, Kostadinka; Hutchings, Natalie; Sorbara, Luigina; Moayed, Alireza A.; Simpson, Trefford
2011-01-01
The limbus is the structurally rich transitional region of tissue between the cornea on one side, and the sclera and conjunctiva on the other. This zone, among other things, contains nerves passing to the cornea, blood and lymph vasculature for oxygen and nutrient delivery and for waste, CO2 removal and drainage of the aqueous humour. In addition, the limbus contains stem cells responsible for the existence and healing of the corneal epithelium. Here we present 3D images of the healthy human limbus, acquired in vivo with a spectral domain optical coherence tomography system operating at 1060nm. Cross-sectional and volumetric images were acquired from temporal and nasal locations in the human limbus with ~3µm x 18µm (axial x lateral) resolution in biological tissue at the rate of 92,000 A-scans/s. The imaging enabled detailed mapping of the corneo-scleral tissue morphology, and visualization of structural details such as the Vogt palisades, the blood and lymph vasculature including the Schlemm’s canal and the trabecular meshwork, as well as corneal nerve fiber bundles. Non-invasive, volumetric, high resolution imaging reveals fine details of the normal human limbal structure, and promises to provide invaluable information about its changes in health and disease as well as during and after corneal surgery. PMID:21750758
Spectral domain optical coherence tomography for ex vivo brain tumor analysis
NASA Astrophysics Data System (ADS)
Lenz, Marcel; Krug, Robin; Jaedicke, Volker; Stroop, Ralf; Schmieder, Kirsten; Hofmann, Martin R.
2015-07-01
Non-contact imaging methods to distinguish between healthy tissue and brain tumor tissue during surgery would be highly desirable but are not yet available. Optical Coherence Tomography (OCT) is a non-invasive imaging technology with a resolution around 1-15 μm and a penetration depth of 1-2 mm that may satisfy the demands. To analyze its potential, we measured ex vivo human brain tumor tissue samples from 10 patients with a Spectral Domain OCT system (Thorlabs Callisto: center wavelength of 930 nm) and compared the results with standard histology. In detail, three different measurements were made for each sample. First the sample was measured directly after surgery. Then it was embedded in paraffin (also H and E staining) and examined for the second time. At last, the slices of each paraffin block cut by the pathology were measured. Each time a B-scan was created and for a better comparison with the histology a 3D image was generated, in order to get the corresponding en face images. In both, histopathological diagnosis and the analysis of the OCT images, different types of brain tumor showed difference in structure. This has been affirmed by two blinded investigators. Nevertheless the difference between two images of samples taken directly after surgery is less distinct. To enhance the contrast in the images further, we employ Spectroscopic OCT and pattern recognition algorithms and compare these results to the histopathological standard.
NASA Astrophysics Data System (ADS)
Lee, Kyungmoo; Abràmoff, Michael D.; Sonka, Milan; Garvin, Mona K.
2011-03-01
Changes in intraretinal layer thickness occur in a variety of diseases such as glaucoma, macular edema and diabetes. To segment the intraretinal layers from macular spectral-domain OCT (SD-OCT) scans, we previously introduced an automated multiscale 3-D graph search method and validated its performance by computing unsigned border positioning differences when compared with human expert tracings. However, it is also important to study the reproducibility of resulting layer thickness measurements, as layer thickness is a commonly used clinical parameter. In this work, twenty eight (14 x 2) repeated macular OCT volumes were acquired from the right eyes of 14 normal subjects using two Zeiss-Cirrus SD-OCT scanners. After segmentation of 10 intraretinal layers and rigid registration of layer thickness maps from the repeated OCT scans, the thickness difference of each layer was calculated. The overall mean global and regional thickness differences of 10 intraretinal layers were 0.46 +/- 0.25 μm (1.70 +/- 0.72 %) and 1.16 +/- 0.84 μm (4.03 +/- 2.05 %), respectively. No specific local region showed a consistent thickness difference across the layers.
NASA Astrophysics Data System (ADS)
Palawong, Kunakorn; Pongchalee, Pornthep; Chuamchaitrakool, Porntip; Tachatraiphop, Sukanya; Widjaja, Joewono; Meemon, Panomsak
2014-06-01
We report the implementation of a high speed and high resolution spectrometer-based spectral domain optical coherence tomography (SD-OCT) system. A high speed near-infrared spectrometer was designed and built, utilizing a high speed line-array CMOS detector and all off-the-shelf optical components. The acquisition speed of more than 100,000 spectra per second was achieved, enabling a high speed 3D imaging of the implemented SD-OCT system. Here, we report the performance characterization, i.e. resolution, imaging depth, and sensitivity of the implemented system. The penetration depth and depth resolution of the system are currently 2 mm and 14.1 μm, respectively. The lateral resolution of the system was quantified by the Modulation transfer function (MTF) measurement to be about 15.5 μm. over the lateral field-of-view (x-y axes) of 30 mm × 30 mm. The acquisition speed of the system was 20 frames per second.
Domain decomposition preconditioners for the spectral collocation method
NASA Technical Reports Server (NTRS)
Quarteroni, Alfio; Sacchilandriani, Giovanni
1988-01-01
Several block iteration preconditioners are proposed and analyzed for the solution of elliptic problems by spectral collocation methods in a region partitioned into several rectangles. It is shown that convergence is achieved with a rate which does not depend on the polynomial degree of the spectral solution. The iterative methods here presented can be effectively implemented on multiprocessor systems due to their high degree of parallelism.
Wang, Hsin-Wei; Hsu, Yen-Chu; Hwang, Jenn-Kang; Lyu, Ping-Chiang; Pai, Tun-Wen; Tang, Chuan Yi
2010-01-01
This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge
Spectral multi-domain for large-scale fluid dynamic simulations
NASA Technical Reports Server (NTRS)
Streett, C. L.; Macaraeg, M. G.
1989-01-01
A number of successful applications of a spectral collocation method extended by a multi-domain patching technique are shown. The multi-domain technique can be used to improve resolution for problems with widely disparate scales, and to reduce the ill-conditioning of the spectral operators for problems in which a large number of points are required for distributed resolution. A new nonreflecting outflow boundary treatment for unsteady transition-to-turbulence simulations is also presented, which relies on the multi-domain technique. The role of multi-domain in improving the efficiency of such calculations is discussed.
NASA Astrophysics Data System (ADS)
Blanco-Roldán, C.; Quirós, C.; Rodriguez-Rodriguez, G.; Vélez, M.; Martín, J. I.; Alameda, J. M.
2016-02-01
Three-dimensional magnetic circuits composed of Co microwires crossed by elevated Co bridges have been patterned on Si substrate by e-beam lithography and lift-off process. The lithographic procedure includes a double resist procedure that optimizes the shape of the bridge, so that 200 nm air gaps can be routinely achieved in between the wire and bridge elements. Microwire magnetization reversal processes have been analyzed by magneto-optical Kerr effect microscopy with different remanent bridge configurations. When the Co bridge is magnetized along the in-plane direction parallel to the wire axis, its stray field induces a marked pinning effect on domain wall propagation along the wire below it, even without being in contact. Changing the sign of the remanent state of the bridge, domain wall pinning can be selected to occur in either the ascending or descending branches of the wire hysteresis loop. Thus, these wire-bridge 3D circuits provide a simple system for tunable domain wall pinning controllable through the pre-recorded bridge remanent state.
Ruggeri, Marco; Major, James C.; McKeown, Craig; Knighton, Robert W.; Puliafito, Carmen A.
2010-01-01
Purpose. To reveal three-dimensional (3-D) information about the retinal structures of birds of prey in vivo. Methods. An ultra-high resolution spectral-domain optical coherence tomography (SD-OCT) system was built for in vivo imaging of retinas of birds of prey. The calibrated imaging depth and axial resolution of the system were 3.1 mm and 2.8 μm (in tissue), respectively. 3-D segmentation was performed for calculation of the retinal nerve fiber layer (RNFL) map. Results. High-resolution OCT images were obtained of the retinas of four species of birds of prey: two diurnal hawks (Buteo platypterus and Buteo brachyurus) and two nocturnal owls (Bubo virginianus and Strix varia). These images showed the detailed retinal anatomy, including the retinal layers and the structure of the deep and shallow foveae. The calculated thickness map showed the RNFL distribution. Traumatic injury to one bird's retina was also successfully imaged. Conclusions. Ultra-high resolution SD-OCT provides unprecedented high-quality 2-D and 3-D in vivo visualization of the retinal structures of birds of prey. SD-OCT is a powerful imaging tool for vision research in birds of prey. PMID:20554605
NASA Astrophysics Data System (ADS)
Subhash, Hrebesh M.; Davila, Viviana; Sun, Hai; Nguyen-Huynh, Anh T.; Nuttall, Alfred L.; Wang, Ruikang K.
2010-05-01
There is considerable interest in developing new methods for in vivo imaging of the complex anatomy of the mammalian cochlea for clinical as well as fundamental studies. In this study, we explored, the feasibility of spectral domain optical coherence tomography (SD-OCT) for 3-D in vivo imaging of the cochlea in mice. The SD-OCT system employed in this study used a broadband light source centered at 1300 nm, and the imaging speed of the system was 47,000 A-scans per second using the InGaAs camera. The system was capable of providing fully processed, high-resolution B-scan images [512 (axial)×128 (lateral) pixels] at 280 frames per sec. The 3-D imaging acquisition time for a whole cochlea was ~0.45 sec. The traditional SD-OCT structural imaging algorithm was used to reconstruct 3-D cochlear morphology. We demonstrated that SD-OCT can be successfully used for in vivo imaging of important morphological features within the mouse cochlea, such as the otic capsule and structures within, including Reissner's membrane, the basilar membrane, tectorial membrane, organ of Corti, and modiolus of the apical and middle turns.
Brosch, Tom; Tam, Roger
2015-01-01
Deep learning has traditionally been computationally expensive, and advances in training methods have been the prerequisite for improving its efficiency in order to expand its application to a variety of image classification problems. In this letter, we address the problem of efficient training of convolutional deep belief networks by learning the weights in the frequency domain, which eliminates the time-consuming calculation of convolutions. An essential consideration in the design of the algorithm is to minimize the number of transformations to and from frequency space. We have evaluated the running time improvements using two standard benchmark data sets, showing a speed-up of up to 8 times on 2D images and up to 200 times on 3D volumes. Our training algorithm makes training of convolutional deep belief networks on 3D medical images with a resolution of up to 128×128×128 voxels practical, which opens new directions for using deep learning for medical image analysis. PMID:25380341
Serohijos, Adrian W R; Hegedus, Tamás; Aleksandrov, Andrei A; He, Lihua; Cui, Liying; Dokholyan, Nikolay V; Riordan, John R
2008-03-01
Deletion of phenylalanine-508 (Phe-508) from the N-terminal nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ATP-binding cassette (ABC) transporter family, disrupts both its folding and function and causes most cystic fibrosis. Most mutant nascent chains do not pass quality control in the ER, and those that do remain thermally unstable, only partially functional, and are rapidly endocytosed and degraded. Although the lack of the Phe-508 peptide backbone diminishes the NBD1 folding yield, the absence of the aromatic side chain is primarily responsible for defective CFTR assembly and channel gating. However, the site of interdomain contact by the side chain is unknown as is the high-resolution 3D structure of the complete protein. Here we present a 3D structure of CFTR, constructed by molecular modeling and supported biochemically, in which Phe-508 mediates a tertiary interaction between the surface of NBD1 and a cytoplasmic loop (CL4) in the C-terminal membrane-spanning domain (MSD2). This crucial cytoplasmic membrane interface, which is dynamically involved in regulation of channel gating, explains the known sensitivity of CFTR assembly to many disease-associated mutations in CL4 as well as NBD1 and provides a sharply focused target for small molecules to treat CF. In addition to identifying a key intramolecular site to be repaired therapeutically, our findings advance understanding of CFTR structure and function and provide a platform for focused biochemical studies of other features of this unique ABC ion channel. PMID:18305154
Serohijos, Adrian W. R.; Hegedűs, Tamás; Aleksandrov, Andrei A.; He, Lihua; Cui, Liying; Dokholyan, Nikolay V.; Riordan, John R.
2008-01-01
Deletion of phenylalanine-508 (Phe-508) from the N-terminal nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ATP-binding cassette (ABC) transporter family, disrupts both its folding and function and causes most cystic fibrosis. Most mutant nascent chains do not pass quality control in the ER, and those that do remain thermally unstable, only partially functional, and are rapidly endocytosed and degraded. Although the lack of the Phe-508 peptide backbone diminishes the NBD1 folding yield, the absence of the aromatic side chain is primarily responsible for defective CFTR assembly and channel gating. However, the site of interdomain contact by the side chain is unknown as is the high-resolution 3D structure of the complete protein. Here we present a 3D structure of CFTR, constructed by molecular modeling and supported biochemically, in which Phe-508 mediates a tertiary interaction between the surface of NBD1 and a cytoplasmic loop (CL4) in the C-terminal membrane-spanning domain (MSD2). This crucial cytoplasmic membrane interface, which is dynamically involved in regulation of channel gating, explains the known sensitivity of CFTR assembly to many disease-associated mutations in CL4 as well as NBD1 and provides a sharply focused target for small molecules to treat CF. In addition to identifying a key intramolecular site to be repaired therapeutically, our findings advance understanding of CFTR structure and function and provide a platform for focused biochemical studies of other features of this unique ABC ion channel. PMID:18305154
NASA Astrophysics Data System (ADS)
Wright, G.; Flyer, N.; Yuen, D. A.; Monnereau, M.; Zhang, S.; Wang, S. M.
2009-05-01
Many numerical methods, such as finite-differences, finite-volume, their yin-yang variants, finite-elements and spectral methods have been employed to study 3-D mantle convection. All have their own strengths, but also serious weaknesses. Spectrally accurate methods do not practically allow for node refinement and often involve cumbersome algebra while finite difference, volume, or element methods are generally low-order, adding excessive numerical diffusion to the model. For the 3-D mantle convection problem, we have introduced a new mesh-free approach, using radial basis functions (RBF). This method has the advantage of being algorithmic simple, spectrally accurate for arbitrary node layouts in multi-dimensions and naturally allows for node-refinement. One virtue of the RBF scheme allows the user to use a simple Cartesian geometry, while implementing the required boundary conditions for the temperature, velocities and stress components on a spherical surface at both the planetary surface and the core-mantle boundary. We have studied time- dependent mantle convection, using both a RBF-pseudospectral code and a code which uses spherical- harmonics in the angular direction and second-order finite volume in the radial direction. We have employed a third code , which uses spherical harmonics and higher-order finite-difference method a la Fornberg in the radial coordinate.We first focus on the onset of time-dependence at Rayleigh number Ra of 70,000. We follow the development of stronger time-dependence to a Ra of one million, using high enough resolution with 120 to 200 points in the radial direction and 128 to 256 spherical harmonics.
NASA Astrophysics Data System (ADS)
Lee, H.; Min, D.; Lim, S.; Yang, J.; Kwon, B.; Yoo, H.
2009-12-01
In a conventional marine seismic data analysis, pressure data have been usually interpreted on the basis of acoustic wave equation. The acoustic wave equation, however, only deals with P-wave propagation, and it cannot correctly describe the wave propagation in acoustic-elastic (fluid-solid) coupled media. Recently, in 4C OBC survey (4-component ocean bottom cable), it is possible to acquire both pressure and 3-component displacements (measured at the sea-bottom). Combining pressure and displacement data allows us to interpret subsurface structures more accurately. In order to accurately simulate wave propagation in fluid-solid coupled media, we need an acoustic-elastic coupled modeling algorithm, which deals with displacements in elastic region and pressure in acoustic region. For waveform inversion and reverse-time migration that require a great number of forward modeling, it is essential to develop an efficient scheme that reduces computing time and computer core memory. In this study, we present a 3D time-domain acoustic-elastic coupled modeling algorithm on the basis of the cell-based finite difference method. The cell-based method has proven to properly describe the free-surface boundary, which indicates that it will also properly describe the fluid-solid interface boundaries. In the acoustic-elastic coupled modeling, we first compose cell-based finite differences individually for the 3D acoustic and elastic media, and then combine the differences using the fluid-solid interface boundary conditions. Considering that the 2D acoustic-elastic coupled modeling algorithm gives numerical solutions comparable to analytic solutions, we expect that the 3D acoustic-elastic coupled modeling will correctly describe wave propagation in the fluid-solid coupled media. We apply our algorithm to 3D horizontal two- and three-layer models. Numerical experiments show that the cell-based coupled modeling algorithm properly describes S- and converted waves as well as P-waves. The
NASA Technical Reports Server (NTRS)
Mittra, R.; Ko, W. L.; Rahmat-Samii, Y.
1979-01-01
This paper presents a brief review of some recent developments on the use of the spectral-domain approach for deriving high-frequency solutions to electromagnetics scattering and radiation problems. The spectral approach is not only useful for interpreting the well-known Keller formulas based on the geometrical theory of diffraction (GTD), it can also be employed for verifying the accuracy of GTD and other asymptotic solutions and systematically improving the results when such improvements are needed. The problem of plane wave diffraction by a finite screen or a strip is presented as an example of the application of the spectral-domain approach.
Lo, William C Y; Villiger, Martin; Golberg, Alexander; Broelsch, G Felix; Khan, Saiqa; Lian, Christine G; Austen, William G; Yarmush, Martin; Bouma, Brett E
2016-01-01
Hypertrophic scars (HTS), frequently seen after traumatic injuries and surgery, remain a major clinical challenge because of the limited success of existing therapies. A significant obstacle to understanding HTS etiology is the lack of tools to monitor scar remodeling longitudinally and noninvasively. We present an in vivo, label-free technique using polarization-sensitive optical frequency domain imaging for the 3D, longitudinal assessment of collagen remodeling in murine HTS. In this study, HTS was induced with a mechanical tension device for 4-10 days on incisional wounds and imaged up to 1 month after device removal; an excisional HTS model was also imaged at 6 months after injury to investigate deeper and more mature scars. We showed that local retardation and degree of polarization provide a robust signature for HTS. Compared with normal skin with heterogeneous local retardation and low degree of polarization, HTS was characterized by an initially low local retardation, which increased as collagen fibers remodeled, and a persistently high degree of polarization. This study demonstrates that polarization-sensitive optical frequency domain imaging offers a powerful tool to gain significant biological insights into HTS remodeling by enabling longitudinal assessment of collagen in vivo, which is critical to elucidating HTS etiology and developing more effective HTS therapies. PMID:26763427
NASA Astrophysics Data System (ADS)
Pathak, Ashish; Raessi, Mehdi
2016-04-01
We present a three-dimensional (3D) and fully Eulerian approach to capturing the interaction between two fluids and moving rigid structures by using the fictitious domain and volume-of-fluid (VOF) methods. The solid bodies can have arbitrarily complex geometry and can pierce the fluid-fluid interface, forming contact lines. The three-phase interfaces are resolved and reconstructed by using a VOF-based methodology. Then, a consistent scheme is employed for transporting mass and momentum, allowing for simulations of three-phase flows of large density ratios. The Eulerian approach significantly simplifies numerical resolution of the kinematics of rigid bodies of complex geometry and with six degrees of freedom. The fluid-structure interaction (FSI) is computed using the fictitious domain method. The methodology was developed in a message passing interface (MPI) parallel framework accelerated with graphics processing units (GPUs). The computationally intensive solution of the pressure Poisson equation is ported to GPUs, while the remaining calculations are performed on CPUs. The performance and accuracy of the methodology are assessed using an array of test cases, focusing individually on the flow solver and the FSI in surface-piercing configurations. Finally, an application of the proposed methodology in simulations of the ocean wave energy converters is presented.
Terahertz Detection Based on Spectral-Domain Interferometry Using Mach-Zehnder Interferometer
NASA Astrophysics Data System (ADS)
Ibrahim, Akram; Sharma, Gargi; Singh, Kanwarpal; Ozaki, Tsuneyuki
2016-04-01
We demonstrate the use of a Mach-Zehnder interferometer (MZI) to improve the performance of terahertz electric field measurements based on spectral-domain interferometry. The interferometer is introduced into the probe beam line to improve the temporal overlap between the two probe pulses. The probe pulse in the sample arm of the interferometer passes through the detection crystal and overlaps with the terahertz pulse, while the probe pulse in the reference arm does not. We measure the phase change between spectral components of these two pulses using spectral-domain interferometry. Using this new technique, we enable an unlimited temporal scanning window without the loss in the signal-to-noise ratio, thus overcoming the major limitation of conventional spectral-domain interferometry techniques for terahertz electric field detection.
Terahertz Detection Based on Spectral-Domain Interferometry Using Mach-Zehnder Interferometer
NASA Astrophysics Data System (ADS)
Ibrahim, Akram; Sharma, Gargi; Singh, Kanwarpal; Ozaki, Tsuneyuki
2016-09-01
We demonstrate the use of a Mach-Zehnder interferometer (MZI) to improve the performance of terahertz electric field measurements based on spectral-domain interferometry. The interferometer is introduced into the probe beam line to improve the temporal overlap between the two probe pulses. The probe pulse in the sample arm of the interferometer passes through the detection crystal and overlaps with the terahertz pulse, while the probe pulse in the reference arm does not. We measure the phase change between spectral components of these two pulses using spectral-domain interferometry. Using this new technique, we enable an unlimited temporal scanning window without the loss in the signal-to-noise ratio, thus overcoming the major limitation of conventional spectral-domain interferometry techniques for terahertz electric field detection.
Eom, Tae Joong; Ahn, Yeh-Chan; Kim, Chang-Seok; Chen, Zhongping
2011-03-01
We present a calibration protocol to obtain the alignment factors of a custom-made spectrometer and the nonlinear fitting function between the measured CCD pixel domain and the wavelength domain to apply to the spectral-domain optical coherence tomography (SD-OCT) using fiber Bragg gratings. We have used five gratings with different center wavelengths covering the broadband source spectral range. All have a narrow spectral bandwidth (0.05 nm) and the same reflectivity (92%) to calibrate and align the custom-made spectrometer. The implemented SD-OCT system following the proposed protocol showed the alignment factors as 44.37 deg incident angle, 53.11 deg diffraction angle, and 70.0-mm focal length. The spectral resolution of 0.187 nm was recalculated from the alignment factors. PMID:21456856
Time-domain calculation of spectral centroid from backscattered ultrasound signals.
Kim, Hyungsuk; Heo, Seo Weon
2012-06-01
Spectral centroid estimation from backscattered ultrasound RF signals is the preliminary step for quantitative ultrasound analysis in many medical applications. The traditional approach of estimating the spectral centroid in the frequency domain takes a long time because discrete Fourier transform (DFT) processing for each RF segment is required. To avoid this, we propose time-domain methods to estimate the spectral centroid in this paper. First, we derive the continuous-time-domain equations for the spectral centroid estimation using Parseval's theorem and Hilbert transform theory. Then, we extend the method to the discrete-time domain to ease the implementation while maintaining the same accuracy as the calculation in the frequency domain. From the result, we observe that it is not practical to apply the discrete-time equations directly, because a high sampling rate is needed to approximate the time derivative in the discrete-time domain. Therefore, we also derive the feasible version of the discrete-time equations using a circular autocorrelation function, which has no constraints on the sampling rate for real RF signals acquired from pulse-echo ultrasound systems. Simulation results using numerical phantoms show that the time-domain calculation is approximately 4.4 times faster on average than the frequency-domain method when the software's built-in functions were used. The average estimation error compared with that of the frequency-domain method using DFT is less than 0.2% for the entire propagation depths. The proposed time-domain approach to estimate the spectral centroid can be easily implemented in real-time ultrasound systems. PMID:22711414
A fluid model simulation of a simplified plasma limiter based on spectral-element time-domain method
Qian, Cheng; Ding, Dazhi Fan, Zhenhong; Chen, Rushan
2015-03-15
A simplified plasma limiter prototype is proposed and the fluid model coupled with Maxwell's equations is established to describe the operating mechanism of plasma limiter. A three-dimensional (3-D) simplified sandwich structure plasma limiter model is analyzed with the spectral-element time-domain (SETD) method. The field breakdown threshold of air and argon at different frequency is predicted and compared with the experimental data and there is a good agreement between them for gas microwave breakdown discharge problems. Numerical results demonstrate that the two-layer plasma limiter (plasma-slab-plasma) has better protective characteristics than a one-layer plasma limiter (slab-plasma-slab) with the same length of gas chamber.
An, Lin; Li, Peng; Shen, Tueng T; Wang, Ruikang
2011-10-01
We present a new development of ultrahigh speed spectral domain optical coherence tomography (SDOCT) for human retinal imaging at 850 nm central wavelength by employing two high-speed line scan CMOS cameras, each running at 250 kHz. Through precisely controlling the recording and reading time periods of the two cameras, the SDOCT system realizes an imaging speed at 500,000 A-lines per second, while maintaining both high axial resolution (~8 μm) and acceptable depth ranging (~2.5 mm). With this system, we propose two scanning protocols for human retinal imaging. The first is aimed to achieve isotropic dense sampling and fast scanning speed, enabling a 3D imaging within 0.72 sec for a region covering 4x4 mm(2). In this case, the B-frame rate is 700 Hz and the isotropic dense sampling is 500 A-lines along both the fast and slow axes. This scanning protocol minimizes the motion artifacts, thus making it possible to perform two directional averaging so that the signal to noise ratio of the system is enhanced while the degradation of its resolution is minimized. The second protocol is designed to scan the retina in a large field of view, in which 1200 A-lines are captured along both the fast and slow axes, covering 10 mm(2), to provide overall information about the retinal status. Because of relatively long imaging time (4 seconds for a 3D scan), the motion artifact is inevitable, making it difficult to interpret the 3D data set, particularly in a way of depth-resolved en-face fundus images. To mitigate this difficulty, we propose to use the relatively high reflecting retinal pigmented epithelium layer as the reference to flatten the original 3D data set along both the fast and slow axes. We show that the proposed system delivers superb performance for human retina imaging. PMID:22025983
Chen, Haoyu; Yang, Jianling; Shi, Fei; Zheng, Ce; Zhu, Weifang; Xiang, Dehui; Chen, Xinjian; Zhang, Mingzhi
2016-01-01
Purpose To investigate the profile and determinants of retinal optical intensity in normal subjects using 3D spectral domain optical coherence tomography (SD OCT). Methods A total of 231 eyes from 231 healthy subjects ranging in age from 18 to 80 years were included and underwent a 3D OCT scan. Forty-four eyes were randomly chosen to be scanned by two operators for reproducibility analysis. Distribution of optical intensity of each layer and regions specified by the Early Treatment of Diabetic Retinopathy Study (ETDRS) were investigated by analyzing the OCT raw data with our automatic graph-based algorithm. Univariate and multivariate analyses were performed between retinal optical intensity and sex, age, height, weight, spherical equivalent (SE), axial length, image quality, disc area and rim/disc area ratio (R/D area ratio). Results For optical intensity measurements, the intraclass correlation coefficient of each layer ranged from 0.815 to 0.941, indicating good reproducibility. Optical intensity was lowest in the central area of retinal nerve fiber layer, ganglion cell layer, inner plexiform layer, inner nuclear layer, outer plexiform layer and photoreceptor layer, except for the retinal pigment epithelium (RPE). Optical intensity was positively correlated with image quality in all retinal layers (0.553<β<0.851, p<0.01), and negatively correlated with age in most retinal layers (-0.362<β<-0.179, p<0.01), except for the RPE (β = 0.456, p<0.01), outer nuclear layer and photoreceptor layer (p>0.05). There was no relationship between retinal optical intensity and sex, height, weight, SE, axial length, disc area and R/D area ratio. Conclusions There was a specific pattern of distribution of retinal optical intensity in different regions. The optical intensity was affected by image quality and age. Image quality can be used as a reference for normalization. The effect of age needs to be taken into consideration when using OCT for diagnosis. PMID:26863010
Automatic online spectral calibration of Fourier-domain OCT for robotic surgery
NASA Astrophysics Data System (ADS)
Liu, Xuan; Balicki, Marcin; Taylor, Russell H.; Kang, Jin U.
2011-03-01
We present a new automatic spectral calibration (ASC) method for spectral Domain optical coherence tomography (SD-OCT). Our ASC method calibrates the spectral mapping of the spectrometer in SD-OCT, and does not require external calibrating light source or a commercial spectral analyzer. The ASC method simultaneously calibrates the physical pixel spacing of the A-scan in static and dynamic environments. Experimental results show that the proposed ASC method can provide satisfactory calibration for SD-OCT to achieve high axial resolution and high ranging accuracy, without increasing hardware complexity.
NASA Astrophysics Data System (ADS)
Gangodagamage, C.; Rowland, J. C.; Skurikhin, A. N.; Wilson, C. J.; Brumby, S. P.; Painter, S. L.; Gable, C. W.; Bui, Q.; Short, L. S.; Liljedahl, A.; Hubbard, S. S.; Wainwright, H. M.; Dafflon, B.; Tweedie, C. E.; Kumar, J.; Wullschleger, S. D.
2013-12-01
. Finally, we show that the developed topographic template curves can be used to synthetically generate 3D model domain polygonal discretizations and characterizations and to predict ice wedge degradation levels - all using commonly available high resolution remotely sensed data where high-resolution LiDAR data is unavailable. Classification scheme for high centered and low centered polygons.
Kothandan, Gugan; Gadhe, Changdev G; Madhavan, Thirumurthy; Choi, Cheol Hee; Cho, Seung Joo
2011-09-01
In order to explore the interactions between flavones and P-gp, in silico methodologies such as docking and 3D-QSAR were performed. CoMFA and CoMSIA analyses were done using ligand based and receptor guided alignment schemes. Validation statistics include leave-one-out cross-validated R(2) (q(2)), internal prediction parameter by progressive scrambling (Q(*2)), external prediction with test set. They show that models derived from this study are quite robust. Ligand based CoMFA (q(2) = 0.747, Q(*2) = 0.639, r(pred)(2)=0.802) and CoMSIA model (q(2) = 0.810, Q(*2) = 0.676, r(pred)(2)=0.785) were developed using atom by atom matching. Receptor guided CoMFA (q(2) = 0.712, Q(*2) = 0.497, r(pred)(2) = 0.841) and for CoMSIA (q(2) = 0.805, Q(*2) = 0.589, r(pred)(2) = 0.937) models were developed by docking of highly active flavone into the proposed NBD (nucleotide binding domain) of P-gp. The 3D-QSAR models generated here predicted that hydrophobic and steric parameters are important for activity toward P-gp. Our studies indicate the important amino acid in NBD crucial for binding in accordance with the previous results. This site forms a hydrophobic site. Since flavonoids have potential without toxicity, we propose to inspect this hydrophobic site including Asn1043 and Asp1049 should be considered for future inhibitor design. PMID:21723648
ICER-3D Hyperspectral Image Compression Software
NASA Technical Reports Server (NTRS)
Xie, Hua; Kiely, Aaron; Klimesh, matthew; Aranki, Nazeeh
2010-01-01
Software has been developed to implement the ICER-3D algorithm. ICER-3D effects progressive, three-dimensional (3D), wavelet-based compression of hyperspectral images. If a compressed data stream is truncated, the progressive nature of the algorithm enables reconstruction of hyperspectral data at fidelity commensurate with the given data volume. The ICER-3D software is capable of providing either lossless or lossy compression, and incorporates an error-containment scheme to limit the effects of data loss during transmission. The compression algorithm, which was derived from the ICER image compression algorithm, includes wavelet-transform, context-modeling, and entropy coding subalgorithms. The 3D wavelet decomposition structure used by ICER-3D exploits correlations in all three dimensions of sets of hyperspectral image data, while facilitating elimination of spectral ringing artifacts, using a technique summarized in "Improving 3D Wavelet-Based Compression of Spectral Images" (NPO-41381), NASA Tech Briefs, Vol. 33, No. 3 (March 2009), page 7a. Correlation is further exploited by a context-modeling subalgorithm, which exploits spectral dependencies in the wavelet-transformed hyperspectral data, using an algorithm that is summarized in "Context Modeler for Wavelet Compression of Hyperspectral Images" (NPO-43239), which follows this article. An important feature of ICER-3D is a scheme for limiting the adverse effects of loss of data during transmission. In this scheme, as in the similar scheme used by ICER, the spatial-frequency domain is partitioned into rectangular error-containment regions. In ICER-3D, the partitions extend through all the wavelength bands. The data in each partition are compressed independently of those in the other partitions, so that loss or corruption of data from any partition does not affect the other partitions. Furthermore, because compression is progressive within each partition, when data are lost, any data from that partition received
NASA Technical Reports Server (NTRS)
Bailey, R. T.; Shih, T. I.-P.; Nguyen, H. L.; Roelke, R. J.
1990-01-01
An efficient computer program, called GRID2D/3D, was developed to generate single and composite grid systems within geometrically complex two- and three-dimensional (2- and 3-D) spatial domains that can deform with time. GRID2D/3D generates single grid systems by using algebraic grid generation methods based on transfinite interpolation in which the distribution of grid points within the spatial domain is controlled by stretching functions. All single grid systems generated by GRID2D/3D can have grid lines that are continuous and differentiable everywhere up to the second-order. Also, grid lines can intersect boundaries of the spatial domain orthogonally. GRID2D/3D generates composite grid systems by patching together two or more single grid systems. The patching can be discontinuous or continuous. For continuous composite grid systems, the grid lines are continuous and differentiable everywhere up to the second-order except at interfaces where different single grid systems meet. At interfaces where different single grid systems meet, the grid lines are only differentiable up to the first-order. For 2-D spatial domains, the boundary curves are described by using either cubic or tension spline interpolation. For 3-D spatial domains, the boundary surfaces are described by using either linear Coon's interpolation, bi-hyperbolic spline interpolation, or a new technique referred to as 3-D bi-directional Hermite interpolation. Since grid systems generated by algebraic methods can have grid lines that overlap one another, GRID2D/3D contains a graphics package for evaluating the grid systems generated. With the graphics package, the user can generate grid systems in an interactive manner with the grid generation part of GRID2D/3D. GRID2D/3D is written in FORTRAN 77 and can be run on any IBM PC, XT, or AT compatible computer. In order to use GRID2D/3D on workstations or mainframe computers, some minor modifications must be made in the graphics part of the program; no
MT3D was first developed by Chunmiao Zheng in 1990 at S.S. Papadopulos & Associates, Inc. with partial support from the U.S. Environmental Protection Agency (USEPA). Starting in 1990, MT3D was released as a pubic domain code from the USEPA. Commercial versions with enhanced capab...
Spatially-dense, multi-spectral, frequency-domain diffuse optical tomography of breast cancer
NASA Astrophysics Data System (ADS)
Ban, Han Yong
Diffuse optical tomography (DOT) employs near-infrared light to image the concentration of chromophores and cell organelles in tissue and thereby providing access to functional parameters that can differentiate cancerous from normal tissues. This thesis describes research at the bench and in the clinic that explores and identifies the potential of DOT breast cancer imaging. The bench and clinic instrumentation differ but share important features: they utilize a very large, spatially dense, set of source-detector pairs (10 7) for imaging in the parallel-plate geometry. The bench experiments explored three-dimensional (3D) image resolution and fidelity as a function of numerous parameters and also ascertained the effects of a chest wall phantom. The chest wall is always present but is typically ignored in breast DOT. My experiments clarified chest wall influences and developed schemes to mitigate these effects. Mostly, these schemes involved selective data exclusion, but their efficacy also depended on reconstruction approach. Reconstruction algorithms based on analytic (fast) Fourier inversion and linear algebraic techniques were explored. The clinical experiments centered around a DOT instrument that I designed, constructed, and have begun to test (in-vitro and in-vivo). This instrumentation offers many features new to the field. Specifically, the imager employs spatially-dense, multi-spectral, frequency-domain data; it possesses the world's largest optical source-detector density yet reported, facilitated by highly-parallel CCD-based frequency-domain imaging based on gain-modulation heterodyne detection. The instrument thus measures both phase and amplitude of the diffusive light waves. Other features include both frontal and sagittal breast imaging capabilities, ancillary cameras for measurement of breast boundary profiles, real-time data normalization, and mechanical improvements for patient comfort. The instrument design and construction is my most significant
Lo, William C. Y.; Villiger, Martin; Golberg, Alexander; Broelsch, G. Felix; Khan, Saiqa; Lian, Christine G.; Austen, William G.; Yarmush, Martin; Bouma, Brett E.
2016-01-01
Hypertrophic scars (HTS), frequently seen after traumatic injuries and surgery, remain a major clinical challenge due to the limited success of existing therapies. A significant obstacle to understanding HTS etiology is the lack of tools to monitor scar remodeling longitudinally and non-invasively. We present an in vivo, label-free technique using polarization-sensitive optical frequency domain imaging (PS-OFDI) for the 3D, longitudinal assessment of collagen remodeling in murine HTS. In this study, HTS was induced with a mechanical tension device for 4 to 10 days on incisional wounds and imaged up to one month after device removal; an excisional HTS model was also imaged at 6 months after injury to investigate deeper and more mature scars. We showed that local retardation (LR) and degree of polarization (DOP) provide a robust signature for HTS. Compared to normal skin with heterogeneous LR and low DOP, HTS was characterized by an initially low LR, which increased as collagen fibers remodeled, and a persistently high DOP. This study demonstrates that PS-OFDI offers a powerful tool to gain significant biological insights into HTS remodeling by enabling longitudinal assessment of collagen in vivo, which is critical to elucidating HTS etiology and developing more effective HTS therapies. PMID:26763427
NASA Astrophysics Data System (ADS)
Ruggeri, Marco; Wehbe, Hassan; Jiao, Shuliang; Gregori, Giovanni; Jockovich, Maria E.; Hackam, Abigail; Duan, Yuanli; Puliafito, Carmen A.
2007-02-01
The purpose of this study is to demonstrate the application of ultrahigh-resolution Spectral Domain Optical Coherence Tomography (SD-OCT) for non contact in vivo imaging of the retina of small animals and quantitative retinal information extraction using 3D segmentation of the OCT images. An ultrahigh-resolution SD-OCT system was specifically designed for in vivo retinal imaging of small animal. En face fundus image was constructed from the measured OCT data, which enables precise registration of the OCT images on the fundus. 3D segmentation algorithms were developed for the calculation of retinal thickness map. High quality OCT images of the retina of mice (B6/SJLF2 for normal retina, Rho -/- for photoreceptor degeneration and LH BETAT AG for retinoblastoma) and rats (Wistar for normal retina) were acquired, where all the retinal layers can be clearly recognized. The calculated retinal thickness map makes successful quantitative comparison of the retinal thickness distribution between normal and degenerative mouse retina. The capabilities of the OCT system provide a valuable tool for longitudinal studies of small animal models of ocular diseases.
Absolute velocity measurement using three-beam spectral-domain Doppler optical coherence tomography
NASA Astrophysics Data System (ADS)
Sharma, P.; Verma, Y.; Kumar, S.; Gupta, P. K.
2015-09-01
We report the development of a three-beam spectral-domain Doppler optical coherence tomography setup that allows single interferometer-based measurement of absolute flow velocity. The setup makes use of galvo-based phase shifting to remove complex conjugate mirror artifact and a beam displacer in the sample arm to avoid cross talk image. The results show that the developed approach allows efficient utilization of the imaging range of the spectral-domain optical coherence tomography setup for three-beam-based velocity measurement.
Sparse OCT: optimizing compressed sensing in spectral domain optical coherence tomography
NASA Astrophysics Data System (ADS)
Liu, Xuan; Kang, Jin U.
2011-03-01
We applied compressed sensing (CS) to spectral domain optical coherence tomography (SD-OCT). Namely, CS was applied to the spectral data in reconstructing A-mode images. This would eliminate the need for a large amount of spectral data for image reconstruction and processing. We tested the CS method by randomly undersampling k-space SD-OCT signal. OCT images are reconstructed by solving an optimization problem that minimizes the l1 norm to enforce sparsity, subject to data consistency constraints. Variable density random sampling and uniform density random sampling were studied and compared, which shows the former undersampling scheme can achieve accurate signal recovery using less data.
Potsaid, Benjamin; Gorczynska, Iwona; Srinivasan, Vivek J; Chen, Yueli; Jiang, James; Cable, Alex; Fujimoto, James G
2008-09-15
We demonstrate ultrahigh speed spectral / Fourier domain optical coherence tomography (OCT) using an ultrahigh speed CMOS line scan camera at rates of 70,000 - 312,500 axial scans per second. Several design configurations are characterized to illustrate trade-offs between acquisition speed, resolution, imaging range, sensitivity and sensitivity roll-off performance. Ultrahigh resolution OCT with 2.5 - 3.0 micron axial image resolution is demonstrated at approximately 100,000 axial scans per second. A high resolution spectrometer design improves sensitivity roll-off and imaging range performance, trading off imaging speed to 70,000 axial scans per second. Ultrahigh speed imaging at >300,000 axial scans per second with standard image resolution is also demonstrated. Ophthalmic OCT imaging of the normal human retina is investigated. The high acquisition speeds enable dense raster scanning to acquire densely sampled volumetric three dimensional OCT (3D-OCT) data sets of the macula and optic disc with minimal motion artifacts. Imaging with approximately 8 - 9 micron axial resolution at 250,000 axial scans per second, a 512 x 512 x 400 voxel volumetric 3D-OCT data set can be acquired in only approximately 1.3 seconds. Orthogonal registration scans are used to register OCT raster scans and remove residual axial eye motion, resulting in 3D-OCT data sets which preserve retinal topography. Rapid repetitive imaging over small volumes can visualize small retinal features without motion induced distortions and enables volume registration to remove eye motion. Cone photoreceptors in some regions of the retina can be visualized without adaptive optics or active eye tracking. Rapid repetitive imaging of 3D volumes also provides dynamic volumetric information (4D-OCT) which is shown to enhance visualization of retinal capillaries and should enable functional imaging. Improvements in the speed and performance of 3D-OCT volumetric imaging promise to enable earlier diagnosis and
Kothari, Nikisha; Kuriyan, Ajay E; Flynn, Harry W
2016-01-01
We report three patients with subretinal bands associated with retinal detachment in chronic retinal detachments who underwent successful retinal reattachment. Subretinal bands before and after surgery can be identified on clinical examination and spectral domain optical coherence tomography. Removal of subretinal bands is not mandatory to achieve retinal reattachment. PMID:27099457
Kamalden, Tengku Ain; Lingam, Gopal; Sundar, Gangadhara
2014-01-01
Choroidal osteoma is a benign ossifying tumor of the choroid, consisting of mature bone tissue. It has been described to enlarge and evolve at varying rates over time. Here, we report and quantify the progression of a unilateral choroidal osteoma in a 7-year-old boy by fundus photography, and document tumor remodeling by spectral domain optical coherence tomography images. PMID:27175357
In-vivo full depth of eye imaging spectral domain optical coherence tomography
NASA Astrophysics Data System (ADS)
Dai, Cuixia; Zhou, Chuanqing; Jiao, Shuliang; Xi, Peng; Ren, Qiushi
2011-09-01
It is necessary to apply the spectral-domain optical coherence tomography (SD-OCT) to image the whole eye segment for practically iatrical application, but the imaging depth of SD-OCT is limited by the spectral resolution of the spectrometer. By now, no result about this research has been reported. In our study, a new dual channel dual focus OCT system is adopted to image the whole eye segment. The cornea and the crystalline lens are simultaneously imaged by using full range complex spectral-domain OCT in one channel, the retina is detected by the other. The new system was successfully tested in imaging of the volunteer' eye in vivo. The preliminary results presented in this paper demonstrated the feasibility of this approach.
Numerical stability analysis of the pseudo-spectral analytical time-domain PIC algorithm
Godfrey, Brendan B.; Vay, Jean-Luc; Haber, Irving
2014-02-01
The pseudo-spectral analytical time-domain (PSATD) particle-in-cell (PIC) algorithm solves the vacuum Maxwell's equations exactly, has no Courant time-step limit (as conventionally defined), and offers substantial flexibility in plasma and particle beam simulations. It is, however, not free of the usual numerical instabilities, including the numerical Cherenkov instability, when applied to relativistic beam simulations. This paper derives and solves the numerical dispersion relation for the PSATD algorithm and compares the results with corresponding behavior of the more conventional pseudo-spectral time-domain (PSTD) and finite difference time-domain (FDTD) algorithms. In general, PSATD offers superior stability properties over a reasonable range of time steps. More importantly, one version of the PSATD algorithm, when combined with digital filtering, is almost completely free of the numerical Cherenkov instability for time steps (scaled to the speed of light) comparable to or smaller than the axial cell size.
A spectral analysis of the domain decomposed Monte Carlo method for linear systems
Slattery, S. R.; Wilson, P. P. H.; Evans, T. M.
2013-07-01
The domain decomposed behavior of the adjoint Neumann-Ulam Monte Carlo method for solving linear systems is analyzed using the spectral properties of the linear operator. Relationships for the average length of the adjoint random walks, a measure of convergence speed and serial performance, are made with respect to the eigenvalues of the linear operator. In addition, relationships for the effective optical thickness of a domain in the decomposition are presented based on the spectral analysis and diffusion theory. Using the effective optical thickness, the Wigner rational approximation and the mean chord approximation are applied to estimate the leakage fraction of stochastic histories from a domain in the decomposition as a measure of parallel performance and potential communication costs. The one-speed, two-dimensional neutron diffusion equation is used as a model problem to test the models for symmetric operators. In general, the derived approximations show good agreement with measured computational results. (authors)
Spectral quantum beating in mixed frequency/time-domain coherent multidimensional spectroscopy.
Pakoulev, Andrei V; Rickard, Mark A; Mathew, Nathan A; Kornau, Kathryn M; Wright, John C
2007-08-01
Coherent multidimensional spectroscopy performed in the mixed frequency/time domain exhibits both temporal and spectral quantum beating when two quantum states are simultaneously excited. The excitation of both quantum states can occur because either the spectral width of the states or the excitation pulse exceeds the frequency separation of the quantum states. The quantum beating appears as a line that broadens and splits into two peaks and then recombines as the time delay between excitation pulses increases. The splitting depends on the spectral width of the excitation pulses. We observe the spectral quantum beating between the two nearly degenerate asymmetric carbonyl stretch modes in a nickel tricarbonyl chelate using the nonrephasing, ground state bleaching coherence pathway in triply vibrationally enhanced four-wave mixing as the time delay between the first two excitation pulses changes. PMID:17628051
Technological aspects of frequency domain data storage using persistent spectral hole burning
NASA Astrophysics Data System (ADS)
Schellenberg, F. M.; Lenth, W.; Bjorklund, G. C.
1986-09-01
Persistent spectral hole burning permits use of optical frequency for encoding digital information at cryogenic temperatures, with storage densities far beyond the limits of conventional laser-disk recording. In the work presented here, several key technological issues of such a storage system have been investigated. Data were encoded with high spatial and spectral resolution using a specially designed cryostat. The fast tuning characteristics of semiconductor diode lasers were studied to test the feasibility of fast data access in the frequency domain. Fast readout was investigated in a simulation experiment using heterodyne detection with frequency modulated diode lasers.
NASA Astrophysics Data System (ADS)
Sablik, Thomas; Velten, Jörg; Kummert, Anton
2015-03-01
An novel system for automatic privacy protection in digital media based on spectral domain watermarking and JPEG compression is described in the present paper. In a first step private areas are detected. Therefore a detection method is presented. The implemented method uses Haar cascades to detects faces. Integral images are used to speed up calculations and the detection. Multiple detections of one face are combined. Succeeding steps comprise embedding the data into the image as part of JPEG compression using spectral domain methods and protecting the area of privacy. The embedding process is integrated into and adapted to JPEG compression. A Spread Spectrum Watermarking method is used to embed the size and position of the private areas into the cover image. Different methods for embedding regarding their robustness are compared. Moreover the performance of the method concerning tampered images is presented.
Wang, Xu; Gao, Zhensen; Kataoka, Nobuyuki; Wada, Naoya
2010-05-10
A novel scheme using single phase modulator for simultaneous time domain spectral phase encoding (SPE) signal generation and DPSK data modulation is proposed and experimentally demonstrated. Array- Waveguide-Grating and Variable-Bandwidth-Spectrum-Shaper based devices can be used for decoding the signal directly in spectral domain. The effects of fiber dispersion, light pulse width and timing error on the coding performance have been investigated by simulation and verified in experiment. In the experiment, SPE signal with 8-chip, 20GHz/chip optical code patterns has been generated and modulated with 2.5 Gbps DPSK data using single modulator. Transmission of the 2.5 Gbps data over 34km fiber with BER<10(-9) has been demonstrated successfully. The proposed scheme has simple configuration and improved flexibility that can significantly improve the data confidentiality for optical code division multiple access (OCDMA) and secure optical communication applications. PMID:20588838
Source-domain spectral EEG analysis of sports-related concussion via Measure Projection Analysis.
Balkan, Ozgur; Virji-Babul, Naznin; Miyakoshi, Makoto; Makeig, Scott; Garudadri, Harinath
2015-01-01
Here, we investigated EEG-based source-level spectral differences between adolescents with sports-related concussions and healthy age matched controls. We transformed resting state EEG collected in both groups to the source domain using Independent Component Analysis (ICA) and computed the component process power spectra. For group-level analysis in the source domain, we used a probabilistic framework, Measure Projection Analysis (MPA), that has advantages over parametric k-means clustering of brain sources. MPA revealed that some frontal brain sources in the concussed group had significantly more power in the beta band (p<;0.005) and significantly less delta (p<;0.01) and theta band power (p<;0.05) than the healthy control group. These results suggest that a shift in spectral profile toward higher frequencies in some frontal brain regions might distinguish individuals with concussion from healthy controls. PMID:26737184
Analysis of multimode fiber bundles for endoscopic spectral-domain optical coherence tomography
Risi, Matthew D.; Makhlouf, Houssine; Rouse, Andrew R.; Gmitro, Arthur F.
2016-01-01
A theoretical analysis of the use of a fiber bundle in spectral-domain optical coherence tomography (OCT) systems is presented. The fiber bundle enables a flexible endoscopic design and provides fast, parallelized acquisition of the OCT data. However, the multimode characteristic of the fibers in the fiber bundle affects the depth sensitivity of the imaging system. A description of light interference in a multimode fiber is presented along with numerical simulations and experimental studies to illustrate the theoretical analysis. PMID:25967012
Improving image quality in intensity-interferometric spectral-domain optical coherence tomography
NASA Astrophysics Data System (ADS)
Shirai, Tomohiro
2016-07-01
Intensity-interferometric spectral-domain optical coherence tomography (I-SD-OCT), devised recently as a classical analog of quantum OCT, enables axially scanless cross-sectional imaging with an immunity to group-velocity dispersion and a factor-of-\\sqrt{2} resolution improvement. However, unwanted artifacts inevitably emerge in the resultant image. In this paper, it is demonstrated theoretically and experimentally that such artifacts can be reduced without any difficulty by means of either a mechanical displacement of the detector for capturing spectral intensity patterns or a numerical displacement of the spectral intensity patterns stored in a computer. Furthermore, it is proved that the I-SD-OCT signal can be extracted from the conventional SD-OCT setup under a certain condition. These two features serve to improve the image quality in I-SD-OCT.
Likelihood Ratios for Glaucoma Diagnosis Using Spectral Domain Optical Coherence Tomography
Lisboa, Renato; Mansouri, Kaweh; Zangwill, Linda M.; Weinreb, Robert N.; Medeiros, Felipe A.
2014-01-01
Purpose To present a methodology for calculating likelihood ratios for glaucoma diagnosis for continuous retinal nerve fiber layer (RNFL) thickness measurements from spectral domain optical coherence tomography (spectral-domain OCT). Design Observational cohort study. Methods 262 eyes of 187 patients with glaucoma and 190 eyes of 100 control subjects were included in the study. Subjects were recruited from the Diagnostic Innovations Glaucoma Study. Eyes with preperimetric and perimetric glaucomatous damage were included in the glaucoma group. The control group was composed of healthy eyes with normal visual fields from subjects recruited from the general population. All eyes underwent RNFL imaging with Spectralis spectral-domain OCT. Likelihood ratios for glaucoma diagnosis were estimated for specific global RNFL thickness measurements using a methodology based on estimating the tangents to the Receiver Operating Characteristic (ROC) curve. Results Likelihood ratios could be determined for continuous values of average RNFL thickness. Average RNFL thickness values lower than 86μm were associated with positive LRs, i.e., LRs greater than 1; whereas RNFL thickness values higher than 86μm were associated with negative LRs, i.e., LRs smaller than 1. A modified Fagan nomogram was provided to assist calculation of post-test probability of disease from the calculated likelihood ratios and pretest probability of disease. Conclusion The methodology allowed calculation of likelihood ratios for specific RNFL thickness values. By avoiding arbitrary categorization of test results, it potentially allows for an improved integration of test results into diagnostic clinical decision-making. PMID:23972303
A spectral analysis of the domain decomposed Monte Carlo method for linear systems
Slattery, Stuart R.; Evans, Thomas M.; Wilson, Paul P. H.
2015-09-08
The domain decomposed behavior of the adjoint Neumann-Ulam Monte Carlo method for solving linear systems is analyzed using the spectral properties of the linear oper- ator. Relationships for the average length of the adjoint random walks, a measure of convergence speed and serial performance, are made with respect to the eigenvalues of the linear operator. In addition, relationships for the effective optical thickness of a domain in the decomposition are presented based on the spectral analysis and diffusion theory. Using the effective optical thickness, the Wigner rational approxi- mation and the mean chord approximation are applied to estimate the leakage frac- tion of random walks from a domain in the decomposition as a measure of parallel performance and potential communication costs. The one-speed, two-dimensional neutron diffusion equation is used as a model problem in numerical experiments to test the models for symmetric operators with spectral qualities similar to light water reactor problems. We find, in general, the derived approximations show good agreement with random walk lengths and leakage fractions computed by the numerical experiments.
A spectral analysis of the domain decomposed Monte Carlo method for linear systems
Slattery, Stuart R.; Evans, Thomas M.; Wilson, Paul P. H.
2015-09-08
The domain decomposed behavior of the adjoint Neumann-Ulam Monte Carlo method for solving linear systems is analyzed using the spectral properties of the linear oper- ator. Relationships for the average length of the adjoint random walks, a measure of convergence speed and serial performance, are made with respect to the eigenvalues of the linear operator. In addition, relationships for the effective optical thickness of a domain in the decomposition are presented based on the spectral analysis and diffusion theory. Using the effective optical thickness, the Wigner rational approxi- mation and the mean chord approximation are applied to estimate the leakagemore » frac- tion of random walks from a domain in the decomposition as a measure of parallel performance and potential communication costs. The one-speed, two-dimensional neutron diffusion equation is used as a model problem in numerical experiments to test the models for symmetric operators with spectral qualities similar to light water reactor problems. We find, in general, the derived approximations show good agreement with random walk lengths and leakage fractions computed by the numerical experiments.« less
NASA Astrophysics Data System (ADS)
Hoelbling, Christian; Zielinski, Christian
2016-07-01
We follow up on a suggestion by Adams and construct explicit domain wall fermion operators with staggered kernels. We compare different domain wall formulations, namely the standard construction as well as Boriçi's modified and Chiu's optimal construction, utilizing both Wilson and staggered kernels. In the process, we generalize the staggered kernels to arbitrary even dimensions and introduce both truncated and optimal staggered domain wall fermions. Some numerical investigations are carried out in the (1 +1 )-dimensional setting of the Schwinger model, where we explore spectral properties of the bulk, effective and overlap Dirac operators in the free-field case, on quenched thermalized gauge configurations and on smooth topological configurations. We compare different formulations using the effective mass, deviations from normality and violations of the Ginsparg-Wilson relation as measures of chirality.
Spectral phase encoding of ultra-short optical pulse in time domain for OCDMA application.
Wang, Xu; Wada, Naoya
2007-06-11
We propose a novel reconfigurable time domain spectral phase encoding (SPE) scheme for coherent optical code-division-multiple-access application. In the proposed scheme, the ultra-short optical pulse is stretched by dispersive device and the SPE is done in time domain using high speed phase modulator. The time domain SPE scheme is robust to wavelength drift of the light source and is very flexible and compatible with the fiber optical system. Proof-of-principle experiments of encoding with 16-chip, 20 GHz/chip binary-phase-shift-keying codes and 1.25 Gbps data transmission have been successfully demonstrated together with an arrayed-wave-guide decoder. PMID:19547055
Ultrahigh-speed imaging of the rat retina using ultrahigh-resolution spectral/Fourier domain OCT
NASA Astrophysics Data System (ADS)
Liu, Jonathan J.; Potsaid, Benjamin; Chen, Yueli; Gorczynska, Iwona; Srinivasan, Vivek J.; Duker, Jay S.; Fujimoto, James G.
2010-02-01
We performed OCT imaging of the rat retina at 70,000 axial scans per second with ~3 μm axial resolution. Three-dimensional OCT (3D-OCT) data sets of the rat retina were acquired. The high speed and high density data sets enable improved en face visualization by reducing eye motion artifacts and improve Doppler OCT measurements. Minimal motion artifacts were visible and the OCT fundus images offer more precise registration of individual OCT images to retinal fundus features. Projection OCT fundus images show features such as the nerve fiber layer, retinal capillary networks and choroidal vasculature. Doppler OCT images and quantitative measurements show pulsatility in retinal blood vessels. Doppler OCT provides noninvasive in vivo quantitative measurements of retinal blood flow properties and may benefit studies of diseases such as glaucoma and diabetic retinopathy. Ultrahigh speed imaging using ultrahigh resolution spectral / Fourier domain OCT promises to enable novel protocols for measuring small animal retinal structure and retinal blood flow. This non-invasive imaging technology is a promising tool for monitoring disease progression in rat and mouse models to assess ocular disease pathogenesis and response to treatment.