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Sample records for 3d spectral domain

  1. Automated multilayer segmentation and characterization in 3D spectral-domain optical coherence tomography images

    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.

  2. 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).

  3. A joint estimation detection of Glaucoma progression in 3D spectral domain optical coherence tomography optic nerve head images

    PubMed Central

    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

  4. A joint estimation detection of Glaucoma progression in 3D spectral domain optical coherence tomography optic nerve head images

    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.

  5. Monitoring adipose-derived stem cells within 3D carrier by combined dielectric spectroscopy and spectral domain optical coherence topography

    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.

  6. Master-slave interferometry for parallel spectral domain interferometry sensing and versatile 3D optical coherence tomography.

    PubMed

    Podoleanu, Adrian Gh; Bradu, Adrian

    2013-08-12

    Conventional spectral domain interferometry (SDI) methods suffer from the need of data linearization. When applied to optical coherence tomography (OCT), conventional SDI methods are limited in their 3D capability, as they cannot deliver direct en-face cuts. Here we introduce a novel SDI method, which eliminates these disadvantages. We denote this method as Master - Slave Interferometry (MSI), because a signal is acquired by a slave interferometer for an optical path difference (OPD) value determined by a master interferometer. The MSI method radically changes the main building block of an SDI sensor and of a spectral domain OCT set-up. The serially provided signal in conventional technology is replaced by multiple signals, a signal for each OPD point in the object investigated. This opens novel avenues in parallel sensing and in parallelization of signal processing in 3D-OCT, with applications in high- resolution medical imaging and microscopy investigation of biosamples. Eliminating the need of linearization leads to lower cost OCT systems and opens potential avenues in increasing the speed of production of en-face OCT images in comparison with conventional SDI.

  7. 3D-spectral CDIs: a fast alternative to 3D inversion?

    NASA Astrophysics Data System (ADS)

    Macnae, James

    2015-09-01

    Virtually all airborne electromagnetic (AEM) data is interpreted using stitched 1D conductivity sections, derived from constrained inversion or fast but fairly accurate approximations. A small subset of this AEM data recently has been inverted using either block 3D models or thin plates, which processes have limitations in terms of cost and accuracy, and the results are in general strongly biased by the choice of starting models. Recent developments in spectral modelling have allowed fast 3D approximations of the EM response of both vortex induction and current gathering for simple geological target geometries. Fitting these spectral responses to AEM data should be sufficient to accurately locate current systems within the ground, and the behaviour of these local current systems can in theory approximately define a conductivity structure in 3D. This paper describes the results of initial testing of the algorithm in fitting vortex induction in a small target at the Forrestania test range, Western Australia, using results from a versatile time-domain electromagnetic (VTEM)-Max survey.

  8. Motion estimation in the 3-D Gabor domain.

    PubMed

    Feng, Mu; Reed, Todd R

    2007-08-01

    Motion estimation methods can be broadly classified as being spatiotemporal or frequency domain in nature. The Gabor representation is an analysis framework providing localized frequency information. When applied to image sequences, the 3-D Gabor representation displays spatiotemporal/spatiotemporal-frequency (st/stf) information, enabling the application of robust frequency domain methods with adjustable spatiotemporal resolution. In this work, the 3-D Gabor representation is applied to motion analysis. We demonstrate that piecewise uniform translational motion can be estimated by using a uniform translation motion model in the st/stf domain. The resulting motion estimation method exhibits both good spatiotemporal resolution and substantial noise resistance compared to existing spatiotemporal methods. To form the basis of this model, we derive the signature of the translational motion in the 3-D Gabor domain. Finally, to obtain higher spatiotemporal resolution for more complex motions, a dense motion field estimation method is developed to find a motion estimate for every pixel in the sequence.

  9. 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.

  10. 3D Vectorial Time Domain Computational Integrated Photonics

    SciTech Connect

    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

  11. Spectral fusing Gabor domain optical coherence microscopy.

    PubMed

    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.

  12. 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.

  13. 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.

  14. Dual-Color 3D Superresolution Microscopy by Combined Spectral-Demixing and Biplane Imaging

    PubMed Central

    Winterflood, Christian M.; Platonova, Evgenia; Albrecht, David; Ewers, Helge

    2015-01-01

    Multicolor three-dimensional (3D) superresolution techniques allow important insight into the relative organization of cellular structures. While a number of innovative solutions have emerged, multicolor 3D techniques still face significant technical challenges. In this Letter we provide a straightforward approach to single-molecule localization microscopy imaging in three dimensions and two colors. We combine biplane imaging and spectral-demixing, which eliminates a number of problems, including color cross-talk, chromatic aberration effects, and problems with color registration. We present 3D dual-color images of nanoscopic structures in hippocampal neurons with a 3D compound resolution routinely achieved only in a single color. PMID:26153696

  15. 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.

  16. Smart 3D Building Infrastructures: Linking GIs with Other Domains

    NASA Astrophysics Data System (ADS)

    Knoth, L.; Mittlböck, M.; Vockner, B.

    2016-10-01

    While digitization as well as new technologies and paradigms such as the Internet of Things (IoT) help solving issues within smart factories, they simultaneously trigger new challenges. The creation of smart factories, whose components communicate in an intelligent manner, is located at the frontier of the virtual and the real world. To connect both worlds, spatio-temporal information can be used to structure and integrate data streams, models and other content such as documents in Enterprise Spatial Data Infrastructures (SDIs). One part of Enterprise SDIs is building information, to support and enhance contextualization of indoor environments and its corresponding information in form of sensor measurements and other digital resources. We identified five major requirements: (1) Three-dimensionality, (2) (Re-)use of available data, (3) Use of GIS-principles and standards, (4) Adaptivity, and (5) Completeness. Our novel approach "OLS3D" addresses these requirements through the use of SDI-principles and linked-data strategies. A prototypical implementation was developed in order to show the potential of our approach.

  17. Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.

    PubMed

    Lees, Jonathan G; Lee, David; Studer, Romain A; Dawson, Natalie L; Sillitoe, Ian; Das, Sayoni; Yeats, Corin; Dessailly, Benoit H; Rentzsch, Robert; Orengo, Christine A

    2014-01-01

    Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of protein domain structure annotations for protein sequences. Domains are predicted using a library of profile HMMs from 2738 CATH superfamilies. Gene3D assigns domain annotations to Ensembl and UniProt sequence sets including >6000 cellular genomes and >20 million unique protein sequences. This represents an increase of 45% in the number of protein sequences since our last publication. Thanks to improvements in the underlying data and pipeline, we see large increases in the domain coverage of sequences. We have expanded this coverage by integrating Pfam and SUPERFAMILY domain annotations, and we now resolve domain overlaps to provide highly comprehensive composite multi-domain architectures. To make these data more accessible for comparative genome analyses, we have developed novel search algorithms for searching genomes to identify related multi-domain architectures. In addition to providing domain family annotations, we have now developed a pipeline for 3D homology modelling of domains in Gene3D. This has been applied to the human genome and will be rolled out to other major organisms over the next year.

  18. 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.

  19. 3D high spectral and spatial resolution imaging of ex vivo mouse brain

    SciTech Connect

    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

  20. From pixel to voxel: a deeper view of biological tissue by 3D mass spectral imaging

    PubMed Central

    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

  1. Efficient global wave propagation adapted to 3-D structural complexity: a pseudospectral/spectral-element approach

    NASA Astrophysics Data System (ADS)

    Leng, Kuangdai; Nissen-Meyer, Tarje; van Driel, Martin

    2016-12-01

    We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridian equations, which is then solved by a 2-D spectral element method (SEM). Computational efficiency of such a hybrid method stems from lateral smoothness of 3-D Earth models and axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. We show novel benchmarks for global wave solutions in 3-D structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period ranging from 34 s down to 11 s. It turns out that our method has run up to two orders of magnitude faster than the 3-D SEM, featured by a computational advantage expanding with seismic frequency.

  2. 3D parallel inversion of time-domain airborne EM data

    NASA Astrophysics Data System (ADS)

    Liu, Yun-He; Yin, Chang-Chun; Ren, Xiu-Yan; Qiu, Chang-Kai

    2016-12-01

    To improve the inversion accuracy of time-domain airborne electromagnetic data, we propose a parallel 3D inversion algorithm for airborne EM data based on the direct Gauss-Newton optimization. Forward modeling is performed in the frequency domain based on the scattered secondary electrical field. Then, the inverse Fourier transform and convolution of the transmitting waveform are used to calculate the EM responses and the sensitivity matrix in the time domain for arbitrary transmitting waves. To optimize the computational time and memory requirements, we use the EM "footprint" concept to reduce the model size and obtain the sparse sensitivity matrix. To improve the 3D inversion, we use the OpenMP library and parallel computing. We test the proposed 3D parallel inversion code using two synthetic datasets and a field dataset. The time-domain airborne EM inversion results suggest that the proposed algorithm is effective, efficient, and practical.

  3. 3D linear inversion of magnetic susceptibility data acquired by frequency domain EMI

    NASA Astrophysics Data System (ADS)

    Thiesson, J.; Tabbagh, A.; Simon, F.-X.; Dabas, M.

    2017-01-01

    Low induction number EMI instruments are able to simultaneously measure a soil's apparent magnetic susceptibility and electrical conductivity. This family of dual measurement instruments is highly useful for the analysis of soils and archeological sites. However, the electromagnetic properties of soils are found to vary over considerably different ranges: whereas their electrical conductivity varies from ≤ 0.1 to ≥ 100 mS/m, their relative magnetic permeability remains within a very small range, between 1.0001 and 1.01 SI. Consequently, although apparent conductivity measurements need to be inverted using non-linear processes, the variations of the apparent magnetic susceptibility can be approximated through the use of linear processes, as in the case of the magnetic prospection technique. Our proposed 3D inversion algorithm starts from apparent susceptibility data sets, acquired using different instruments over a given area. A reference vertical profile is defined by considering the mode of the vertical distributions of both the electrical resistivity and of the magnetic susceptibility. At each point of the mapped area, the reference vertical profile response is subtracted to obtain the apparent susceptibility variation dataset. A 2D horizontal Fourier transform is applied to these variation datasets and to the dipole (impulse) response of each instrument, a (vertical) 1D inversion is performed at each point in the spectral domain, and finally the resulting dataset is inverse transformed to restore the apparent 3D susceptibility variations. It has been shown that when applied to synthetic results, this method is able to correct the apparent deformations of a buried object resulting from the geometry of the instrument, and to restore reliable quantitative susceptibility contrasts. It also allows the thin layer solution, similar to that used in magnetic prospection, to be implemented. When applied to field data it initially delivers a level of contrast

  4. 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.

  5. Snapshot Spectral Domain Optical Coherence Tomography

    NASA Astrophysics Data System (ADS)

    Valdez, Ashley

    Optical coherence tomography systems are used to image the retina in 3D to allow ophthalmologists diagnose ocular disease. These systems yield large data sets that are often labor-intensive to analyze and require significant expertise in order to draw conclusions, especially when used over time to monitor disease progression. Spectral Domain Optical Coherence Tomography (SD-OCT) instantly acquires depth profiles at a single location with a broadband source. These systems require mechanical scanning to generate two- or three-dimensional images. Instead of mechanically scanning, a beamlet array was used to permit multiple depth measurements on the retina with a single snapshot using a 3x 3 beamlet array. This multi-channel system was designed, assembled, and tested using a 1 x 2 beamlet lens array instead of a 3 x 3 beamlet array as a proof of concept prototype. The source was a superluminescent diode centered at 840nm with a 45nm bandwidth. Theoretical axial resolution was 6.92um and depth of focus was 3.45mm. Glass samples of varying thickness ranging from 0.18mm to 1.14mm were measured with the system to validate that correct depth profiles can be acquired for each channel. The results demonstrated the prototype system performed as expected, and is ready to be modified for in vivo applicability.

  6. 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping.

    PubMed

    Shameer, Khader; Shingate, Prashant N; Manjunath, S C P; Karthika, M; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

    2011-01-01

    Three-dimensional domain swapping is a unique protein structural phenomenon where two or more protein chains in a protein oligomer share a common structural segment between individual chains. This phenomenon is observed in an array of protein structures in oligomeric conformation. Protein structures in swapped conformations perform diverse functional roles and are also associated with deposition diseases in humans. We have performed in-depth literature curation and structural bioinformatics analyses to develop an integrated knowledgebase of proteins involved in 3D domain swapping. The hallmark of 3D domain swapping is the presence of distinct structural segments such as the hinge and swapped regions. We have curated the literature to delineate the boundaries of these regions. In addition, we have defined several new concepts like 'secondary major interface' to represent the interface properties arising as a result of 3D domain swapping, and a new quantitative measure for the 'extent of swapping' in structures. The catalog of proteins reported in 3DSwap knowledgebase has been generated using an integrated structural bioinformatics workflow of database searches, literature curation, by structure visualization and sequence-structure-function analyses. The current version of the 3DSwap knowledgebase reports 293 protein structures, the analysis of such a compendium of protein structures will further the understanding molecular factors driving 3D domain swapping.

  7. The crystal structure of Aspergillus fumigatus cyclophilin reveals 3D domain swapping of a central element.

    PubMed

    Limacher, Andreas; Kloer, Daniel P; Flückiger, Sabine; Folkers, Gerd; Crameri, Reto; Scapozza, Leonardo

    2006-02-01

    The crystal structure of Aspergillus fumigatus cyclophilin (Asp f 11) was solved by the multiwavelength anomalous dispersion method and was refined to a resolution of 1.85 A with R and R(free) values of 18.9% and 21.4%, respectively. Many cyclophilin structures have been solved to date, all showing the same monomeric conformation. In contrast, the structure of A. fumigatus cyclophilin reveals dimerization by 3D domain swapping and represents one of the first proteins with a swapped central domain. The domain-swapped element consists of two beta strands and a subsequent loop carrying a conserved tryptophan. The tryptophan binds into the active site, inactivating cis-trans isomerization. This might be a means of biological regulation. The two hinge loops leave the protein prone to misfolding. In this context, alternative forms of 3D domain swapping that can lead to N- or C-terminally swapped dimers, oligomers, and aggregates are discussed.

  8. 3D LTE spectral line formation with scattering in red giant stars

    NASA Astrophysics Data System (ADS)

    Hayek, W.; Asplund, M.; Collet, R.; Nordlund, Å.

    2011-05-01

    Aims: We investigate the effects of coherent isotropic continuum scattering on the formation of spectral lines in local thermodynamic equilibrium (LTE) using 3D hydrodynamical and 1D hydrostatic model atmospheres of red giant stars. Methods: Detailed radiative transfer with coherent and isotropic continuum scattering is computed for 3D hydrodynamical and 1D hydrostatic models of late-type stellar atmospheres using the SCATE code. Opacities are computed in LTE, while a coherent and isotropic scattering term is added to the continuum source function. We investigate the effects of scattering by comparing continuum flux levels, spectral line profiles and curves of growth for different species with calculations that treat scattering as absorption. Results: Rayleigh scattering is the dominant source of scattering opacity in the continuum of red giant stars. Photons may escape from deeper, hotter layers through scattering, resulting in significantly higher continuum flux levels beneath a wavelength of λ ≲ 5000 Å. The magnitude of the effect is determined by the importance of scattering opacity with respect to absorption opacity; we observe the largest changes in continuum flux at the shortest wavelengths and lowest metallicities; intergranular lanes of 3D models are more strongly affected than granules. Continuum scattering acts to increase the profile depth of LTE lines: continua gain more brightness than line cores due to their larger thermalization depth in hotter layers. We thus observe the strongest changes in line depth for high-excitation species and ionized species, which contribute significantly to photon thermalization through their absorption opacity near the continuum optical surface. Scattering desaturates the line profiles, leading to larger abundance corrections for stronger lines, which reach -0.5 dex at 3000 Å for Fe ii lines in 3D with excitation potential χ = 2 eV at [Fe/H] = -3.0. The corrections are less severe for low-excitation lines, longer

  9. Discoidin domain receptor 2 regulates the adhesion of fibroblasts to 3D collagen matrices.

    PubMed

    Kim, Daehwan; You, Eunae; Min, Na Young; Lee, Kwang-Ho; Kim, Hyoung Kyu; Rhee, Sangmyung

    2013-05-01

    The collagen matrix constitutes the primary extracellular matrix (ECM) portion of mammalian connective tissues in which the interaction of the cell and the surrounding collagen fibers has a significant impact on cell and tissue physiology, including morphogenesis, development and motility. Discoidin domain receptors (DDR1 and DDR2) have been identified as the receptor tyrosine kinases that are activated upon collagen binding. However, there is a lack of evidence regarding the effect of DDRs on the mechanical interaction between fibroblasts and ECM. In this study, we demonstrated that one of the major phosphotyrosine proteins in human fibroblasts during 3D collagen matrix polymerization is DDR2. Treatment of fibroblasts in 3D collagen matrices with platelet-derived growth factor (PDFG) has been shown to increase DDR2 phosphorylation. Silencing of DDR2 with siRNA in fibroblasts significantly reduced the number of dendritic extensions regardless of whether cells were cultured in the collagen or fibronectin 3D matrices. Decreasing dendritic extensions in DDR2-silenced cells has also been shown to decrease the ability of fibroblast entanglement to collagen fibrils in 3D collagen matrices. Finally, we also showed that the silencing of DDR2 decreased the cell migration in 3D nested collagen matrices but had no effect on 3D floating matrix contraction. Collectively, these results suggest that DDR2 functioning is required for the membrane dynamics to control the mechanical attachment of fibroblasts to the 3D collagen matrices in an integrin-independent manner.

  10. Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

    PubMed Central

    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

  11. 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.

  12. Spectral triangulation: a 3D method for locating single-walled carbon nanotubes in vivo.

    PubMed

    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.

  13. Solving Dirac equations on a 3D lattice with inverse Hamiltonian and spectral methods

    NASA Astrophysics Data System (ADS)

    Ren, Z. X.; Zhang, S. Q.; Meng, J.

    2017-02-01

    A new method to solve the Dirac equation on a 3D lattice is proposed, in which the variational collapse problem is avoided by the inverse Hamiltonian method and the fermion doubling problem is avoided by performing spatial derivatives in momentum space with the help of the discrete Fourier transform, i.e., the spectral method. This method is demonstrated in solving the Dirac equation for a given spherical potential in a 3D lattice space. In comparison with the results obtained by the shooting method, the differences in single-particle energy are smaller than 10-4 MeV, and the densities are almost identical, which demonstrates the high accuracy of the present method. The results obtained by applying this method without any modification to solve the Dirac equations for an axial-deformed, nonaxial-deformed, and octupole-deformed potential are provided and discussed.

  14. Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

    PubMed Central

    Buchan, Daniel W.A.; Shepherd, Adrian J.; Lee, David; Pearl, Frances M.G.; Rison, Stuart C.G.; Thornton, Janet M.; Orengo, Christine A.

    2002-01-01

    We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies. PMID:11875040

  15. Spectral element method for band-structure calculations of 3D phononic crystals

    NASA Astrophysics Data System (ADS)

    Shi, Linlin; Liu, Na; Zhou, Jianyang; Zhou, Yuanguo; Wang, Jiamin; Huo Liu, Qing

    2016-11-01

    The spectral element method (SEM) is a special kind of high-order finite element method (FEM) which combines the flexibility of a finite element method with the accuracy of a spectral method. In contrast to the traditional FEM, the SEM exhibits advantages in the high-order accuracy as the error decreases exponentially with the increase of interpolation degree by employing the Gauss-Lobatto-Legendre (GLL) polynomials as basis functions. In this study, the spectral element method is developed for the first time for the determination of band structures of 3D isotropic/anisotropic phononic crystals (PCs). Based on the Bloch theorem, we present a novel, intuitive discretization formulation for Navier equation in the SEM scheme for periodic media. By virtue of using the orthogonal Legendre polynomials, the generalized eigenvalue problem is converted to a regular one in our SEM implementation to improve the efficiency. Besides, according to the specific geometry structure, 8-node and 27-node hexahedral elements as well as an analytic mesh have been used to accurately capture curved PC models in our SEM scheme. To verify its accuracy and efficiency, this study analyses the phononic-crystal plates with square and triangular lattice arrangements, and the 3D cubic phononic crystals consisting of simple cubic (SC), bulk central cubic (BCC) and faced central cubic (FCC) lattices with isotropic or anisotropic scatters. All the numerical results considered demonstrate that SEM is superior to the conventional FEM and can be an efficient alternative method for accurate determination of band structures of 3D phononic crystals.

  16. 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.

  17. Digital holographic tomography method for 3D observation of domain patterns in ferroelectric single crystals

    NASA Astrophysics Data System (ADS)

    Mokrý, Pavel; Psota, Pavel; Steiger, Kateřina; Václavík, Jan; Vápenka, David; Doleček, Roman; Vojtíšek, Petr; Sládek, Juraj; Lédl, Vít.

    2016-11-01

    We report on the development and implementation of the digital holographic tomography for the three-dimensio- nal (3D) observations of the domain patterns in the ferroelectric single crystals. Ferroelectric materials represent a group of materials, whose macroscopic dielectric, electromechanical, and elastic properties are greatly in uenced by the presence of domain patterns. Understanding the role of domain patterns on the aforementioned properties require the experimental techniques, which allow the precise 3D measurements of the spatial distribution of ferroelectric domains in the single crystal. Unfortunately, such techniques are rather limited at this time. The most frequently used piezoelectric atomic force microscopy allows 2D observations on the ferroelectric sample surface. Optical methods based on the birefringence measurements provide parameters of the domain patterns averaged over the sample volume. In this paper, we analyze the possibility that the spatial distribution of the ferroelectric domains can be obtained by means of the measurement of the wavefront deformation of the transmitted optical wave. We demonstrate that the spatial distribution of the ferroelectric domains can be determined by means of the measurement of the spatial distribution of the refractive index. Finally, it is demonstrated that the measurements of wavefront deformations generated in ferroelectric polydomain systems with small variations of the refractive index provide data, which can be further processed by means of the conventional tomographic methods.

  18. 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.

  19. 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

  20. Frequency Domain Beamformer for a 3-D Sediment Volume Imaging Synthetic Aperture Sonar

    DTIC Science & Technology

    2010-06-01

    Frequency Domain Beamformer for a 3-D Sediment Volume Imaging Synthetic Aperture Sonar Jonathan R. Pearson Magoon,a Matthew A. Nelson,a Daniel D...synthetic aperture sonars (SAS). The beamformer, designed for systems with receiver arrays oriented transverse to the vehicle, performs standard delay and...volume imaging synthetic aperture sonars (SAS). The beamformer is designed for systems with receiver arrays oriented transverse to the vehicle such

  1. Active monomeric and dimeric forms of Pseudomonas putida glyoxalase I: evidence for 3D domain swapping.

    PubMed

    Saint-Jean, A P; Phillips, K R; Creighton, D J; Stone, M J

    1998-07-21

    3D domain swapping of proteins involves the interconversion of a monomer containing a single domain-domain interface and a 2-fold symmetrical dimer containing two equivalent intermolecular interfaces. Human glyoxalase I has the structure of a domain-swapped dimer [Cameron, A. D., Olin, B., Ridderström, M., Mannervik, B., and Jones, T. A. (1997) EMBO J. 16, 3386-3395] but Pseudomonas putida glyoxalase I has been reported to be monomeric [Rhee, H.-I., Murata, K., and Kimura, A. (1986) Biochem. Biophys. Res. Commun. 141, 993-999]. We show here that recombinant P. putida glyoxalase I is an active dimer (kcat approximately 500 +/- 100 s-1; KM approximately 0.4 +/- 0.2 mM) with two zinc ions per dimer. The zinc is required for structure and function. However, treatment of the dimer with glutathione yields an active monomer (kcat approximately 115 +/- 40 s-1; KM approximately 1.4 +/- 0.4 mM) containing a single zinc ion. The monomer is metastable and slowly reverts to the active dimer in the absence of glutathione. Thus, glyoxalase I appears to be a novel example of a single protein able to exist in two alternative domain-swapped forms. It is unique among domain-swapped proteins in that the active site and an essential metal binding site are apparently disassembled and reassembled by the process of domain swapping. Furthermore, it is the only example to date in which 3D domain swapping can be regulated by a small organic ligand.

  2. Early detection of skin cancer via terahertz spectral profiling and 3D imaging.

    PubMed

    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.

  3. 3D face recognition system using cylindrical hidden-layer neural network: spatial domain and its eigenspace domain

    NASA Astrophysics Data System (ADS)

    Kusumoputro, Benyamin; Pangabean, Martha Y.; Rachman, Leila F.

    2001-09-01

    In this paper, a 3-D face recognition system is developed using a modified neural network. This modified neural network is constructed by substituting each of neuron in its hidden layer of conventional multilayer perceptron with a circular-structure of neurons. This neural system is then called as cylindrical-structure of hidden layer neural network (CHL-NN). The neural system is then applied on a real 3-D face image database that consists of 5 Indonesian persons. The images are taken under four different expressions such as neutral, smile, laugh and free expression. The 2-D images is taken from the human face images by gradually changing visual points, which is done by successively varies the camera position from - 90 to +90 with an interval of 15 degree. The experimental result has shown that the average recognition rate of 60% could be achieved when we used the image in its spatial domain. Improvement of the system is then developed, by transforming the image in its spatial domain into its eigenspace domain. Karhunen Loeve transformation technique is used, and each image in the spatial domain is represented as a point in the eigenspace domain. Fisherface method is then utilized as a feature extraction on the eigenspace domain, and using the same database and experimental procedure, the recognition rate of the system could be increased into 84% in average.

  4. Validation of 3D Seismic Velocity Models Using the Spectral Element Method

    NASA Astrophysics Data System (ADS)

    Maceira, M.; Larmat, C. S.; Porritt, R. W.; Higdon, D.; Allen, R. M.

    2012-12-01

    For over a decade now, many research institutions have been focusing on addressing the Earth's 3D heterogeneities and complexities by improving tomographic methods. Utilizing dense array datasets, these efforts have led to unprecedented 3D seismic images, but little is done in terms of model validation or to provide any absolute assessment of model uncertainty. Furthermore, the question of "How good is a 3D geophysical model at representing the Earth's true physics? " remains largely not addressed in a time when 3D Earth models are used for societal and energy security. In the last few years, new horizons have opened up in earth structure imaging, with the advent of new numerical and mathematical methods in computational seismology and statistical sciences. We use these methods to tackle the question of model validation taking advantage of unique and extensive High Performance Computing resources available at Los Alamos National Laboratory. We present results from a study focused on validating 3D models for the Western USA generated using both ray-theoretical and finite-frequency approximations. In this manner we do not validate just the model but also the imaging technique. For this test case, we utilize the Dynamic North America (DNA) model family of UC Berkeley, as they are readily available in both formulations. We evaluate model performances by comparing observed and synthetic seismograms generated using the Spectral Element Method. Results show that both, finite-frequency and ray-theoretical DNA09 models, predict the observations well. Waveform cross-correlation coefficients show a difference in performance between models obtained with the finite-frequency or ray-theory limited to smallest periods (<15s), with no perceptible difference at longer periods (50-200s). At those shortest periods, and based on statistical analyses on S-wave phase delay measurements, finite-frequency shows an improvement over ray theory. We are also investigating the breakdown of ray

  5. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cuff, Alison; Dana, Jose M.; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Rackham, Owen J. L.; Smith, James; Sternberg, Michael J. E.; Velankar, Sameer; Yeats, Corin; Orengo, Christine

    2013-01-01

    Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker’s yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs). PMID:23203986

  6. 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.

  7. 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

  8. Spectral selectivity of 3D magnetophotonic crystal film fabricated from single butterfly wing scales.

    PubMed

    Peng, Wenhong; Zhu, Shenmin; Zhang, Wang; Yang, Qingqing; Zhang, Di; Chen, Zhixin

    2014-06-07

    3D magnetophotonic crystal (3D-MPC) film is an excellent platform for tailoring the magneto-optical response of magnetic materials. However, its fabrication is a great challenge due to the limitation of commonly used artificial synthesis methods. Inspired by the unique structures of biospecies, we hereby manipulate the pristine single wing scales of Morpho didius precisely and successfully fabricate Fe3O4 films with photonic structure. The synthesis strategy involves the fabrication of Fe2O3 film from a single wing scale using an improved sol-gel method followed by a subsequent reduction. The intrinsic hierarchical photonic structures as well as the anisotropic optical properties of the pristine butterfly wing scale have been retained in the obtained Fe2O3 and Fe3O4 films. When investigated under an external magnetic field, a spectral blue shift about 43 nm is observed in the designated orientation of the Fe3O4 film, which is useful for the design and creation of novel magnetic-optical modulator devices. Furthermore, these single scales can be used as building blocks to fabricate designable and more complicated assembled nano systems. This biomimetic technique combined with the variety of structures of butterfly wing scales provides an effective approach to produce magneto-photonic films with desired structure, paving a new way for theoretical research and practical applications.

  9. 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.

  10. Application of high resolution 2D/3D spectral induced polarization (SIP) in metalliferous ore exploration

    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

  11. Induced Polarization with Electromagnetic Coupling: 3D Spectral Imaging Theory EMSP Project No. 73836

    SciTech Connect

    Morgan, F. Dale

    2003-06-01

    This report summarizes the research work completed on the project between December 2001 and September 2002. (1) A model of all Spectral IP capacitive couplings revealed that potential bearing electrodes should be carefully chosen to obviate some of the capacitive coupling problems. This need becomes more important for borehole sampling. Thus, work had been done to design a porous pot electrode hat has all the desired characteristics (low input impedance = 100{Omega}, low noise = 1 {micro}V/{radical} z, low temperature sensitivity = 10{micro}V/{sup o}C) and that can be implanted in a borehole for up to two ears. Further constructional/fabrication details will be given in the final report. The attached pictures are rom a sample of the prototype electrode. Four strings, each consisting of 14 electrodes (7 potential electrodes alternated with 7 metallic-copper current electrodes, each electrode 6ft apart), were constructed and are to be employed into the four boreholes. (They were eventually deployed in Dec. 2002 and measurements acquired in March 2003). (2) The MIT's Earth Resources Laboratory (ERL) performed Spectral Induced Polarization SIP and Time Domain Induced Polarization (TDIP) measurements at the A-14 Outfall during the summer of Y01 as a participant in a DOE-sponsored exercise to assess the state-of-the-art in cross-borehole IP technology for delineating subsurface contaminants. To demonstrate the utility of SIP to map DNAPL contaminants, we inverted cross-borehole SIP data, taken within a very narrow frequency bandwidth of 1/32 o 9/32 Hz. The narrow bandwidth was selected after carefully studying when effects of emc, electrode polarization, etc. begin to set in. The upper frequency is limited by electromagnetic couplings (emc) and strong capacitive behavior observed for the electrodes and the low-frequency limit is set by the time to take measurements. Because below 9/32 Hz, the IP response seems to be greater than emc in all our measurements, the data was

  12. Mapping of the C3d receptor (CR2)-binding site and a neoantigenic site in the C3d domain of the third component of complement.

    PubMed Central

    Lambris, J D; Ganu, V S; Hirani, S; Müller-Eberhard, H J

    1985-01-01

    The C3d domain of C3 contains the site that binds to the C3d receptor (CR2) which is expressed on B lymphocytes. It also contains a neoantigenic determinant that is recognized by monoclonal antibody (mAb) 130 and is expressed when C3b is cleaved to iC3b and subsequently to C3dg or C3d. mAb 130 inhibits the binding of C3d to CR2. In this study, the locations of the CR2-binding site and of the neoantigen recognized by mAb 130 within the C3d domain were investigated. Treatment of human C3d with CNBr generated two major fragments with Mrs of 12,500 and 8600. Binding studies showed that only the Mr 8600 fragment was capable of binding to both CR2 and mAb 130. Amino-terminal sequence analysis of the Mr 8600 fragment and comparison with the amino acid sequence derived from human C3 cDNA [de Bruijn, M. H. L. & Fey, G. H. (1985) Proc. Natl. Acad. Sci. USA 82, 708-712] placed it between residues 1199 and 1274 of the C3 sequence. Several peptides were synthesized according to the derived C3 sequence of amino acid residues 1209-1236. Based on their differential binding to CR2 and mAb 130, we localized the CR2-binding site and mAb 130 neoantigenic site, respectively, to residues 1227-1232 and 1217-1232 of the C3 sequence. PMID:2408276

  13. Accurate 2D/3D electromagnetic modeling for time-domain airborne EM systems

    NASA Astrophysics Data System (ADS)

    Yin, C.; Hodges, G.

    2012-12-01

    The existing industry software cannot deliver correct results for 3D time-domain airborne EM responses. In this paper, starting from the Fourier transform and convolution, we compare the stability of different modeling techniques and analyze the reason for instable calculations of the time-domain airborne EM responses. We find that the singularity of the impulse responses of EM systems at very early time that are used in the convolution is responsible for the instability of the modeling (Fig.1). Based on this finding, we put forward an algorithm that uses step response rather than impulse response of the airborne EM system for the convolution and create a stable algorithm that delivers precise results and maintains well the integral/derivative relationship between the magnetic field B and the magnetic induction dB/dt. A three-step transformation procedure for the modeling is proposed: 1) output the frequency-domain EM response data from the existing software; 2) transform into step-response by digital Fourier/Hankel transform; 3) convolve the step response with the transmitting current or its derivatives. The method has proved to be working very well (Fig. 2). The algorithm can be extended to the modeling of other time-domain ground and airborne EM system responses.Fig. 1: Comparison of impulse and step responses for an airborne EM system Fig. 2: Bz and dBz/dt calculated from step (middle panel) and impulse responses (lower panel) for the same 3D model as in Fig.1.

  14. Induced Polarization with Electromagnetic Coupling: 3D Spectral Imaging Theory, EMSP Project No. 73836

    SciTech Connect

    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

  15. 3D time-domain airborne EM forward modeling with topography

    NASA Astrophysics Data System (ADS)

    Yin, Changchun; Qi, Yanfu; Liu, Yunhe; Cai, Jing

    2016-11-01

    The time-domain finite-difference method has been widely used in simulation of the electromagnetic field diffusion. However, this method is severely restricted by the mesh size and time step. To overcome the defect, we adopted edge finite-element method for unstructured grid with Backward Euler method to conduct 3D airborne electromagnetic forward modeling directly in time-domain. The tetrahedral meshes provide the flexibility required for representing the rugged topography and complex-shape anomalous bodies. We simulated the practical shape, size and attitude of transmitting source by directly setting the loop into the well-generated grids. The characteristic properties of vector basic functions guarantee automatic satisfaction of divergence-free property of electric fields. The Galerkin's method is used to discretize the governing equations and a direct solver is adopted to solve the large sparse linear system. We adopted an algorithm with constant step in each time segment to speed up the forward modeling. Further we introduced the local mesh strategy to reduce the calculations, in which an optimized grid is designed for each sounding station. We check the accuracy of our 3D modeling results against the solution for a homogenous half-space and those for a buried vertical plate model using integral equation. The numerical experiments for a hill, a valley or undulating topography model with buried anomalous bodies were further studied that show that the topography has a serious effect on airborne EM data.

  16. 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.

  17. Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization.

    PubMed

    Ea, Vuthy; Baudement, Marie-Odile; Lesne, Annick; Forné, Thierry

    2015-07-27

    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.

  18. Crack identification by 3D time-domain elastic or acoustic topological sensitivity

    NASA Astrophysics Data System (ADS)

    Bellis, Cédric; Bonnet, Marc

    2009-03-01

    The topological sensitivity analysis, based on the asymptotic behavior of a cost functional associated with the creation of a small trial flaw in a defect-free solid, provides a computationally-fast, non-iterative approach for identifying flaws embedded in solids. This concept is here considered for crack identification using time-dependent measurements on the external boundary. The topological derivative of a cost function under the nucleation of a crack of infinitesimal size is established, in the framework of time-domain elasticity or acoustics. The simplicity and efficiency of the proposed formulation is enhanced by the recourse to an adjoint solution. Numerical results obtained on a 3-D elastodynamic example using the conventional FEM demonstrate the usefulness of the topological derivative as a crack indicator function. To cite this article: C. Bellis, M. Bonnet, C. R. Mecanique 337 (2009).

  19. Automated segmentation of 3-D spectral OCT retinal blood vessels by neural canal opening false positive suppression.

    PubMed

    Hu, Zhihong; Niemeijer, Meindert; Abràmoft, Michael D; Lee, Kyungmoo; Garvin, Mona K

    2010-01-01

    We present a method for automatically segmenting the blood vessels in optic nerve head (ONH) centered spectral-domain optical coherence tomography (SD-OCT) volumes, with a focus on the ability to segment the vessels in the region near the neural canal opening (NCO). The algorithm first pre-segments the NCO using a graph-theoretic approach. Oriented Gabor wavelets rotated around the center of the NCO are applied to extract features in a 2-D vessel-aimed projection image. Corresponding oriented NCO-based templates are utilized to help suppress the false positive tendency near the NCO boundary. The vessels are identified in a vessel-aimed projection image using a pixel classification algorithm. Based on the 2-D vessel profiles, 3-D vessel segmentation is performed by a triangular-mesh-based graph search approach in the SD-OCT volume. The segmentation method is trained on 5 and is tested on 10 randomly chosen independent ONH-centered SD-OCT volumes from 15 subjects with glaucoma. Using ROC analysis, for the 2-D vessel segmentation, we demonstrate an improvement over the closest previous work with an area under the curve (AUC) of 0.81 (0.72 for previously reported approach) for the region around the NCO and 0.84 for the region outside the NCO (0.81 for previously reported approach).

  20. A time-space domain stereo finite difference method for 3D scalar wave propagation

    NASA Astrophysics Data System (ADS)

    Chen, Yushu; Yang, Guangwen; Ma, Xiao; He, Conghui; Song, Guojie

    2016-11-01

    The time-space domain finite difference methods reduce numerical dispersion effectively by minimizing the error in the joint time-space domain. However, their interpolating coefficients are related with the Courant numbers, leading to significantly extra time costs for loading the coefficients consecutively according to velocity in heterogeneous models. In the present study, we develop a time-space domain stereo finite difference (TSSFD) method for 3D scalar wave equation. The method propagates both the displacements and their gradients simultaneously to keep more information of the wavefields, and minimizes the maximum phase velocity error directly using constant interpolation coefficients for different Courant numbers. We obtain the optimal constant coefficients by combining the truncated Taylor series approximation and the time-space domain optimization, and adjust the coefficients to improve the stability condition. Subsequent investigation shows that the TSSFD can suppress numerical dispersion effectively with high computational efficiency. The maximum phase velocity error of the TSSFD is just 3.09% even with only 2 sampling points per minimum wavelength when the Courant number is 0.4. Numerical experiments show that to generate wavefields with no visible numerical dispersion, the computational efficiency of the TSSFD is 576.9%, 193.5%, 699.0%, and 191.6% of those of the 4th-order and 8th-order Lax-Wendroff correction (LWC) method, the 4th-order staggered grid method (SG), and the 8th-order optimal finite difference method (OFD), respectively. Meanwhile, the TSSFD is compatible to the unsplit convolutional perfectly matched layer (CPML) boundary condition for absorbing artificial boundaries. The efficiency and capability to handle complex velocity models make it an attractive tool in imaging methods such as acoustic reverse time migration (RTM).

  1. 3D imaging of tomato seeds using frequency domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Fan, Chuanmao; Yao, Gang

    2012-05-01

    A fast imaging system that can reveal internal sample structures is important for research and quality controls of seeds. Optical coherence tomography (OCT) is a non-invasive optical imaging technique that can acquire high speed, high resolution depth-resolved images in scattering samples. It has found numerous applications in studying various biological tissues and other materials in vivo. A few studies have reported the use of OCT in studying seed morphology. However, 3D imaging of internal seed structure has not been reported before. In this study, we used a frequency domain OCT system to image tomato seeds. The system has a central wavelength of 844nm with a 46.8 nm FWHM bandwidth. The requirement for depth scan was eliminated by using a Fourier domain implementation. The B-scan imaging speed was limited by the spectroscopic imaging CCD at 52 kHz. The calibrated system has a 6.7μm depth resolution and a 15.4μm lateral resolution. Our results show that major seed structures can be clearly visualized in OCT images.

  2. 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.

  3. Variation in spectral and mass dimension on 3D soil image processing

    NASA Astrophysics Data System (ADS)

    Sanchez, M. E.; Tarquis, A. M.; Fabregat, J.; Andina, D.; Jimenez, J.; Crawford, J. W.

    2009-04-01

    Knowledge on three dimensional soil pore architecture is important for understanding soil processes as it controls biological, chemical and physical processes on various scales. Recent advances in non-destructive imaging, such as X-ray Computed Tomography (CT), provide several ways to analyze pore space features mainly concentrating on the visualization of soil structure. Fractal formalism has revealed as useful tool in these cases where highly complex and heterogeneous medium are studied. One of these quantifications is mass dimension (Dm) and spectral dimension (d) applied for water and gas diffusion coefficient in soil. At the same time that these techniques give a unique opportunity to quantify and describe pore space, they presents steps in their procedures on which the results depend. In this work, intact soil samples were collected from four horizons of a Brazilian soil and 3D images, of 45.1 micro-m resolution (256x256x256 voxels), were obtained. Four different threshold criteria were used to transform CT grey-scale imagery in binary imagery (pore/solid), based on the frequency of CT units. Then the threshold effect on the estimation of Dm and d, as well as their ratio was studied. Each threshold criteria had a direct influence on Dm as it has been previously reported [1], through the increase on porosity obtained. Meanwhile Dm showed a clear logarithmic relation with the apparent porosity in the image obtained for each threshold, d showed an almost linear one. In any case the increase of each one of them respect to porosity was different for each horizon. The Dm/d ratio was practically constant through all the porosity achieved in this study when Dm was estimated using all the scale range available. On the other hand, when Dm was estimated based on smaller scales this ratio depended on the threshold criteria applied to the image. This fact has a direct implication in diffusion parameters for a pore network modeling based on both fractal dimensions. [1] A

  4. Self-spectral calibration for spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zhang, Xianling; Gao, Wanrong; Bian, Haiyi; Chen, Chaoliang; Liao, Jiuling

    2013-06-01

    A different real-time self-wavelength calibration method for spectral domain optical coherence tomography is presented in which interference spectra measured from two arbitrary points on the tissue surface are used for calibration. The method takes advantages of two favorable conditions of optical coherence tomography (OCT) signal. First, the signal back-scattered from the tissue surface is generally much stronger than that from positions in the tissue interior, so the spectral component of the surface interference could be extracted from the measured spectrum. Second, the tissue surface is not a plane and a phase difference exists between the light reflected from two different points on the surface. Compared with the zero-crossing automatic method, the introduced method has the advantage of removing the error due to dispersion mismatch or the common phase error. The method is tested experimentally to demonstrate the improved signal-to-noise ratio, higher axial resolution, and slower sensitivity degradation with depth when compared to the use of the zero-crossing method and applied to two-dimensional cross-sectional images of human finger skin.

  5. Use of the ARM Measurements of Spectral Zenith Radiance for Better Understanding of 3D Cloud-Radiation Processes & Aerosol-Cloud Interaction

    SciTech Connect

    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: • 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. • Provide cloud property retrievals from the ARM sites and the ARM Mobile Facility for studies of aerosol-cloud interactions. • Assess impact of 3D cloud structures on aerosol properties using passive and active remote sensing techniques from both ARM and satellite measurements.

  6. 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.

  7. 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.

  8. Real Time Gabor-Domain Optical Coherence Microscopy for 3D Imaging.

    PubMed

    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.

  9. 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.

  10. The crystal structure of the dimeric colicin M immunity protein displays a 3D domain swap.

    PubMed

    Usón, Isabel; Patzer, Silke I; Rodríguez, Dayté Dayana; Braun, Volkmar; Zeth, Kornelius

    2012-04-01

    Bacteriocins are proteins secreted by many bacterial cells to kill related bacteria of the same niche. To avoid their own suicide through reuptake of secreted bacteriocins, these bacteria protect themselves by co-expression of immunity proteins in the compartment of colicin destination. In Escherichia coli the colicin M (Cma) is inactivated by the interaction with the Cma immunity protein (Cmi). We have crystallized and solved the structure of Cmi at a resolution of 1.95Å by the recently developed ab initio phasing program ARCIMBOLDO. The monomeric structure of the mature 10kDa protein comprises a long N-terminal α-helix and a four-stranded C-terminal β-sheet. Dimerization of this fold is mediated by an extended interface of hydrogen bond interactions between the α-helix and the four-stranded β-sheet of the symmetry related molecule. Two intermolecular disulfide bridges covalently connect this dimer to further lock this complex. The Cmi protein resembles an example of a 3D domain swapping being stalled through physical linkage. The dimer is a highly charged complex with a significant surplus of negative charges presumably responsible for interactions with Cma. Dimerization of Cmi was also demonstrated to occur in vivo. Although the Cmi-Cma complex is unique among bacteria, the general fold of Cmi is representative for a class of YebF-like proteins which are known to be secreted into the external medium by some Gram-negative bacteria.

  11. Study of Shortwave Spectra in Fully 3D Environment: Synergy Between Scanning Radars and Spectral Radiation Measurements

    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.

  12. 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.

  13. ShipMo3D Version 1.0 User Manual for Frequency Domain Analysis of Ship Seakeeping in a Seaway

    DTIC Science & Technology

    2007-11-01

    earth -fixed axes ν mean wave direction (from) in earth -fixed axes νi mean wave direction (from) for spectral component i ρ water density σ standard...values are given relative to their position when the ship is moving at speed in calm water . earthFixed - Output values are given in earth -fixed axes...domain for a freely maneuvering ship in calm water or in waves. Several ShipMo3D applications are used for obtaining ship motion predictions in the

  14. An attempt at 3-D imaging of a small domain (Almeria, southern Spain)

    NASA Astrophysics Data System (ADS)

    Badal, J.; Sabadell, F. J.; Serón, F. J.

    2000-11-01

    When applying a methodology for obtaining the 3-D shear-wave velocity structure of a medium from surface wave dispersion data, the problem must be considered with caution since one inverts path-averaged velocities and the use of any inversion method entails some drawbacks such as lack of uniqueness, unwarranted stability and constraints affecting the data. Several imaging techniques aimed at volumetric modeling and the visualization of data can be used to overcome these drawbacks. Actually, some spatial prediction techniques are especially useful for analyzing short-range variability between scattered points. We use here a pathwise reconstruction by means of an algorithm that, from a mathematical viewpoint, can be understood through the application of the orthogonal projection theorem onto convex sets (POCS). In particular, we are interested in exploring the possibilities of a POCS algorithm operating on a very unfavorable case constrained by a lack of available data. In this paper, we have tackled a small-sized problem and we present the results based on ray-path seismic velocities that we have obtained in the case of a sparsely sampled study area like Almeria (southeastern Spain) by way of tomographic images obtained by application of such an algorithm. The main goal of this procedure is the reconstruction of the very shallow Rg-wave velocity structure of a small domain strongly constrained by the data. The method has allowed us to examine the sharply contrasting geology between neighboring geological formations. Although the relationship between lateral changes in Rg-wave dispersion and geologic structure may not be straightforward, we have observed a correlation between the velocity structure of very shallow soils and the local geology at surface. The good agreement between our results and the field observations prove the versatility of the method and the reliability of the imaging.

  15. 3-D frequency-domain seismic wave modelling in heterogeneous, anisotropic media using a Gaussian Quadrature Grid (GQG) approach

    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

  16. Final Report – Study of Shortwave Spectra in Fully 3D Environment. Synergy Between Scanning Radars and Spectral Radiation Measurements

    SciTech Connect

    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.

  17. 3D coaxial out-of-plane metallic antennas for filtering and multi-spectral imaging in the infrared range.

    PubMed

    Jacassi, Andrea; Bozzola, Angelo; Zilio, Pierfrancesco; Tantussi, Francesco; De Angelis, Francesco

    2016-06-27

    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.

  18. 3D coaxial out-of-plane metallic antennas for filtering and multi-spectral imaging in the infrared range

    PubMed Central

    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

  19. A General Method for Evaluation of 2D and 3D Domain Integrals Without Domain Discretization and its Application in BEM

    NASA Astrophysics Data System (ADS)

    Hematiyan, M. R.

    2007-03-01

    A robust method is presented to evaluate 2D and 3D domain integrals without domain discretization. Each domain integral is transformed into a double integral, a boundary integral and a 1D integral. Both integrals are evaluated by adaptive Simpson quadrature method. The method can be used to evaluate domain integrals over simply or multiply connected regions with any arbitrary form of integrands. As an application of the method, domain integrals produced in boundary element formulation of potential and elastostatic problems are analyzed. Several examples are provided to show the validity and accuracy of the method.

  20. Spectrally encoded fiber-based structured lighting probe for intraoperative 3D imaging

    PubMed Central

    Clancy, Neil T.; Stoyanov, Danail; Maier-Hein, Lena; Groch, Anja; Yang, Guang-Zhong; Elson, Daniel S.

    2011-01-01

    Three dimensional quantification of organ shape and structure during minimally invasive surgery (MIS) could enhance precision by allowing the registration of multi-modal or pre-operative image data (US/MRI/CT) with the live optical image. Structured illumination is one technique to obtain 3D information through the projection of a known pattern onto the tissue, although currently these systems tend to be used only for macroscopic imaging or open procedures rather than in endoscopy. To account for occlusions, where a projected feature may be hidden from view and/or confused with a neighboring point, a flexible multispectral structured illumination probe has been developed that labels each projected point with a specific wavelength using a supercontinuum laser. When imaged by a standard endoscope camera they can then be segmented using their RGB values, and their 3D coordinates calculated after camera calibration. The probe itself is sufficiently small (1.7 mm diameter) to allow it to be used in the biopsy channel of commonly used medical endoscopes. Surgical robots could therefore also employ this technology to solve navigation and visualization problems in MIS, and help to develop advanced surgical procedures such as natural orifice translumenal endoscopic surgery. PMID:22076272

  1. Low-Amplitude Craniofacial EMG Power Spectral Density and 3D Muscle Reconstruction from MRI

    PubMed Central

    Wiedemann, Lukas; Chaberova, Jana; Edmunds, Kyle; Einarsdóttir, Guðrún; Ramon, Ceon

    2015-01-01

    Improving EEG signal interpretation, specificity, and sensitivity is a primary focus of many current investigations, and the successful application of EEG signal processing methods requires a detailed knowledge of both the topography and frequency spectra of low-amplitude, high-frequency craniofacial EMG. This information remains limited in clinical research, and as such, there is no known reliable technique for the removal of these artifacts from EEG data. The results presented herein outline a preliminary investigation of craniofacial EMG high-frequency spectra and 3D MRI segmentation that offers insight into the development of an anatomically-realistic model for characterizing these effects. The data presented highlights the potential for confounding signal contribution from around 60 to 200 Hz, when observed in frequency space, from both low and high-amplitude EMG signals. This range directly overlaps that of both low γ (30-50 Hz) and high γ (50-80 Hz) waves, as defined traditionally in standatrd EEG measurements, and mainly with waves presented in dense-array EEG recordings. Likewise, average EMG amplitude comparisons from each condition highlights the similarities in signal contribution of low-activity muscular movements and resting, control conditions. In addition to the FFT analysis performed, 3D segmentation and reconstruction of the craniofacial muscles whose EMG signals were measured was successful. This recapitulation of the relevant EMG morphology is a crucial first step in developing an anatomical model for the isolation and removal of confounding low-amplitude craniofacial EMG signals from EEG data. Such a model may be eventually applied in a clinical setting to ultimately help to extend the use of EEG in various clinical roles. PMID:26913150

  2. CONTINUUM INTENSITY AND [O i] SPECTRAL LINE PROFILES IN SOLAR 3D PHOTOSPHERIC MODELS: THE EFFECT OF MAGNETIC FIELDS

    SciTech Connect

    Fabbian, D.; Moreno-Insertis, F. E-mail: fmi@iac.es

    2015-04-01

    The importance of magnetic fields in three-dimensional (3D) magnetoconvection models of the Sun’s photosphere is investigated in terms of their influence on the continuum intensity at different viewing inclination angles and on the intensity profile of two [O i] spectral lines. We use the RH numerical radiative transfer code to perform a posteriori spectral synthesis on the same time series of magnetoconvection models used in our publications on the effect of magnetic fields on abundance determination. We obtain a good match of the synthetic disk-center continuum intensity to the absolute continuum values from the Fourier Transform Spectrometer (FTS) observational spectrum; the match of the center-to-limb variation synthetic data to observations is also good, thanks, in part, to the 3D radiation transfer capabilities of the RH code. The different levels of magnetic flux in the numerical time series do not modify the quality of the match. Concerning the targeted [O i] spectral lines, we find, instead, that magnetic fields lead to nonnegligible changes in the synthetic spectrum, with larger average magnetic flux causing both of the lines to become noticeably weaker. The photospheric oxygen abundance that one would derive if instead using nonmagnetic numerical models would thus be lower by a few to several centidex. The inclusion of magnetic fields is confirmed to be important for improving the current modeling of the Sun, here in particular in terms of spectral line formation and of deriving consistent chemical abundances. These results may shed further light on the still controversial issue regarding the precise value of the solar oxygen abundance.

  3. 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.

  4. Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

    SciTech Connect

    Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Ng, C.; Schussman, G.; Ko, K.; Syratchev, I.; /CERN

    2009-06-19

    In recent years, SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively parallel processing allow unprecedented simulation accuracy for wakefield computations and simulations of transient effects in realistic accelerator structures. Applications include simulation of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).

  5. Determination and validation of mTOR kinase-domain 3D structure by homology modeling.

    PubMed

    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.

  6. 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.

  7. Implications of 3D domain swapping for protein folding, misfolding and function.

    PubMed

    Rousseau, Frederic; Schymkowitz, Joost; Itzhaki, Laura S

    2012-01-01

    Three-dimensional domain swapping is the process by which two identical protein chains exchange a part of their structure to form an intertwined dimer or higher-order oligomer. The phenomenon has been observed in the crystal structures of a range of different proteins. In this chapter we review the experiments that have been performed in order to understand the sequence and structural determinants of domain-swapping and these show how the general principles obtained can be used to engineer proteins to domain swap. We discuss the role of domain swapping in regulating protein function and as one possible mechanism of protein misfolding that can lead to aggregation and disease. We also review a number of interesting pathways of macromolecular assembly involving β-strand insertion or complementation that are related to the domain-swapping phenomenon.

  8. 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.

  9. 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.

  10. Polycomb silencing: from linear chromatin domains to 3D chromosome folding.

    PubMed

    Cheutin, Thierry; Cavalli, Giacomo

    2014-04-01

    Polycomb group (PcG) proteins are conserved chromatin factors that regulate key developmental genes. Genome wide studies have shown that PcG proteins and their associated H3K27me3 histone mark cover long genomic domains. PcG proteins and H3K27me3 accumulate in Pc nuclear foci, which are the cellular counterparts of genomic domains silenced by PcG proteins. One explanation for how large genomic domains form nuclear foci may rely on loops occurring between specific elements located within domains. However, recent improvement of the chromosome conformation capture (3C) technology, which allowed monitoring genome wide contacts depicts a more complex picture in which chromosomes are composed of many topologically associating domains (TADs). Chromatin regions marked with H3K27me3 correspond to one class of TADs and PcG proteins participate in long-range interactions of H3K27me3 TADs, whereas insulator proteins seem to be important for separating TADs and may also participate in the regulation of intra TAD architecture. Recent data converge to suggest that this hierarchical organization of chromosome domains plays an important role in genome function during cell proliferation and differentiation.

  11. Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information

    PubMed Central

    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

  12. On domain decomposition preconditioner of BPS type for finite element discretizations of 3D elliptic equations

    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.

  13. Synthesis, spectral characterization and 3D molecular modeling of some novel nickel(II) complexes derived from 4-aminoantipyrine

    NASA Astrophysics Data System (ADS)

    Nair, M. L. Harikumaran; Lalitha, K. P.

    2014-10-01

    Some novel Ni(II) complexes with the ligand (z)-4-((2-hydroxy-4-methoxyphenyl)diazenyl)-1,5-dimethyl-2-phenyl-1H-pyrazole-3(2H)-one, 3-methoxy phenol azoantipyrine, L having the formulae [Ni(L)2X2] and [Ni(L)2(Y)Cl] where X = 450 Cl-/NO3; Y = NCS- were synthesized and characterized by elemental analysis, molar conductance measurements, magnetic susceptibility measurements, spectral (IR, UV-Visible, EPR, FAB-mass) studies, thermo gravimetric analysis and by TEM image. Energy minimized configuration of the complex [Ni(L)2Cl2] was made with CHEM Bio 3D Ultra 11.0 and the respective parameters were computed. The ligand and the complex [Ni(L)2(Y)Cl] were screened for their antibacterial activities. An octahedral structure is tentatively proposed for the complexes.

  14. Haralick Texture Features Expanded Into The Spectral Domain

    DTIC Science & Technology

    2006-01-01

    Haralick Texture Features Expanded Into The Spectral Domain Angela M. Puetz, R. C. Olsen U.S. Naval Postgraduate School, 833 Dyer Road...Monterey, CA 93943 ABSTRACT Robert M. Haralick, et. al., described a technique for computing texture features based on gray-level spatial... Texture is modeled on Haralick’s texture features . This Spectral Texture Method uses spectral-similarity spatial dependencies (rather than gray-level

  15. [HRV-Spectral analysis of Pain, by 3D Evaluation and by Balance Index in the Pain Rehabilitation Field].

    PubMed

    Goto, Yukio

    2015-07-01

    Pain signaling is achieved by electrical impulses in the body; however, some electrical abnormalities can cause pain in the body without generating any visible symptoms. This phenomenon is sensed by the brain and a signal that may affect cardiac rhythms is immediately transmitted to the heart. To evaluate heart rate variability (HRV), the balance correction between an increase and decrease of heart rate was recorded in real time. Using a special method for spectral-analysis of the HRV, techniques for analyzing the essence of pain were developed, namely, the 'Balance index' and the '3D spectrum evaluation method'. Using these techniques, an alpha wave-like factor or a beta wave-like reaction can be obtained, and the nature and strength of pain can be displayed as spectral zones, as in a rainbow. The balance reaction can be shown by analyzing data in the frequency band using a 1/f-like spectral-analysis method. Additionally, emotional reactions can be detected using a 'Balance index' that can demonstrate imbalance responding to the pain. The mental state of the subject can also be inferred because this technique is adapted from the 1/f fluctuation theory related to the best balanced 1/f-sound wave in nature that comforts the human mind, similar to music (artificial sound wave). In this study, the variety and intensity of pain were determined from the frequency band resulting from the 1/f-spectral analysis of HRV fluctuation. These techniques could explain several situations related to medication or anesthesia and can be helpful in preventative treatment and/or explaining the differences in the effectiveness of various techniques for the rehabilitation of chronic pain.

  16. 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.

  17. 3D Velocity and Density Model of the Los Angeles Basin and Spectral Element Method Earthquake Simulations

    NASA Astrophysics Data System (ADS)

    Suess, P.; Shaw, J. H.; Komatitsch, D.; Tromp, J.

    2001-12-01

    We present a 3D velocity model and a 3D density model of the LA basin. The LA basin velocity model was constructed using sonic log and stacking velocity information, provided by oil industry sources and not previously incorporated into southern California velocity models. The density model is based upon a new database of approximately 300 oil industry density logs from across the Los Angeles basin. These logs use gamma ray emissions to determine formation density at samples of about one meter. We have developed an empirical relation between sonic velocity and density by comparing data from approximately 30 wells in which we have both sonic and density logs. For the remaining wells, we have derived relationships between depth and density, and characterized this relationship for the three main stratigraphic sub-divisions of the SCEC Phase 2 model (Quaternary to base Pico Fm., top Repetto Fm. to top Mohnian, and top Mohnian to basement). The density-depth and density-velocity relations will provide independent rules that can be employed to define density and velocity structure in areas where data does not exist, or in other areas with similar lithology to the Los Angeles basin. We use a spectral element method (SEM) for simulation of seismic wave propagation which is currently being implemented on a 156-node Pentium PC cluster at Cal Tech. Preliminary work shows that SEM results using a 1D velocity model for southern California compare very well to discrete-wavenumber results. Both the density structure and velocity structure must be defined in a 3D model for its use in simulations of seismic wave propagation with a spectral element method, to predict the distribution of hazardous ground shaking during large events. Previous work has typically used density values which were predicted by the sonic velocity values; use of our measured density values should provide more accurate ground shaking predictions, and comparison to previous results will provide a useful

  18. Practical alignment method for X-ray spectral measurement in micro-CT system based on 3D printing technology.

    PubMed

    Ren, Liqiang; Wu, Di; Li, Yuhua; Zheng, Bin; Chen, Yong; Yang, Kai; Liu, Hong

    2016-06-01

    This study presents a practical alignment method for X-ray spectral measurement in a rotating gantry based micro-computed tomography (micro-CT) system using three-dimensional (3D) printing technology. In order to facilitate the spectrometer placement inside the gantry, supporting structures including a cover and a stand were dedicatedly designed and printed using a 3D printer. According to the relative position between the spectrometer and the stand, the upright projection of the spectrometer collimator onto the stand was determined and then marked by a tungsten pinhole. Thus, a visible alignment indicator of the X-ray central beam and the spectrometer collimator represented by the pinhole was established in the micro-CT live mode. Then, a rough alignment could be achieved through repeatedly adjusting and imaging the stand until the pinhole was located at the center of the acquired projection image. With the spectrometer being positioned back onto the stand, the precise alignment was completed by slightly translating the spectrometer-stand assembly around the rough location, until finding a "sweet spot" with the highest photon rate and proper distribution of the X-ray photons in the resultant spectrum. The spectra were acquired under precise alignment and misalignment of approximately 0.2, 0.5, and 1.0mm away from the precise alignment position, and then were compared in qualitative and quantitative analyses. Qualitative analysis results show that, with slight misalignment, the photon rate is reduced from 1302 to 1098, 1031, and 416 photons/second (p/s), respectively, and the characteristic peaks in the acquired spectra are gradually deteriorated. Quantitative analysis indicates that the energy resolutions for characteristic peak of Kα1 were calculated as 1.56% for precise alignment, while were 1.84% and 2.40% for slight misalignment of 0.2mm and 0.5mm. The mean energies were reduced from 43.93keV under precise alignment condition to 40.97, 39.63 and 37.78keV when

  19. Formulation and implementation of a high-order 3-D domain integral method for the extraction of energy release rates

    NASA Astrophysics Data System (ADS)

    Ozer, H.; Duarte, C. A.; Al-Qadi, I. L.

    2012-04-01

    This article presents a three dimensional (3-D) formulation and implementation of a high-order domain integral method for the computation of energy release rate. The method is derived using surface and domain formulations of the J-integral and the weighted residual method. The J-integral along 3-D crack fronts is approximated by high-order Legendre polynomials. The proposed implementation is tailored for the Generalized/eXtended Finite Element Method and can handle discontinuities arbitrarily located within a finite element mesh. The domain integral calculations are based on the same integration elements used for the computation of the stiffness matrix. Discontinuities of the integrands across crack surfaces and across computational element boundaries are fully accounted for. The proposed method is able to deliver smooth approximations and to capture the boundary layer behavior of the J-integral using tetrahedral meshes. Numerical simulations of mode-I and mixed mode benchmark fracture mechanics examples verify expected convergence rates for the computed energy release rates. The results are also in good agreement with other numerical solutions available in the literature.

  20. 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.

  1. 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.

  2. 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

    PubMed Central

    Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S.; Carazo, Jose Maria

    2016-01-01

    Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application—3DIANA—specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es. PMID:26772592

  3. Global classical solutions to the 3D isentropic compressible Navier-Stokes equations in a bounded domain

    NASA Astrophysics Data System (ADS)

    Yu, Haibo; Zhao, Junning

    2017-01-01

    In this paper, we study the global existence for classical solutions to the 3D isentropic compressible Navier-Stokes equations in a cuboid domain. Compared to the Cauchy problem studied in Hoff (1995 J. Differ. Equ. 120 215-54), Hoff (2005 J. Math. Fluid Mech. 7 315-38), Huang et al (2012 Commun. Pure Appl. Math. 65 549-85), some new thoughts are applied to obtain upper bounds for density. Precisely, through piecewise estimation and some time-depending a priori estimates, we establish time-uniform upper bounds for density under the assumption that the initial energy is small. The initial vacuum is allowed.

  4. Massive parallelization of a 3D finite difference electromagnetic forward solution using domain decomposition methods on multiple CUDA enabled GPUs

    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

  5. 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.

  6. 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.

  7. First 3D radiative transfer with scattering for domain-decomposed MHD simulations

    NASA Astrophysics Data System (ADS)

    Hayek, W.

    2008-12-01

    This paper presents an implementation of the Gauss Seidel solver for radiative transfer with scattering in the Oslo Stagger Code. It fully supports MPI parallelism through domain decomposition of the simulation box, enabling fast computation of radiative transfer at a high resolution. Continuum and line opacities are treated with either a multigroup method or opacity sampling. Line scattering probabilities are estimated using the van Regemorter approximation for de-excitation rates of electron collisions. A solar-type test simulation with continuum and line scattering exhibits a steeper temperature gradient due to decreased radiative heating above the optical surface when compared with the strict local thermodynamic equilibrium (LTE) case. The classical van Regemorter approximation may overestimate the importance of line scattering, implying that the true temperature structure will be in between the LTE case and the scattering case considered here. It is demonstrated that continuum scattering is unimportant in the case of the Sun.

  8. A framework for discrete stochastic simulation on 3D moving boundary domains

    NASA Astrophysics Data System (ADS)

    Drawert, Brian; Hellander, Stefan; Trogdon, Michael; Yi, Tau-Mu; Petzold, Linda

    2016-11-01

    We have developed a method for modeling spatial stochastic biochemical reactions in complex, three-dimensional, and time-dependent domains using the reaction-diffusion master equation formalism. In particular, we look to address the fully coupled problems that arise in systems biology where the shape and mechanical properties of a cell are determined by the state of the biochemistry and vice versa. To validate our method and characterize the error involved, we compare our results for a carefully constructed test problem to those of a microscale implementation. We demonstrate the effectiveness of our method by simulating a model of polarization and shmoo formation during the mating of yeast. The method is generally applicable to problems in systems biology where biochemistry and mechanics are coupled, and spatial stochastic effects are critical.

  9. Dynamic rupture modeling of the 2011 M9 Tohoku earthquake with an unstructured 3D spectral element method

    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

  10. Encrypting 2D/3D image using improved lensless integral imaging in Fresnel domain

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Wei; Wang, Qiong-Hua; Kim, Seok-Tae; Lee, In-Kwon

    2016-12-01

    We propose a new image encryption technique, for the first time to our knowledge, combined Fresnel transform with the improved lensless integral imaging technique. In this work, before image encryption, the input image is first recorded into an elemental image array (EIA) by using the improved lensless integral imaging technique. The recorded EIA is encrypted into random noise by use of two phase masks located in the Fresnel domain. The positions of phase masks and operation wavelength, as well as the integral imaging system parameters are used as encryption keys that can ensure security. Compared with previous works, the main novelty of this proposed method resides in the fact that the elemental images possess distributed memory characteristic, which greatly improved the robustness of the image encryption algorithm. Meanwhile, the proposed pixel averaging algorithm can effectively address the overlapping problem existing in the computational integral imaging reconstruction process. Numerical simulations are presented to demonstrate the feasibility and effectiveness of the proposed method. Results also indicate the high robustness against data loss attacks.

  11. An accurate multimodal 3-D vessel segmentation method based on brightness variations on OCT layers and curvelet domain fundus image analysis.

    PubMed

    Kafieh, Raheleh; Rabbani, Hossein; Hajizadeh, Fedra; Ommani, Mohammadreza

    2013-10-01

    This paper proposes a multimodal approach for vessel segmentation of macular optical coherence tomography (OCT) slices along with the fundus image. The method is comprised of two separate stages; the first step is 2-D segmentation of blood vessels in curvelet domain, enhanced by taking advantage of vessel information in crossing OCT slices (named feedback procedure), and improved by suppressing the false positives around the optic nerve head. The proposed method for vessel localization of OCT slices is also enhanced utilizing the fact that retinal nerve fiber layer becomes thicker in the presence of the blood vessels. The second stage of this method is axial localization of the vessels in OCT slices and 3-D reconstruction of the blood vessels. Twenty-four macular spectral 3-D OCT scans of 16 normal subjects were acquired using a Heidelberg HRA OCT scanner. Each dataset consisted of a scanning laser ophthalmoscopy (SLO) image and limited number of OCT scans with size of 496 × 512 (namely, for a data with 19 selected OCT slices, the whole data size was 496 × 512 × 19). The method is developed with least complicated algorithms and the results show considerable improvement in accuracy of vessel segmentation over similar methods to produce a local accuracy of 0.9632 in area of SLO, covered with OCT slices, and the overall accuracy of 0.9467 in the whole SLO image. The results are also demonstrative of a direct relation between the overall accuracy and percentage of SLO coverage by OCT slices.

  12. 3D shape tracking of minimally invasive medical instruments using optical frequency domain reflectometry

    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.

  13. A Parameter-Free Dynamic Alternative to Hyper-Viscosity for Coupled Transport Equations: Application to the Simulation of 3D Squall Lines Using Spectral Elements

    DTIC Science & Technology

    2015-06-04

    that involve physics coupling with phase change in the simulation of 3D deep convection . We show that the VMS+DC approach is a robust technique that can...of 3D deep convection . We show that the VMS+DC approach is a robust technique that can damp the high order modes characterizing the spectral element...of Spectral Elements, Deep Convection , Kessler Microphysics Preprint J. Comput. Phys. 283 (2015) 360-373 June 4, 2015 1. Introduction In the field of

  14. Volumetric three-dimensional reconstruction and segmentation of spectral-domain OCT.

    PubMed

    Aaker, Grant D; Gracia, Luis; Myung, Jane S; Borcherding, Vanessa; Banfelder, Jason R; D'Amico, Donald J; Kiss, Szilárd

    2011-07-01

    Despite advances in optical coherence tomography (OCT), three-dimensional (3D) renderings of OCT images remain limited to scanning consecutive two-dimensional (2D) OCT slices. The authors describe a method of reconstructing 2D OCT data for 3D retinal analysis and visualization in a Computer Assisted Virtual Environment (CAVE). Using customized signal processing software, raw data from 2D slice-based spectral-domain OCT images were rendered into high-resolution 3D images for segmentation and quantification analysis. Reconstructed OCT images were projected onto a four-walled space and viewed through stereoscopic glasses, resulting in a virtual reality perception of the retina. These 3D retinal renderings offer a novel method for segmentation and isolation of volumetric images. The ability to manipulate the images in a virtual reality environment allows visualization of complex spatial relationships that may aid our understanding of retinal pathology. More importantly, these 3D retinal renderings can be viewed, manipulated, and analyzed on traditional 2D monitors independent of the CAVE.

  15. A new efficient 3D Discontinuous Galerkin Time Domain (DGTD) method for large and multiscale electromagnetic simulations

    NASA Astrophysics Data System (ADS)

    Tobón, Luis E.; Ren, Qiang; Liu, Qing Huo

    2015-02-01

    A new Discontinuous Galerkin Time Domain (DGTD) method for solving the 3D time dependent Maxwell's equations via the electric field intensity E and magnetic flux density B fields is proposed for the first time. It uses curl-conforming and divergence-conforming basis functions for E and B, respectively, with the same order of interpolation. In this way, higher accuracy is achieved at lower memory consumption than the conventional approach based on the field variables E and H. The centered flux and Riemann solver are both used to treat interfaces with non-conforming meshes, and both explicit Runge-Kutta method and implicit Crank-Nicholson method are implemented for time integration. Numerical examples for realistic cases will be presented to verify that the proposed method is a non-spurious and efficient DGTD scheme.

  16. A Non-Linear Mixed Spectral Finite-Difference 3-D Model of Planetary Boundary-Layer Flow over Complex Terrain and Its Application

    NASA Astrophysics Data System (ADS)

    Weng, W.; Taylor, P. A.

    2010-09-01

    Based on the early linear and Non-Linear Mixed Spectral Finite-Difference (MSFD and NLMSFD) models, a 3-D non-linear model of planetary boundary-layer flow (NLMSFD-PBL) was developed to study neutral PBL flow over complex terrain. The model assumes upwind or zero-order profiles of mean and turbulence variables about which perturbation quantities are calculated due to the effects of the terrain. In early models, the mean zero-order wind profile was assumed to be a simple logarithmic surface-layer profile and Reynolds stresses were constant throughout the depth of the model domain. This formally limits the applications of model to the surface-layer flow. The new model utilizes the results of early 1-D planetary boundary layer model of Weng and Taylor as the zero-order or upstream profiles of mean and turbulent quantities. The limitations associated with the original MSFD/NLMSFD model (e.g. logarithmic wind profile and constant shear stress layer) are relaxed. The effect of earth's rotation is also included in the model. Model results for planetary boundary-layer flow over complex terrain are discussed, particularly, the flow over Askervein hill - the site of a detailed and much referenced field study of flow over hills in the 1980s. This type of modelling of flow over complex terrain has important applications for wind energy resource assessment and wind farm design.

  17. 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.

  18. Spectral domain detection in low-coherence spectroscopy

    PubMed Central

    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

  19. Development of quantitative diagnostic observables for age-related macular degeneration using Spectral Domain OCT

    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.

  20. Predicting Gilthead Sea Bream (Sparus aurata) Freshness by a Novel Combined Technique of 3D Imaging and SW-NIR Spectral Analysis.

    PubMed

    Ivorra, Eugenio; Verdu, Samuel; Sánchez, Antonio J; Grau, Raúl; Barat, José M

    2016-10-19

    A technique that combines the spatial resolution of a 3D structured-light (SL) imaging system with the spectral analysis of a hyperspectral short-wave near infrared system was developed for freshness predictions of gilthead sea bream on the first storage days (Days 0-6). This novel approach allows the hyperspectral analysis of very specific fish areas, which provides more information for freshness estimations. The SL system obtains a 3D reconstruction of fish, and an automatic method locates gilthead's pupils and irises. Once these regions are positioned, the hyperspectral camera acquires spectral information and a multivariate statistical study is done. The best region is the pupil with an R² of 0.92 and an RMSE of 0.651 for predictions. We conclude that the combination of 3D technology with the hyperspectral analysis offers plenty of potential and is a very promising technique to non destructively predict gilthead freshness.

  1. Predicting Gilthead Sea Bream (Sparus aurata) Freshness by a Novel Combined Technique of 3D Imaging and SW-NIR Spectral Analysis

    PubMed Central

    Ivorra, Eugenio; Verdu, Samuel; Sánchez, Antonio J.; Grau, Raúl; Barat, José M.

    2016-01-01

    A technique that combines the spatial resolution of a 3D structured-light (SL) imaging system with the spectral analysis of a hyperspectral short-wave near infrared system was developed for freshness predictions of gilthead sea bream on the first storage days (Days 0–6). This novel approach allows the hyperspectral analysis of very specific fish areas, which provides more information for freshness estimations. The SL system obtains a 3D reconstruction of fish, and an automatic method locates gilthead’s pupils and irises. Once these regions are positioned, the hyperspectral camera acquires spectral information and a multivariate statistical study is done. The best region is the pupil with an R2 of 0.92 and an RMSE of 0.651 for predictions. We conclude that the combination of 3D technology with the hyperspectral analysis offers plenty of potential and is a very promising technique to non destructively predict gilthead freshness. PMID:27775556

  2. Optimal fourth-order staggered-grid finite-difference scheme for 3D frequency-domain viscoelastic wave modeling

    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.

  3. Biofunctionalization of electrospun PCL-based scaffolds with perlecan domain IV peptide to create a 3-D pharmacokinetic cancer model

    PubMed Central

    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

  4. GRID3D-v2: An updated version of the GRID2D/3D computer program for generating grid systems in complex-shaped three-dimensional spatial domains

    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.

  5. GRID2D/3D: A computer program for generating grid systems in complex-shaped two- and three-dimensional spatial domains. Part 1: Theory and method

    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

  6. Fast Volumetric Spatial-Spectral MR Imaging of Hyperpolarized 13C-Labeled Compounds using Multiple Echo 3D bSSFP

    PubMed Central

    Perman, William H.; Bhattacharya, Pratip; Leupold, Jochen; Lin, Alexander P.; Harris, Kent C.; Norton, Valerie A.; Hovener, Jan B.; Ross, Brian D.

    2010-01-01

    PURPOSE The goal of this work was to develop a fast 3D chemical shift imaging technique for the non-invasive measurement of hyperpolarized 13C-labeled substrates and metabolic products at low concentration. MATERIALS AND METHODS Multiple echo 3D balanced steady state MR imaging (ME-3DbSSFP) was performed in vitro on a syringe containing hyperpolarized [1,3,3-2H3; 1-13C]2-hydroxyethylpropionate (HEP) adjacent to a 13C-enriched acetate phantom, and in vivo on a rat before and after IV injection of hyperpolarized HEP at 1.5 T. Chemical shift images of the hyperpolarized HEP were derived from the multiple echo data by Fourier transformation along the echoes on a voxel by voxel basis for each slice of the 3D data set. RESULTS ME-3DbSSFP imaging was able to provide chemical shift images of hyperpolarized HEP in vivo, and in a rat with isotropic 7 mm spatial resolution, 93 Hz spectral resolution and 16 second temporal resolution for a period greater than 45 seconds. CONCLUSION Multiple echo 3D bSSFP imaging can provide chemical shift images of hyperpolarized 13C-labeled compounds in vivo with relatively high spatial resolution and moderate spectral resolution. The increased signal-to-noise ratio (SNR) of this 3D technique will enable the detection of hyperpolarized 13C-labeled metabolites at lower concentrations as compared to a 2D technique. PMID:20171034

  7. Dynamic spectral-domain optical coherence elastography for tissue characterization.

    PubMed

    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.

  8. 3D Simulation of Elastic Wave Propagation in Heterogeneous Anisotropic Media in Laplace Domain for Electromagnetic-Seismic Inverse Modeling

    NASA Astrophysics Data System (ADS)

    Petrov, P.; Newman, G. A.

    2011-12-01

    Recent developments in high resolution imaging technology of subsurface objects involves a combination of different geophysical measurements (gravity, EM and seismic). A joint image of the subsurface geophysical attributes (velocity, electrical conductivity and density) requires the consistent treatment of the different geophysical data due to their differing physical nature. For example, in conducting media, which is typical of the Earth's interior, EM energy propagation is defined by a diffusive mechanism and may be characterized by two specific length scales: wavelength and skin depth. However, the propagation of seismic signals is a multiwave process and is characterized by a set of wavelengths. Thus, to consistently treat seismic and electromagnetic data an additional length scale is needed for seismic data that does not directly depend on a wavelength and describes a diffusive process, similar to EM wave propagation in the subsurface. Works by Brown et al.(2005), Shin and Cha(2008), and Shin and Ha(2008) suggest that an artificial damping of seismic wave fields via Laplace-Fourier transformation can be an effective approach to obtain a seismic data that have similar spatial resolution to EM data. The key benefit of such transformation is that diffusive wave-field inversion works well for both data sets: seismic (Brown et al.,2005; Shin and Cha,2008) and electromagnetic (Commer and Newman,2008; Newman et al.,2010). With the recent interest in the Laplace-Fourier domain full waveform inversion, 3D fourth and second-order finite-difference schemes for modeling of seismic wave propagation have been developed (Petrov and Newman, 2010). Incorporation of attenuation and anisotropy into a velocity model is a necessary step for a more realistic description of subsurface media. Here we consider the extension of our method which includes attenuation and VTI anisotropy. Our approach is based on the integro-interpolation technique for velocity-stress formulation. Seven

  9. 3D Non-destructive Imaging of Punctures in Polyethylene Composite Armor by THz Time Domain Spectroscopy

    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.

  10. An example of a harmonizable process whose spectral domain is not complete

    NASA Technical Reports Server (NTRS)

    Miamee, A. G.; Salehi, H.

    1989-01-01

    The question of completeness of the spectral domain of harmonizable processes has been open for some years. An example is given of a harmonizable process whose spectral domain is not complete. This shows that a recent result which claims the completeness of all such spectral domains is false.

  11. Gabor-domain optical coherence microscopy with integrated dual-axis MEMS scanner for fast 3D imaging and metrology

    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.

  12. A numerical method for solving the 3D unsteady incompressible Navier Stokes equations in curvilinear domains with complex immersed boundaries

    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

  13. Europeana and 3D

    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.

  14. Using 3D Simulation of Elastic Wave Propagation in Laplace Domain for Electromagnetic-Seismic Inverse Modeling

    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.

  15. On-line surface inspection using cylindrical lens-based spectral domain low-coherence interferometry.

    PubMed

    Tang, Dawei; Gao, Feng; Jiang, X

    2014-08-20

    We present a spectral domain low-coherence interferometry (SD-LCI) method that is effective for applications in on-line surface inspection because it can obtain a surface profile in a single shot. It has an advantage over existing spectral interferometry techniques by using cylindrical lenses as the objective lenses in a Michelson interferometric configuration to enable the measurement of long profiles. Combined with a modern high-speed CCD camera, general-purpose graphics processing unit, and multicore processors computing technology, fast measurement can be achieved. By translating the tested sample during the measurement procedure, real-time surface inspection was implemented, which is proved by the large-scale 3D surface measurement in this paper. ZEMAX software is used to simulate the SD-LCI system and analyze the alignment errors. Two step height surfaces were measured, and the captured interferograms were analyzed using a fast Fourier transform algorithm. Both 2D profile results and 3D surface maps closely align with the calibrated specifications given by the manufacturer.

  16. Balanced detection for spectral domain optical coherence tomography.

    PubMed

    Kuo, Wen-Chuan; Lai, Chih-Ming; Huang, Yi-Shiang; Chang, Cheng-Yi; Kuo, Yue-Ming

    2013-08-12

    The use and advantages of applying balanced-detection (BD) operation method to high speed spectral domain optical coherence tomography (SDOCT) are presented in this study, which we believe is the first such demonstration. Compared to conventional SDOCT, BD-SDOCT provides two unique advantages. First, the method can suppress background noise and autocorrelation artifacts in biological tissues. Second, it is a power-efficient method which is particularly helpful for high speed SDOCT to eliminate random intensity noise and to achieve shot noise limited detection. This performance allows in vivo three-dimensional tissue visualization with high imaging quality and high speed.

  17. Spectral domain optical coherence tomography finding in posterior microphthalmos.

    PubMed

    Kumar, Mukesh; Das, Taraprasad; Kesarwani, Siddharth

    2012-11-01

    An eight-year-old boy presented with decreased vision in both eyes. At presentation, the visual acuity was 6/60 in both eyes with high plus spheres. Anterior segment examination was normal. Fundus examination and spectral domain optical coherence tomography were consistent with posterior microphthalmos and showed an elevated foveal contour and fold in the outer plexiform layer. External limiting membrane, photoreceptor and retinal pigment epithelium were not involved in the fold. To the best of our knowledge this is the first such case report with optical coherence tomography imaging of the retinal layer involved in a case of posterior microphthalmos.

  18. ShipMo3D Version 1.0 User Manual for Simulating Time Domain Motions of a Freely Maneuvering Ship in a Seaway

    DTIC Science & Technology

    2007-10-01

    from) in earth -fixed axes ν mean wave direction (from) in earth -fixed axes νi mean wave direction (from) for spectral component i ρ water density {σ...Kennedy Abstract This report serves as a user manual for simulating ship motions in waves and in calm water using ShipMo3D Version 1.0. ShipMo3D is...with associated user applica- tions for predicting ship motions in calm water and in waves. Motion predictions are available in both the frequency

  19. A New Method to Explore the Spectral Impact of the Piriform Fossae on the Singing Voice: Benchmarking Using MRI-Based 3D-Printed Vocal Tracts

    PubMed Central

    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

  20. A new method to explore the spectral impact of the piriform fossae on the singing voice: benchmarking using MRI-based 3D-printed vocal tracts.

    PubMed

    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.

  1. Solution structure of the calponin CH domain and fitting to the 3D-helical reconstruction of F-actin:calponin.

    PubMed

    Bramham, Janice; Hodgkinson, Julie L; Smith, Brian O; Uhrín, Dusan; Barlow, Paul N; Winder, Steven J

    2002-02-01

    Calponin is involved in the regulation of contractility and organization of the actin cytoskeleton in smooth muscle cells. It is the archetypal member of the calponin homology (CH) domain family of actin binding proteins that includes cytoskeletal linkers such as alpha-actinin, spectrin, and dystrophin, and regulatory proteins including VAV, IQGAP, and calponin. We have determined the first structure of a CH domain from a single CH domain-containing protein, that of calponin, and have fitted the NMR-derived coordinates to the 3D-helical reconstruction of the F-actin:calponin complex using cryo-electron microscopy. The tertiary fold of this single CH domain is typical of, yet significantly different from, those of the CH domains that occur in tandem pairs to form high-affinity ABDs in other proteins. We thus provide a structural insight into the mode of interaction between F-actin and CH domain-containing proteins.

  2. Online monitoring of printed electronics by Spectral-Domain Optical Coherence Tomography

    PubMed Central

    Alarousu, Erkki; AlSaggaf, Ahmed; Jabbour, Ghassan E.

    2013-01-01

    Spectral-Domain Optical Coherence Tomography (SD-OCT) is an optical method capable of 3D imaging of object's internal structure with micron-scale resolution. Modern SD-OCT tools offer the speed capable of online monitoring of printed devices. This paper demonstrates the use of SD-OCT in a simulated roll-to-roll (R2R) process through monitoring some structural properties of moving screen printed interdigitated electrodes. It is shown that structural properties can be resolved for speeds up to ca. 1 m/min, which is the first step towards application of this method in real manufacturing processes, including roll-to-roll (R2R) printing. PMID:23536206

  3. Online monitoring of printed electronics by Spectral-Domain Optical Coherence Tomography.

    PubMed

    Alarousu, Erkki; AlSaggaf, Ahmed; Jabbour, Ghassan E

    2013-01-01

    Spectral-Domain Optical Coherence Tomography (SD-OCT) is an optical method capable of 3D imaging of object's internal structure with micron-scale resolution. Modern SD-OCT tools offer the speed capable of online monitoring of printed devices. This paper demonstrates the use of SD-OCT in a simulated roll-to-roll (R2R) process through monitoring some structural properties of moving screen printed interdigitated electrodes. It is shown that structural properties can be resolved for speeds up to ca. 1 m/min, which is the first step towards application of this method in real manufacturing processes, including roll-to-roll (R2R) printing.

  4. 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.

  5. Spectral domain of large nonsymmetric correlated Wishart matrices.

    PubMed

    Vinayak; Benet, Luis

    2014-10-01

    We study complex eigenvalues of the Wishart model for nonsymmetric correlation matrices. The model is defined for two statistically equivalent but different Gaussian real matrices, as C=AB(t)/T, where B(t) is the transpose of B and both matrices A and B are of dimensions N×T. If A and B are uncorrelated, or equivalently if C vanishes on average, it is known that at large matrix dimension the domain of the eigenvalues of C is a circle centered-at-origin and the eigenvalue density depends only on the radial distances. We consider actual correlation in A and B and derive a result for the contour describing the domain of the bulk of the eigenvalues of C in the limit of large N and T where the ratio N/T is finite. In particular, we show that the eigenvalue domain is sensitive to the correlations. For example, when C is diagonal on average with the same element c≠0, the contour is no longer a circle centered at origin but a shifted ellipse. In this case we explicitly derive a result for the spectral density which again depends only on the radial distances. For more general cases, we show that the contour depends on the symmetric and antisymmetric parts of the correlation matrix resulting from the ensemble-averaged C. If the correlation matrix is normal, then the contour depends only on its spectrum. We also provide numerics to justify our analytics.

  6. Spectral domain of large nonsymmetric correlated Wishart matrices

    NASA Astrophysics Data System (ADS)

    Vinayak, Benet, Luis

    2014-10-01

    We study complex eigenvalues of the Wishart model for nonsymmetric correlation matrices. The model is defined for two statistically equivalent but different Gaussian real matrices, as C =ABt/T, where Bt is the transpose of B and both matrices A and B are of dimensions N ×T. If A and B are uncorrelated, or equivalently if C vanishes on average, it is known that at large matrix dimension the domain of the eigenvalues of C is a circle centered-at-origin and the eigenvalue density depends only on the radial distances. We consider actual correlation in A and B and derive a result for the contour describing the domain of the bulk of the eigenvalues of C in the limit of large N and T where the ratio N /T is finite. In particular, we show that the eigenvalue domain is sensitive to the correlations. For example, when C is diagonal on average with the same element c ≠0, the contour is no longer a circle centered at origin but a shifted ellipse. In this case we explicitly derive a result for the spectral density which again depends only on the radial distances. For more general cases, we show that the contour depends on the symmetric and antisymmetric parts of the correlation matrix resulting from the ensemble-averaged C. If the correlation matrix is normal, then the contour depends only on its spectrum. We also provide numerics to justify our analytics.

  7. Spectral, Magnetic and Biological Studie on Some Bivalent 3d Metal Complexes of Hydrazine Derived Schiff-Base Ligands

    PubMed Central

    Sherazi, Syed K. A.

    1997-01-01

    Metal(II) complexes of hydrazine derived Schiff-base ligands of the type M(L)2Cl2 where M = Co, Cu, Ni and Zn and L = L1 and L2 have been prepared and characterised by molar conductance, magnetic moment, elemental analysis and electronic, IR, H-NMR and 13C spectral data.The different modes of chelation of the ligands and their comparative biological properties against different bacterial species are reported. PMID:18475770

  8. 3-D spectral IP imaging: Non-invasive characterization of contaminant plumes. Annual progress report, September 15, 1996--September 14, 1997

    SciTech Connect

    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.'

  9. iVirtualWorld: A Domain-Oriented End-User Development Environment for Building 3D Virtual Chemistry Experiments

    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…

  10. Automated vessel shadow segmentation of fovea-centered spectral-domain images from multiple OCT devices

    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

  11. Sparsity based denoising of spectral domain optical coherence tomography images

    PubMed Central

    Fang, Leyuan; Li, Shutao; Nie, Qing; Izatt, Joseph A.; Toth, Cynthia A.; Farsiu, Sina

    2012-01-01

    In this paper, we make contact with the field of compressive sensing and present a development and generalization of tools and results for reconstructing irregularly sampled tomographic data. In particular, we focus on denoising Spectral-Domain Optical Coherence Tomography (SDOCT) volumetric data. We take advantage of customized scanning patterns, in which, a selected number of B-scans are imaged at higher signal-to-noise ratio (SNR). We learn a sparse representation dictionary for each of these high-SNR images, and utilize such dictionaries to denoise the low-SNR B-scans. We name this method multiscale sparsity based tomographic denoising (MSBTD). We show the qualitative and quantitative superiority of the MSBTD algorithm compared to popular denoising algorithms on images from normal and age-related macular degeneration eyes of a multi-center clinical trial. We have made the corresponding data set and software freely available online. PMID:22567586

  12. A line integration method for the treatment of 3D domain integrals and accelerated by the fast multipole method in the BEM

    NASA Astrophysics Data System (ADS)

    Wang, Qiao; Zhou, Wei; Cheng, Yonggang; Ma, Gang; Chang, Xiaolin

    2017-04-01

    A line integration method (LIM) is proposed to calculate the domain integrals for 3D problems. In the proposed method, the domain integrals are transformed into boundary integrals and only line integrals on straight lines are needed to be computed. A background cell structure is applied to further simplify the line integrals and improve the accuracy. The method creates elements only on the boundary, and the integral lines are created from the boundary elements. The procedure is quite suitable for the boundary element method, and we have applied it to 3D situations. Directly applying the method is time-consuming since the complexity of the computational time is O( NM), where N and M are the numbers of nodes and lines, respectively. To overcome this problem, the fast multipole method is used with the LIM for large-scale computation. The numerical results show that the proposed method is efficient and accurate.

  13. Spectral tomography with diffuse near-infrared light: inclusion of broadband frequency domain spectral data

    PubMed Central

    Wang, Jia; Davis, Scott C.; Srinivasan, Subhadra; Jiang, Shudong; Pogue, Brian W.; Paulsen, Keith D.

    2010-01-01

    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

  14. Combining Public Domain and Professional Panoramic Imagery for the Accurate and Dense 3d Reconstruction of the Destroyed Bel Temple in Palmyra

    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.

  15. Global existence and asymptotic behavior for the 3D compressible Navier-Stokes equations without heat conductivity in a bounded domain

    NASA Astrophysics Data System (ADS)

    Wu, Guochun

    2017-01-01

    In this paper, we investigate the global existence and uniqueness of strong solutions to the initial boundary value problem for the 3D compressible Navier-Stokes equations without heat conductivity in a bounded domain with slip boundary. The global existence and uniqueness of strong solutions are obtained when the initial data is near its equilibrium in H2 (Ω). Furthermore, the exponential convergence rates of the pressure and velocity are also proved by delicate energy methods.

  16. 3-D Quantum Transport Solver Based on the Perfectly Matched Layer and Spectral Element Methods for the Simulation of Semiconductor Nanodevices

    PubMed Central

    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

  17. Reconstruction for Time-Domain In Vivo EPR 3D Multigradient Oximetric Imaging—A Parallel Processing Perspective

    PubMed Central

    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

  18. Imaging patients with glaucoma using spectral-domain optical coherence tomography and optical microangiography

    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.

  19. Tunable acousto-optic spectral imager for atmospheric composition measurements in the visible spectral domain.

    PubMed

    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.

  20. 3D nanopillar optical antenna photodetectors.

    PubMed

    Senanayake, Pradeep; Hung, Chung-Hong; Shapiro, Joshua; Scofield, Adam; Lin, Andrew; Williams, Benjamin S; Huffaker, Diana L

    2012-11-05

    We demonstrate 3D surface plasmon photoresponse in nanopillar arrays resulting in enhanced responsivity due to both Localized Surface Plasmon Resonances (LSPRs) and Surface Plasmon Polariton Bloch Waves (SPP-BWs). The LSPRs are excited due to a partial gold shell coating the nanopillar which acts as a 3D Nanopillar Optical Antenna (NOA) in focusing light into the nanopillar. Angular photoresponse measurements show that SPP-BWs can be spectrally coincident with LSPRs to result in a x2 enhancement in responsivity at 1180 nm. Full-wave Finite Difference Time Domain (FDTD) simulations substantiate both the spatial and spectral coupling of the SPP-BW / LSPR for enhanced absorption and the nature of the LSPR. Geometrical control of the 3D NOA and the self-aligned metal hole lattice allows the hybridization of both localized and propagating surface plasmon modes for enhanced absorption. Hybridized plasmonic modes opens up new avenues in optical antenna design in nanoscale photodetectors.

  1. Three-Dimensional Spectral-Domain Optical Coherence Tomography Data Analysis for Glaucoma Detection

    PubMed Central

    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

  2. Retinal photoreceptor imaging with high-speed line-field parallel spectral domain OCT (Conference Presentation)

    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.

  3. Retinal photoreceptor imaging with high-speed line-field parallel spectral domain OCT (Conference Presentation)

    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.

  4. Automated retinal fovea type distinction in spectral-domain optical coherence tomography of retinal vein occlusion

    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

  5. The Stagger-grid: A grid of 3D stellar atmosphere models. II. Horizontal and temporal averaging and spectral line formation

    NASA Astrophysics Data System (ADS)

    Magic, Z.; Collet, R.; Hayek, W.; Asplund, M.

    2013-12-01

    Aims: We study the implications of averaging methods with different reference depth scales for 3D hydrodynamical model atmospheres computed with the Stagger-code. The temporally and spatially averaged (hereafter denoted as ⟨3D⟩) models are explored in the light of local thermodynamic equilibrium (LTE) spectral line formation by comparing spectrum calculations using full 3D atmosphere structures with those from ⟨3D⟩ averages. Methods: We explored methods for computing mean ⟨3D⟩ stratifications from the Stagger-grid time-dependent 3D radiative hydrodynamical atmosphere models by considering four different reference depth scales (geometrical depth, column-mass density, and two optical depth scales). Furthermore, we investigated the influence of alternative averages (logarithmic, enforced hydrostatic equilibrium, flux-weighted temperatures). For the line formation we computed curves of growth for Fe i and Fe ii lines in LTE. Results: The resulting ⟨3D⟩ stratifications for the four reference depth scales can be very different. We typically find that in the upper atmosphere and in the superadiabatic region just below the optical surface, where the temperature and density fluctuations are highest, the differences become considerable and increase for higher Teff, lower log g, and lower [Fe / H]. The differential comparison of spectral line formation shows distinctive differences depending on which ⟨3D⟩ model is applied. The averages over layers of constant column-mass density yield the best mean ⟨3D⟩ representation of the full 3D models for LTE line formation, while the averages on layers at constant geometrical height are the least appropriate. Unexpectedly, the usually preferred averages over layers of constant optical depth are prone to increasing interference by reversed granulation towards higher effective temperature, in particular at low metallicity. Appendix A is available in electronic form at http://www.aanda.orgMean ⟨3D⟩ models are

  6. Spectral Domain Optical Coherence Tomography for Glaucoma (An AOS Thesis)

    PubMed Central

    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

  7. Using a time-domain higher-order boundary element method to simulate wave and current diffraction from a 3-D body

    NASA Astrophysics Data System (ADS)

    Liu, Zhen; Teng, Bin; Ning, De-Zhi; Sun, Liang

    2010-06-01

    To study wave-current actions on 3-D bodies a time-domain numerical model was established using a higher-order boundary element method (HOBEM). By assuming small flow velocities, the velocity potential could be expressed for linear and higher order components by perturbation expansion. A 4th-order Runge-Kutta method was applied for time marching. An artificial damping layer was adopted at the outer zone of the free surface mesh to dissipate scattering waves. Validation of the numerical method was carried out on run-up, wave exciting forces, and mean drift forces for wave-currents acting on a bottom-mounted vertical cylinder. The results were in close agreement with the results of a frequency-domain method and a published time-domain method. The model was then applied to compute wave-current forces and run-up on a Seastar mini tension-leg platform.

  8. Crystal Structure of the Mycoplasma arthritidis-Derived Mitogen in Apo Form Reveals a 3D Domain-Swapped Dimer

    SciTech Connect

    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.

  9. Retinal Imaging of Infants on Spectral Domain Optical Coherence Tomography

    PubMed Central

    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

  10. Isoparametric fitting: A method for approximating full-field experimental data distributed on any shaped 3D domain

    NASA Astrophysics Data System (ADS)

    Bruno, Luigi

    2016-12-01

    With the present paper, the author proposes a fitting method for approximating experimental data retrieved from any full-field technique. Unlike most of the fitting procedures, the method works on data distributed on a surface of any shape, and the mathematical model is able to take into account of both the 3D shape of the surface and of the experimental quantity to be fitted. The paper reports all the mathematical steps necessary for applying the method, which was tested on two sets of experimental data obtained by an out-of-plane speckle interferometer working in two different conditions of noise. Experimental results showed the capability of the method to work in presence of high level of noise.

  11. Imaging of eye tumor in the mouse model of retinoblastoma with spectral-domain optical coherence tomography

    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.

  12. Quantification of airway thickness changes in smoke-inhalation injury using in-vivo 3-D endoscopic frequency-domain optical coherence tomography

    PubMed Central

    Lee, Sang-Won; Heidary, Andrew E.; Yoon, David; Mukai, David; Ramalingam, Tirunelveli; Mahon, Sari; Yin, Jiechen; Jing, Joseph; Liu, Gangjun; Chen, Zhongping; Brenner, Matthew

    2011-01-01

    Smoke inhalation injury is frequently accompanied by cyanide poisoning that may result in substantial morbidity and mortality, and methods are needed to quantitatively determine extent of airway injury. We utilized a 3-D endoscopic frequency-domain optical coherence tomography (FD-OCT) constructed with a swept-source laser to investigate morphological airway changes following smoke and cyanide exposure in rabbits. The thickness of the mucosal area between the epithelium and cartilage in the airway was measured and quantified. 3-D endoscopic FD-OCT was able to detect significant increases in the thickness of the tracheal walls of the rabbit beginning almost immediately after smoke inhalation injuries which were similar to those with combined smoke and cyanide poisoning. PMID:21339870

  13. RAPID COMMUNICATION: Processing of single domain Y Ba Cu O with pre-defined 3D interconnected porosity for bulk reinforcement

    NASA Astrophysics Data System (ADS)

    Sudhakar Reddy, E.; Babu, N. Hari; Shi, Y.; Cardwell, D. A.; Schmitz, G. J.

    2003-11-01

    A simple method for processing large, single domain Y-Ba-Cu-O (YBCO) bulks containing pre-defined 3D interconnected porosity is reported. The process involves the preparation of solid Y2BaCuO5 (Y-211) pre-form bodies by casting a water-based slurry into a mould containing a 3D wax model. The cast, composite sample is dried and heated to 600 °C to burn out organic binders and remove the wax component. The resulting Y-211 green body is then sintered at 1080 °C to produce a self-supporting ceramic sample containing an interconnected porous structure that replicates the initial wax model. Finally, the porous Y-211 body is transformed into near net shaped single domain YBa2Cu3O7-dgr (Y-123) by a seeded infiltration and growth processing technique and oxygenated to produce a superconducting sample. The as-produced, porous single YBCO domains can be reinforced with resins or alloys for improved mechanical and thermal properties.

  14. The structural domains of Pseudomonas aeruginosa phosphorylcholine phosphatase cooperate in substrate hydrolysis: 3D structure and enzymatic mechanism.

    PubMed

    Infantes, Lourdes; Otero, Lisandro Horacio; Beassoni, Paola Rita; Boetsch, Cristhian; Lisa, Angela Teresita; Domenech, Carlos Eduardo; Albert, Armando

    2012-11-02

    Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen. It colonizes different tissues by the utilization of diverse mechanisms. One of these may involve the breakdown of the host cell membrane through the sequential action of hemolytic phospholipase C and phosphorylcholine phosphatase (PchP). The action of hemolytic phospholipase C on phosphatidylcholine produces phosphorylcholine, which is hydrolyzed to choline (Cho) and inorganic phosphate by PchP. The available biochemical data on this enzyme demonstrate the involvement of two Cho-binding sites in the catalytic cycle and in enzyme regulation. The crystal structure of P. aeruginosa PchP has been determined. It folds into three structural domains. The first domain harbors all the residues involved in catalysis and is well conserved among the haloacid dehalogenase superfamily of proteins. The second domain is characteristic of PchP and is involved in the recognition of the Cho moiety of the substrate. The third domain stabilizes the relative position of the other two. Fortuitously, the crystal structure of PchP captures molecules of Bistris (2-[bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)propane-1,3-diol) at the active site and at an additional site. This represents two catalytically relevant complexes with just one or two inhibitory Bistris molecules and provides the basis of the PchP function and regulation. Site-directed mutagenesis along with biochemical experiments corroborates the structural observations and demonstrates the interplay between different sites for Cho recognition and inhibition. The structural comparison of PchP with other phosphatases of the haloacid dehalogenase family provides a three-dimensional picture of the conserved catalytic cycle and the structural basis for the recognition of the diverse substrate molecules.

  15. Development of Spectral Domain Optical Coherence Tomography for in vivo Functional Imaging of Biological Tissues

    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.)

  16. Linear-wavenumber spectrometer for high-speed spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Gelikonov, V. M.; Gelikonov, G. V.; Shilyagin, P. A.

    2009-03-01

    An equidistant (in the wavenumber) spectrometer based on a diffraction grating, a compensation prism, and a CCD linear array is developed and implemented for spectral-domain optical coherence tomography. A criterion is introduced for estimating the level of residual nonequidistance. This criterion allows one to determine the threshold compensation level necessary for obtaining the spectrally limited spatial resolution. The method is tested in spectral-domain optical coherent tomography systems at wavelengths of 1270 and 830 nm.

  17. Assessment of Artifacts and Reproducibility across Spectral and Time Domain Optical Coherence Tomography Devices

    PubMed Central

    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

  18. A high-order 3D spectral-element method for the forward modelling and inversion of gravimetric data - Application to the western Pyrenees

    NASA Astrophysics Data System (ADS)

    Martin, Roland; Chevrot, Sébastien; Komatitsch, Dimitri; Seoane, Lucia; Spangenberg, Hannah; Wang, Yi; Dufréchou, Grégory; Bonvalot, Sylvain; Bruinsma, Sean

    2017-01-01

    We image the internal density structure of the Pyrenees by inverting gravity data using an a priori density model derived by scaling a Vp model obtained by full waveform inversion of teleseismic P-waves. Gravity anomalies are computed via a 3D high-order finite-element integration in the same high-order spectral-element grid as the one used to solve the wave equation and thus to obtain the velocity model. The curvature of the Earth and surface topography are taken into account in order to obtain a density model as accurate as possible. The method is validated through comparisons with exact semi-analytical solutions. We show that the spectral element method drastically accelerates the computations when compared to other more classical methods. Different scaling relations between compressional velocity and density are tested, and the Nafe-Drake relation is the one that leads to the best agreement between computed and observed gravity anomalies. Gravity data inversion is then performed and the results allow us to put more constraints on the density structure of the shallow crust and on the deep architecture of the mountain range.

  19. A Parallel 3D Spectral Difference Method for Solutions of Compressible Navier Stokes Equations on Deforming Grids and Simulations of Vortex Induced Vibration

    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.

  20. Macular Surgery Using Intraoperative Spectral Domain Optical Coherence Tomography

    PubMed Central

    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

  1. Polymer model with Epigenetic Recoloring Reveals a Pathway for the de novo Establishment and 3D Organization of Chromatin Domains

    NASA Astrophysics Data System (ADS)

    Michieletto, D.; Orlandini, E.; Marenduzzo, D.

    2016-10-01

    One of the most important problems in development is how epigenetic domains can first be established, and then maintained, within cells. To address this question, we propose a framework that couples three-dimensional chromatin folding dynamics to a "recoloring" process modeling the writing of epigenetic marks. Because many intrachromatin interactions are mediated by bridging proteins, we consider a "two-state" model with self-attractive interactions between two epigenetic marks that are alike (either active or inactive). This model displays a first-order-like transition between a swollen, epigenetically disordered phase and a compact, epigenetically coherent chromatin globule. If the self-attraction strength exceeds a threshold, the chromatin dynamics becomes glassy, and the corresponding interaction network freezes. By modifying the epigenetic read-write process according to more biologically inspired assumptions, our polymer model with recoloring recapitulates the ultrasensitive response of epigenetic switches to perturbations and accounts for long-lived multidomain conformations, strikingly similar to the topologically associating domains observed in eukaryotic chromosomes.

  2. 3D structural conformation and functional domains of polysialyltransferase ST8Sia IV required for polysialylation of neural cell adhesion molecules.

    PubMed

    Zhou, Guo-Ping; Huang, Ri-Bo; Troy, Frederic A

    2015-01-01

    Synthesis of α2,8-polysialic acid (polySia) glycans are catalyzed by two highly homologous mammalian polysialyltransferases (polySTs), ST8Sia II (STX) and ST8Sia IV (PST), which are two members of the ST8Sia gene family of sialytransferases. During polysialylation, both STX and PST catalyze the transfer of multiple Sia residues from the activated sugar nucleotide precursor, CMP-Neu5Ac (Sia), to terminal Sia residues on N- and Olinked oligosaccharide chains on acceptor glycoproteins, including the neural cell adhesion molecule (NCAM), which is the major carrier protein of polySia. Based on our new findings and previously published studies, this review summarizes the present concepts regarding the molecular mechanism underlying regulation of protein-specific polysialylation of NCAM that includes the following: (1) Determination of the catalytic domains and specific regions within ST8Sia IV for recognizing and catalyzing the efficient polysialylation of NCAM; (2) Identification of key amino acid residues within the PSTD motif of ST8Sia IV that are essential for polysialylation; (3) Verification of key amino acids in the PBR domain of ST8Sia IV required for NCAM-specific polysialylation; and (4) a 3D conformational study of ST8Sia IV based on the Phyre2 server to discover the relationship between the structure and its functional domains of the polyST. Based on these results, our 3D model of ST8Sia IV was used to identify and characterize the catalytic domains and amino acid residues critical for catalyzing polysialylation, and have provided new structural information for supporting a detailed mechanism of polyST-NCAM interaction required for polysialylation of NCAM, findings that have not been previously reported.

  3. S4EI (Spectral Sampling with Slicer for Stellar and Extragalactical Instrumentation), a new-generation of 3D spectro-imager dedicated to night astronomy

    NASA Astrophysics Data System (ADS)

    Sayède, Frédéric; Puech, Mathieu; Mein, Pierre; Bonifacio, Piercarlo; Malherbe, Jean-Marie; Galicher, Raphaël.; Amans, Jean-Philippe; Fasola, Gilles

    2014-07-01

    Multichannel Subtractive Double Pass (MSDP) spectrographs have been widely used in solar spectroscopy because of their ability to provide an excellent compromise between field of view and spatial and spectral resolutions. Compared with other types of spectrographs, MSDP can deliver simultaneous monochromatic images at higher spatial and spectral resolutions without any time-scanning requirement (as with Fabry-Perot spectrographs), and with limited loss of flux. These performances are obtained thanks to a double pass through the dispersive element. Recent advances with VPH (Volume phase holographic) Grisms as well as with image slicers now make MSDP potentially sensitive to much smaller fluxes. We present S4EI (Spectral Sampling with Slicer for Stellar and Extragalactical Instrumentation), which is a new concept for extending MSDP to night-time astronomy. It is based on new generation reflecting plane image slicers working with large apertures specific to night-time telescopes. The resulting design could be potentially very attractive and innovative for different domains of astronomy, e.g., the simultaneous spatial mapping of accurately flux-calibrated emission lines between OH sky lines in extragalactic astronomy or the simultaneous imaging of stars, exoplanets and interstellar medium. We present different possible MSDP/S4EI configurations for these science cases and expected performances on telescopes such as the VLT.

  4. Full-range k-domain linearization in spectral-domain optical coherence tomography

    PubMed Central

    Jeon, Mansik; Kim, Jeehyun; Jung, Unsang; Lee, Changho; Jung, Woonggyu; Boppart, Stephen A.

    2011-01-01

    A full-bandwidth k-domain linearization method for spectral-domain optical coherence tomography (SD-OCT) is demonstrated. The method uses information of the wavenumber–pixel-position provided by a translating-slit-based wavelength filter. For calibration purposes, the filter is placed either after a broadband source or at the end of the sample path, and the filtered spectrum with a narrowed line width (~0.5 nm) is incident on a line-scan camera in the detection path. The wavelength-swept spectra are co-registered with the pixel positions according to their central wavelengths, which can be automatically measured with an optical spectrum analyzer. For imaging, the method does not require a filter or a software recalibration algorithm; it simply resamples the OCT signal from the detector array without employing rescaling or interpolation methods. The accuracy of k-linearization is maximized by increasing the k-linearization order, which is known to be a crucial parameter for maintaining a narrow point-spread function (PSF) width at increasing depths. The broadening effect is studied by changing the k-linearization order by undersampling to search for the optimal value. The system provides more position information, surpassing the optimum without compromising the imaging speed. The proposed full-range k-domain linearization method can be applied to SD-OCT systems to simplify their hardware/software, increase their speed, and improve the axial image resolution. The experimentally measured width of PSF in air has an FWHM of 8 μm at the edge of the axial measurement range. At an imaging depth of 2.5 mm, the sensitivity of the full-range calibration case drops less than 10 dB compared with the uncompensated case. PMID:21394187

  5. 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.

  6. In vivo volumetric imaging of the human corneo-scleral limbus with spectral domain OCT

    PubMed Central

    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

  7. Automated segmentation of intraretinal layers from spectral-domain macular OCT: reproducibility of layer thickness measurements

    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.

  8. Electroretinography combined with spectral domain optical coherence tomography to detect retinal damage in shaken baby syndrome.

    PubMed

    Nakayama, Yuri; Yokoi, Tadashi; Sachiko, Nishina; Okuyama, Makiko; Azuma, Noriyuki

    2013-08-01

    In order to correlate anatomical changes with visual function in shaken baby syndrome, we performed electroretinography and spectral domain optical coherence tomography on a 2-month-old girl and a 9-month-old girl after the retinal hemorrhages absorbed. Both patients had significant abnormalities in spectral domain optical coherence tomography images of the macular area. The amplitudes of the focal macular electroretinograms were more severely decreased than those of the full-field electroretinograms. Combining spectral domain coherence tomography with focal macular electroretinograms might better estimate the functional damage to the macula in patients with shaken baby syndrome.

  9. Spatioangular Prefiltering for Multiview 3D Displays.

    PubMed

    Ramachandra, Vikas; Hirakawa, Keigo; Zwicker, Matthias; Nguyen, Truong

    2011-05-01

    In this paper, we analyze the reproduction of light fields on multiview 3D displays. A three-way interaction between the input light field signal (which is often aliased), the joint spatioangular sampling grids of multiview 3D displays, and the interview light leakage in modern multiview 3D displays is characterized in the joint spatioangular frequency domain. Reconstruction of light fields by all physical 3D displays is prone to light leakage, which means that the reconstruction low-pass filter implemented by the display is too broad in the angular domain. As a result, 3D displays excessively attenuate angular frequencies. Our analysis shows that this reduces sharpness of the images shown in the 3D displays. In this paper, stereoscopic image recovery is recast as a problem of joint spatioangular signal reconstruction. The combination of the 3D display point spread function and human visual system provides the narrow-band low-pass filter which removes spectral replicas in the reconstructed light field on the multiview display. The nonideality of this filter is corrected with the proposed prefiltering. The proposed light field reconstruction method performs light field antialiasing as well as angular sharpening to compensate for the nonideal response of the 3D display. The union of cosets approach which has been used earlier by others is employed here to model the nonrectangular spatioangular sampling grids on a multiview display in a generic fashion. We confirm the effectiveness of our approach in simulation and in physical hardware, and demonstrate improvement over existing techniques.

  10. Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques

    PubMed Central

    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

  11. 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.

  12. Switchable field-tuned control of magnetic domain wall pinning along Co microwires by 3D e-beam lithographed structures

    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.

  13. Asymptotic behaviour of optimal spectral planar domains with fixed perimeter

    NASA Astrophysics Data System (ADS)

    Bucur, Dorin; Freitas, Pedro

    2013-05-01

    We consider the problem of minimizing the kth Dirichlet eigenvalue of planar domains with fixed perimeter and show that, as k goes to infinity, the optimal domain converges to the ball with the same perimeter. We also consider this problem within restricted classes of domains such as n-polygons and tiling domains, for which we show that the optimal asymptotic domain is that which maximises the area for fixed perimeter within the given family, i.e., the regular n-polygon and the regular hexagon, respectively. Physically, the above problems correspond to the determination of the shapes within a given class which will support the largest number of modes below a given frequency.

  14. Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function.

    PubMed

    Serohijos, Adrian W R; Hegedus, Tamás; Aleksandrov, Andrei A; He, Lihua; Cui, Liying; Dokholyan, Nikolay V; Riordan, John R

    2008-03-04

    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.

  15. NMR spectroscopy reveals that RNase A is chiefly denatured in 40% acetic acid: implications for oligomer formation by 3D domain swapping.

    PubMed

    López-Alonso, Jorge Pedro; Bruix, Marta; Font, Josep; Ribó, Marc; Vilanova, Maria; Jiménez, María Angeles; Santoro, Jorge; González, Carlos; Laurents, Douglas V

    2010-02-10

    Protein self-recognition is essential in many biochemical processes and its study is of fundamental interest to understand the molecular mechanism of amyloid formation. Ribonuclease A (RNase A) is a monomeric protein that may form several oligomers by 3D domain swapping of its N-terminal alpha-helix, C-terminal beta-strand, or both. RNase A oligomerization is induced by 40% acetic acid, which has been assumed to mildly unfold the protein by detaching the terminal segments and consequently facilitating intersubunit swapping, once the acetic acid is removed by lyophilization and the protein is redissolved in a benign buffer. Using UV difference, near UV circular dichroism, folding kinetics, and multidimensional heteronuclear NMR spectroscopy, the conformation of RNase A in 40% acetic acid and in 8 M urea has been characterized. These studies demonstrate that RNase A is chiefly unfolded in 40% acetic acid; it partially retains the native helices, whereas the beta-sheet is fully denatured and all X-Pro peptide bonds are predominantly in the trans conformation. Refolding occurs via an intermediate, I(N), with non-native X-Pro peptide bonds. I(N) is known to be populated during RNase A refolding following denaturation in concentrated solutions of urea or guanidinium chloride, and we find that urea- or GdmCl-denatured RNase A can oligomerize during refolding. By revealing the importance of a chiefly denaturated state and a refolding intermediate with non-native X-Pro peptide bonds, these findings revise the model for RNase A oligomerization via 3D domain swapping and have general implications for amyloid formation.

  16. Volumetric in vivo imaging of intracochlear microstructures in mice by high-speed spectral domain optical coherence tomography

    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.

  17. Partial least square and k-nearest neighbor algorithms for improved 3D quantitative spectral data-activity relationship consensus modeling of acute toxicity.

    PubMed

    Stoyanova-Slavova, Iva B; Slavov, Svetoslav H; Pearce, Bruce; Buzatu, Dan A; Beger, Richard D; Wilkes, Jon G

    2014-06-01

    A diverse set of 154 chemicals that included US Food and Drug Administration-regulated compounds tested for their aquatic toxicity in Daphnia magna were modeled by a 3-dimensional quantitative spectral data-activity relationship (3D-QSDAR). Two distinct algorithms, partial least squares (PLS) and Tanimoto similarity-based k-nearest neighbors (KNN), were used to process bin occupancy descriptor matrices obtained after tessellation of the 3D-QSDAR space into regularly sized bins. The performance of models utilizing bins ranging in size from 2 ppm × 2 ppm × 0.5 Å to 20 ppm × 20 ppm × 2.5 Å was explored. Rigorous quality-control criteria were imposed: 1) 100 randomized 20% hold-out test sets were generated and the average R(2) test of the respective models was used as a measure of their performance, and 2) a Y-scrambling procedure was used to identify chance correlations. A consensus between the best-performing composite PLS model using 0.5 Å × 14 ppm × 14 ppm bins and 10 latent variables (average R(2) test  = 0.770) and the best composite KNN model using 0.5 Å × 8 ppm × 8 ppm and 2 neighbors (average R(2) test  = 0.801) offered an improvement of about 7.5% (R(2) test consensus  = 0.845). Projection of the most frequently occurring bins on the standard coordinate space indicated that the presence of a primary or secondary amino group-substituted aromatic systems-would result in an increased toxic effect in Daphnia. The presence of a second aromatic ring with highly electronegative substituents 5 Å to 7 Å apart from the first ring would lead to a further increase in toxicity.

  18. Longitudinal, 3D Imaging of Collagen Remodeling in Murine Hypertrophic Scars In Vivo Using Polarization-Sensitive Optical Frequency Domain Imaging.

    PubMed

    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.

  19. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model

    PubMed Central

    Zhou, Jian; Qi, Jinyi

    2014-01-01

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D TOF PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon's raytracer, we propose another more simplified geometrical projector based on the Bresenham's raytracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a nonfactored model such as the analytical model while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve optimal reconstruction performance based on a sparse factorization model with an only image domain resolution model. PMID:24434568

  20. A 3D, fully Eulerian, VOF-based solver to study the interaction between two fluids and moving rigid bodies using the fictitious domain method

    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.

  1. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model.

    PubMed

    Zhou, Jian; Qi, Jinyi

    2014-02-07

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D time-of-flight PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon's ray-tracer, we propose another more simplified geometrical projector based on the Bresenham's ray-tracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a non-factored model, while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve the optimal reconstruction performance based on a sparse factorization model with an image domain resolution model.

  2. Solution of electromagnetic scattering and radiation problems using a spectral domain approach - A review

    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.

  3. 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

  4. 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.

  5. A fluid model simulation of a simplified plasma limiter based on spectral-element time-domain method

    SciTech Connect

    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.

  6. The absorption spectrum of monodeuterated methane /CH3D/ in the 6000-12000 A spectral region. [in atmospheres of outer planets

    NASA Technical Reports Server (NTRS)

    Danehy, R. G.; Lutz, B. L.; Owen, T.; Scattergood, T. W.; Goetz, W.

    1977-01-01

    Preliminary results of a laboratory study of the absorption spectrum of CH3D are presented. Three new parallel-type bands are reported at 8379 A, 9613 A, and 1.065 microns. The application of this work to the search for CH3D in the atmospheres of the outer planets is discussed.

  7. GRID2D/3D: A computer program for generating grid systems in complex-shaped two- and three-dimensional spatial domains. Part 2: User's manual and program listing

    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

  8. A spectral multi-domain technique with application to generalized curvilinear coordinates

    NASA Technical Reports Server (NTRS)

    Macaraeg, M. G.; Streett, C. L.

    1986-01-01

    Spectral collocation methods have proven to be efficient discretization schemes for many aerodynamic and fluid mechanic problems. The high order accuracy and resolution shown by these methods allows one to obtain engineering accuracy solutions on coarse meshes, or alternatively, to obtain solutions with very small error. One drawback to these techniques was the requirement that a complicated physical domain must map into a simple computational domain for discretization. This mapping must be smooth if the high order accuracy and expontential convergence rates associated with spectral methods are to be preserved. Additionally even smooth stretching transformations can decrease the accuracy of a spectral method, if the stretching is severe. A further difficulty with spectral methods was in their implementation on parallel processing computers, where efficient spectral algorithms were lacking. The above restrictions are overcome by splitting the domain into regions, each of which preserve the advantages of spectral collocation, and allow the ratio of the mesh spacing between regions to be several orders of magnitude higher than allowable in a single domain. Such stretchings would be required to resolve the thin viscous region in an external aerodynamic problem. Adjoining regions are interfaced by enforcing a global flux balance which preserves high-order continuity of the solution, regardless of the type of the equations being solved.

  9. Spectral element method for elastic and acoustic waves in frequency domain

    NASA Astrophysics Data System (ADS)

    Shi, Linlin; Zhou, Yuanguo; Wang, Jia-Min; Zhuang, Mingwei; Liu, Na; Liu, Qing Huo

    2016-12-01

    Numerical techniques in time domain are widespread in seismic and acoustic modeling. In some applications, however, frequency-domain techniques can be advantageous over the time-domain approach when narrow band results are desired, especially if multiple sources can be handled more conveniently in the frequency domain. Moreover, the medium attenuation effects can be more accurately and conveniently modeled in the frequency domain. In this paper, we present a spectral-element method (SEM) in frequency domain to simulate elastic and acoustic waves in anisotropic, heterogeneous, and lossy media. The SEM is based upon the finite-element framework and has exponential convergence because of the use of GLL basis functions. The anisotropic perfectly matched layer is employed to truncate the boundary for unbounded problems. Compared with the conventional finite-element method, the number of unknowns in the SEM is significantly reduced, and higher order accuracy is obtained due to its spectral accuracy. To account for the acoustic-solid interaction, the domain decomposition method (DDM) based upon the discontinuous Galerkin spectral-element method is proposed. Numerical experiments show the proposed method can be an efficient alternative for accurate calculation of elastic and acoustic waves in frequency domain.

  10. Blind spectral unmixing in terahertz domain using nonnegative matrix factorization

    NASA Astrophysics Data System (ADS)

    Li, Xian; Huang, Ping J.; Ma, Ye H.; Hou, Di B.; Zhang, Guangxin

    2015-11-01

    Recovering component spectra from terahertz measurements of unknown mixtures has been studied in this paper using nonnegative matrix factorization (NMF). NMF mathematically decomposes the spectra data into two nonnegative matrixes which describe the component spectra and the corresponding fractional abundance. Two basic algorithms in the class of this method, NMF and NMF with smoothness constraint (cNMF), were adopted to resolve the terahertz absorption spectra matrix obtained from a ternary mixture with varying compositions of Nitrofurantoin, L-Leucine and D-Tyrosine. The quality of the decomposition results was evaluated. The performance of the two algorithms on extracting component terahertz spectra was compared. The optimal result reached by cNMF in this study implies the capability of the NMF method for blind terahertz spectral unmixing. The attempt made in our work helps to further investigate unknown mixtures by terahertz spectroscopy.

  11. The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections.

    PubMed

    Chen, Delei; Goris, Bart; Bleichrodt, Folkert; Mezerji, Hamed Heidari; Bals, Sara; Batenburg, Kees Joost; de With, Gijsbertus; Friedrich, Heiner

    2014-12-01

    In electron tomography, the fidelity of the 3D reconstruction strongly depends on the employed reconstruction algorithm. In this paper, the properties of SIRT, TVM and DART reconstructions are studied with respect to having only a limited number of electrons available for imaging and applying different angular sampling schemes. A well-defined realistic model is generated, which consists of tubular domains within a matrix having slab-geometry. Subsequently, the electron tomography workflow is simulated from calculated tilt-series over experimental effects to reconstruction. In comparison with the model, the fidelity of each reconstruction method is evaluated qualitatively and quantitatively based on global and local edge profiles and resolvable distance between particles. Results show that the performance of all reconstruction methods declines with the total electron dose. Overall, SIRT algorithm is the most stable method and insensitive to changes in angular sampling. TVM algorithm yields significantly sharper edges in the reconstruction, but the edge positions are strongly influenced by the tilt scheme and the tubular objects become thinned. The DART algorithm markedly suppresses the elongation artifacts along the beam direction and moreover segments the reconstruction which can be considered a significant advantage for quantification. Finally, no advantage of TVM and DART to deal better with fewer projections was observed.

  12. Longitudinal, 3D Imaging of Collagen Remodeling in Murine Hypertrophic Scars In Vivo using Polarization-sensitive Optical Frequency Domain Imaging

    PubMed Central

    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

  13. Spectral domain optical coherence tomography for in-vivo three-dimensional retinal imaging of small animals

    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.

  14. Wave propagation numerical models in damage detection based on the time domain spectral element method

    NASA Astrophysics Data System (ADS)

    Ostachowicz, W.; Kudela, P.

    2010-06-01

    A Spectral Element Method is used for wave propagation modelling. A 3D solid spectral element is derived with shape functions based on Lagrange interpolation and Gauss-Lobatto-Legendre points. This approach is applied for displacement approximation suited for fundamental modes of Lamb waves as well as potential distribution in piezoelectric transducers. The novelty is the model geometry extension from flat to curved elements for application in shell-like structures. Exemplary visualisations of waves excited by the piezoelectric transducers in curved shell structure made of aluminium alloy are presented. Simple signal analysis of wave interaction with crack is performed. The crack is modelled by separation of appropriate nodes between elements. An investigation of influence of the crack length on wave propagation signals is performed. Additionally, some aspects of the spectral element method implementation are discussed.

  15. 3-D finite-difference, finite-element, discontinuous-Galerkin and spectral-element schemes analysed for their accuracy with respect to P-wave to S-wave speed ratio

    NASA Astrophysics Data System (ADS)

    Moczo, Peter; Kristek, Jozef; Galis, Martin; Chaljub, Emmanuel; Etienne, Vincent

    2011-12-01

    We analyse 13 3-D numerical time-domain explicit schemes for modelling seismic wave propagation and earthquake motion for their behaviour with a varying P-wave to S-wave speed ratio (VP/VS). The second-order schemes include three finite-difference, three finite-element and one discontinuous-Galerkin schemes. The fourth-order schemes include three finite-difference and two spectral-element schemes. All schemes are second-order in time. We assume a uniform cubic grid/mesh and present all schemes in a unified form. We assume plane S-wave propagation in an unbounded homogeneous isotropic elastic medium. We define relative local errors of the schemes in amplitude and the vector difference in one time step and normalize them for a unit time. We also define the equivalent spatial sampling ratio as a ratio at which the maximum relative error is equal to the reference maximum error. We present results of the extensive numerical analysis. We theoretically (i) show how a numerical scheme sees the P and S waves if the VP/VS ratio increases, (ii) show the structure of the errors in amplitude and the vector difference and (iii) compare the schemes in terms of the truncation errors of the discrete approximations to the second mixed and non-mixed spatial derivatives. We find that four of the tested schemes have errors in amplitude almost independent on the VP/VS ratio. The homogeneity of the approximations to the second mixed and non-mixed spatial derivatives in terms of the coefficients of the leading terms of their truncation errors as well as the absolute values of the coefficients are key factors for the behaviour of the schemes with increasing VP/VS ratio. The dependence of the errors in the vector difference on the VP/VS ratio should be accounted for by a proper (sufficiently dense) spatial sampling.

  16. Persistent Monitoring of Urban Infrasound Phenomenology. Report 1: Modeling an Urban Environment for Acoustical Analyses using the 3-D Finite-Difference Time-Domain Program PSTOP3D

    DTIC Science & Technology

    2015-08-01

    information systems (GIS) software. A smaller 6.25 square kilometer area around the Southern Methodist University was extracted from the larger...area and analyzed using an acoustic finite- difference time-domain (FDTD) code. The procedures to model the area using GIS software, extract required...create directories. .................................................. 127 Figure 8.4. Choose section cut to extract data

  17. Spectral domain optical coherence tomography imaging of subretinal bands associated with chronic retinal detachments

    PubMed Central

    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

  18. 3-D adaptive nonlinear complex-diffusion despeckling filter.

    PubMed

    Rodrigues, Pedro; Bernardes, Rui

    2012-12-01

    This work aims to improve the process of speckle noise reduction while preserving edges and other relevant features through filter expansion from 2-D to 3-D. Despeckling is very important for data visual inspection and as a preprocessing step for other algorithms, as they are usually notably influenced by speckle noise. To that intent, a 3-D approach is proposed for the adaptive complex-diffusion filter. This 3-D iterative filter was applied to spectral-domain optical coherence tomography medical imaging volumes of the human retina and a quantitative evaluation of the results was performed to allow a demonstration of the better performance of the 3-D over the 2-D filtering and to choose the best total diffusion time. In addition, we propose a fast graphical processing unit parallel implementation so that the filter can be used in a clinical setting.

  19. Numerical stability analysis of the pseudo-spectral analytical time-domain PIC algorithm

    SciTech Connect

    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.

  20. Adaptive time-domain filtering for real-time spectral discrimination in a Michelson interferometer.

    PubMed

    Bhalotra, Sameer R; Kung, Helen L; Jiao, Yang; Miller, David A B

    2002-07-01

    We present a method of spectral discrimination that employs time-domain processing instead of the typical frequency-domain analysis and implement the method in a Michelson interferometer with a nonlinear mirror scan. The technique yields one analog output value per scan instead of a complete interferogram by directly filtering a measured scan with a reference function in the time domain. Such a procedure drastically reduces data-processing requirements downstream. Additionally, using prerecorded interferograms as references eliminates the need to compensate for scan nonlinearities, which broadens the field of usable components for implementation in miniaturized sensing systems. With our efficient use of known spectral signatures, we demonstrate real-time discrimination of 633- and 663-nm laser sources with a mirror scan length of 1 microm , compared with the Rayleigh criterion of 7 microm.

  1. A spectral analysis of the domain decomposed Monte Carlo method for linear systems

    SciTech Connect

    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)

  2. A domain decomposition method for pseudo-spectral electromagnetic simulations of plasmas

    SciTech Connect

    Vay, Jean-Luc; Haber, Irving; Godfrey, Brendan B.

    2013-06-15

    Pseudo-spectral electromagnetic solvers (i.e. representing the fields in Fourier space) have extraordinary precision. In particular, Haber et al. presented in 1973 a pseudo-spectral solver that integrates analytically the solution over a finite time step, under the usual assumption that the source is constant over that time step. Yet, pseudo-spectral solvers have not been widely used, due in part to the difficulty for efficient parallelization owing to global communications associated with global FFTs on the entire computational domains. A method for the parallelization of electromagnetic pseudo-spectral solvers is proposed and tested on single electromagnetic pulses, and on Particle-In-Cell simulations of the wakefield formation in a laser plasma accelerator. The method takes advantage of the properties of the Discrete Fourier Transform, the linearity of Maxwell’s equations and the finite speed of light for limiting the communications of data within guard regions between neighboring computational domains. Although this requires a small approximation, test results show that no significant error is made on the test cases that have been presented. The proposed method opens the way to solvers combining the favorable parallel scaling of standard finite-difference methods with the accuracy advantages of pseudo-spectral methods.

  3. The Time-Domain Matched Filter and the Spectral-Domain Matched Filter in 1-Dimensional NMR Spectroscopy

    PubMed Central

    Spencer, Richard G.

    2010-01-01

    A type of “matched filter” (MF), used extensively in the processing of one-dimensional spectra, is defined by multiplication of a free-induction decay (FID) by a decaying exponential with the same time constant as that of the FID. This maximizes, in a sense to be defined, the signal-to-noise ratio (SNR) in the spectrum obtained after Fourier transformation. However, a different entity known also as the matched filter was introduced by van Vleck in the context of pulse detection in the 1940's and has become widely integrated into signal processing practice. These two types of matched filters appear to be quite distinct. In the NMR case, the “filter”, that is, the exponential multiplication, is defined by the characteristics of, and applied to, a time domain signal in order to achieve improved SNR in the spectral domain. In signal processing, the filter is defined by the characteristics of a signal in the spectral domain, and applied in order to improve the SNR in the temporal (pulse) domain. We reconcile these two distinct implementations of the matched filter, demonstrating that the NMR “matched filter” is a special case of the matched filter more rigorously defined in the signal processing literature. In addition, two limitations in the use of the MF are highlighted. First, application of the MF distorts resonance ratios as defined by amplitudes, although not as defined by areas. Second, the MF maximizes SNR with respect to resonance amplitude, while intensities are often more appropriately defined by areas. Maximizing the SNR with respect to area requires a somewhat different approach to matched filtering. PMID:21765806

  4. Spectral domain optical coherence tomography findings in CNGB3-associated achromatopsia and therapeutic implications.

    PubMed

    McClintock, Michael; Peden, Marc C; Kay, Christine N

    2014-01-01

    We describe the spectral domain OCT findings in two siblings with CNGB3-associated achromatopsia. A 33-year-old female and her 31-year-old sibling were evaluated for mild nystagmus and decreased visual acuity which had been present since childhood. They were each evaluated with full field Ganzfeld electroretinography which demonstrated flat photopic responses and preserved rod function. Genetic testing performed at Carver lab at the University of Iowa confirmed a diagnosis of achromatopsia with identical mutations in the CNGB3 gene. Spectral domain optical coherence tomography was performed which revealed foveal changes in both siblings, with slight phenotypic variations in these genotypically identical siblings. OCT findings in achromatopsia emphasize the importance of early identification and treatment in this disorder.

  5. Descemet membrane endothelial keratoplasty: intraoperative and postoperative imaging spectral-domain optical coherence tomography.

    PubMed

    Ang, Marcus; Dubis, Adam M; Wilkins, Mark R

    2015-01-01

    We describe a case report of using the same handheld spectral-domain anterior segment optical coherence tomography (ASOCT) for rapid intraoperative and postoperative imaging in a case of Descemet membrane endothelial keratoplasty (DMEK). A 67-year-old woman, with Fuchs dystrophy and corneal decompensation, underwent DMEK with intraoperative ASOCT imaging using the handheld Envisu spectral domain ASOCT system (Bioptigen, Inc., Morrisville, NC, USA). We found that this easy-to-use portable system with handheld probe allowed for rapid imaging of the anterior segment during donor manipulation to visualize the orientation of the DMEK donor, as well as to confirm the initial adhesion of the DMEK donor. Moreover, the same system may be used for postoperative monitoring of graft adhesion, corneal thickness, and stromal remodeling in the clinic with very high-definition images.

  6. Analysis of multimode fiber bundles for endoscopic spectral-domain optical coherence tomography

    PubMed Central

    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

  7. Molecular Electronics for Frequency Domain Optical Storage. Persistent Spectral Hole-Burning. A Review.

    DTIC Science & Technology

    1985-03-25

    if applicable) Office of Naval Research IBM Almaden Research Center Chemistry Division, Code 1113 6c. ADDRESS (City, State, and ZIP Code) 7b...NOTATION Journal of Molecular Electronics 17. .* COSATI CODES 18. SUBJECT TERMS (Continue on reverse of necessary and identify by block number) FIEL GRUP SB...GOUP Molecular electronics, spectral hole-burning, frequency I I domain. optical storage, solid state photo chemistry , * I photon gating. 19. ABSTRACT

  8. Euro3D Science Conference

    NASA Astrophysics Data System (ADS)

    Walsh, J. R.

    2004-02-01

    The Euro3D RTN is an EU funded Research Training Network to foster the exploitation of 3D spectroscopy in Europe. 3D spectroscopy is a general term for spectroscopy of an area of the sky and derives its name from its two spatial + one spectral dimensions. There are an increasing number of instruments which use integral field devices to achieve spectroscopy of an area of the sky, either using lens arrays, optical fibres or image slicers, to pack spectra of multiple pixels on the sky (``spaxels'') onto a 2D detector. On account of the large volume of data and the special methods required to reduce and analyse 3D data, there are only a few centres of expertise and these are mostly involved with instrument developments. There is a perceived lack of expertise in 3D spectroscopy spread though the astronomical community and its use in the armoury of the observational astronomer is viewed as being highly specialised. For precisely this reason the Euro3D RTN was proposed to train young researchers in this area and develop user tools to widen the experience with this particular type of data in Europe. The Euro3D RTN is coordinated by Martin M. Roth (Astrophysikalisches Institut Potsdam) and has been running since July 2002. The first Euro3D science conference was held in Cambridge, UK from 22 to 23 May 2003. The main emphasis of the conference was, in keeping with the RTN, to expose the work of the young post-docs who are funded by the RTN. In addition the team members from the eleven European institutes involved in Euro3D also presented instrumental and observational developments. The conference was organized by Andy Bunker and held at the Institute of Astronomy. There were over thirty participants and 26 talks covered the whole range of application of 3D techniques. The science ranged from Galactic planetary nebulae and globular clusters to kinematics of nearby galaxies out to objects at high redshift. Several talks were devoted to reporting recent observations with newly

  9. 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.

  10. High-speed high-precision and ultralong-range complex spectral domain dimensional metrology.

    PubMed

    Bao, Wen; Shen, Yi; Chen, Tao; Li, Peng; Ding, Zhihua

    2015-05-04

    A precise, nondestructive dimensional metrological system is crucial to manufacturing and packaging of multi-component optical system. To this end, an orthogonal dispersive spectrometer based complex spectral domain interferometric system for high-speed high-precision and ultralong-range dimensional metrology is developed. An improved complex method based on actual spectral phase shift is proposed to achieve ultrahigh suppression of artifacts. Suppression ratios of 80 dB for DC and 60 dB for mirror images are realized, the highest ratios among existing complex methods. To ensure high-precision in distance determination, an averaged spectral phase measurement algorithm is adopted. A precision of 60 nm within a measurement range of 200 mm without axial movement of the sample is demonstrated. The measurement range is readily extendable if axial movement of the sample and range cascading are involved. The system holds potential applications in various areas for real-time nondestructive testing and evaluation.

  11. Imaging the living retina at the cellular level with AO parallel spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Miller, Donald T.; Zhang, Yan; Rha, Jungtae; Jonnal, Ravi S.; Gao, Weihua

    2005-12-01

    We investigate a novel camera that incorporates adaptive optics (AO) and optical coherence tomography (OCT) to determine if it can achieve the necessary 3-D resolution, sensitivity, and speed for imaging individual cells in the living human retina. An AO spectral-domain OCT system was constructed that is based on a free-space Michelson interferometer design. The OCT sub-system consists of a broadband superluminescent diode whose beam passes through an astigmatic lens to form a line illumination pattern on the retina, which is then imaged onto the slit of an imaging spectrometer. The detector of the spectrometer is a scientific-grade areal CCD. Conventional flood illumination, also with AO, was integrated into the camera and provided confirmation of the focus position in the retina. Short bursts of narrow B-scans (100x560 microns) of the living retina were subsequently acquired at 500 Hz during dynamic compensation that corrected the most significant ocular aberrations across a dilated 6 mm pupil. Camera sensitivity (up to 94 dB) was sufficient for observing reflections from essentially all neural layers of the retina. The 3-D resolution of the B-scans (3.0x3.0x5.7 microns) is the highest reported to date in the living human eye. It was sufficient to observe the interface between the inner and outer segments of individual photoreceptor cells, resolved in both lateral and axial dimensions. The waveguiding nature of the photoreceptors is suggestive at multiple reflective sites. Micro-movements of the retina during short burst imaging allow averaging to reduce speckle contrast, but they appear insufficient for significant speckle reduction.

  12. A spectral analysis of the domain decomposed Monte Carlo method for linear systems

    SciTech Connect

    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.

  13. A spectral analysis of the domain decomposed Monte Carlo method for linear systems

    DOE PAGES

    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

  14. Spectral properties and chiral symmetry violations of (staggered) domain wall fermions in the Schwinger model

    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.

  15. 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.

  16. Horizontal structure and propagation characteristics of mesospheric gravity waves observed by Antarctic Gravity Wave Imaging/Instrument Network (ANGWIN), using a 3-D spectral analysis technique

    NASA Astrophysics Data System (ADS)

    Matsuda, Takashi S.; Nakamura, Takuji; Murphy, Damian; Tsutsumi, Masaki; Moffat-Griffin, Tracy; Zhao, Yucheng; Pautet, Pierre-Dominique; Ejiri, Mitsumu K.; Taylor, Michael

    2016-07-01

    ANGWIN (Antarctic Gravity Wave Imaging/Instrument Network) is an international airglow imager/instrument network in the Antarctic, which commenced observations in 2011. It seeks to reveal characteristics of mesospheric gravity waves, and to study sources, propagation, breaking of the gravity waves over the Antarctic and the effects on general circulation and upper atmosphere. In this study, we compared distributions of horizontal phase velocity of the gravity waves at around 90 km altitude observed in the mesospheric airglow imaging over different locations using our new statistical analysis method of 3-D Fourier transform, developed by Matsuda et al. (2014). Results from the airglow imagers at four stations at Syowa (69S, 40E), Halley (76S, 27W), Davis (69S, 78E) and McMurdo (78S, 156E) out of the ANGWIN imagers have been compared, for the observation period between April 6 and May 21 in 2013. In addition to the horizontal distribution of propagation and phase speed, gravity wave energies have been quantitatively compared, indicating a smaller GW activity in higher latitude stations. We further investigated frequency dependence of gravity wave propagation direction, as well as nightly variation of the gravity wave direction and correlation with the background wind variations. We found that variation of propagation direction is partly due to the effect of background wind in the middle atmosphere, but variation of wave sources could play important role as well. Secondary wave generation is also needed to explain the observed results.

  17. Use of the ARM Measurement of Spectral Zenith Radiance For Better Understanding Of 3D Cloud-Radiation Processes and Aerosol-Cloud Interaction

    SciTech Connect

    Chiu, Jui-Yuan

    2010-10-19

    Our proposal focuses on cloud-radiation processes in a general 3D cloud situation, with particular emphasis on cloud optical depth and effective particle size. We also focus on zenith radiance measurements, both active and passive. The proposal has three main parts. Part One exploits the "solar-background" mode of ARM lidars to allow them to retrieve cloud optical depth not just for thin clouds but for all clouds. This also enables the study of aerosol cloud interactions with a single instrument. Part Two exploits the large number of new wavelengths offered by ARM's zenith-pointing ShortWave Spectrometer (SWS), especially during CLASIC, to develop better retrievals not only of cloud optical depth but also of cloud particle size. We also propose to take advantage of the SWS's 1 Hz sampling to study the "twilight zone" around clouds where strong aerosol-cloud interactions are taking place. Part Three involves continuing our cloud optical depth and cloud fraction retrieval research with ARM's 2NFOV instrument by, first, analyzing its data from the AMF-COPS/CLOWD deployment, and second, making our algorithms part of ARM's operational data processing.

  18. Application of Spectral Filtering scheme for Spherical Limited-Area domain to Regional forecast model

    NASA Astrophysics Data System (ADS)

    Park, J.-R.; Cheong, H.-. B.; Kang, H.-. G.

    2012-04-01

    The spectral filter for spherical limited-area domain was applied to time integration procedure of regional model as a numerical scheme to remove small scale noises, which cannot be properly resolved in numerical models. This filter is designed to provide the sharp filter response, selective scale decomposition, and the isotropy on the limited-area domain by using the filter equation with high-order spherical Laplacian operator. The high-order filter equation is solved by low-order elliptic equations with the first or the second spherical Laplacian operator. It is controlled by the order of the spherical Laplacian operator and wave cutoff scale parameter. For the application to the regional weather forecast model, the filter is reconstructed into the regional map projection, e.g., Mercator map projection. The weather research and forecasting (WRF) model is used and the spectral filter works on the vertical velocity field in which the unresolved kinematic features appear prominently. The filter parameters are set to damp the amplitude of wave component with wavelength of two times the grid interval by half in every time step. The effect of the filter on the removal of small-scale waves was evaluated through the tropical cyclone (TC) track and intensity prediction. For the accurate prediction of typhoon, the TC initialization scheme, named the structure adjustable balanced vortex (SABV) scheme, is used for all test cases. In comparison with the simulated result using the diffusion scheme provided in the model for the same purpose, the model performance was improved, especially in track prediction. The 1-day accumulated precipitation of the test simulation using the spectral filter exhibits the most similar pattern to the observation. The spectra analysis of vertical velocity field showed that the spectral filtering scheme restrains the undesirable small upturned spectral energy usually produced in limited-area models.

  19. Test target for characterizing 3D resolution of optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Hu, Zhixiong; Hao, Bingtao; Liu, Wenli; Hong, Baoyu; Li, Jiao

    2014-12-01

    Optical coherence tomography (OCT) is a non-invasive 3D imaging technology which has been applied or investigated in many diagnostic fields including ophthalmology, dermatology, dentistry, cardiovasology, endoscopy, brain imaging and so on. Optical resolution is an important characteristic that can describe the quality and utility of an image acquiring system. We employ 3D printing technology to design and fabricate a test target for characterizing 3D resolution of optical coherence tomography. The test target which mimics USAF 1951 test chart was produced with photopolymer. By measuring the 3D test target, axial resolution as well as lateral resolution of a spectral domain OCT system was evaluated. For comparison, conventional microscope and surface profiler were employed to characterize the 3D test targets. The results demonstrate that the 3D resolution test targets have the potential of qualitatively and quantitatively validating the performance of OCT systems.

  20. Achromatic registration of quadrature components of the optical spectrum in spectral domain optical coherence tomography

    SciTech Connect

    Shilyagin, P A; Gelikonov, G V; Gelikonov, V M; Moiseev, A A; Terpelov, D A

    2014-07-31

    We have thoroughly investigated the method of simultaneous reception of spectral components with the achromatised quadrature phase shift between two portions of a reference wave, designed for the effective suppression of the 'mirror' artefact in the resulting image obtained by means of spectral domain optical coherence tomography (SD OCT). We have developed and experimentally tested a phase-shifting element consisting of a beam divider, which splits the reference optical beam into the two beams, and of delay lines being individual for each beam, which create a mutual phase difference of π/2 in the double pass of the reference beam. The phase shift achromatism over a wide spectral range is achieved by using in the delay lines the individual elements with different dispersion characteristics. The ranges of admissible adjustment parameters of the achromatised delay line are estimated for exact and inexact conformity of the geometric characteristics of its components to those calculated. A possibility of simultaneous recording of the close-to-quadrature spectral components with a single linear photodetector element is experimentally confirmed. The suppression of the artefact mirror peak in the OCT-signal by an additional 9 dB relative to the level of its suppression is experimentally achieved when the air delay line is used. Two-dimensional images of the surface positioned at an angle to the axis of the probe beam are obtained with the correction of the 'mirror' artefact while maintaining the dynamic range of the image. (laser biophotonics)

  1. Domain decomposition methods for systems of conservation laws: Spectral collocation approximations

    NASA Technical Reports Server (NTRS)

    Quarteroni, Alfio

    1989-01-01

    Hyperbolic systems of conversation laws are considered which are discretized in space by spectral collocation methods and advanced in time by finite difference schemes. At any time-level a domain deposition method based on an iteration by subdomain procedure was introduced yielding at each step a sequence of independent subproblems (one for each subdomain) that can be solved simultaneously. The method is set for a general nonlinear problem in several space variables. The convergence analysis, however, is carried out only for a linear one-dimensional system with continuous solutions. A precise form of the error reduction factor at each iteration is derived. Although the method is applied here to the case of spectral collocation approximation only, the idea is fairly general and can be used in a different context as well. For instance, its application to space discretization by finite differences is straight forward.

  2. Spectral domain optical coherence tomography imaging with an integrated optics spectrometer.

    PubMed

    Nguyen, V Duc; Akca, B Imran; Wörhoff, Kerstin; de Ridder, René M; Pollnau, Markus; van Leeuwen, Ton G; Kalkman, Jeroen

    2011-04-01

    We designed and fabricated an arrayed-waveguide grating (AWG) in silicon oxynitride as a spectrometer for spectral domain optical coherence tomography (SD-OCT). The AWG has a footprint of only 3.0 cm × 2.5 cm, operates at a center wavelength of 1300 nm, and has 78 nm free spectral range. OCT measurements are performed that demonstrate imaging up to a maximum depth of 1 mm with an axial resolution of 19 μm, both in agreement with the AWG design parameters. Using the AWG spectrometer combined with a fiber-based SD-OCT system, we demonstrate cross-sectional OCT imaging of a multilayered scattering phantom.

  3. Three-dimensional Segmentation of Retinal Cysts from Spectral-domain Optical Coherence Tomography Images by the Use of Three-dimensional Curvelet Based K-SVD.

    PubMed

    Esmaeili, Mahdad; Dehnavi, Alireza Mehri; Rabbani, Hossein; Hajizadeh, Fedra

    2016-01-01

    This paper presents a new three-dimensional curvelet transform based dictionary learning for automatic segmentation of intraretinal cysts, most relevant prognostic biomarker in neovascular age-related macular degeneration, from 3D spectral-domain optical coherence tomography (SD-OCT) images. In particular, we focus on the Spectralis SD-OCT (Heidelberg Engineering, Heidelberg, Germany) system, and show the applicability of our algorithm in the segmentation of these features. For this purpose, we use recursive Gaussian filter and approximate the corrupted pixels from its surrounding, then in order to enhance the cystoid dark space regions and future noise suppression we introduce a new scheme in dictionary learning and take curvelet transform of filtered image then denoise and modify each noisy coefficients matrix in each scale with predefined initial 3D sparse dictionary. Dark pixels between retinal pigment epithelium and nerve fiber layer that were extracted with graph theory are considered as cystoid spaces. The average dice coefficient for the segmentation of cystoid regions in whole 3D volume and with-in central 3 mm diameter on the MICCAI 2015 OPTIMA Cyst Segmentation Challenge dataset were found to be 0.65 and 0.77, respectively.

  4. Three-dimensional Segmentation of Retinal Cysts from Spectral-domain Optical Coherence Tomography Images by the Use of Three-dimensional Curvelet Based K-SVD

    PubMed Central

    Esmaeili, Mahdad; Dehnavi, Alireza Mehri; Rabbani, Hossein; Hajizadeh, Fedra

    2016-01-01

    This paper presents a new three-dimensional curvelet transform based dictionary learning for automatic segmentation of intraretinal cysts, most relevant prognostic biomarker in neovascular age-related macular degeneration, from 3D spectral-domain optical coherence tomography (SD-OCT) images. In particular, we focus on the Spectralis SD-OCT (Heidelberg Engineering, Heidelberg, Germany) system, and show the applicability of our algorithm in the segmentation of these features. For this purpose, we use recursive Gaussian filter and approximate the corrupted pixels from its surrounding, then in order to enhance the cystoid dark space regions and future noise suppression we introduce a new scheme in dictionary learning and take curvelet transform of filtered image then denoise and modify each noisy coefficients matrix in each scale with predefined initial 3D sparse dictionary. Dark pixels between retinal pigment epithelium and nerve fiber layer that were extracted with graph theory are considered as cystoid spaces. The average dice coefficient for the segmentation of cystoid regions in whole 3D volume and with-in central 3 mm diameter on the MICCAI 2015 OPTIMA Cyst Segmentation Challenge dataset were found to be 0.65 and 0.77, respectively. PMID:27563573

  5. Three-dimensional (3D) structure prediction and function analysis of the chitin-binding domain 3 protein HD73_3189 from Bacillus thuringiensis HD73.

    PubMed

    Zhan, Yiling; Guo, Shuyuan

    2015-01-01

    Bacillus thuringiensis (Bt) is capable of producing a chitin-binding protein believed to be functionally important to bacteria during the stationary phase of its growth cycle. In this paper, the chitin-binding domain 3 protein HD73_3189 from B. thuringiensis has been analyzed by computer technology. Primary and secondary structural analyses demonstrated that HD73_3189 is negatively charged and contains several α-helices, aperiodical coils and β-strands. Domain and motif analyses revealed that HD73_3189 contains a signal peptide, an N-terminal chitin binding 3 domains, two copies of a fibronectin-like domain 3 and a C-terminal carbohydrate binding domain classified as CBM_5_12. Moreover, analysis predicted the protein's associated localization site to be the cell wall. Ligand site prediction determined that amino acid residues GLU-312, TRP-334, ILE-341 and VAL-382 exposed on the surface of the target protein exhibit polar interactions with the substrate.

  6. 3d-3d correspondence revisited

    DOE PAGES

    Chung, Hee -Joong; Dimofte, Tudor; Gukov, Sergei; ...

    2016-04-21

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d N = 2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. As a result, we also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  7. Spectral-domain optical coherence tomography appearance of a retinal nematode.

    PubMed

    Masudi, Ali; Soheilian, Masoud; Nourinia, Ramin; Soheilian, Rasam; Peyman, Gholam A

    2013-11-25

    A 65-year-old man presented with decreased visual acuity in his left eye of 10 days' duration. Ocular examination revealed visual acuity of 20/200 in the left eye caused by a visible retinal nematode (roundworm) located close to the fovea. Spectral-domain optical coherence tomography imaging showed the nematode in the retinal nerve fiber layer. The patient was followed up without treatment, and the nematode disappeared spontaneously after 5 weeks. Visual acuity in the affected eye improved to 20/25.

  8. Multifunctional 1050 nm Spectral Domain OCT System at 147 kHz for Posterior Eye Imaging

    PubMed Central

    Zhang, Anqi; Zhang, Qinqin; Huang, Yanping; Zhong, Zhiwei; Wang, Ruikang K.

    2015-01-01

    We report a newly developed multifunctional 1050 nm spectral domain optical coherence tomography (SD-OCT) system working at 147 kHz A-scan rate for posterior eye imaging. It is demonstrated through in-vivo experiments that this system delivers not only superior performance of posterior eye structural imaging but also detailed visualization of microcirculation network in retina. The choroid of the eye with either myopic or normal conditions can clearly be visualized through the entire scanning volume. These results indicate great potential in applying this new system for clinical studies. PMID:26623142

  9. Error estimate of Taylor's frozen-in flow hypothesis in the spectral domain

    NASA Astrophysics Data System (ADS)

    Narita, Yasuhito

    2017-03-01

    The quality of Taylor's frozen-in flow hypothesis can be measured by estimating the amount of the fluctuation energy mapped from the streamwise wavenumbers onto the Doppler-shifted frequencies in the spectral domain. For a random sweeping case with a Gaussian variation of the large-scale flow, the mapping quality is expressed by the error function which depends on the mean flow speed, the sweeping velocity, the frequency bin, and the frequency of interest. Both hydrodynamic and magnetohydrodynamic treatments are presented on the error estimate of Taylor's hypothesis with examples from the solar wind measurements.

  10. Spectral-domain moment-method analysis of coplanar microstrip parasitic subarrays

    NASA Technical Reports Server (NTRS)

    Chen, Wei; Lee, Kai-Fong; Lee, R. Q.

    1993-01-01

    Basic characteristics of several configurations of coplanar microstrip parasitic subarrays consisting of one fed patch and two or more parasitic patches were investigated by means of a spectral-domain full-wave analysis and the moment method analysis. Results are presented for radiating- and nonradiating edge-coupled three-element linear subarrays and for a five-patch cross. A comparison of the theoretical input impedance results obtained by the analysis of a three-element linear array showed a reasonable agreement between computed and measured R and X values.

  11. Spectral-domain and swept-source OCT imaging of asteroid hyalosis: a case report.

    PubMed

    Alasil, Tarek; Adhi, Mehreen; Liu, Jonathan J; Fujimoto, James G; Duker, Jay S; Baumal, Caroline R

    2014-01-01

    A 72-year-old man with diabetes was referred to the retina clinic for diabetic retinopathy. Detailed funduscopic examination of the left eye was limited by prominent asteroid hyalosis. Spectral-domain (SD) and swept-source (SS) optical coherence tomography (OCT) were utilized to examine the vitreous, vitreoretinal interface, and the morphology of the retina. Asteroid hyalosis induced artifacts of the OCT images, which resolved when the appropriate imaging protocols were applied. SS-OCT may show superior diagnostic and preoperative capabilities when compared to SD-OCT in the settings of asteroid hyalosis-induced media opacity.

  12. Suppression of image autocorrelation artefacts in spectral domain optical coherence tomography and multiwave digital holography

    SciTech Connect

    Gelikonov, V M; Gelikonov, G V; Terpelov, D A; Shabanov, D V; Shilyagin, P A

    2012-05-31

    An improved method for suppressing image artefacts in spectral domain optical coherence tomography (SD OCT) and multiwave digital holography, caused by the influence of coherent noise in the course of successive registration of an autocorrelation component and informative signal is reported. The method allows complete suppression of all types of coherent noises, provided that the sample of values used to record the autocorrelation component satisfies the conditions of Kotelnikov's theorem: in SD OCT - for the transverse structure of the studied medium, in multiwave digital holography - for the envelop function of the radiation source frequency tuning spectrum.

  13. Extended depth of focus adaptive optics spectral domain optical coherence tomography

    PubMed Central

    Sasaki, Kazuhiro; Kurokawa, Kazuhiro; Makita, Shuichi; Yasuno, Yoshiaki

    2012-01-01

    We present an adaptive optics spectral domain optical coherence tomography (AO-SDOCT) with a long focal range by active phase modulation of the pupil. A long focal range is achieved by introducing AO-controlled third-order spherical aberration (SA). The property of SA and its effects on focal range are investigated in detail using the Huygens-Fresnel principle, beam profile measurement and OCT imaging of a phantom. The results indicate that the focal range is extended by applying SA, and the direction of extension can be controlled by the sign of applied SA. Finally, we demonstrated in vivo human retinal imaging by altering the applied SA. PMID:23082278

  14. Photothermal spectral-domain optical coherence reflectometry for direct measurement of hemoglobin concentration of erythrocytes.

    PubMed

    Yim, Jinyeong; Kim, Hun; Ryu, Suho; Song, Sungwook; Kim, Hyun Ok; Hyun, Kyung-A; Jung, Hyo-Il; Joo, Chulmin

    2014-07-15

    A novel optical detection method for hemoglobin concentration is described. The hemoglobin molecules consisting mainly of iron generate heat upon their absorption of light energy at 532 nm, which subsequently changes the refractive index of the blood. We exploit this photothermal effect to determine the hemoglobin concentration of erythrocytes without any preprocessing of blood. Highly sensitive measurement of refractive index alteration of blood samples is enabled by a spectral-domain low coherence reflectometric sensor with subnanometer-level optical path-length sensitivity. The performance and validity of the sensor are presented by comparing the measured results against the reference data acquired from an automatic hematology analyzer.

  15. Human ex-vivo oral tissue imaging using spectral domain polarization sensitive optical coherence tomography.

    PubMed

    Sharma, Priyanka; Verma, Yogesh; Sahu, Khageswar; Kumar, Sudhir; Varma, Amit V; Kumawat, Jyoti; Gupta, Pradeep Kumar

    2017-01-01

    We report the use of spectral domain polarization sensitive optical coherence tomography for ex-vivo imaging of human oral mandibular tissue samples. Our results show that compared to the changes observed in the epithelium thickness and the decay constant of A-scan intensity profile, a much larger degree of change was observed in the phase retardation for tissue sites progressing from normal to the malignant state. These results suggest that monitoring of tissue retardance can help in better differentiation of normal and cancerous oral tissue sites.

  16. Spectral-Domain Optical Coherence Tomography of Polypoidal Choroidal Vasculopathy Associated With Benign Choroidal Nevus.

    PubMed

    De Salvo, Gabriella; Vaz-Pereira, Sara; Sehmi, Kulwant S; Andrews, Richard M; Sagoo, Mandeep S

    2015-01-01

    Two cases of polypoidal choroidal vasculopathy (PCV) complicating benign choroidal nevus and their tomographic features at spectral-domain optical coherence tomography (SD-OCT) are reported. Two eyes with choroidal nevus and associated subretinal fluid underwent complete ophthalmological examination, SD-OCT, fundus fluorescein angiography, and indocyanine green angiography (ICGA). SD-OCT and ICGA confirmed the diagnosis of PCV in both cases. Ophthalmologists should be aware of this rare combination between choroidal nevus and PCV. If a choroidal nevus presents with subretinal fluid, this does not always herald malignant transformation, and PCV should be ruled out so that the correct treatment can be planned.

  17. Fast Domain Partitioning Method for dynamic boundary integral equations applicable to non-planar faults dipping in 3-D elastic half-space

    NASA Astrophysics Data System (ADS)

    Ando, Ryosuke

    2016-11-01

    The elastodynamic boundary integral equation method (BIEM) in real space and in the temporal domain is an accurate semi-analytical tool to investigate the earthquake rupture dynamics on non-planar faults. However, its heavy computational demand for a historic integral generally increases with a time complexity of O(MN3)for the number of time steps N and elements M due to volume integration in the causality cone. In this study, we introduce an efficient BIEM, termed the `Fast Domain Partitioning Method' (FDPM), which enables us to reduce the computation time to the order of the surface integral, O(MN2), without degrading the accuracy. The memory requirement is also reduced to O(M2) from O(M2N). FDPM uses the physical nature of Green's function for stress to partition the causality cone into the domains of the P and S wave fronts, the domain in-between the P and S wave fronts, and the domain of the static equilibrium, where the latter two domains exhibit simpler dependences on time and/or space. The scalability of this method is demonstrated on the large-scale parallel computing environments of distributed memory systems. It is also shown that FDPM enables an efficient use of memory storage, which makes it possible to reduce computation times to a previously unprecedented level. We thus present FDPM as a powerful tool to break through the current fundamental difficulties in running dynamic simulations of coseismic ruptures and earthquake cycles under realistic conditions of fault geometries.

  18. Extending the effective imaging depth in spectral domain optical coherence tomography by dual spatial frequency encoding

    NASA Astrophysics Data System (ADS)

    Wu, Tong; Wang, Qingqing; Liu, Youwen; Wang, Jiming

    2016-03-01

    We present a spatial frequency domain multiplexing method for extending the imaging depth range of a SDOCT system without any expensive device. This method uses two reference arms with different round-trip optical delay to probe different depth regions within the sample. Two galvo scanners with different pivot-offset distances in the reference arms are used for spatial frequency modulation and multiplexing. While simultaneously driving the galvo scanners in the reference arms and the sample arm, the spatial spectrum of the acquired two-dimensional OCT spectral interferogram corresponding to the shallow and deep depth of the sample will be shifted to the different frequency bands in the spatial frequency domain. After data filtering, image reconstruction and fusion the spatial frequency multiplexing SDOCT system can provide an approximately 1.9 fold increase in the effective ranging depth compared with that of a conventional single-reference-arm full-range SDOCT system.

  19. Spectral Domain OCT Documented Resolution of Pseudophakic Cystoid Macular Edema after Intravitreal Triamcinolone

    PubMed Central

    Murthy, Ravi K; Chalam, Kakarla V.

    2010-01-01

    Cystoid macular edema (CME) is an important cause of visual loss after cataract surgery. Treatment is usually with topical anti-inflammatory agents, with anti-vascular endothelial growth factor agents and steroids used intravitreally in resistant cases. Even though time-domain Stratus OCT can quantify the macular thickness, it cannot prognosticate visual outcomes due to the poor resolution of images, especially the outer segment-inner segment junction. Spectral-domain OCT (SD-OCT) by its ability to acquire large number of images in a short span of time provides high resolution cross-sectional images of the retina, which not only highlights the underlying pathological changes, but in addition can prognosticate visual recovery. We describe pre and post SD-OCT features of a case of refractory CME who was treated with intravitreal triamcinolone actetonide. PMID:23861610

  20. Polarization-sensitive spectral-domain optical coherence tomography using a single line scan camera

    NASA Astrophysics Data System (ADS)

    Cense, Barry; Mujat, Mircea; Chen, Teresa C.; Park, B. H.; de Boer, Johannes F.

    2007-03-01

    Polarization-sensitive optical coherence tomography can be used to measure the birefringence of biological tissue such as the human retina. Previous measurements with a time-domain polarization-sensitive optical coherence tomography system revealed that the birefringence of the human retinal nerve fiber layer is not constant, but varies as a function of location around the optic nerve head. Here we present a spectral-domain polarization-sensitive optical coherence tomography system that uses a spectrometer configuration with a single line scan camera and a Wollaston prism in the detection arm. Since only one camera has to be synchronized with other components in the system, the design is simplified considerably. This system is 60 times faster than a time-domain polarization-sensitive optical coherence tomography system. Data was acquired using concentric circular scans around the optic nerve head of a young healthy volunteer and the acquisition time for 12 circular scans was reduced from 72 s to 1.2 s. The acquired data sets demonstrate variations in retinal thickness and double pass phase retardation per unit depth that were similar to data from the same volunteer taken with a time-domain polarization-sensitive system. The double pass phase retardation per unit depth of the retinal nerve fiber layer varied between 0.18 and 0.40 degrees/μm, equivalent to a birefringence of 2.2 • 10-4 and 4.8 • 10-4 respectively, measured at 840 nm.

  1. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

    Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?

  2. Anterior segment spectral domain optical coherence tomography imaging of patients with anterior scleritis.

    PubMed

    Levison, Ashleigh L; Lowder, Careen Y; Baynes, Kimberly M; Kaiser, Peter K; Srivastava, Sunil K

    2016-08-01

    The purpose of the study was to describe the findings seen on anterior segment spectral domain optical coherence tomography (SD-OCT) in patients with anterior scleritis and determine the feasibility of using SD-OCT to image and grade the degree of scleral inflammation and monitor response to treatment. All patients underwent slit lamp examination by a uveitis specialist, and the degree of scleral inflammation was recorded. Spectral domain OCT imaging was then performed of the conjunctiva and scleral tissue using a standardized acquisition protocol. The scans were graded and compared to clinical findings. Twenty-eight patients with anterior scleritis and ten patients without ocular disease were included in the study. Seventeen of the scleritis patients were followed longitudinally. Common findings on SD-OCT in patients with active scleritis included changes in hyporeflectivity within the sclera, nodules, and visible vessels within the sclera. There was significant variation in findings on SD-OCT within each clinical grade of active scleritis. These changes on SD-OCT improved with treatment and clinical improvement. SD-OCT imaging provided various objective measures that could be used in the future to grade inflammatory activity in patients with anterior scleritis. Longitudinal imaging of patients with active scleritis demonstrated that SD-OCT may have great utility in monitoring response to treatment.

  3. Cutting Edge of Traumatic Maculopathy with Spectral-domain Optical Coherence Tomography – A Review

    PubMed Central

    Mendes, Sílvia; Campos, António; Campos, Joana; Neves, Arminda; Beselga, Diana; Fernandes, Cristina; Castro Sousa, João Paulo

    2015-01-01

    This article reviews clinically relevant data regarding traumatic maculopathy (TM), frequently observed in clinical practice, especially due to sport or traffic accident injuries. It is characterized by transient gray-whitish retinal coloration and reduction of visual acuity (VA) with closed, blunt object globe trauma of their prior. It may be limited to the posterior pole (Berlin’s edema), or peripheral areas of the retina. Spectral-domain optical coherence tomography (SD-OCT) provides detail insight using high resolution cross-sectional tomographs of the ocular tissue. It is a potent non-invasive tool for the clinician to follow-up. Clinicians are, thereby empowered with a tool that enables evaluation of the retinal status and allows for prediction of the prognosis. Spectral-domain optical coherence tomography supports the idea that the major site of injury is in the photoreceptor and layers of the retinal pigment epithelium (RPE). Depending on the severity of the trauma, SD-OCT may reveal differential optical densities of intraretinal spaces ranging from disappearance of the thin hyporeflective optical space in mild lesions, or areas of disruption of the inner segment/outer segment (IS/OS) junction and hyperreflectivity of the overlying retina, pigment disorders and retinal atrophy, in more severe cases. The prognosis for recovery of vision is generally good, and improvement occurs within 3-4 weeks. PMID:26060831

  4. Defining the spectral and amplitude domain of music---a window into audio

    NASA Astrophysics Data System (ADS)

    Nam, Myoung W.

    In terms of 'visualizing music', this thesis presents the first critical measurements for the selected musical instruments (piano, violin, cello, flute, piccolo, drums, double bass, electric bass, and electric guitar) seeking to describe their place in the spectral and amplitude domain. All data presented as a part of this research were measured with Z-weighting (un-weighted) from 12.5Hz to 20kHz along the frequency axis, in 1/3 octave bands, evaluated statistically and in equivalent sound level. Measuring musical performances can be a very subjective process. Therefore, this research proceeded under some strategically chosen conditions and limitations. The measurements were made with each musician playing at several different intensities of musical performance. Chosen musical genres were classical, pop and jazz for the selected musical instruments. To obtain data representative of real world conditions, musical instrument measurements were made mostly in professional recording studios by professional players. The results seek to define the spectral and amplitude domain occupied by these instruments when playing typical works.

  5. Imaging of the intact mouse cochlea by spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Gao, Simon S.; Yuan, Tao; Xia, Anping; Raphael, Patrick; Shelton, Ryan L.; Applegate, Brian E.; Oghalai, John S.

    2011-03-01

    Current medical imaging modalities, such as MRI and CT, do not provide high enough resolution to detect many changes within the cochlea that cause hearing loss. We sought to develop the technique of optical coherence tomography (OCT) to image the cochlea noninvasively and within its native environment. We used spectral domain OCT with 950 nm as the center wavelength and a bandwidth of ~100 nm to image freshly excised normal mouse cochlea at different developmental ages. The OCT system has an axial resolution of ~4 μm (in air) and a lateral resolution of ~10 μm. When we imaged normal adult mouse cochleae through the round window membrane, Reissner's membrane, the basilar membrane, the tectorial membrane, the spiral ligament, the spiral limbus, and the modiolus could be clearly identified. When we imaged intact adult cochleae, we were able to image through ~130 μm of bone and tissue to see up to a depth of ~600 μm, and all of the previously identified structures were still visible. Imaging of early postnatal mice during the timeline of cochlear development permitted visualization of the expected structural differences from adult cochleae. Therefore, we conclude that spectral domain OCT is an effective technique for noninvasive imaging of the murine cochlea.

  6. Terrain Dynamics Analysis Using Space-Time Domain Hypersurfaces and Gradient Trajectories Derived From Time Series of 3D Point Clouds

    DTIC Science & Technology

    2015-08-01

    CONTRACT NUMBER Form Approved OMB NO. 0704-0188 3. DATES COVERED (From - To) - UU UU UU UU 01-08-2015 1-Apr-2011 31- Mar -2014 Approved for Public Release...Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 landscape dynamics, lidar time series, space time cube, tangible interface...2701 Sullivan Drive Suite 240 Raleigh, NC 27695 -7514 31- Mar -2014 ABSTRACT Terrain Dynamics Analysis Using Space-Time Domain Hypersurfaces and

  7. Ultra-high resolution spectral domain optical coherence tomography using supercontinuum light source

    NASA Astrophysics Data System (ADS)

    Lim, Yiheng; Yatagai, Toyohiko; Otani, Yukitoshi

    2016-04-01

    An ultra-high resolution spectral domain optical coherence tomography (SD-OCT) was developed using a cost-effective supercontinuum laser. A spectral filter consists of a dispersive prism, a cylindrical lens and a right-angle prism was built to transmit the wavelengths in range 680-940 nm to the OCT system. The SD-OCT has achieved 1.9 μm axial resolution and the sensitivity was estimated to be 91.5 dB. A zero-crossing fringes matching method which maps the wavelengths to the pixel indices of the spectrometer was proposed for the OCT spectral calibration. A double sided foam tape as a static sample and the tip of a middle finger as a biological sample were measured by the OCT. The adhesive and the internal structure of the foam of the tape were successfully visualized in three dimensions. Sweat ducts was clearly observed in the OCT images at very high resolution. To the best of our knowledge, this is the first demonstration of ultra-high resolution visualization of sweat duct by OCT.

  8. Comparison of perceptual properties of auditory streaming between spectral and amplitude modulation domains.

    PubMed

    Yamagishi, Shimpei; Otsuka, Sho; Furukawa, Shigeto; Kashino, Makio

    2017-03-18

    The two-tone sequence (ABA_), which comprises two different sounds (A and B) and a silent gap, has been used to investigate how the auditory system organizes sequential sounds depending on various stimulus conditions or brain states. Auditory streaming can be evoked by differences not only in the tone frequency ("spectral cue": ΔFTONE, TONE condition) but also in the amplitude modulation rate ("AM cue": ΔFAM, AM condition). The aim of the present study was to explore the relationship between the perceptual properties of auditory streaming for the TONE and AM conditions. A sequence with a long duration (400 repetitions of ABA_) was used to examine the property of the bistability of streaming. The ratio of feature differences that evoked an equivalent probability of the segregated percept was close to the ratio of the Q-values of the auditory and modulation filters, consistent with a "channeling theory" of auditory streaming. On the other hand, for values of ΔFAM and ΔFTONE evoking equal probabilities of the segregated percept, the number of perceptual switches was larger for the TONE condition than for the AM condition, indicating that the mechanism(s) that determine the bistability of auditory streaming are different between or sensitive to the two domains. Nevertheless, the number of switches for individual listeners was positively correlated between the spectral and AM domains. The results suggest a possibility that the neural substrates for spectral and AM processes share a common switching mechanism but differ in location and/or in the properties of neural activity or the strength of internal noise at each level.

  9. Resolving spectral information from time domain induced polarization data through 2-D inversion

    NASA Astrophysics Data System (ADS)

    Fiandaca, Gianluca; Ramm, James; Binley, Andrew; Gazoty, Aurélie; Christiansen, Anders Vest; Auken, Esben

    2013-02-01

    Field-based time domain (TD) induced polarization (IP) surveys are usually modelled by taking into account only the integral chargeability, thus disregarding spectral content. Furthermore, the effect of the transmitted waveform is commonly neglected, biasing inversion results. Given these limitations of conventional approaches, a new 2-D inversion algorithm has been developed using the full voltage decay of the IP response, together with an accurate description of the transmitter waveform and receiver transfer function. This allows reconstruction of the spectral information contained in the TD decay series. The inversion algorithm is based around a 2-D complex conductivity kernel that is computed over a range of frequencies and converted to the TD through a fast Hankel transform. Two key points in the implementation ensure that computation times are minimized. First, the speed of the Jacobian computation, time transformed from frequency domain through the same transformation adopted for the forward response is optimized. Secondly, the reduction of the number of frequencies where the forward response and Jacobian are calculated: cubic splines are used to interpolate the responses to the frequency sampling necessary in the fast Hankel transform. These features, together with parallel computation, ensure inversion times comparable with those of direct current algorithms. The algorithm has been developed in a laterally constrained inversion scheme, and handles both smooth and layered inversions; the latter being helpful in sedimentary environments, where quasi-layered models often represent the actual geology more accurately than smooth minimum-structure models. In the layered inversion approach, a general method to derive the thickness derivative from the complex conductivity Jacobian is also proposed. One synthetic example of layered inversion and one field example of smooth inversion show the capability of the algorithm and illustrates a complete uncertainty

  10. 3D THz hyperspectrum applied in security check-in

    NASA Astrophysics Data System (ADS)

    Damian, V.; Logofǎtu, P. C.; Vasile, T.

    2016-12-01

    We developed a measuring technology using a TDS-THz system to construct hyperspectral images of some objects, including hazardous materials. "T-rays" (the THz spectral domain of the light) have a growing importance in security and imagistic domain. Due to their property of penetrating through dielectric objects, and using non-ionizing radiations, the THz systems have become a standard for "hot-places" (airports, train stations etc.). The hyperspectral images are 3D images having 2D spatial dimension and one spectral dimension. In this way, we obtain simultaneously information about the form of the object and its molecular composition. For discriminating between substances, we must first build a database of spectra for hazardous and dangerous substances. We experiment our system on some items (among them a firecracker, a cigarette and a metal collar) and we tried to discriminate between them using the database of spectra.

  11. Comparison of choroidal thickness measurements between spectral-domain OCT and swept-source OCT in normal and diseased eyes

    PubMed Central

    Zafar, Sidra; Siddiqui, MA Rehman; Shahzad, Rida

    2016-01-01

    Purpose Sub-foveal choroidal thickness (SFCT) is affected in many ocular diseases. The aim of this study was to compare SFCT measurements between Topcon 3D 2000 spectral-domain optical coherence tomography (SD-OCT) and Topcon swept-source OCT (SS-OCT), with different laser wavelengths, in normal and diseased populations. Materials and methods This was a prospective, cross-sectional, noninterventional study including 27 normal volunteers and 27 participants with retinal disease. OCT scans were performed sequentially and under standardized conditions using both SD-OCT and SS-OCT. The OCT scans were evaluated by two independent graders. Paired t-tests and intraclass correlation coefficients (ICCs) were used to assess the statistically significant difference between SFCT measurements as measured by the two devices. Results Mean SFCT measurements for all 54 participants were 264.9±103.1 μm using SD-OCT (range: 47–470 μm) and 278.5±110.5 μm using SS-OCT (range: 56–502 μm), with an inter-device ICC of 0.850. Greater variability was noted in the diseased eyes. Inter-device ICCs were 0.870 (95% CI; 0.760–0.924) and 0.840 (95% CI; 0.654–0.930) for normal and diseased eyes, respectively. However, the difference was not statistically significant (P=0.132). Conclusion Both machines reliably measure SFCT. Larger studies are needed to confirm these findings. PMID:27881909

  12. Large depth-high resolution full 3D imaging of the anterior segments of the eye using high speed optical frequency domain imaging

    NASA Astrophysics Data System (ADS)

    Kerbage, C.; Lim, H.; Sun, W.; Mujat, M.; de Boer, J. F.

    2007-06-01

    Three dimensional rapid large depth range imaging of the anterior segments of the human eye by an optical frequency domain imaging system is presented. The tunable source spans from 1217 to 1356 nm with an average output power of 60 mW providing a measured axial resolution of 10 μm in air based on the coherence envelope. The effective depth range is 4 mm, defined as the distance over which the sensitivity drops by 6 dB, achieved by frequency shifting the optical signal using acousto-optic modulators. The measured maximum sensitivity is 109 dB at a sample arm power of 14.7mW and A-lines rate of 43,900 per second. Images consisting of 512 depth profiles are acquired at an acquisition rate of 85 frames per second. We demonstrate an optical frequency domain imaging system capable of mapping in vivo the entire area of the human anterior segment (13.4 x 12 x 4.2 mm) in 1.4 seconds.

  13. Spectral-domain optical coherence tomography staging and autofluorescence imaging in achromatopsia.

    PubMed

    Greenberg, Jonathan P; Sherman, Jerome; Zweifel, Sandrine A; Chen, Royce W S; Duncker, Tobias; Kohl, Susanne; Baumann, Britta; Wissinger, Bernd; Yannuzzi, Lawrence A; Tsang, Stephen H

    2014-04-01

    IMPORTANCE Evidence is mounting that achromatopsia is a progressive retinal degeneration, and treatments for this condition are on the horizon. OBJECTIVES To categorize achromatopsia into clinically identifiable stages using spectral-domain optical coherence tomography and to describe fundus autofluorescence imaging in this condition. DESIGN, SETTING, AND PARTICIPANTS A prospective observational study was performed between 2010 and 2012 at the Edward S. Harkness Eye Institute, New York-Presbyterian Hospital. Participants included 17 patients (aged 10-62 years) with full-field electroretinography-confirmed achromatopsia. MAIN OUTCOMES AND MEASURES Spectral-domain optical coherence tomography features and staging system, fundus autofluorescence and near-infrared reflectance features and their correlation to optical coherence tomography, and genetic mutations served as the outcomes and measures. RESULTS Achromatopsia was categorized into 5 stages on spectral-domain optical coherence tomography: stage 1 (2 patients [12%]), intact outer retina; stage 2 (2 patients [12%]), inner segment ellipsoid line disruption; stage 3 (5 patients [29%]), presence of an optically empty space; stage 4 (5 patients [29%]), optically empty space with partial retinal pigment epithelium disruption; and stage 5 (3 patients [18%]), complete retinal pigment epithelium disruption and/or loss of the outer nuclear layer. Stage 1 patients showed isolated hyperreflectivity of the external limiting membrane in the fovea, and the external limiting membrane was hyperreflective above each optically empty space. On near infrared reflectance imaging, the fovea was normal, hyporeflective, or showed both hyporeflective and hyperreflective features. All patients demonstrated autofluorescence abnormalities in the fovea and/or parafovea: 9 participants (53%) had reduced or absent autofluorescence surrounded by increased autofluorescence, 4 individuals (24%) showed only reduced or absent autofluorescence, 3

  14. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

    Discusses 3 D imaging as it relates to digital representations in virtual library collections. Highlights include X-ray computed tomography (X-ray CT); the National Science Foundation (NSF) Digital Library Initiatives; output peripherals; image retrieval systems, including metadata; and applications of 3 D imaging for libraries and museums. (LRW)

  15. Identification of nucleolus-associated chromatin domains reveals the role of the nucleolus in the 3D organisation of the A. thaliana genome

    PubMed Central

    Pontvianne, Frédéric; Carpentier, Marie-Christine; Durut, Nathalie; Pavlištová, Veronika; Jaške, Karin; Schořová, Šárka; Parrinello, Hugues; Rohmer, Marine; Pikaard, Craig S; Fojtová, Miloslava; Fajkus, Jiří; Saez-Vasquez, Julio

    2017-01-01

    The nucleolus is the site of ribosomal RNA (rRNA) gene transcription, rRNA processing and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli by Fluorescence Activated Cell Sorting (FACS) and identified Nucleolus-Associated Chromatin Domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein, NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions and mostly inactive protein-coding genes. However, NADs also include active ribosomal RNA genes, and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance. PMID:27477271

  16. Spectral-domain optical coherence phase microscopy for label-free multiplexed protein microarray assay.

    PubMed

    Joo, Chulmin; Ozkumur, Emre; Unlü, M Selim; Boer, Johannes F de

    2009-10-15

    Quantitative measurement of affinities and kinetics of various biomolecular interactions such as protein-protein, protein-DNA and receptor-ligand is central to our understanding of basic molecular and cellular functions and is useful for therapeutic evaluation. Here, we describe a laser-scanning quantitative imaging method, referred to as spectral-domain optical coherence phase microscopy, as an optical platform for label-free detection of biomolecular interactions. The instrument is based on a confocal interferometric microscope that enables depth-resolved quantitative phase measurements on sensor surface with high spatial resolution and phase stability. We demonstrate picogram per square millimeter surface mass sensitivity, and show its sensing capability by presenting static and dynamic detection of multiplexed protein microarray as immobilized antigens capture their corresponding antibodies.

  17. Spectral-domain optical coherence tomography features of mild and severe acute solar retinopathy.

    PubMed

    Hossein, Mohammad; Jabbarpoor Bonyadi, Mohammad Hossein; Bonyadi, Jabbarpour; Soheilian, Rasam; Soheilian, Masoud; Peyman, Gholam A

    2011-09-08

    Photochemical/thermal retinal damage that results from unprotected solar eclipse viewing has vague presentations and sometimes misleading diagnosis, especially in cases with unclear history. Spectral-domain optical coherence tomography (SD-OCT) is a non-invasive imaging technique useful in differential diagnosis that can reveal characteristic foveal alterations in solar retinopathy to an unprecedented quasi histologic level. The authors present high-resolution SD-OCT findings correlated with clinical findings in three eyes of two cases with acute solar retinopathy. SD-OCT can precisely define the site and extent of damage in acute solar retinopathy. In mild forms, damage may be limited to the outer retina with inner segment/outer segment disruption. In severe forms, full thickness macular damage may be seen. Advances in retinal imaging have improved our ability to provide precise correlation with clinical presentation and prognosis.

  18. Achromatopsia: case presentation and literature review emphasising the value of spectral domain optical coherence tomography.

    PubMed

    Yu, Xiao Xi; Rego, Robert E; Shechtman, Diana

    2014-11-01

    A literature review and case presentation are used to discuss the diagnostic value of spectral domain optical coherence tomography (SD-OCT) in the assessment and management of congenital achromatopsia. A 24-year-old Hispanic man presented to the clinic with a longstanding history of decreased vision and associated possible recent progression. A comprehensive eye examination and a battery of tests including SD-OCT, fundus photography, electroretinogram (ERG) and Farnsworth D-15 were completed. SD-OCT and photopic ERG confirmed the clinical diagnosis of congenital achromatopsia. There was the classic subfoveal flattened hyporeflective 'punched out' zone, resulting from an absence of inner segment/outer segment junction. SD-OCT findings associated with congenital achromatopsia have been documented recently, helping in the diagnosis of the condition. The SD-OCT findings have further expanded our knowledge of congenital achromatopsia, while also aiding in the management of the disease.

  19. An FC-based spectral solver for elastodynamic problems in general three-dimensional domains

    NASA Astrophysics Data System (ADS)

    Amlani, Faisal; Bruno, Oscar P.

    2016-02-01

    This paper presents a spectral numerical algorithm for the solution of elastodynamics problems in general three-dimensional domains. Based on a recently introduced "Fourier continuation" (FC) methodology for accurate Fourier expansion of non-periodic functions, the proposed approach possesses a number of appealing properties: it yields results that are essentially free of dispersion errors, it entails mild CFL constraints, it runs at a cost that scales linearly with the discretization sizes, and it lends itself easily to efficient parallelization in distributed-memory computing clusters. The proposed algorithm is demonstrated in this paper by means of a number of applications to problems of isotropic elastodynamics that arise in the fields of materials science and seismology. These examples suggest that the new approach can yield solutions within a prescribed error tolerance by means of significantly smaller discretizations and shorter computing times than those required by other methods.

  20. Clinical Usefulness of Spectral-Domain Optical Coherence Tomography in Glaucoma and NAION

    PubMed Central

    Lee, Tae Hee; Heo, Hwan

    2016-01-01

    The development of optical coherence tomography (OCT) has changed the clinical management of ophthalmic diseases by furthering the understanding of pathogenesis, as well as improving the monitoring of their progression and assisting in quantifying the response to treatment modalities in ophthalmic diseases. Initially, the two-dimensional configuration of the optic nerve head (ONH) and the thickness of the retinal nerve fiber layer (RNFL) were the main OCT structural parameters used in clinical management of optic nerve diseases. Now, with higher resolution power and faster acquisition times, the details of ONH and the retina including the macular area can be measured using spectral domain OCT (SD-OCT) with high reproducibility and increased diagnostic ability. OCT can provide structural information to improve the understanding and management of optic nerve diseases. In this review, we will briefly summarize the clinical applications of SD-OCT in glaucoma and nonarteritic anterior ischemic optic neuropathy, which are two representative optic nerve diseases. PMID:27689029

  1. Precision of the IAS monitoring system based on the elapsed time method in the spectral domain

    NASA Astrophysics Data System (ADS)

    André, H.; Girardin, F.; Bourdon, A.; Antoni, J.; Rémond, D.

    2014-02-01

    Instantaneous Angular Speed (IAS) has recently appeared as an original and promising tool for monitoring mechanical parts of rotating machines. Mechanisms running under non-stationary conditions, such as wind turbine, are especially suited to this method since the issued signal is intrinsically sampled in the angular domain. Although processing tools are developed to enhance its use in the industry, this method is lacking a proper identification of its limitations and this paper aims at precisely understanding two of its main shortcomings: the aliasing and the quantization phenomena. After having presented the measurement method, both the aliasing and the quantization error are theoretically dissected. Formula is proposed to estimate their influence in the spectral observation of the IAS, and a good signal-to-noise ratio appraisal for this measurement technique is finally obtained. It can eventually be used as a first guide to conveniently design an IAS based control/monitoring system.

  2. Spectral analysis of GEOS-3 altimeter data and frequency domain collocation. [to estimate gravity anomalies

    NASA Technical Reports Server (NTRS)

    Eren, K.

    1980-01-01

    The mathematical background in spectral analysis as applied to geodetic applications is summarized. The resolution (cut-off frequency) of the GEOS 3 altimeter data is examined by determining the shortest wavelength (corresponding to the cut-off frequency) recoverable. The data from some 18 profiles are used. The total power (variance) in the sea surface topography with respect to the reference ellipsoid as well as with respect to the GEM-9 surface is computed. A fast inversion algorithm for matrices of simple and block Toeplitz matrices and its application to least squares collocation is explained. This algorithm yields a considerable gain in computer time and storage in comparison with conventional least squares collocation. Frequency domain least squares collocation techniques are also introduced and applied to estimating gravity anomalies from GEOS 3 altimeter data. These techniques substantially reduce the computer time and requirements in storage associated with the conventional least squares collocation. Numerical examples given demonstrate the efficiency and speed of these techniques.

  3. Polarization maintaining fiber based ultra-high resolution spectral domain polarization sensitive optical coherence tomography

    PubMed Central

    2010-01-01

    We present a new ultra high resolution spectral domain polarization sensitive optical coherence tomography (PS-OCT) system based on polarization maintaining (PM) fibers. The method transfers the principles of our previous bulk optic PS-OCT systems to a fiberized setup. The phase shift between the orthogonal polarization states travelling in the two orthogonal modes of the PM fiber is compensated by software in post processing. Thereby, the main advantage of our bulk optics setups, i.e. the use of only a single input polarization state to simultaneously acquire reflectivity, retardation, optic axis orientation, and Stokes vector, is maintained. The use of a broadband light source of 110 nm bandwidth provides improved depth resolution and smaller speckle size. The latter is important for improved resolution of depolarization imaging. We demonstrate our instrument for high-resolution PS-OCT imaging of the healthy human retina. PMID:20052196

  4. Speckle noise reduction in high speed polarization sensitive spectral domain optical coherence tomography

    PubMed Central

    Götzinger, Erich; Pircher, Michael; Baumann, Bernhard; Schmoll, Tilman; Sattmann, Harald; Leitgeb, Rainer A.; Hitzenberger, Christoph K.

    2015-01-01

    We present a high speed polarization sensitive spectral domain optical coherence tomography system based on polarization maintaining fibers and two high speed CMOS line scan cameras capable of retinal imaging with up to 128 k A-lines/s. This high imaging speed strongly reduces motion artifacts and therefore averaging of several B-scans is possible, which strongly reduces speckle noise and improves image quality. We present several methods for averaging retardation and optic axis orientation, the best one providing a 5 fold noise reduction. Furthermore, a novel scheme of calculating images of degree of polarization uniformity is presented. We quantitatively compare the noise reduction depending on the number of averaged frames and discuss the limits of frame numbers that can usefully be averaged. PMID:21934820

  5. Monitoring small changes in blood hematocrit using phase sensitive spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Manne, Venu G. R.; Manapuram, Ravi Kiran; Sudheendran, Narendran; Larin, Kirill V.

    2010-02-01

    A new method for monitoring ultra-small changes in blood hematocrit (~0.2%) based on measurement of refractive index changes in vitro using Phase Sensitive Spectral Domain Optical Coherence Tomography modality (PhS-SDOCT) is introduced. The developed system has an axial resolution of ~8 μm, phase sensitivity of +/-0.01 radians, imaging depth of 3.4 +/- 0.01 mm in air, and image acquisition speed of 29 kHz. The experimental accuracy for monitoring refractive index changes as a function of hematocrit level in blood is found to be +/-1.5x10-4 (+/-0.2%). Obtained results indicate that the PhS-SDOCT can be used to monitor ultra-small changes in the hematocrit and in vitro and, potentially, in tissue blood vessels in vivo.

  6. Spectral-domain phase microscopy with improved sensitivity using two-dimensional detector arrays

    SciTech Connect

    Singh, K.; Dion, C.; Ozaki, T.; Lesk, M. R.; Costantino, S.

    2011-02-15

    In this work we demonstrate the use of two-dimensional detectors to improve the signal-to-noise ratio (SNR) and sensitivity in spectral-domain phase microscopy for subnanometer accuracy measurements. We show that an increase in SNR can be obtained, from 82 dB to 105 dB, using 150 pixel lines of a low-cost CCD camera as compared to a single line, to compute an averaged axial scan. In optimal mechanical conditions, phase stability as small as 92 {mu}rad, corresponding to 6 pm displacement accuracy, could be obtained. We also experimentally demonstrate the benefit of spatial-averaging in terms of the reduction of signal fading due to an axially moving sample. The applications of the improved system are illustrated by imaging live cells in culture.

  7. Efficient evaluation of the inner products in the spectral domain analysis of microstrip discontinuities

    NASA Astrophysics Data System (ADS)

    McNay, Dan; Mittra, Raj

    1990-11-01

    The current trend in microwave and millimeter-wave integrated circuits (MICs) is toward higher operating frequencies, high packing densities, and more stringent performance requirements. As a result, earlier models based on approximate analysis techniques are becoming insufficiently accurate for use in computer-aided design (CAD) packages. In particular, simplifying assumptions, such as the quasi-static approximation and the magnetic wall approximation, are becoming inappropriate in the analysis of microstrip discontinuities such as bends, steps, and stubs. Instead, a rigorous full-wave analysis is needed to obtain a more accurate characterization of thes passive circuits. Such an analysis captures the increasingly significant effects of coupling, dispersion, and radiation. The objective of this study is to develop an asymptotic acceleration technique for the efficient evaluation of the integrals involved in the full-wave spectral domain method for analyzing microstrip discontinuity problems. (kr)

  8. Fast retinal layer segmentation of spectral domain optical coherence tomography images

    NASA Astrophysics Data System (ADS)

    Zhang, Tianqiao; Song, Zhangjun; Wang, Xiaogang; Zheng, Huimin; Jia, Fucang; Wu, Jianhuang; Li, Guanglin; Hu, Qingmao

    2015-09-01

    An approach to segment macular layer thicknesses from spectral domain optical coherence tomography has been proposed. The main contribution is to decrease computational costs while maintaining high accuracy via exploring Kalman filtering, customized active contour, and curve smoothing. Validation on 21 normal volumes shows that 8 layer boundaries could be segmented within 5.8 s with an average layer boundary error <2.35 μm. It has been compared with state-of-the-art methods for both normal and age-related macular degeneration cases to yield similar or significantly better accuracy and is 37 times faster. The proposed method could be a potential tool to clinically quantify the retinal layer boundaries.

  9. Polarization-based balanced detection for spectral-domain optical coherence tomography.

    PubMed

    Black, Adam J; Akkin, Taner

    2015-08-20

    We present a new design for spectral-domain optical coherence tomography that allows balanced detection using a single camera. The design uses polarization optics to encode the light in reference and sample arms. Two parallel and highly aligned spectra, which carry out-of-phase interference signals, in-phase common noise, and auto-interference terms, are focused on the camera, which performs the digital balanced detection for each wavelength. The optical system is characterized and tested for tissue imaging. Results demonstrate consistent signal gains in depth and suppression of DC and sample auto-interference. The design could be further amended for polarization-sensitive imaging and might demonstrate a market for manufacturing dual-line cameras with analog-balanced detection capability.

  10. Areas of activity in biofilms through the biospeckle and the spectral domain

    NASA Astrophysics Data System (ADS)

    Marques, J. K.; Braga, R. A.; Pereira, J.

    2010-09-01

    The dynamic laser speckle or biospeckle laser has been used to analyze the activity of biological and non-biological material by means of various statistical techniques and image processing. However, a challenge to adopt this technique is the ability to identify, in the same material, an area of low activity immersed in an environment of a higher activity. This work was carried out to evaluate the spectral approach associated to biospeckle laser technique as an alternative to identify distinct activities areas in the same material. Biofilm samples, which present well known protocols to be prepared, and a simpler structure than vegetal and animal tissues, were prepared with potato starch and corn starch with areas of different levels of moisture and were analyzed using the biospeckle laser associated with the wavelets transform in order to evaluate the data in the spectral domain. The effect of a black or white background below the samples was also tested. The image analysis was conducted using Generalized Difference and Fujii techniques before and after the implementation of the wavelets transform producing the filtration of the data. The results allowed the visualization of different activities areas in different frequency bands. The areas of activity were presented clearer than the traditional procedures without filtering. A new way to present the results of the biospeckle and the frequency domain information was proposed to enhance the visualization of a whole picture. It was also noted that the greatest contrast between areas of different activity were promoted by materials of different compositions. In some experimental configurations there were possible to tag the relationship between the frequency and depth of the active or inactive material. The influence of the color, black or white, of the background was also noticed in the results, but with white background better in some configurations and with the black better in others.

  11. A parallel domain decomposition-based implicit method for the Cahn-Hilliard-Cook phase-field equation in 3D

    NASA Astrophysics Data System (ADS)

    Zheng, Xiang; Yang, Chao; Cai, Xiao-Chuan; Keyes, David

    2015-03-01

    We present a numerical algorithm for simulating the spinodal decomposition described by the three dimensional Cahn-Hilliard-Cook (CHC) equation, which is a fourth-order stochastic partial differential equation with a noise term. The equation is discretized in space and time based on a fully implicit, cell-centered finite difference scheme, with an adaptive time-stepping strategy designed to accelerate the progress to equilibrium. At each time step, a parallel Newton-Krylov-Schwarz algorithm is used to solve the nonlinear system. We discuss various numerical and computational challenges associated with the method. The numerical scheme is validated by a comparison with an explicit scheme of high accuracy (and unreasonably high cost). We present steady state solutions of the CHC equation in two and three dimensions. The effect of the thermal fluctuation on the spinodal decomposition process is studied. We show that the existence of the thermal fluctuation accelerates the spinodal decomposition process and that the final steady morphology is sensitive to the stochastic noise. We also show the evolution of the energies and statistical moments. In terms of the parallel performance, it is found that the implicit domain decomposition approach scales well on supercomputers with a large number of processors.

  12. A parallel domain decomposition-based implicit method for the Cahn–Hilliard–Cook phase-field equation in 3D

    SciTech Connect

    Zheng, Xiang; Yang, Chao; Cai, Xiao-Chuan; Keyes, David

    2015-03-15

    We present a numerical algorithm for simulating the spinodal decomposition described by the three dimensional Cahn–Hilliard–Cook (CHC) equation, which is a fourth-order stochastic partial differential equation with a noise term. The equation is discretized in space and time based on a fully implicit, cell-centered finite difference scheme, with an adaptive time-stepping strategy designed to accelerate the progress to equilibrium. At each time step, a parallel Newton–Krylov–Schwarz algorithm is used to solve the nonlinear system. We discuss various numerical and computational challenges associated with the method. The numerical scheme is validated by a comparison with an explicit scheme of high accuracy (and unreasonably high cost). We present steady state solutions of the CHC equation in two and three dimensions. The effect of the thermal fluctuation on the spinodal decomposition process is studied. We show that the existence of the thermal fluctuation accelerates the spinodal decomposition process and that the final steady morphology is sensitive to the stochastic noise. We also show the evolution of the energies and statistical moments. In terms of the parallel performance, it is found that the implicit domain decomposition approach scales well on supercomputers with a large number of processors.

  13. 3D model for Cancerous Inhibitor of Protein Phosphatase 2A armadillo domain unveils highly conserved protein-protein interaction characteristics.

    PubMed

    Dahlström, Käthe M; Salminen, Tiina A

    2015-12-07

    Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A) is a human oncoprotein, which exerts its cancer-promoting function through interaction with other proteins, for example Protein Phosphatase 2A (PP2A) and MYC. The lack of structural information for CIP2A significantly prevents the design of anti-cancer therapeutics targeting this protein. In an attempt to counteract this fact, we modeled the three-dimensional structure of the N-terminal domain (CIP2A-ArmRP), analyzed key areas and amino acids, and coupled the results to the existing literature. The model reliably shows a stable armadillo repeat fold with a positively charged groove. The fact that this conserved groove highly likely binds peptides is corroborated by the presence of a conserved polar ladder, which is essential for the proper peptide-binding mode of armadillo repeat proteins and, according to our results, several known CIP2A interaction partners appropriately possess an ArmRP-binding consensus motif. Moreover, we show that Arg229Gln, which has been linked to the development of cancer, causes a significant change in charge and surface properties of CIP2A-ArmRP. In conclusion, our results reveal that CIP2A-ArmRP shares the typical fold, protein-protein interaction site and interaction patterns with other natural armadillo proteins and that, presumably, several interaction partners bind into the central groove of the modeled CIP2A-ArmRP. By providing essential structural characteristics of CIP2A, the present study significantly increases our knowledge on how CIP2A interacts with other proteins in cancer progression and how to develop new therapeutics targeting CIP2A.

  14. AE3D

    SciTech Connect

    Spong, Donald A

    2016-06-20

    AE3D solves for the shear Alfven eigenmodes and eigenfrequencies in a torodal magnetic fusion confinement device. The configuration can be either 2D (e.g. tokamak, reversed field pinch) or 3D (e.g. stellarator, helical reversed field pinch, tokamak with ripple). The equations solved are based on a reduced MHD model and sound wave coupling effects are not currently included.

  15. 3D change detection - Approaches and applications

    NASA Astrophysics Data System (ADS)

    Qin, Rongjun; Tian, Jiaojiao; Reinartz, Peter

    2016-12-01

    Due to the unprecedented technology development of sensors, platforms and algorithms for 3D data acquisition and generation, 3D spaceborne, airborne and close-range data, in the form of image based, Light Detection and Ranging (LiDAR) based point clouds, Digital Elevation Models (DEM) and 3D city models, become more accessible than ever before. Change detection (CD) or time-series data analysis in 3D has gained great attention due to its capability of providing volumetric dynamics to facilitate more applications and provide more accurate results. The state-of-the-art CD reviews aim to provide a comprehensive synthesis and to simplify the taxonomy of the traditional remote sensing CD techniques, which mainly sit within the boundary of 2D image/spectrum analysis, largely ignoring the particularities of 3D aspects of the data. The inclusion of 3D data for change detection (termed 3D CD), not only provides a source with different modality for analysis, but also transcends the border of traditional top-view 2D pixel/object-based analysis to highly detailed, oblique view or voxel-based geometric analysis. This paper reviews the recent developments and applications of 3D CD using remote sensing and close-range data, in support of both academia and industry researchers who seek for solutions in detecting and analyzing 3D dynamics of various objects of interest. We first describe the general considerations of 3D CD problems in different processing stages and identify CD types based on the information used, being the geometric comparison and geometric-spectral analysis. We then summarize relevant works and practices in urban, environment, ecology and civil applications, etc. Given the broad spectrum of applications and different types of 3D data, we discuss important issues in 3D CD methods. Finally, we present concluding remarks in algorithmic aspects of 3D CD.

  16. Phase sensitive spectral domain interferometry for label free biomolecular interaction analysis and biosensing applications

    NASA Astrophysics Data System (ADS)

    Chirvi, Sajal

    Biomolecular interaction analysis (BIA) plays vital role in wide variety of fields, which include biomedical research, pharmaceutical industry, medical diagnostics, and biotechnology industry. Study and quantification of interactions between natural biomolecules (proteins, enzymes, DNA) and artificially synthesized molecules (drugs) is routinely done using various labeled and label-free BIA techniques. Labeled BIA (Chemiluminescence, Fluorescence, Radioactive) techniques suffer from steric hindrance of labels on interaction site, difficulty of attaching labels to molecules, higher cost and time of assay development. Label free techniques with real time detection capabilities have demonstrated advantages over traditional labeled techniques. The gold standard for label free BIA is surface Plasmon resonance (SPR) that detects and quantifies the changes in refractive index of the ligand-analyte complex molecule with high sensitivity. Although SPR is a highly sensitive BIA technique, it requires custom-made sensor chips and is not well suited for highly multiplexed BIA required in high throughput applications. Moreover implementation of SPR on various biosensing platforms is limited. In this research work spectral domain phase sensitive interferometry (SD-PSI) has been developed for label-free BIA and biosensing applications to address limitations of SPR and other label free techniques. One distinct advantage of SD-PSI compared to other label-free techniques is that it does not require use of custom fabricated biosensor substrates. Laboratory grade, off-the-shelf glass or plastic substrates of suitable thickness with proper surface functionalization are used as biosensor chips. SD-PSI is tested on four separate BIA and biosensing platforms, which include multi-well plate, flow cell, fiber probe with integrated optics and fiber tip biosensor. Sensitivity of 33 ng/ml for anti-IgG is achieved using multi-well platform. Principle of coherence multiplexing for multi

  17. On the detection and monitoring of reduced water content in plants using spectral responses in the visible domain

    NASA Astrophysics Data System (ADS)

    Baranoski, Gladimir V. G.; Van Leeuwen, Spencer; Chen, Tenn F.

    2016-05-01

    The water status of cultivated plants can have a significant impact not only on food production, but also on the appropriate usage of increasingly scarce freshwater supplies. Accordingly, the cost-effective detection and monitoring of changes in their water content are longstanding remote sensing goals. Existing procedures employed to achieve these goals are largely based on the spectral responses of plant leaves in the infrared domain where the light absorption within the foliar tissues is dominated by water. Recently, it has been suggested that such procedures could be implemented using spectral responses, more specifically spectral subsurface reflectance to transmittance ratios, obtained in the visible domain. The basis for this proposition resides on the premise that a reduced water content (RWC) can result in histological changes whose effects on the foliar optical properties may not be limited to the infrared domain. However, the experiments leading to this proposition were performed on detached leaves, which were not influenced by the whole plant's adaptation mechanisms to water stress. In this work, we investigate whether the spectral responses of living plant leaves in the visible domain can lead to reliable RWC estimations. We employ measured biophysical data and predictive light transport simulations in order to extend qualitatively and quantitatively the scope of previous studies in this area. Our findings indicate that the living specimens' physiological responses to water stress should be taken into account in the design of new procedures for the cost-effective RWC estimation using visible subsurface reflectance to transmittance ratios.

  18. 3-D Seismic Interpretation

    NASA Astrophysics Data System (ADS)

    Moore, Gregory F.

    2009-05-01

    This volume is a brief introduction aimed at those who wish to gain a basic and relatively quick understanding of the interpretation of three-dimensional (3-D) seismic reflection data. The book is well written, clearly illustrated, and easy to follow. Enough elementary mathematics are presented for a basic understanding of seismic methods, but more complex mathematical derivations are avoided. References are listed for readers interested in more advanced explanations. After a brief introduction, the book logically begins with a succinct chapter on modern 3-D seismic data acquisition and processing. Standard 3-D acquisition methods are presented, and an appendix expands on more recent acquisition techniques, such as multiple-azimuth and wide-azimuth acquisition. Although this chapter covers the basics of standard time processing quite well, there is only a single sentence about prestack depth imaging, and anisotropic processing is not mentioned at all, even though both techniques are now becoming standard.

  19. Radiochromic 3D Detectors

    NASA Astrophysics Data System (ADS)

    Oldham, Mark

    2015-01-01

    Radiochromic materials exhibit a colour change when exposed to ionising radiation. Radiochromic film has been used for clinical dosimetry for many years and increasingly so recently, as films of higher sensitivities have become available. The two principle advantages of radiochromic dosimetry include greater tissue equivalence (radiologically) and the lack of requirement for development of the colour change. In a radiochromic material, the colour change arises direct from ionising interactions affecting dye molecules, without requiring any latent chemical, optical or thermal development, with important implications for increased accuracy and convenience. It is only relatively recently however, that 3D radiochromic dosimetry has become possible. In this article we review recent developments and the current state-of-the-art of 3D radiochromic dosimetry, and the potential for a more comprehensive solution for the verification of complex radiation therapy treatments, and 3D dose measurement in general.

  20. Frozen Gaussian approximation for 3-D seismic wave propagation

    NASA Astrophysics Data System (ADS)

    Chai, Lihui; Tong, Ping; Yang, Xu

    2017-01-01

    We present a systematic introduction on applying frozen Gaussian approximation (FGA) to compute synthetic seismograms in 3-D earth models. In this method, seismic wavefield is decomposed into frozen (fixed-width) Gaussian functions, which propagate along ray paths. Rather than the coherent state solution to the wave equation, this method is rigorously derived by asymptotic expansion on phase plane, with analysis of its accuracy determined by the ratio of short wavelength over large domain size. Similar to other ray-based beam methods (e.g. Gaussian beam methods), one can use relatively small number of Gaussians to get accurate approximations of high-frequency wavefield. The algorithm is embarrassingly parallel, which can drastically speed up the computation with a multicore-processor computer station. We illustrate the accuracy and efficiency of the method by comparing it to the spectral element method for a 3-D seismic wave propagation in homogeneous media, where one has the analytical solution as a benchmark. As another proof of methodology, simulations of high-frequency seismic wave propagation in heterogeneous media are performed for 3-D waveguide model and smoothed Marmousi model, respectively. The second contribution of this paper is that, we incorporate the Snell's law into the FGA formulation, and asymptotically derive reflection, transmission and free surface conditions for FGA to compute high-frequency seismic wave propagation in high contrast media. We numerically test these conditions by computing traveltime kernels of different phases in the 3-D crust-over-mantle model.

  1. Bootstrapping 3D fermions

    DOE PAGES

    Iliesiu, Luca; Kos, Filip; Poland, David; ...

    2016-03-17

    We study the conformal bootstrap for a 4-point function of fermions <ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge CT. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  2. Bootstrapping 3D fermions

    SciTech Connect

    Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran

    2016-03-17

    We study the conformal bootstrap for a 4-point function of fermions <ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge CT. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  3. Spectral-Domain Optical Coherence Tomography of Preclinical Chloroquine Maculopathy in Egyptian Rheumatoid Arthritis Patients

    PubMed Central

    Allam, Riham S. H. M.; Abd-Elmohsen, Mai N.; Khafagy, Mohamed M.; Raafat, Karim A.; Sheta, Sherif M.

    2015-01-01

    Purpose. To evaluate the role of spectral-domain optical coherence tomography (SD-OCT) in early detection of Chloroquine maculopathy in rheumatoid arthritis (RA) patients. Methods. 40 left eyes of 40 female rheumatoid arthritis patients who received treatment chloroquine for more than one year were recruited in the study. All patients had no symptoms or signs of Chloroquine retinopathy. They were evaluated using SD-OCT, where the Central Foveal Thickness (CFT), parafoveal thickness and perifoveal thickness, average Retinal Nerve Fiber Layer (RNFL) thickness, and Ganglion Cell Complex (GCC) measurements were measured and compared to 40 left eyes of 40 normal females. Results. The mean CFT was found to be thinner in the Chloroquine group (238.15 µm ± 22.49) than the normal controls (248.2 µm ± 19.04), which was statistically significant (p value = 0.034). The mean parafoveal thickness was lesser in the Chloroquine group than the control group in all quadrants (p value <0.05). The perifoveal thickness in both groups showed no statistically significant difference (p value >0.05) in all quadrants. No significant difference was detected between the two groups regarding RNFL, GCC, or IS/OS junction. Conclusions. Preclinical Chloroquine toxicity can lead to early thinning in the central fovea as well as the parafoveal regions that is detected by SD-OCT. PMID:26301102

  4. Accommodation-induced variations in retinal thickness measured by spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Fan, Shanhui; Sun, Yong; Dai, Cuixia; Zheng, Haihua; Ren, Qiushi; Jiao, Shuliang; Zhou, Chuanqing

    2014-09-01

    To research retinal stretching or distortion with accommodation, accommodation-induced changes in retinal thickness (RT) in the macular area were investigated in a population of young adults (n=23) by using a dual-channel spectral domain optical coherence tomography (SD-OCT) system manufactured in-house for this study. This dual-channel SD-OCT is capable of imaging the cornea and retina simultaneously with an imaging speed of 24 kHz A-line scan rate, which can provide the anatomical dimensions of the eye, including the RT and axial length. Thus, the modification of the RT with accommodation can be calculated. A significant decrease in the RT (13.50±1.25 μm) was observed during maximum accommodation. In the 4 mm×4 mm macular area centered at the fovea, we did not find a significant quadrant-dependent difference in retinal volume change, which indicates that neither retinal stretching nor distortion was quadrant-dependent during accommodation. We speculate that the changes in RT with maximum accommodation resulted from accommodation-induced ciliary muscle contractions.

  5. Myocardial imaging using ultrahigh-resolution spectral domain optical coherence tomography

    PubMed Central

    Yao, Xinwen; Gan, Yu; Marboe, Charles C.; Hendon, Christine P.

    2016-01-01

    Abstract. We present an ultrahigh-resolution spectral domain optical coherence tomography (OCT) system in 800 nm with a low-noise supercontinuum source (SC) optimized for myocardial imaging. The system was demonstrated to have an axial resolution of 2.72  μm with a large imaging depth of 1.78 mm and a 6-dB falloff range of 0.89 mm. The lateral resolution (5.52  μm) was compromised to enhance the image penetration required for myocardial imaging. The noise of the SC source was analyzed extensively and an imaging protocol was proposed for SC-based OCT imaging with appreciable contrast. Three-dimensional datasets were acquired ex vivo on the endocardium side of tissue specimens from different chambers of fresh human and swine hearts. With the increased resolution and contrast, features such as elastic fibers, Purkinje fibers, and collagen fiber bundles were observed. The correlation between the structural information revealed in the OCT images and tissue pathology was discussed as well. PMID:27001162

  6. Measurement of strain and strain rate in embryonic chick heart using spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Dou, Shidan; Suo, Yanyan; Liang, Chengbo; Wang, Yi; Zhao, Yuqian; Liu, Jian; Xu, Tao; Wang, Ruikang; Ma, Zhenhe

    2016-03-01

    It is important to measure embryonic heart myocardial wall strain and strain rate for understanding the mechanisms of embryonic heart development. Optical coherence tomography (OCT) can provide depth resolved images with high spatial and temporal resolution, which makes it have the potential to reveal the complex myocardial activity in the early stage embryonic heart. We develop a novel method to measure strain in embryonic chick heart based on spectral domain OCT images and subsequent image processing. We perform 4D(x,y,z,t) scanning on the outflow tract (OFT) of chick embryonic hearts in HH18 stage (~3 days of incubation). Only one image sequence acquired at the special position is selected based on the Doppler blood flow information where the probe beam penetrates through the OFT perpendicularly. For each image of the selected sequence, the cross-section of the myocardial wall can be approximated as an annulus. The OFT is segmented with a semi-automatic boundary detection algorithm, thus the area and mean circumference of the annular myocardial wall can be achieved. The myocardial wall thickness was calculated using the area divided by the mean circumference, and then the strain was obtained. The results demonstrate that OCT can be a useful tool to describe the biomechanical characteristics of the embryonic heart.

  7. Myocardial imaging using ultrahigh-resolution spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Yao, Xinwen; Gan, Yu; Marboe, Charles C.; Hendon, Christine P.

    2016-06-01

    We present an ultrahigh-resolution spectral domain optical coherence tomography (OCT) system in 800 nm with a low-noise supercontinuum source (SC) optimized for myocardial imaging. The system was demonstrated to have an axial resolution of 2.72 μm with a large imaging depth of 1.78 mm and a 6-dB falloff range of 0.89 mm. The lateral resolution (5.52 μm) was compromised to enhance the image penetration required for myocardial imaging. The noise of the SC source was analyzed extensively and an imaging protocol was proposed for SC-based OCT imaging with appreciable contrast. Three-dimensional datasets were acquired ex vivo on the endocardium side of tissue specimens from different chambers of fresh human and swine hearts. With the increased resolution and contrast, features such as elastic fibers, Purkinje fibers, and collagen fiber bundles were observed. The correlation between the structural information revealed in the OCT images and tissue pathology was discussed as well.

  8. Signal generation and mixing electronics for frequency-domain lifetime and spectral fluorometry

    NASA Technical Reports Server (NTRS)

    Cruce, Tommy Clay (Inventor); Hallidy, William H. (Inventor); Chin, Robert C. (Inventor)

    2007-01-01

    The present invention additionally comprises a method and apparatus for generating and mixing signals for frequency-domain lifetime and spectral fluorometry. The present invention comprises a plurality of signal generators that generate a plurality of signals where the signal generators modulate the amplitude and/or the frequency of the signals. The present invention uses one of these signals to drive an excitation signal that the present invention then directs and transmits at a target mixture, which absorbs the energy from the excitation signal. The property of fluorescence causes the target mixture to emit an emitted signal that the present invention detects with a signal detector. The present invention uses a plurality of mixers to produce a processor reference signal and a data signal. The present invention then uses a processor to compare the processor reference signal with the data signal by analyzing the differences in the phase and the differences in the amplitude between the two signals. The processor then extracts the fluorescence lifetime and fluorescence spectrum of the emitted signal from the phase and amplitude information using a chemometric analysis.

  9. Evaluation of the Lower Punctum Parameters and Morphology Using Spectral Domain Anterior Segment Optical Coherence Tomography.

    PubMed

    Allam, Riham S H M; Ahmed, Rania A

    2015-01-01

    Purpose. To study features of the lower punctum in normal subjects using spectral domain anterior segment optical coherence tomography (SD AS-OCT). Methods. Observational cross-sectional study that included 147 punctae (76 subjects). Punctae were evaluated clinically for appearance, position, and size. AS-OCT was used to evaluate the punctal shape, contents, and junction with the vertical canaliculus. Inner and outer diameters as well as depth were measured. Results. 24 males and 52 females (mean age 44 ± 14.35 y) were included. Lower punctum was perceived by OCT to be an area with an outer diameter (mean 412.16 ± 163 μm), inner diameter (mean 233.67 ± 138.73 μm), and depth (mean 251.7 ± 126.58 μm). The OCT measured outer punctum diameter was significantly less than that measured clinically (P: 0.000). Seven major shapes were identified. The junction with the vertical canaliculus was detectable in 44%. Fluid was detected in 34%, one of which had an air bubble; however, 63% of punctae showed no contents and 4% had debris. Conclusions. AS-OCT can be a useful tool in understanding the anatomy of the punctum and distal lacrimal system as well as tear drainage physiology. Measuring the punctum size may play a role in plugs fitting.

  10. Real-time Functional Analysis of Inertial Microfluidic Devices via Spectral Domain Optical Coherence Tomography

    PubMed Central

    Dong, Biqin; Chen, Siyu; Zhou, Fan; Chan, Christina H. Y.; Yi, Ji; Zhang, Hao F.; Sun, Cheng

    2016-01-01

    We report the application of spectral-domain optical coherence tomography (SD-OCT) technology that enables real-time functional analysis of sorting microparticles and cells in an inertial microfluidic device. We demonstrated high-speed, high-resolution acquisition of cross-sectional images at a frame rate of 350 Hz, with a lateral resolution of 3 μm and an axial resolution of 1 μm within the microfluidic channel filled with water. We analyzed the temporal sequence of cross-sectional SD-OCT images to determine the position and diameter of microspheres in a spiral microfluidic channel under various flow rates. We used microspheres with known diameters to validate the sub-micrometer precision of the particle size analysis based on a scattering model of spherical microparticles. An additional investigation of sorting live HT-29 cells in the spiral microfluidic channel indicated that the distribution of cells within in the microchannel has a close correspondence with the cells’ size distribution. The label-free real-time imaging and analysis of microscale particles in flow offers robustness for practical applications with live cells and allows us to better understand the mechanisms of particle separations in microfluidic sorting systems. PMID:27619202

  11. Macular Findings Obtained by Spectral Domain Optical Coherence Tomography in Retinopathy of Prematurity

    PubMed Central

    Erol, Muhammet Kazim; Ozdemir, Ozdemir; Turgut Coban, Deniz; Bilgin, Ahmet Burak; Dogan, Berna; Sogutlu Sari, Esin; Toslak, Devrim

    2014-01-01

    Purpose. To examine the macular findings obtained with spectral domain optical coherence tomography (SD OCT) in infants with retinopathy of prematurity (ROP). Materials and Methods. The macular SD OCT images of 190 premature infants were analyzed. Data regarding central foveal thickness (CFT), cystoid macular edema (CME), and cyst grading were compared. The relationships of CFT with gestational age and birth weight were investigated. Results. The results were obtained from 358 eyes of 179 infants (81 females and 98 males) of a mean gestational age of 30.9 ± 2.7 weeks and a mean birth weight of 1609 ± 477 g. ROP was diagnosed in 126 eyes and CME in 139 eyes. A significantly greater percentage of eyes with ROP were found to have CME (54%) compared to eyes without ROP (31%; P = 0.001). The incidence of CME was 46.3% for stage 1 ROP, 57.1% for stage 2, and 87.5% for stage 3. There was a weakly inverse correlation between CFT, gestational age, and birth weight (P = 0.025, r = −0.227; P = 0.002, r = −0.182, resp., Spearman correlation test). Conclusions. High-quality SD OCT images can be obtained from premature infants using the iVue system. Severity and frequency of CME in premature infants increase as stage of ROP increases. PMID:25544895

  12. Visualization of vitreoretinal surgical manipulations using intraoperative spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Tao, Yuankai K.; Ehlers, Justis P.; Toth, Cynthia A.; Izatt, Joseph A.

    2011-03-01

    Vitreoretinal surgical visualization by ophthalmic microscopy is limited in its ability to distinguish thin translucent tissues from other retinal substructures. Conventional methods for supplementing poor contrast, such as with increased illumination and application of exogenous contrast agents, have been limited by the risks of toxicity at the retina. Spectral domain optical coherence tomography (SDOCT) has demonstrated strong clinical success in retinal imaging, enabling high-resolution, motion-artifact-free cross-sectional imaging and rapid accumulation of volumetric macular datasets. Current generation SDOCT systems achieve <5 μm axial resolutions in tissue, and have been used to obtain high resolution datasets from patients with neovascular AMD, high risk drusen, and geographic atrophy. Recently, an intraoperative microscope-mounted OCT system (MMOCT) was presented as a method of augmenting a surgical microscope to concurrently acquire high-resolution, high-contrast SDOCT volumetric datasets. Here, we demonstrated the utility of intraoperative MMOCT for the visualization of vitreoretinal surgical procedures. Vitreoretinal surgery was simulated by performing procedures, through an ophthalmic surgical microscope, on cadaveric porcine eyes. The datasets acquired with the MMOCT show both instrument-tissue interaction as well as the ability of OCT to image certain surgical tools, which would directly translate to better surgical visualization and impact the treatment of ocular diseases.

  13. Spectral domain optical coherence tomography with extended depth-of-focus by aperture synthesis

    NASA Astrophysics Data System (ADS)

    Bo, En; Liu, Linbo

    2016-10-01

    We developed a spectral domain optical coherence tomography (SD-OCT) with an extended depth-of-focus (DOF) by synthetizing aperture. For a designated Gaussian-shape light source, the lateral resolution was determined by the numerical aperture (NA) of the objective lens and can be approximately maintained over the confocal parameter, which was defined as twice the Rayleigh range. However, the DOF was proportional to the square of the lateral resolution. Consequently, a trade-off existed between the DOF and lateral resolution, and researchers had to weigh and judge which was more important for their research reasonably. In this study, three distinct optical apertures were obtained by imbedding a circular phase spacer in the sample arm. Due to the optical path difference between three distinct apertures caused by the phase spacer, three images were aligned with equal spacing along z-axis vertically. By correcting the optical path difference (OPD) and defocus-induced wavefront curvature, three images with distinct depths were coherently summed together. This system digitally refocused the sample tissue and obtained a brand new image with higher lateral resolution over the confocal parameter when imaging the polystyrene calibration beads.

  14. Design and implementation of random noise radar with spectral-domain correlation for moving target detection

    NASA Astrophysics Data System (ADS)

    Kim, Jeong Phill; Jeong, Chi Hyun; Kim, Cheol Hoo

    2011-06-01

    A correlation processing algorithm in the spectral domain is proposed for detecting moving targets with random noise radar. AD converted reference and Rx signals are passed through FFT block, and they are multiplied after the reference signal is complex conjugated. Now inverse FFT yields the sub-correlation results, and range and velocity information can be accurately extracted by an additional FFT processing. In this design procedure, specific considerations have to be made for correlation length, averaging number, and number of sub-correlation data for Doppler processing. The proposed algorithm was verified by Simulink (Mathworks) simulation, and its logic was implemented with Xilinx FPGA device (Vertex5 series) by System Generator block sets (Xilinx) in the Simulink environment. A CW X-band random-FM noise radar prototype with an instantaneous bandwidth of 100 MHz was designed and implemented, and laboratory and field tests were conducted to detect moving targets, and the observed results showed the validity of the proposed algorithm and the operation of implemented FPGA logics.

  15. Identification of surface defects on glass by parallel spectral domain optical coherence tomography.

    PubMed

    Chen, Zhiyan; Shen, Yi; Bao, Wen; Li, Peng; Wang, Xiaoping; Ding, Zhihua

    2015-09-07

    Defects can dramatically degrade glass quality, and automatic inspection is a trend of quality control in modern industry. One challenge in inspection in an uncontrolled environment is the misjudgment of fake defects (such as dust particles) as surface defects. Fortunately, optical changes within the periphery of a surface defect are usually introduced while those of a fake defect are not. The existence of changes within the defect peripheries can be adopted as a criterion for defect identification. However, modifications within defect peripheries can be too small to be noticeable in intensity based optical image of the glass surface, and misjudgments of modifications may occur due to the incorrectness in defect demarcation. Thus, a sensitive and reliable method for surface defect identification is demanded. To this end, a nondestructive method based on optical coherence tomography (OCT) is proposed to precisely demarcate surface defects and sensitively measure surface deformations. Suspected surface defects are demarcated using the algorithm based on complex difference from expectation. Modifications within peripheries of suspected surface defects are mapped by phase information from complex interface signal. In this way, surface defects are discriminated from fake defects using a parallel spectral domain OCT (SD-OCT) system. Both simulations and experiments are conducted, and these preliminary results demonstrate the advantage of the proposed method to identify glass surface defects.

  16. Signal generation and mixing electronics for frequency-domain lifetime and spectral fluorometry

    NASA Technical Reports Server (NTRS)

    Cruce, Tommy C. (Inventor); Hallidy, William H. (Inventor); Chin, Robert C. (Inventor)

    1999-01-01

    The present invention additionally comprises a method and apparatus for generating and mixing signals for frequency-domain lifetime and spectral fluorometry. The present invention comprises a plurality of signal generators that generate a plurality of signals where the signal generators modulate the amplitude and/or the frequency of the signals. The present invention uses one of these signals to drive an excitation signal that the present invention then directs and transmits at a target mixture, which absorbs the energy from the excitation signal. The property of fluorescence causes the target mixture to emit an emitted signal that the present invention detects with a signal detector. The present invention uses a plurality of mixers to produce a processor reference signal and a data signal. The present invention then uses a processor to compare the processor reference signal with the data signal by analyzing the differences in the phase and the differences in the amplitude between the two signals. The processor then extracts the fluorescence lifetime and fluorescence spectrum of the emitted signal from the phase and amplitude information using a chemometric analysis.

  17. Quantitative Diagnosis of Colorectal Polyps by Spectral Domain Optical Coherence Tomography

    PubMed Central

    Wang, Chen; Zhang, Qinqin; Wu, Xiaojing; Tang, Tao; Liu, Hong; Zhu, S. W.; Gao, Bruce Z.; Yuan, X.-C.

    2014-01-01

    The principal aim of this study is to investigate the scattering coefficient of colorectal polyp tissues using an optical coherence tomography (OCT) technique. It combines the existing scattering coefficient model and spectral domain OCT to achieve method of early diagnosis of colorectal polyp in hospitals. Seventeen patients were studied, and a total of 1456 data points were extracted by curve-fitting the OCT signals into a confocal single-backscattering model. The results show that the mean scattering coefficient value for colorectal polyps is 1.91 mm−1 (std: ±0.54 mm−1), which is between the values for normal and malignant tissues. In addition, we studied the difference between adenomatous polyps (n = 15) and inflammatory polyps (n = 2) quantitatively and found that the adenomatous tissues had lower scattering coefficients than the inflammatory ones. The quantitative measurements confirmed that OCT can be used in primary diagnosis to compensate for the deficiencies in methods of pathological diagnosis, with a great potential for early diagnosis of tissues. PMID:24818145

  18. In-line quality control of moving objects by means of spectral-domain OCT

    NASA Astrophysics Data System (ADS)

    Markl, Daniel; Hannesschläger, Günther; Buchsbaum, Andreas; Sacher, Stephan; Khinast, Johannes G.; Leitner, Michael

    2014-08-01

    In-line quality control of intermediate and final products is essential in various industries. This may imply determining the thickness of a foil or evaluating the homogeneity of coating applied to a pharmaceutical tablet. Such a qualitative and quantitative monitoring in a depth-resolved manner can be accomplished using optical coherence tomography (OCT). In-line quality control based on OCT requires additional consideration of motion effects for the system design as well as for data interpretation. This study focuses on transverse motion effects that can arise in spectral-domain (SD-) OCT systems. The impact of a transverse movement is analyzed for a constant relative speed difference up to 0.7 m/s between sample and sensor head. In particular, transverse motion is affecting OCT system properties such as the beam displacement (distance between adjacent A-scans) and transverse resolution. These properties were evaluated theoretically and experimentally for OCT images of a resolution target and pharmaceutical film-coated tablets. Both theoretical and experimental analyses highlight the shift of the transverse resolution limiting factor from the optics to the beam displacement above a relative speed difference between sensor head and sample of 0.42 m/s (for the presented SD-OCT setup). Speeds above 0.4 m/s are often demanded when monitoring industrial processes, such as a coating process when producing film-coated tablets. This emphasizes the importance of a fast data acquisition when using OCT as in-line quality control tool.

  19. Parabolic BM-scan technique for full range Doppler spectral domain optical coherence tomography.

    PubMed

    Jaillon, Franck; Makita, Shuichi; Yabusaki, Masaki; Yasuno, Yoshiaki

    2010-01-18

    A full range spectral domain optical coherence tomography (SD-OCT) technique that relies on the linear phase modulation of one of the interferometer arms has been widely utilized. Although this method is useful, the mirror image elimination is not perfect for samples in which regions with high axial motion exist. In this paper, we introduce a new modulation pattern to overcome this mirror image elimination failure. This new modulation is a parabolic phase modulation in the transverse scanning direction, and is applied to the SD-OCT reference beam by an electro-optic modulator. Flow phantom and in vivo experiments demonstrate that for moving structures with large velocities, this parabolic phase modulation technique presents better mirror image elimination than a standard linear phase modulation method. A direct consequence of this enhanced mirror image removal is an improved velocity range obtained with phase-resolved Doppler imaging. Consequently, applying the proposed technique in retinal blood flow measurements may be useful for ophthalmologic diagnosis.

  20. Differentiating Mild Papilledema and Buried Optic Nerve Head Drusen Using Spectral Domain Optical Coherence Tomography

    PubMed Central

    Kulkarni, Kaushal M.; Pasol, Joshua; Rosa, Potyra R.; Lam, Byron L.

    2013-01-01

    Purpose To evaluate the clinical utility of spectral domain optical coherence tomography (SD-OCT) in differentiating mild papilledema from buried optic nerve head drusen (ONHD). Design Comparative case series. Participants 16 eyes of 9 patients with ultrasound-proven buried ONHD, 12 eyes of 6 patients with less than or equal to Frisén grade 2 papilledema due to idiopathic intracranial hypertension. 2 normal fellow eyes of patients with buried ONHD were included. Methods A raster scan on the optic nerve and retinal nerve fiber layer (RNFL) thickness analysis was performed on each eye using SD-OCT. Eight eyes underwent enhanced depth imaging SD-OCT. Images were assessed qualitatively and quantitatively to identify differentiating features between buried ONHD and papilledema. Five clinicians trained with a tutorial and masked to the underlying diagnosis reviewed the SD-OCT images of each eye independently to determine the diagnosis. Main outcome measures Differences in RNFL thickness in each quadrant between the two groups, and diagnostic accuracy of five independent clinicians based on the SD-OCT images alone. Results We found no statistically significant difference in RNFL thickness between buried ONHD and papilledema in any of the four quadrants. Diagnostic accuracy among the readers was low and ranged from 50–64%. The kappa coefficient of agreement among the readers was 0.35 (95% Confidence interval: 0.19, 0.54). Conclusions SD-OCT is not clinically reliable in differentiating buried ONHD and mild papilledema. PMID:24321144

  1. Combined spectrally encoded confocal microscopy and optical frequency domain imaging system

    NASA Astrophysics Data System (ADS)

    Kang, DongKyun; Suter, Melissa J.; Boudoux, Caroline; Yachimski, Patrick S.; Bouma, Brett E.; Nishioka, Norman S.; Tearney, Guillermo J.

    2009-02-01

    Spectrally encoded confocal microscopy (SECM) and optical frequency domain imaging (OFDI) are two reflectancebased imaging technologies that may be utilized for high-resolution microscopic screening of internal organs. SECM provides en face images of tissues with a high lateral resolution of 1-2 μm, and a penetration depth of up to 300 μm. OFDI generates cross-sectional images of tissue architecture with a resolution of 10-20 μm and a penetration depth of 1- 2 mm. Since the two technologies yield complementary microscopic information on two different size scales (SECM-cellular and OFDI-architectural) that are commonly used for histopathologic evaluation, their combination may allow for more accurate optical diagnosis. Here, we report the integration of these two imaging modalities in a single bench top system. SECM images of swine small intestine showed the presence of goblet cells, and OFDI images revealed the finger-shaped villous architecture. In clinical study of 9 gastroesophageal biopsies from 8 patients, a diverse set of architectural and cellular features was observed, including squamous mucosa with mild hyperplasia and gastric antral mucosa with gastric pits and crypts. The capability of this multimodality device to enable the visualization of microscopic features on these two size scales supports our hypothesis that improved diagnostic accuracy may be obtained by merging these two technologies into a single instrument.

  2. In vivo imaging of raptor retina with ultra high resolution spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Ruggeri, Marco; Major, James C., Jr.; McKeown, Craig; Wehbe, Hassan; Jiao, Shuliang; Puliafito, Carmen A.

    2008-02-01

    Among birds, raptors are well known for their exceptional eyesight, which is partly due to the unique structure of their retina. Because the raptor retina is the most advanced of any animal species, in vivo examination of its structure would be remarkable. Furthermore, a noticeable percentage of traumatic ocular injuries are identified in birds of prey presented to rehabilitation facilities. Injuries affecting the posterior segment have been considered as a major impact on raptor vision. Hence, in vivo examination of the structure of the posterior segment of the raptors would be helpful for the diagnosis of traumatized birds. 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 birds of prey, which to the best of our knowledge has never been attempted. For the first time we present high quality OCT images of the retina of two species of bird of prey, one diurnal hawk and one nocturnal owl.

  3. Methodology for assessment of structural vibrations by spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Gao, Simon S.; Raphael, Patrick; Xia, Anping; Park, Jesung; Carbajal, Esteban; Applegate, Brian E.; Oghalai, John S.

    2012-02-01

    Clinical diagnosis of cochlear dysfunction typically remains incomplete due to a lack of proper diagnostic methods. Medical imaging modalities can only detect gross changes in the cochlea, and non-invasive in vivo cochlear measurements are scarce. As a result, extensive efforts have been made to adapt optical coherence tomography (OCT) techniques to analyze and study the cochlea. Herein, we detail the methods for measuring vibration using OCT. We used spectral domain OCT with ~950 nm as the center wavelength and a bandwidth of ~80 nm. The custom spectrometer used was based on a high speed line scan camera which is capable of line rates up to 28 kHz. The signal-to- noise ratio of the system was ~90 dB. The data collection and processing software was written in LabVIEW and MATLAB. We tested whether streaming directly from the camera, writing the data to multiple hard drives in the RAID- 0 configuration, and processing using the GPU shortened experiment times. We then analyzed the A-line phase noise over several hundred milliseconds and growth curves from a piezoelectric element. We believe this is the first step towards a diagnostic device which generates vibration information of cochlear structures.

  4. In vivo assessment of wall strain in embryonic chick heart by spectral domain optical coherence tomography.

    PubMed

    Ma, Zhenhe; Dou, Shidan; Zhao, Yuqian; Guo, Ce; Liu, Jian; Wang, Qiaoyun; Xu, Tao; Wang, Ruikang K; Wang, Yi

    2015-11-01

    The ability to measure in vivo wall strain in embryonic hearts is important for fully understanding the mechanisms of cardiac development. Optical coherence tomography (OCT) is a powerful tool for the three-dimensional imaging of complex myocardial activities in early-stage embryonic hearts with high spatial and temporal resolutions. We describe a method to analyze periodic deformations of myocardial walls and evaluate in vivo myocardial wall strains with a high-speed spectral domain OCT system. We perform four-dimensional scanning on the outflow tract (OFT) of chick embryonic hearts and determine a special cross-section in which the OFT can be approximated as an annulus by analyzing Doppler blood-flow velocities. For each image acquired at the special cross-section, the annular myocardial wall is segmented with a semiautomatic boundary-detection algorithm, and the fluctuation myocardial wall thickness is calculated from the area and mean circumference of the myocardial wall. The experimental results shown with the embryonic chick hearts demonstrate that the proposed method is a useful tool for studying the biomechanical characteristics of embryonic hearts.

  5. High resolution retinal imaging with a compact adaptive optics spectral domain optical coherence tomography system

    NASA Astrophysics Data System (ADS)

    Hammer, Daniel X.; Iftimia, Nicusor V.; Bigelow, Chad E.; Ustun, Teoman E.; Bloom, Benjamin; Ferguson, R. Daniel; Burns, Stephen A.

    2007-02-01

    Adaptive optics (AO) is used to correct ocular aberrations primarily in the cornea, lens, and tear film of every eye. Among other applications, AO allows high lateral resolution images to be acquired with scanning laser ophthalmoscopy (SLO) and optical coherence tomography (OCT). Spectral domain optical coherence tomography (SDOCT) is a high-speed imaging technique that can acquire cross-sectional scans with micron-scale axial resolution at tens to hundreds of kHz line rates. We present a compact clinical AO-SDOCT system that achieves micron-scale axial and lateral resolution of retinal structures. The system includes a line scanning laser ophthalmscope (LSLO) for simultaneous wide-field retinal viewing and selection of regions-of-interest. OCT and LSLO imaging and AO correction performance are characterized. We present a case study of a single subject with hyper-reflective lesions associated with stable, resolved central serous retinopathy to compare and contrast AO as applied to scanning laser ophthalmoscopy and optical coherence tomography. The two imaging modes are found to be complementary in terms of information on structure morphology. Both provide additional information lacking in the other. This preliminary finding points to the power of combining SLO and SDOCT in a single research instrument for exploration of disease mechanisms, retinal cellular architecture, and visual psychophysics.

  6. Macular thickness and macular volume measurements using spectral domain optical coherence tomography in normal Nepalese eyes

    PubMed Central

    Pokharel, Amrit; Shrestha, Gauri Shankar; Shrestha, Jyoti Baba

    2016-01-01

    Purpose To record the normative values for macular thickness and macular volume in normal Nepalese eyes. Methods In all, 126 eyes of 63 emmetropic subjects (mean age: 21.17±6.76 years; range: 10–37 years) were assessed for macular thickness and macular volume, using spectral domain-optical coherence tomography over 6×6 mm2 in the posterior pole. A fast macular thickness protocol was employed. Statistics such as the mean, median, standard deviation, percentiles, and range were used, while a P-value was set at 0.05 to test significance. Results Average macular thickness and total macular volume were larger in males compared to females. With each year of increasing age, these variables decreased by 0.556 μm and 0.0156 mm3 for average macular thickness and total macular volume, respectively. The macular thickness was greatest in the inner superior section and lowest at the center of the fovea. The volume was greatest in the outer nasal section and thinnest in the fovea. The central subfield thickness (r=−0.243, P=0.055) and foveal volume (r=0.216, P=0.09) did not correlate with age. Conclusion Males and females differ significantly with regard to macular thickness and macular volume measurements. Reports by other studies that the increase in axial length reduced thickness and volume, were negated by this study which found a positive correlation among axial length, thickness, and volume. PMID:27041990

  7. Venus in 3D

    NASA Technical Reports Server (NTRS)

    Plaut, Jeffrey J.

    1993-01-01

    Stereographic images of the surface of Venus which enable geologists to reconstruct the details of the planet's evolution are discussed. The 120-meter resolution of these 3D images make it possible to construct digital topographic maps from which precise measurements can be made of the heights, depths, slopes, and volumes of geologic structures.

  8. 3D photoacoustic imaging

    NASA Astrophysics Data System (ADS)

    Carson, Jeffrey J. L.; Roumeliotis, Michael; Chaudhary, Govind; Stodilka, Robert Z.; Anastasio, Mark A.

    2010-06-01

    Our group has concentrated on development of a 3D photoacoustic imaging system for biomedical imaging research. The technology employs a sparse parallel detection scheme and specialized reconstruction software to obtain 3D optical images using a single laser pulse. With the technology we have been able to capture 3D movies of translating point targets and rotating line targets. The current limitation of our 3D photoacoustic imaging approach is its inability ability to reconstruct complex objects in the field of view. This is primarily due to the relatively small number of projections used to reconstruct objects. However, in many photoacoustic imaging situations, only a few objects may be present in the field of view and these objects may have very high contrast compared to background. That is, the objects have sparse properties. Therefore, our work had two objectives: (i) to utilize mathematical tools to evaluate 3D photoacoustic imaging performance, and (ii) to test image reconstruction algorithms that prefer sparseness in the reconstructed images. Our approach was to utilize singular value decomposition techniques to study the imaging operator of the system and evaluate the complexity of objects that could potentially be reconstructed. We also compared the performance of two image reconstruction algorithms (algebraic reconstruction and l1-norm techniques) at reconstructing objects of increasing sparseness. We observed that for a 15-element detection scheme, the number of measureable singular vectors representative of the imaging operator was consistent with the demonstrated ability to reconstruct point and line targets in the field of view. We also observed that the l1-norm reconstruction technique, which is known to prefer sparseness in reconstructed images, was superior to the algebraic reconstruction technique. Based on these findings, we concluded (i) that singular value decomposition of the imaging operator provides valuable insight into the capabilities of

  9. Electrostatic effects in the folding of the SH3 domain of the c-Src tyrosine kinase: pH-dependence in 3D-domain swapping and amyloid formation.

    PubMed

    Bacarizo, Julio; Martinez-Rodriguez, Sergio; Martin-Garcia, Jose Manuel; Andujar-Sanchez, Montserrat; Ortiz-Salmeron, Emilia; Neira, Jose Luis; Camara-Artigas, Ana

    2014-01-01

    The SH3 domain of the c-Src tyrosine kinase (c-Src-SH3) aggregates to form intertwined dimers and amyloid fibrils at mild acid pHs. In this work, we show that a single mutation of residue Gln128 of this SH3 domain has a significant effect on: (i) its thermal stability; and (ii) its propensity to form amyloid fibrils. The Gln128Glu mutant forms amyloid fibrils at neutral pH but not at mild acid pH, while Gln128Lys and Gln128Arg mutants do not form these aggregates under any of the conditions assayed. We have also solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6₅22 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P2₁2₁2₁, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. Analysis of these crystallographic structures shows that the residue at position 128 is connected to Glu106 at the diverging β-turn through a cluster of water molecules. Changes in this hydrogen-bond network lead to the displacement of the c-Src-SH3 distal loop, resulting also in conformational changes of Leu100 that might be related to the binding of proline rich motifs. Our findings show that electrostatic interactions and solvation of residues close to the folding nucleation site of the c-Src-SH3 domain might play an important role during the folding reaction and the amyloid fibril formation.

  10. Electrostatic Effects in the Folding of the SH3 Domain of the c-Src Tyrosine Kinase: pH-Dependence in 3D-Domain Swapping and Amyloid Formation

    PubMed Central

    Bacarizo, Julio; Martinez-Rodriguez, Sergio; Martin-Garcia, Jose Manuel; Andujar-Sanchez, Montserrat; Ortiz-Salmeron, Emilia; Neira, Jose Luis; Camara-Artigas, Ana

    2014-01-01

    The SH3 domain of the c-Src tyrosine kinase (c-Src-SH3) aggregates to form intertwined dimers and amyloid fibrils at mild acid pHs. In this work, we show that a single mutation of residue Gln128 of this SH3 domain has a significant effect on: (i) its thermal stability; and (ii) its propensity to form amyloid fibrils. The Gln128Glu mutant forms amyloid fibrils at neutral pH but not at mild acid pH, while Gln128Lys and Gln128Arg mutants do not form these aggregates under any of the conditions assayed. We have also solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6522 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P212121, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. Analysis of these crystallographic structures shows that the residue at position 128 is connected to Glu106 at the diverging β-turn through a cluster of water molecules. Changes in this hydrogen-bond network lead to the displacement of the c-Src-SH3 distal loop, resulting also in conformational changes of Leu100 that might be related to the binding of proline rich motifs. Our findings show that electrostatic interactions and solvation of residues close to the folding nucleation site of the c-Src-SH3 domain might play an important role during the folding reaction and the amyloid fibril formation. PMID:25490095

  11. Efficient 3-D frequency-domain mono-parameter full-waveform inversion of ocean-bottom cable data: application to Valhall in the visco-acoustic vertical transverse isotropic approximation

    NASA Astrophysics Data System (ADS)

    Operto, S.; Miniussi, A.; Brossier, R.; Combe, L.; Métivier, L.; Monteiller, V.; Ribodetti, A.; Virieux, J.

    2015-08-01

    Computationally efficient 3-D frequency-domain full waveform inversion (FWI) is applied to ocean-bottom cable data from the Valhall oil field in the visco-acoustic vertical transverse isotropic (VTI) approximation. Frequency-domain seismic modelling is performed with a parallel sparse direct solver on a limited number of computer nodes. A multiscale imaging is performed by successive inversions of single frequencies in the 3.5-10 Hz frequency band. The vertical wave speed is updated during FWI while density, quality factor QP and anisotropic Thomsen's parameters δ and ɛ are kept fixed to their initial values. The final FWI model shows the resolution improvement that was achieved compared to the initial model that was built by reflection traveltime tomography. This FWI model shows a glacial channel system at 175 m depth, the footprint of drifting icebergs on the palaeo-seafloor at 500 m depth, a detailed view of a gas cloud at 1 km depth and the base cretaceous reflector at 3.5 km depth. The relevance of the FWI model is assessed by frequency-domain and time-domain seismic modelling and source wavelet estimation. The agreement between the modelled and recorded data in the frequency domain is excellent up to 10 Hz although amplitudes of modelled wavefields propagating across the gas cloud are overestimated. This might highlight the footprint of attenuation, whose absorption effects are underestimated by the homogeneous background QP model (QP = 200). The match between recorded and modelled time-domain seismograms suggests that the inversion was not significantly hampered by cycle skipping. However, late arrivals in the synthetic seismograms, computed without attenuation and with a source wavelet estimated from short-offset early arrivals, arrive 40 ms earlier than the recorded seismograms. This might result from dispersion effects related to attenuation. The repeatability of the source wavelets inferred from data that are weighted by a linear gain with offset is

  12. Enhanced spectral domain optical coherence tomography for pathological and functional studies

    NASA Astrophysics Data System (ADS)

    Yuan, Zhijia

    Optical coherence tomography (OCT) is a novel technique that enables noninvasive or minimally invasive, cross-sectional imaging of biological tissue at sub-10mum spatial resolution and up to 2-3mm imaging depth. Numerous technological advances have emerged in recent years that have shown great potential to develop OCT into a powerful imaging and diagnostic tools. In particular, the implementation of Fourier-domain OCT (FDOCT) is a major step forward that leads to greatly improved imaging rate and image fidelity of OCT. This dissertation summarizes the work that focuses on enhancing the performances and functionalities of spectral radar based FDOCT (SDOCT) for pathological and functional applications. More specifically, chapters 1-4 emphasize on the development of SDOCT and its utility in pathological studies, including cancer diagnosis. The principle of SDOCT is first briefly outlined, followed by the design of our bench-top SDOCT systems with emphasis on spectral linear interpolation, calibration and system dispersion compensation. For ultrahigh-resolution SDOCT, time-lapse image registration and frame averaging is introduced to effectively reduce speckle noise and uncover subcellular details, showing great promise for enhancing the diagnosis of carcinoma in situ. To overcome the image depth limitation of OCT, a dual-modal imaging method combing SDOCT with high-frequency ultrasound is proposed and examined in animal cancer models to enhance the sensitivity and staging capabilities for bladder cancer diagnosis. Chapters 5-7 summarize the work on developing Doppler SDOCT for functional studies. Digital-frequency-ramping OCT (DFR-OCT) is developed in the study, which has demonstrated the ability to significantly improve the signal-to-noise ratio and thus sensitivity for retrieving subsurface blood flow imaging. New DFR algorithms and imaging processing methods are discussed to further enhance cortical CBF imaging. Applications of DFR-OCT for brain functional studies

  13. A spectral collocation time-domain solver for Maxwell's equations of electromagnetics with application to radar cross-section computation

    NASA Astrophysics Data System (ADS)

    Kabakian, Adour Vahe

    1998-12-01

    Most time-domain solvers of Maxwell's equations that are applied to electromagnetic wave scattering problems are based on second- or third-order finite-difference and finite-volume schemes. Since linear wave propagation phenomena tend to be very susceptible to numerical dissipation and dispersion errors, they place high accuracy demands on the numerical methods employed. Starting with the premise that the required accuracy can be achieved more efficiently with high-order methods, a new numerical scheme based on spectral collocation is developed for solving Maxwell's equations in the time domain. The three-dimensional method is formulated over generalized curvilinear coordinates. It employs Fourier and Chebyshev spectral collocation for the spatial derivatives, while time advancement is achieved by the explicit third-order Adams-Moulton-Bashforth scheme. A domain decomposition method supplementing the spectral solver is also developed, extending its range of applications to geometries more complex than those traditionally associated with spectral methods. Reflective and absorbing boundary conditions are developed specifically for the spectral scheme. Finally, a grid stretching function is incorporated into the solver, which can be used, when needed, to relieve the stability restriction associated with the Chebyshev spacing of the collocation points, at the expense of only moderate loss in accuracy. The numerical method is applied to solve electromagnetic wave scattering problems from perfectly conducting solid targets, using both single and multi-domain grids. The geometries considered are the circular cylinder, the square cylinder, and the sphere. Solutions are evaluated and validated by the accuracy of the radar cross-section and, in some instances, the surface currents. Compared to commonly used finite-difference and finite-volume solvers, the spectral scheme produces results that are one to two orders of magnitude more accurate, using grids that are an order of

  14. Spectral induced polarization of disseminated electronic conductors: laboratory data obtained through time domain measurements

    NASA Astrophysics Data System (ADS)

    Gurin, G.; Ilyin, Yu.; Tarasov, A.; Titov, K.

    2012-04-01

    With a time domain (TD) technique, we measured Spectral Induced Polarization responses of 19 models of ore. The models were mixtures of calibrated sand (0.2 - 0.3 mm) with calibrated electron-conductive grains (average radii: 0.045, 0.055, 0.13, 0.20, 0.38 and 0.50 mm). The grains represent a mixture of pyrrhotite (30 %), pyrite (30 %), magnetite (30 %) and chalcopyrite (10 %). In the models the grain concentration varied from 0.6 to 30 % by volume. We measured IP decay with a conventional TD measuring setup and a lab low-current transmitter in the time range from 0.3 ms to 64 s. The IP decays obtained with various current wavelength forms were inverted on the basis of the Debye decomposition, which allowed obtaining the relaxation time distribution. The following results were obtained: The total chargeability, m, was found to be independent of the grain size; it is related to the grain fraction, χ, according to the power law, m=6.28.10-2.χ0.78(m is dimensionless, and χ is in per cents; R2=0.98); The grain size, r, was found to be closely related to the mean IP relaxation time, τ, according to the square law, r2=10-5.τ (r is in meters, and τ is in seconds; R2=0.74); the square law corresponds to the diffusion kinetics, but contains the unrealistically large value of the diffusion coefficient; The maximum values of the relaxation time distributions, Zmax, was found to be closely related to the specific surface of the grains, Sv, according to the power law, Zmax=1.82 10-2 Sv0.65 (Zmax is dimensionless, and Sv is in cm-1; R2=0.94); The relaxation time distribution for disseminated ores can be safely recovered on the basis of TD measurements with relatively short pulse lengths (or using frequency domain measurements with relatively high frequency values).

  15. ShowMe3D

    SciTech Connect

    Sinclair, Michael B

    2012-01-05

    ShowMe3D is a data visualization graphical user interface specifically designed for use with hyperspectral image obtained from the Hyperspectral Confocal Microscope. The program allows the user to select and display any single image from a three dimensional hyperspectral image stack. By moving a slider control, the user can easily move between images of the stack. The user can zoom into any region of the image. The user can select any pixel or region from the displayed image and display the fluorescence spectrum associated with that pixel or region. The user can define up to 3 spectral filters to apply to the hyperspectral image and view the image as it would appear from a filter-based confocal microscope. The user can also obtain statistics such as intensity average and variance from selected regions.

  16. Macular changes of neuromyelitis optica through spectral-domain optical coherence tomography

    PubMed Central

    Cheng, Lu; Wang, Jing; He, Xu; Xu, Xun; Ling, Zhen-Fen

    2016-01-01

    AIM To evaluate the thickness of the retinal layers in the macula using spectral-domain optical coherence tomography (SD-OCT) in patients with neuromyelitis optica (NMO). METHODS Spectralis SD-OCT, utilizing automated macular layer segmentation, was performed in 26 NMO patients and 26 healthy controls. Visual function including visual field tests and pattern visual evoked potential were recorded in study subjects. RESULTS Forty-one eyes from 26 NMO patients and 52 eyes from 26 age- and sex-matched healthy controls were included. Besides total macular volume, peri-paipillary retinal nerve fiber layer (RNFL) thickness, the thickness of macular RNFL, ganglion cell layer (GCL) and inner plexiform layer (IPL) were also significantly reduced in NMO patients compared to those inhealthy controls (P<0.000). No differences were found in the thickness of macular inner nuclear layer (INL), outer plexiform layer (OPL), and outer nuclear layer (ONL) between the two groups. Reversely, the outer retinal layer (ORL) was shown to be thicker in NMO than controls (P<0.05). Compared with the peri-papillary RNFL thickness, the GCL thickness was demonstrated to correlate with visual function better. CONCLUSION The study provides in vivo evidence of retinal neural loss in NMO patients and demonstrates a better structure-function correlation between retinal ganglion cell and visual function than peri-papillary RNFL does. In addition, no evidence of primary neural damage is found. Besides, the photoreceptor cells and retinal pigments epithelial (RPE) cells presumably proliferated in compensation in NMO after retinal neural loss. PMID:27990369

  17. Keraring Intrastromal Segment Depth Measured by Spectral-Domain Optical Coherence Tomography in Eyes with Keratoconus

    PubMed Central

    Lavia, Carlo; D'Amelio, Savino

    2017-01-01

    Purpose. To evaluate agreement between measured and intended distance of Keraring (Mediphacos, Belo Horizonte, Brazil) intracorneal ring segments from the anterior and posterior corneal surfaces. Methods. Twenty-six Keraring ICRS implanted in 24 keratoconic eyes were examined. The distance from the Keraring apex to the anterior corneal surface and the distance from the inner and the outer corners to the posterior corneal surface were measured 3 months postoperatively using spectral-domain optical coherence tomography. Agreement between measured distance and intended distance was assessed by calculating the absolute differences and 95% limits of agreement (95% LoA). Results. The mean absolute difference was significantly lower (p < 0.001) for the measurements taken at the inner corner (23.54 ± 15.90 μm) than that for those taken at the apex (108.92 ± 62.72 μm) and the outer corner (108.35 ± 56.99 μm). The measurements taken at the inner corner were within ±25 and ±50 μm of the intended distance in 15/26 (57.7%) and 24/26 (92.3%) cases, respectively, and showed the narrowest 95% LoA with the intended distance (−57.61 to 55.15 μm). Conclusions. The distance of the inner corner from the posterior corneal surface showed the best agreement with the intended distance. This measurement is suitable for determining whether the actual Keraring depth matches the intended depth. PMID:28261495

  18. Retinal ganglion cell complex changes using spectral domain optical coherence tomography in diabetic patients without retinopathy

    PubMed Central

    Hegazy, Ahmed I.; Zedan, Rasha H.; Macky, Tamer A.; Esmat, Soheir M.

    2017-01-01

    AIM To assess the ganglion cell complex (GCC) thickness in diabetic eyes without retinopathy. METHODS Two groups included 45 diabetic eyes without retinopathy and 21 non diabetic eyes. All subjects underwent full medical and ophthalmological history, full ophthalmological examination, measuring GCC thickness and central foveal thickness (CFT) using the RTVue® spectral domain-optical coherence tomography (SD-OCT), and HbA1C level. RESULTS GCC focal loss volume (FLV%) was significantly more in diabetic eyes (22.2% below normal) than normal eyes (P=0.024). No statistically significant difference was found between the diabetic group and the control group regarding GCC global loss volume (GLV%) (P=0.160). CFT was positively correlated to the average, superior and inferior GCC (P=0.001, 0.000 and 0.001 respectively) and negatively correlated to GLV% and FLV% (P=0.002 and 0.031 respectively) in diabetic eyes. C/D ratio in diabetic eyes was negatively correlated to average, superior and inferior GCC (P=0.015, 0.007 and 0.017 respectively). The FLV% was negatively correlated to the refraction and level of HbA1c (P=0.019 and 0.013 respectively) and positively correlated to the best corrected visual acuity (BCVA) in logMAR in diabetic group (P=0.004). CONCLUSION Significant GCC thinning in diabetes predates retinal vasculopathy, which is mainly focal rather than diffuse. It has no preference to either the superior or inferior halves of the macula. Increase of myopic error is significantly accompanied with increased focal GCC loss. GCC loss is accompanied with increased C/D ratio in diabetic eyes. PMID:28393035

  19. Multimodal retinal vessel segmentation from spectral-domain optical coherence tomography and fundus photography.

    PubMed

    Hu, Zhihong; Niemeijer, Meindert; Abràmoff, Michael D; Garvin, Mona K

    2012-10-01

    Segmenting retinal vessels in optic nerve head (ONH) centered spectral-domain optical coherence tomography (SD-OCT) volumes is particularly challenging due to the projected neural canal opening (NCO) and relatively low visibility in the ONH center. Color fundus photographs provide a relatively high vessel contrast in the region inside the NCO, but have not been previously used to aid the SD-OCT vessel segmentation process. Thus, in this paper, we present two approaches for the segmentation of retinal vessels in SD-OCT volumes that each take advantage of complimentary information from fundus photographs. In the first approach (referred to as the registered-fundus vessel segmentation approach), vessels are first segmented on the fundus photograph directly (using a k-NN pixel classifier) and this vessel segmentation result is mapped to the SD-OCT volume through the registration of the fundus photograph to the SD-OCT volume. In the second approach (referred to as the multimodal vessel segmentation approach), after fundus-to-SD-OCT registration, vessels are simultaneously segmented with a k -NN classifier using features from both modalities. Three-dimensional structural information from the intraretinal layers and neural canal opening obtained through graph-theoretic segmentation approaches of the SD-OCT volume are used in combination with Gaussian filter banks and Gabor wavelets to generate the features. The approach is trained on 15 and tested on 19 randomly chosen independent image pairs of SD-OCT volumes and fundus images from 34 subjects with glaucoma. Based on a receiver operating characteristic (ROC) curve analysis, the present registered-fundus and multimodal vessel segmentation approaches [area under the curve (AUC) of 0.85 and 0.89, respectively] both perform significantly better than the two previous OCT-based approaches (AUC of 0.78 and 0.83, p < 0.05). The multimodal approach overall performs significantly better than the other three approaches (p < 0.05).

  20. Repeated, noninvasive, high resolution spectral domain optical coherence tomography imaging of zebrafish embryos

    PubMed Central

    Kagemann, Larry; Ishikawa, Hiroshi; Zou, Jian; Charukamnoetkanok, Puwat; Wollstein, Gadi; Townsend, Kelly A.; Gabriele, Michelle L.; Bahary, Nathan; Wei, Xiangyun; Fujimoto, James G.

    2008-01-01

    Purpose To demonstrate a new imaging method for high resolution spectral domain optical coherence tomography (SD-OCT) for small animal developmental imaging. Methods Wildtype zebrafish that were 24, 48, 72, and 120 h post fertilization (hpf) and nok gene mutant (48 hpf) embryos were imaged in vivo. Three additional embryos were imaged twice, once at 72 hpf and again at 120 hpf. Images of the developing eye, brain, heart, whole body, proximal yolk sac, distal yolk sac, and tail were acquired. Three-dimensional OCT data sets (501×180 axial scans) were obtained as well as oversampled frames (8,100 axial scans) and repeated line scans (180 repeated frames). Scan volumes ranged from 750×750 µm to 3×3 mm, each 1.8 mm thick. Three-dimenstional data sets allowed construction of C-mode slabs of the embryo. Results SD-OCT provided ultra-high resolution visualization of the eye, brain, heart, ear, and spine of the developing embryo as early as 24 hpf, and allowed development to be documented in each of these organ systems in consecutive sessions. Repeated line scanning with averaging optimized the visualization of static and dynamic structures contained in SD-OCT images. Structural defects caused by a mutation in the nok gene were readily observed as impeded ocular development, and enlarged pericardial cavities. Conclusions SD-OCT allowed noninvasive, in vivo, ultra-high resolution, high-speed imaging of zebrafish embryos in their native state. The ability to measure structural and functional features repeatedly on the same specimen, without the need to sacrifice, promises to be a powerful tool in small animal developmental imaging. PMID:19052656

  1. The comparison of manual vs automated disc margin delineation using spectral-domain optical coherence tomography

    PubMed Central

    Iverson, S M; Sehi, M

    2013-01-01

    Aims To examine the impact of manual vs automated disc margin delineation on optic nerve head (ONH) and retinal nerve fiber layer (RNFL) parameters using spectral-domain optical coherence tomography (SDOCT). Methods A prospective cohort study consisting of normal, glaucoma suspect (GS) and glaucoma patients who underwent ONH and RNFL measurements using SDOCT technology (RTVue; Optovue Inc.). The retinal pigment epithelium/Bruch's membrane (RPE/BM) complex end points were automatically determined first, and were manually redefined subsequently. Analysis of variance, coefficient of variation (COV), concordance correlation coefficient (CCC), and Bland–Altman plots were used for the analyses. Results Ninety-nine eyes of 50 subjects (age 68±10 years) consisting of 36 glaucoma, 56 GS, and 7 normal eyes were included. The RNFL thickness measurements were similar (P>0.05) between the two methods of demarcation, except for the inferior-nasal sector (P=0.04). For the ONH measurements, the cup-to-disc (C/D) ratio and rim area showed significant differences between the two methods (P<0.001). COV/CCC values for the ONH parameters were as follows: cup area 17.6%/0.88; cup volume 7.4%/0.91; average C/D ratio 18.1%/0.78; rim area 25.3%/0.69; and rim volume 42.6%/0.71, respectively. CCC/COV values for the RNFL parameters were as follows: average 2.1%/0.98; inferior-temporal quadrant 8.1%/0.79; inferior-nasal quadrant INQ quadrant 12.6%/0.67; SNQ quadrant 7.8%/0.83; and STQ quadrant 7.8%/0.88, respectively. Conclusion An overall high agreement and moderate–substantial concordance was observed between the demarcation methods. Automated disc margin delineation of SDOCT can be used reliably in clinical practice. PMID:23907624

  2. Entire contact lens imaged in vivo and in vitro with spectral domain optical coherence tomography

    PubMed Central

    Shen, Meixiao; Wang, Michael R.; Wang, Jianhua; Yuan, Yimin; Chen, Feng

    2010-01-01

    Objective To demonstrate the capability of directly visualizing the entire ocular surface and the entire contact lens on the eye using spectral domain optical coherence tomography (SD-OCT). Methods A custom built, high speed and high resolution SD-OCT was developed with extended scan depth and width. The eye was imaged before and after wearing a toric soft contact lens (PureVision, Bausch & Lomb, Rochester, NY). A lubricant eye drop (Soothe, Bausch & Lomb) was instilled in the eye to enhance the image contrast on the lens. The same toric soft contact lens immersed in the contact lens solution was also imaged with a contrast enhancement medium (0.5% Intralipid). Results Cross-sectional OCT images of the entire ocular surface were acquired with high resolution 2048×2048 pixels. Quantitative surface height map of the ocular surface was obtained from a radial scan dataset containing 32 B-scans. With the contrast enhancement agent, the entire toric soft contact lens was clearly visualized both in vitro and on the eye. The surfaces of the lens were detected and used to generate the thickness maps of the soft contact lens. Conclusions SD-OCT with extended scan depth and width is a promising tool for imaging the entire ocular surface shape and soft contact lenses. This successful demonstration suggests that the extended depth SD-OCT is effective in studying ocular surface shape and its interaction with a soft contact lens. The novel method is helpful for contact lens fitting evaluation and lens design. PMID:20093938

  3. Interobserver Agreement in Detecting Spectral-Domain Optical Coherence Tomography Features of Diabetic Macular Edema

    PubMed Central

    Heng, Ling Zhi; Pefianaki, Maria; Hykin, Philip; Patel, Praveen J.

    2015-01-01

    Purpose To evaluate interobserver agreement for the detection of spectral-domain optical coherence tomography (SDOCT) features of diabetic macular edema (DME). Method Cross-sectional study in which 2 retinal specialists evaluated SDOCT scans from eyes receiving treatment for DME. Scans from 50 eyes with DME of 39 patients were graded for features of DME including intra-retinal fluid (IRF), diffuse retinal oedema (DRE), hyper-reflective foci (HRF), subretinal fluid (SRF), macular fluid and vitreomacular traction (VMT). Features were graded as present or absent at zones involving the fovea, 1mm from the fovea and the whole scan of 49 line scans. Analysis was performed using cross-tabulations for percentage concordance and kappa values (κ). Results In the 2950 line scans analysed, there was an increase in percentage concordance for DRE and HRF when moving from a foveal line scan, 1mm zone and then to a whole scan analysis (88% vs 94% vs 96%) and (88% vs 94% vs 94%) respectively with κ ranging from substantial to almost perfect. Percentage concordance for SRF was 96% at all 3 regions analysed, whilst IRF was 96% at fovea and 98% at higher number of line-scans analysed. Concordance for MF was 100% at fovea and 98% at 1mm zone and whole scan with almost perfect and substantial κ respectively. κ agreement was substantial for VMT at all regions analysed. Conclusion We report a high level of interobserver agreement in the detection of SDOCT features of DME. This finding is important as detection of macular fluid is used to guide retreatment with anti-angiogenic agents. PMID:25996150

  4. Volume Averaging of Spectral-Domain Optical Coherence Tomography Impacts Retinal Segmentation in Children

    PubMed Central

    Trimboli-Heidler, Carmelina; Vogt, Kelly; Avery, Robert A.

    2016-01-01

    Purpose To determine the influence of volume averaging on retinal layer thickness measures acquired with spectral-domain optical coherence tomography (SD-OCT) in children. Methods Macular SD-OCT images were acquired using three different volume settings (i.e., 1, 3, and 9 volumes) in children enrolled in a prospective OCT study. Total retinal thickness and five inner layers were measured around an Early Treatment Diabetic Retinopathy Scale (ETDRS) grid using beta version automated segmentation software for the Spectralis. The magnitude of manual segmentation required to correct the automated segmentation was classified as either minor (<12 lines adjusted), moderate (>12 and <25 lines adjusted), severe (>26 and <48 lines adjusted), or fail (>48 lines adjusted or could not adjust due to poor image quality). The frequency of each edit classification was assessed for each volume setting. Thickness, paired difference, and 95% limits of agreement of each anatomic quadrant were compared across volume density. Results Seventy-five subjects (median age 11.8 years, range 4.3–18.5 years) contributed 75 eyes. Less than 5% of the 9- and 3-volume scans required more than minor manual segmentation corrections, compared with 71% of 1-volume scans. The inner (3 mm) region demonstrated similar measures across all layers, regardless of volume number. The 1-volume scans demonstrated greater variability of the retinal nerve fiber layer (RNLF) thickness, compared with the other volumes in the outer (6 mm) region. Conclusions In children, volume averaging of SD-OCT acquisitions reduce retinal layer segmentation errors. Translational Relevance This study highlights the importance of volume averaging when acquiring macula volumes intended for multilayer segmentation. PMID:27570711

  5. Automated segmentation of retinal blood vessels in spectral domain optical coherence tomography scans.

    PubMed

    Pilch, Matthäus; Wenner, Yaroslava; Strohmayr, Elisabeth; Preising, Markus; Friedburg, Christoph; Meyer Zu Bexten, Erdmuthe; Lorenz, Birgit; Stieger, Knut

    2012-07-01

    The correct segmentation of blood vessels in optical coherence tomography (OCT) images may be an important requirement for the analysis of intra-retinal layer thickness in human retinal diseases. We developed a shape model based procedure for the automatic segmentation of retinal blood vessels in spectral domain (SD)-OCT scans acquired with the Spectralis OCT system. The segmentation procedure is based on a statistical shape model that has been created through manual segmentation of vessels in a training phase. The actual segmentation procedure is performed after the approximate vessel position has been defined by a shadowgraph that assigns the lateral vessel positions. The active shape model method is subsequently used to segment blood vessel contours in axial direction. The automated segmentation results were validated against the manual segmentation of the same vessels by three expert readers. Manual and automated segmentations of 168 blood vessels from 34 B-scans were analyzed with respect to the deviations in the mean Euclidean distance and surface area. The mean Euclidean distance between the automatically and manually segmented contours (on average 4.0 pixels respectively 20 µm against all three experts) was within the range of the manually marked contours among the three readers (approximately 3.8 pixels respectively 18 µm for all experts). The area deviations between the automated and manual segmentation also lie within the range of the area deviations among the 3 clinical experts. Intra reader variability for the experts was between 0.9 and 0.94. We conclude that the automated segmentation approach is able to segment blood vessels with comparable accuracy as expert readers and will provide a useful tool in vessel analysis of whole C-scans, and in particular in multicenter trials.

  6. Cystic macular oedema on spectral-domain optical coherence tomography in choroideremia patients without cystic changes on fundus examination

    PubMed Central

    Genead, M A; Fishman, G A

    2011-01-01

    Purpose To determine the prevalence of cystic macular oedema (CME) in patients with choroideremia (CHM) by using spectral-domain optical coherence tomography (SD-OCT). Methods A total 16 patients affected with CHM were enroled in the study. All patients underwent a complete eye examination. SD-OCT was performed using an OPKO spectral-domain OCT/SLO instrument. Results The average age of the study patients was 44.0±16.0 years (range, 13–63 years). Out of the 16 patients with CHM, 10 patients (62.5%) showed a degree of CME on SD-OCT testing in at least one eye, and 8 patients (50%) showed CME in both eyes. Conclusions Because of its notable prevalence, it would seem prudent to screen CHM patients by SD-OCT for the possible presence of CME and to identify those amenable to future treatment strategies for their macular oedema. PMID:20966974

  7. Diffuse shear wave imaging: toward passive elastography using low-frame rate spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Nguyen, Thu-Mai; Zorgani, Ali; Lescanne, Maxime; Boccara, Claude; Fink, Mathias; Catheline, Stefan

    2016-12-01

    Optical coherence tomography (OCT) can map the stiffness of biological tissue by imaging mechanical perturbations (shear waves) propagating in the tissue. Most shear wave elastography (SWE) techniques rely on active shear sources to generate controlled displacements that are tracked at ultrafast imaging rates. Here, we propose a noise-correlation approach to retrieve stiffness information from the imaging of diffuse displacement fields using low-frame rate spectral-domain OCT. We demonstrated the method on tissue-mimicking phantoms and validated the results by comparison with classic ultrafast SWE. Then we investigated the in vivo feasibility on the eye of an anesthetized rat by applying noise correlation to naturally occurring displacements. The results suggest a great potential for passive elastography based on the detection of natural pulsatile motions using conventional spectral-domain OCT systems. This would facilitate the transfer of OCT-elastography to clinical practice, in particular, in ophthalmology or dermatology.

  8. Change in Drusen Area Over Time Compared Using Spectral-Domain Optical Coherence Tomography and Color Fundus Imaging

    PubMed Central

    Gregori, Giovanni; Yehoshua, Zohar; Garcia Filho, Carlos Alexandre de Amorim; Sadda, SriniVas R.; Portella Nunes, Renata; Feuer, William J.; Rosenfeld, Philip J.

    2014-01-01

    Purpose. To investigate the relationship between drusen areas measured with color fundus images (CFIs) and those with spectral-domain optical coherence tomography (SDOCT). Methods. Forty-two eyes from thirty patients with drusen in the absence of geographic atrophy were recruited to a prospective study. Digital color fundus images and SDOCT images were obtained at baseline and at follow-up visits at 3 and 6 months. Registered, matched circles centered on the fovea with diameters of 3 mm and 5 mm were identified on both CFIs and SDOCT images. Spectral-domain OCT drusen measurements were obtained using a commercially available proprietary algorithm. Drusen boundaries on CFIs were traced manually at the Doheny Eye Institute Image Reading Center. Results. Mean square root drusen area (SQDA) measurements for the 3-mm circles on the SDOCT images were 1.451 mm at baseline and 1.464 mm at week 26, whereas the measurements on CFIs were 1.555 mm at baseline and 1.584 mm at week 26. Mean SQDA measurements from CFIs were larger than those from the SDOCT measurements at all time points (P = 0.004 at baseline, P = 0.003 at 26 weeks). Changes in SQDA over 26 weeks measured with SDOCT were not different from those measured with CFIs (mean difference = 0.014 mm, P = 0.5). Conclusions. Spectral-domain OCT drusen area measurements were smaller than the measurements obtained from CFIs. However, there were no differences in the change in drusen area over time between the two imaging modalities. Spectral-domain OCT measurements were considerably more sensitive in assessing drusen area changes. PMID:25335982

  9. Quantitative Assessment of Anterior Segment Inflammation in a Rat Model of Uveitis Using Spectral-Domain Optical Coherence Tomography

    PubMed Central

    Pepple, Kathryn L.; Choi, Woo June; Wilson, Leslie; Van Gelder, Russell N.; Wang, Ruikang K.

    2016-01-01

    Purpose To develop anterior segment spectral-domain optical coherence tomography (SD-OCT) and quantitative image analysis for use in experimental uveitis in rats. Methods Acute anterior uveitis was generated in Lewis rats. A spectral domain anterior segment OCT system was used to image the anterior chamber (AC) and ciliary body at baseline and during peak inflammation 2 days later. Customized MatLab image analysis algorithms were developed to segment the AC, count AC cells, calculate central corneal thickness (CCT), segment the ciliary body and zonules, and quantify the level of ciliary body inflammation with the ciliary body index (CBI). Images obtained at baseline and during peak inflammation were compared. Finally, longitudinal imaging and image analysis was performed over the 2-week course of inflammation. Results Spectral-domain optical coherence tomography identifies structural features of inflammation. Anterior chamber cell counts at peak inflammation obtained by automated image analysis and human grading were highly correlated (r = 0.961), and correlated well with the histologic score of inflammation (r = 0.895). Inflamed eyes showed a significant increase in average CCT (27 μm, P = 0.02) and an increase in average CBI (P < 0.0001). Longitudinal imaging and quantitative image analysis identified a significant change in AC cell and CBI on day 2 with spontaneous resolution of inflammation by day 14. Conclusions Spectral-domain optical coherence tomography provides high-resolution images of the structural changes associated with anterior uveitis in rats. Anterior chamber cell count and CBI determined by semi-automated image analysis strongly correlates with inflammation, and can be used to quantify inflammation longitudinally in single animals. PMID:27388049

  10. Relationship Between Optic Nerve Appearance and Retinal Nerve Fiber Layer Thickness as Explored with Spectral Domain Optical Coherence Tomography

    PubMed Central

    Aleman, Tomas S.; Huang, Jiayan; Garrity, Sean T.; Carter, Stuart B.; Aleman, Wendy D.; Ying, Gui-shuang; Tamhankar, Madhura A.

    2014-01-01

    Purpose To study the relationship between the appearance of the optic nerve and the retinal nerve fiber layer (RNFL) thickness determined by spectral domain optical coherence tomography (OCT). Methods Records from patients with spectral domain-OCT imaging in a neuro-ophthalmology practice were reviewed. Eyes with glaucoma/glaucoma suspicion, macular/optic nerve edema, pseudophakia, and with refractive errors > 6D were excluded. Optic nerve appearance by slit lamp biomicroscopy was related to the RNFL thickness by spectral domain-OCT and to visual field results. Results Ninety-one patients (176 eyes; mean age: 49 ± 15 years) were included. Eighty-three eyes (47%) showed optic nerve pallor; 89 eyes (50.6%) showed RNFL thinning (sectoral or average peripapillary). Average peripapillary RNFL thickness in eyes with pallor (mean ± SD = 76 ± 17 μm) was thinner compared to eyes without pallor (91 ± 14 μm, P < 0.001). Optic nerve pallor predicted RNFL thinning with a sensitivity of 69% and a specificity of 75%. Optic nerve appearance predicted RNFL thinning (with a sensitivity and specificity of 81%) when RNFL had thinned by ∼ 40%. Most patients with pallor had RNFL thinning with (66%) or without (25%) visual field loss; the remainder had normal RNFL and fields (5%) or with visual field abnormalities (4%). Conclusions Optic nerve pallor as a predictor of RNFL thinning showed fair sensitivity and specificity, although it is optimally sensitive/specific only when substantial RNFL loss has occurred. Translational Relevance Finding an acceptable relationship between the optic nerve appearance by ophthalmoscopy and spectral domain-OCT RNFL measures will help the clinician's interpretation of the information provided by this technology, which is gaining momentum in neuro-ophthalmic research. PMID:25374773

  11. Twin Peaks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The two hills in the distance, approximately one to two kilometers away, have been dubbed the 'Twin Peaks' and are of great interest to Pathfinder scientists as objects of future study. 3D glasses are necessary to identify surface detail. The white areas on the left hill, called the 'Ski Run' by scientists, may have been formed by hydrologic processes.

    The IMP is a stereo imaging system with color capability provided by 24 selectable filters -- twelve filters per 'eye.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  12. 3D and beyond

    NASA Astrophysics Data System (ADS)

    Fung, Y. C.

    1995-05-01

    This conference on physiology and function covers a wide range of subjects, including the vasculature and blood flow, the flow of gas, water, and blood in the lung, the neurological structure and function, the modeling, and the motion and mechanics of organs. Many technologies are discussed. I believe that the list would include a robotic photographer, to hold the optical equipment in a precisely controlled way to obtain the images for the user. Why are 3D images needed? They are to achieve certain objectives through measurements of some objects. For example, in order to improve performance in sports or beauty of a person, we measure the form, dimensions, appearance, and movements.

  13. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Ames Research Center research into virtual reality led to the development of the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. It consists of a two-card set designed for use with a personal computer. The Convolvotron's primary application is presentation of 3D audio signals over headphones. Four independent sound sources are filtered with large time-varying filters that compensate for motion. The perceived location of the sound remains constant. Possible applications are in air traffic control towers or airplane cockpits, hearing and perception research and virtual reality development.

  14. 3D Human cartilage surface characterization by optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Brill, Nicolai; Riedel, Jörn; Schmitt, Robert; Tingart, Markus; Truhn, Daniel; Pufe, Thomas; Jahr, Holger; Nebelung, Sven

    2015-10-01

    Early diagnosis and treatment of cartilage degeneration is of high clinical interest. Loss of surface integrity is considered one of the earliest and most reliable signs of degeneration, but cannot currently be evaluated objectively. Optical Coherence Tomography (OCT) is an arthroscopically available light-based non-destructive real-time imaging technology that allows imaging at micrometre resolutions to millimetre depths. As OCT-based surface evaluation standards remain to be defined, the present study investigated the diagnostic potential of 3D surface profile parameters in the comprehensive evaluation of cartilage degeneration. To this end, 45 cartilage samples of different degenerative grades were obtained from total knee replacements (2 males, 10 females; mean age 63.8 years), cut to standard size and imaged using a spectral-domain OCT device (Thorlabs, Germany). 3D OCT datasets of 8  ×  8, 4  ×  4 and 1  ×  1 mm (width  ×  length) were obtained and pre-processed (image adjustments, morphological filtering). Subsequent automated surface identification algorithms were used to obtain the 3D primary profiles, which were then filtered and processed using established algorithms employing ISO standards. The 3D surface profile thus obtained was used to calculate a set of 21 3D surface profile parameters, i.e. height (e.g. Sa), functional (e.g. Sk), hybrid (e.g. Sdq) and segmentation-related parameters (e.g. Spd). Samples underwent reference histological assessment according to the Degenerative Joint Disease classification. Statistical analyses included calculation of Spearman’s rho and assessment of inter-group differences using the Kruskal Wallis test. Overall, the majority of 3D surface profile parameters revealed significant degeneration-dependent differences and correlations with the exception of severe end-stage degeneration and were of distinct diagnostic value in the assessment of surface integrity. None of the 3D

  15. Comprehensive Three-Dimensional Analysis of the Neuroretinal Rim in Glaucoma Using High-Density Spectral-Domain Optical Coherence Tomography Volume Scans

    PubMed Central

    Tsikata, Edem; Lee, Ramon; Shieh, Eric; Simavli, Huseyin; Que, Christian J.; Guo, Rong; Khoueir, Ziad; de Boer, Johannes; Chen, Teresa C.

    2016-01-01

    Purpose To describe spectral-domain optical coherence tomography (OCT) methods for quantifying neuroretinal rim tissue in glaucoma and to compare these methods to the traditional retinal nerve fiber layer thickness diagnostic parameter. Methods Neuroretinal rim parameters derived from three-dimensional (3D) volume scans were compared with the two-dimensional (2D) Spectralis retinal nerve fiber layer (RNFL) thickness scans for diagnostic capability. This study analyzed one eye per patient of 104 glaucoma patients and 58 healthy subjects. The shortest distances between the cup surface and the OCT-based disc margin were automatically calculated to determine the thickness and area of the minimum distance band (MDB) neuroretinal rim parameter. Traditional 150-μm reference surface–based rim parameters (volume, area, and thickness) were also calculated. The diagnostic capabilities of these five parameters were compared with RNFL thickness using the area under the receiver operating characteristic (AUROC) curves. Results The MDB thickness had significantly higher diagnostic capability than the RNFL thickness in the nasal (0.913 vs. 0.818, P = 0.004) and temporal (0.922 vs. 0.858, P = 0.026) quadrants and the inferonasal (0.950 vs. 0.897, P = 0.011) and superonasal (0.933 vs. 0.868, P = 0.012) sectors. The MDB area and the three neuroretinal rim parameters based on the 150-μm reference surface had diagnostic capabilities similar to RNFL thickness. Conclusions The 3D MDB thickness had a high diagnostic capability for glaucoma and may be of significant clinical utility. It had higher diagnostic capability than the RNFL thickness in the nasal and temporal quadrants and the inferonasal and superonasal sectors. PMID:27768203

  16. Spectral representation: a core aspect of modelling the response characteristics of time-domain EMI mine detectors

    NASA Astrophysics Data System (ADS)

    West, G. F.; Bailey, R. C.

    2006-05-01

    Most modern EMI mine detectors can detect the very small conductive and/or ferromagnetic parts of typical mines with relative ease. However, they also respond significantly to certain soils that contain lossy ferromagnetic minerals. In some special environments such as ocean beaches, conductivity of the host soil may also cause a response. Characterizing and modelling both the various target response mechanisms and the EMI detectors quantitatively would be relatively straightforward if it were not for the fact that most modern EMI detectors operate in time domain and use different current waveforms and time gates to observe response. Furthermore, much of the information about targets and interferences and even instrumental spectral limitations is observational rather than analytical data. In this paper, we put forward a spectral representation method that can be incorporated into both EMI data gathering and instrument modelling and which facilitates efficient quantitative simulation of arbitrary time- domain detection systems. The methodology and examples of its use are presented. Pure induction response from the ground is modelled with a sum-over-N-elements transfer function in which the kernel elements are single pole, pure damping responses which are log-spaced over the spectral range of interest. Instrument transfer functions can be described with a standard sparse pole and zero representation (located anywhere in the damped frequency half plane), if required. Model fitting techniques employing generalized inversion controls are used to go back and forth between frequency and time domain and the set of model parameters.

  17. Coseismic slip distribution of the 2015 Mw7.8 Gorkha, Nepal, earthquake from joint inversion of GPS and InSAR data for slip within a 3-D heterogeneous Domain

    NASA Astrophysics Data System (ADS)

    Tung, Sui; Masterlark, Timothy

    2016-05-01

    We derive a coseismic slip model of the 2015 Mw7.8 Gorkha earthquake on the basis of GPS and line-of-sight displacements from ALOS-2 descending interferograms, using Green's functions calculated with a 3-D finite element model (FEM). The FEM simulates a nonuniform distribution of elastic material properties and a precise geometric configuration of the irregular topographical surface. The rupturing fault is modeled as a low-angle and north dipping surface within the Main Frontal Thrust along the convergent margin of the Himalayas. The optimal model that inherits heterogeneous material properties provides a significantly better solution than that in a homogenous domain at the 95% confidence interval. The best fit solution for the domain having a nonuniform distribution of material properties reveals a rhombus-shaped slip zone of three composite asperities. Slip is primarily concentrated at a depth of 15 km with both dip-slip (maximum 6.54 m) and strike-slip (maximum 2.0 m) components, giving rise to a geodetic-based moment of 1.09 × 1021 Nm in general agreement with the seismological estimate. The optimal relative weights among GPS and interferometric synthetic aperture radar (InSAR) are deduced from a new method, MC-HVCE which combines a Monte Carlo search and a Helmert Method of Variance Components Estimation. This method determines the relative weights in a systemic approach which preserves the intrinsic solution smoothness. The joint solution is significantly better than those inverted from each individual data set. This methodology allows us to integrate multiple data sets of geodetic observations with seismic tomography, in an effort to achieve a better understanding of seismic ruptures within crustal heterogeneity.

  18. The role of 3-D interactive visualization in blind surveys of H I in galaxies

    NASA Astrophysics Data System (ADS)

    Punzo, D.; van der Hulst, J. M.; Roerdink, J. B. T. M.; Oosterloo, T. A.; Ramatsoku, M.; Verheijen, M. A. W.

    2015-09-01

    Upcoming H I surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize H I objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. We discuss how Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain. The requirements for a fully interactive visualization tool are: coupled 1-D/2-D/3-D visualization, quantitative and comparative capabilities, combined with supervised semi-automated analysis. Moreover, the source code must have the following characteristics for enabling collaborative work: open, modular, well documented, and well maintained. We review four state of-the-art, 3-D visualization packages assessing their capabilities and feasibility for use in the case of 3-D astronomical data.

  19. 3D Surgical Simulation

    PubMed Central

    Cevidanes, Lucia; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael

    2009-01-01

    This paper discusses the development of methods for computer-aided jaw surgery. Computer-aided jaw surgery allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery (CAS) system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3D surface models from Cone-beam CT (CBCT), dynamic cephalometry, semi-automatic mirroring, interactive cutting of bone and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intra-operative guidance. The system provides further intra-operative assistance with the help of a computer display showing jaw positions and 3D positioning guides updated in real-time during the surgical procedure. The CAS system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training and assessing the difficulties of the surgical procedures prior to the surgery. CAS has the potential to make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. Supported by NIDCR DE017727, and DE018962 PMID:20816308

  20. Martian terrain - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    An area of rocky terrain near the landing site of the Sagan Memorial Station can be seen in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. This image is part of a 3D 'monster' panorama of the area surrounding the landing site.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  1. Detection of retinal changes in Parkinson’s disease with spectral-domain optical coherence tomography

    PubMed Central

    Aaker, Grant D; Myung, Jane S; Ehrlich, Joshua R; Mohammed, Mujtaba; Henchcliffe, Claire; Kiss, Szilárd

    2010-01-01

    Purpose This pilot study investigated whether high-resolution spectral-domain optical coherence tomography (SD-OCT) could detect differences in inner retinal layer (IRL), peripapillary retinal nerve fiber layer (RNFL), and macular thickness between patients with Parkinson’s disease (PD) and controls. Methods Both eyes of patients with PD and age-matched controls were imaged with the Heidelberg Spectralis® HRA + OCT. RNFL, IRL, and macular thickness were measured for each eye using Heidelberg software. These measurements were compared with validated, published normal values for macular and RNFL thickness, and compared with matched controls for IRL thickness. Results Eighteen eyes from nine subjects with PD and 19 eyes of 16 control subjects were evaluated using SD-OCT. The average age of PD patients was 64 years with a range of 52–75 years. The average age of controls was 67 years with a range of 50–81 years. No significant reduction in IRL thickness was detected between PD patients and age-matched controls at 13 points along a 6 mm horizontal section through the fovea. No significant difference in RNFL thickness was detected between PD patients and published normal values. Overall average RNFL thickness was 97 μm for PD patients, which exactly matched the normative database value. However, significant differences in macular thickness were detected in three of nine subfields between PD subjects and published normal values. In PD subjects, the outer superior subfield was 2.8% thinner (P = 0.026), while the outer nasal and inner inferior subfields were 2.8% (P = 0.016) and 2.7% (P = 0.001) thicker compared to published normal values. Conclusion In this pilot study, significant differences in macular thickness were detected in three of nine subfields by SD-OCT. However, SD-OCT did not detect significant reductions in peripapillary RNFL and IRL thickness between PD patients and controls. This suggests that macular thickness measurements by SD-OCT may potentially

  2. Applicability of automatic spectral domain optical coherence tomography for glaucoma mass screening

    PubMed Central

    Nakano, Tadashi; Hayashi, Takeshi; Nakagawa, Toru; Honda, Toru; Owada, Satoshi; Endo, Hitoshi; Tatemichi, Masayuki

    2017-01-01

    Purpose To perform a preliminary evaluation of the applicability of automatic spectral domain optical coherence tomography (ASD-OCT) for glaucoma mass screening in a population-based setting. Methods Information using ASD-OCT (thicknesses of the macular retinal nerve fiber layer [mRNFL], disc retinal nerve fiber layer [dRNFL], ganglion cell layer [GCL] + inner plexiform layer [IPL]; GCL+, and ganglion cell complex [GCL + IPL + RNFL; GCL++]) was obtained from 245 eyes of 123 glaucomatous subjects and 1,454 eyes of 727 normal subjects. For all four measurements, each grid was scored as follows: 2= within 95% of the normal database; 1= within 5%; and 0= within 1%. The sums of each grid (mRNFLs, dRNFLs, GCL+s, and GCL++s) were used as indicators. The effectiveness was estimated by the area under the receiver operating characteristic curve (AUC-ROC). The appropriate algorithm was then applied to 10,145 eyes of 5,088 subjects from the general population (mean age: 50.1±10.3 years). Results AUC-ROC of mRNFLs, dRNFLs, GCL+s, and GCL++s was 0.927 (95% confidence interval [CI] =0.903–0.950), 0.919 (95% CI =0.899–0.940), 0.972 (95% CI =0.958–0.986), and 0.972 (95% CI =0.957–0.986), respectively. The discriminant analysis demonstrated that the canonical correlation coefficients of mRNFLs, dRNFLs, GCL+s, and dGCL++s were 0.07, 0.255, 0.661, and 0.207, respectively. AUC-ROC of the discriminant value was 0.971 (95% CI =0.956–0.986). The sensitivity/specificity using GCL+s (cutoff =160) was 81.6%/99.9%. This algorithm was applied to the general population, and 1,658 eyes (16.3%) were found to be positive for glaucoma. Conclusion In the case–control setting, ASD-OCT showed a relatively high performance, and the thickness of the GCL + IPL was the best predictor. However, further prospective studies are needed, in which the results of this study are compared to the general population, because the false-positive rate of glaucoma seems to be high. PMID:28096653

  3. Wide-field spectral domain-optical coherence tomography in central serous chorioretinopathy.

    PubMed

    Carrai, Paola; Pichi, Francesco; Bonsignore, Francesco; Ciardella, Antonio P; Nucci, Paolo

    2015-04-01

    The aim the study was to describe wide-field spectral-domain optical coherence tomography morphologic relationships of the vitreous, retina, and choroid in central serous chorioretinopathy (CSCR) eyes. Standardized horizontal, vertical, and two oblique (supertemporal to inferonasal and supranasal to inferotemporal) SD-OCT sections were collected for 40 patient with CSCR. For extramacular imaging, images were obtained from eight locations: (1) nasal to the optic disk, (2) extreme nasal periphery, (3) superior to the superotemporal vascular arcade, (4) extreme superior periphery, (5) inferior to the inferotemporal vascular arcade, (6) extreme inferior periphery, (7) temporal to the macula, and (8) extreme temporal periphery. Wide-angle montage images of OCT from equator to equator were composed with a montaging software. Average subfoveal choroidal thickness was 478 ± 114 µm (range 232-695 µm) at the macular level, 367 ± 94 µm in the superior periphery, 257 ± 103 µm in the inferior periphery, 431 ± 121 and 280 ± 88 µm in the nasal and in the temporal periphery, respectively. Wide-field EDI-OCT revealed a relative thinning of the inner choroidal layer in the periphery, including the small and medium large vessels, which ranged from 86 µm nasally to 120.1 µm superiorly, with a mean of 98.8 ± 13.6 µm. Beneath the thinned inner choroidal layer, hyporeflective lumina, corresponding to the outer choroidal layer, were identified in the periphery of all eyes. The outer choroidal layer thickness ranged from 175.5 µm temporally to 235.5 µm superiorly, with a mean of 217.8 ± 41.4 µm. The novel approach of montaging SD-OCT images to examine relationships between the choroid, retina, and associated structures adjacent to and outside of the macula may have a number of relevant applications in the study of pathologic features of central serous chorioretinopathy.

  4. Automated Analysis of Vitreous Inflammation Using Spectral-Domain Optical Coherence Tomography

    PubMed Central

    Keane, Pearse A.; Balaskas, Konstantinos; Sim, Dawn A.; Aman, Kiran; Denniston, Alastair K.; Aslam, Tariq; and for the EQUATOR Study Group

    2015-01-01

    Purpose To develop an automated method for quantifying vitreous signal intensity on optical coherence tomography (OCT), with particular application for use in the assessment of vitreous inflammation. Methods This retrospective, observational case-control series comprised 30 patients (30 eyes), with vitreous haze secondary to intermediate, posterior, or panuveitis; 12 patients (12 eyes) with uveitis without evidence of vitreous haze; and 18 patients (18 eyes) without intraocular inflammation or vitreoretinal disease. The presence and severity of vitreous haze was classified according to the National Eye Institute system; other inflammatory indices and clinical parameters were also documented. Spectral-domain OCT images were analyzed using custom VITreous ANalysis software (termed ‘VITAN'), which is fully automated and avoids the need for manual segmentation. Results VITAN performed accurate segmentation in all scans. Automated measurements of the vitreous:retinal pigment epithelium (RPE) signal ratio showed a moderate correlation with clinical vitreous haze scores (r = 0.585, P < 0.001), comparable to that reported using manual segmentation in our previous study (r = 0.566, P = 0.0001). The novel parameter of vitreous:RPE textural ratio showed a marginally stronger correlation (r = 0.604, P < 0.001) with clinical vitreous haze scores than the Vitreous:RPE signal ratio. Conclusions The custom OCT image analysis software (VITAN) allows rapid and automated measurement of vitreous parameters, that is comparable to our previously reported vitreous:RPE index, and correlates with clinically measured disease activity. Such OCT-based indices may provide the much needed objective markers of vitreous activity, which may be used in both clinical assessment, and as outcome measures in clinical trials for intermediate, posterior, and panuveitis. Translational Relevance We describe a rapid automated method for quantifying vitreous signal intensity on optical coherence tomography

  5. Retinal nerve fiber layer evaluation in multiple sclerosis with spectral domain optical coherence tomography

    PubMed Central

    Khanifar, Aziz A; Parlitsis, George J; Ehrlich, Joshua R; Aaker, Grant D; D’Amico, Donald J; Gauthier, Susan A; Kiss, Szilárd

    2010-01-01

    Purpose: Histopathologic studies have reported retinal nerve fiber layer (RNFL) thinning in various neurodegenerative diseases. Attempts to quantify this loss in vivo have relied on time-domain optical coherence tomography (TDOCT), which has low resolution and requires substantial interpolation of data for volume measurements. We hypothesized that the significantly higher resolution of spectral-domain optical coherence tomography (SDOCT) would better detect RNFL changes in patients with multiple sclerosis, and that RNFL thickness differences between eyes with and without optic neuritis might be identified more accurately. Methods: In this retrospective case series, patients with multiple sclerosis were recruited from the Judith Jaffe Multiple Sclerosis Center at Weill Cornell Medical College in New York. Patients with a recent clinical diagnosis of optic neuritis (less than three months) were excluded. Eyes with a history of glaucoma, optic neuropathy (other than multiple sclerosis-related optic neuritis), age-related macular degeneration, or other relevant retinal and/or optic nerve disease were excluded. Both eyes of each patient were imaged with the Heidelberg Spectralis® HRA + OCT. RNFL and macular thickness were measured for each eye using the Heidelberg OCT software. These measurements were compared with validated published normal values, and were modeled as linear functions of duration of disease. The odds of an optic neuritis diagnosis as a function of RNFL and macular thickness were calculated. Results: Ninety-four eyes were prospectively evaluated using OCT. Ages of patients ranged from 26 to 69 years, with an average age of 39 years. Peripapillary RNFL thinning was demonstrated in multiple sclerosis patients; mean RNFL thickness was 88.5 μm for individuals with multiple sclerosis compared with a reported normal value of 97 μm (P < 0.001). Eyes with a history of optic neuritis had more thinning compared with those without optic neuritis (83.0

  6. 3D field harmonics

    SciTech Connect

    Caspi, S.; Helm, M.; Laslett, L.J.

    1991-03-30

    We have developed an harmonic representation for the three dimensional field components within the windings of accelerator magnets. The form by which the field is presented is suitable for interfacing with other codes that make use of the 3D field components (particle tracking and stability). The field components can be calculated with high precision and reduced cup time at any location (r,{theta},z) inside the magnet bore. The same conductor geometry which is used to simulate line currents is also used in CAD with modifications more readily available. It is our hope that the format used here for magnetic fields can be used not only as a means of delivering fields but also as a way by which beam dynamics can suggest correction to the conductor geometry. 5 refs., 70 figs.

  7. Optically rewritable 3D liquid crystal displays.

    PubMed

    Sun, J; Srivastava, A K; Zhang, W; Wang, L; Chigrinov, V G; Kwok, H S

    2014-11-01

    Optically rewritable liquid crystal display (ORWLCD) is a concept based on the optically addressed bi-stable display that does not need any power to hold the image after being uploaded. Recently, the demand for the 3D image display has increased enormously. Several attempts have been made to achieve 3D image on the ORWLCD, but all of them involve high complexity for image processing on both hardware and software levels. In this Letter, we disclose a concept for the 3D-ORWLCD by dividing the given image in three parts with different optic axis. A quarter-wave plate is placed on the top of the ORWLCD to modify the emerging light from different domains of the image in different manner. Thereafter, Polaroid glasses can be used to visualize the 3D image. The 3D image can be refreshed, on the 3D-ORWLCD, in one-step with proper ORWLCD printer and image processing, and therefore, with easy image refreshing and good image quality, such displays can be applied for many applications viz. 3D bi-stable display, security elements, etc.

  8. Molecular docking and 3D-QSAR study on 4-(1H-indazol-4-yl) phenylamino and aminopyrazolopyridine urea derivatives as kinase insert domain receptor (KDR) inhibitors.

    PubMed

    Wu, Xiaoyun; Wu, Shuguang; Chen, Wen-Hua

    2012-03-01

    Vascular endothselial growth factor (VEGF) and its receptor tyrosine kinase VEGFR-2 or kinase insert domain receptor (KDR) have been identified as new promising targets for the design of novel anticancer agents. It is reported that 4-(1H-indazol-4-yl)phenylamino and aminopyrazolopyridine urea derivatives exhibit potent inhibitory activities toward KDR. To investigate how their chemical structures relate to the inhibitory activities and to identify the key structural elements that are required in the rational design of potential drug candidates of this class, molecular docking simulations and three-dimensional quantitative structure-activity relationship (3D-QSAR) methods were performed on 78 4-(1H-indazol-4-yl)phenylamino and aminopyrazolopyridine urea derivatives as KDR inhibitors. Surflex-dock was used to determine the probable binding conformations of all the compounds at the active site of KDR. As a result, multiple hydrophobic and hydrogen-bonding interactions were found to be two predominant factors that may be used to modulate the inhibitory activities. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) 3D-QSAR models were developed based on the docking conformations. The CoMFA model produced statistically significant results with the cross-validated correlation coefficient q(2) of 0.504 and the non-cross-validated correlation coefficient r(2) of 0.913. The best CoMSIA model was obtained from the combination of steric, electrostatic and hydrophobic fields. Its q(2) and r(2) being 0.595 and 0.947, respectively, indicated that it had higher predictive ability than the CoMFA model. The predictive abilities of the two models were further validated by 14 test compounds, giving the predicted correction coefficients r (pred) (2) of 0.727 for CoMFA and 0.624 for CoMSIA, respectively. In addition, the CoMFA and CoMSIA models were used to guide the design of a series of new inhibitors of this class with

  9. Measuring time-domain spectral induced polarization in the on-time: decreasing acquisition time and increasing signal-to-noise ratio

    NASA Astrophysics Data System (ADS)

    Olsson, Per-Ivar; Dahlin, Torleif; Fiandaca, Gianluca; Auken, Esben

    2015-12-01

    Combined resistivity and time-domain direct current induced polarization (DCIP) measurements are traditionally carried out with a 50% duty cycle current waveform, taking the resistivity measurements during the on-time and the IP measurements during the off-time. One drawback with this method is that only half of the acquisition time is available for resistivity and IP measurements, respectively. In this paper, this limitation is solved by using a current injection with 100% duty cycle and also taking the IP measurements in the on-time. With numerical modelling of current waveforms with 50% and 100% duty cycles we show that the waveforms have comparable sensitivity for the spectral Cole-Cole parameters and that signal level is increased up to a factor of 2 if the 100% duty cycle waveform is used. The inversion of field data acquired with both waveforms confirms the modelling results and shows that it is possible to retrieve similar inversion models with either of the waveforms when inverting for the spectral Cole-Cole parameters with the waveform of the injected current included in the forward computations. Consequently, our results show that on-time measurements of IP can reduce the acquisition time by up to 50% and increase the signal-to-noise ratio by up to 100% almost without information loss. Our findings can contribute and have a large impact for DCIP surveys in general and especially for surveys where time and reliable data quality are important factors. Specifically, the findings are of value for DCIP surveys conducted in urban areas where anthropogenic noise is an issue and the heterogeneous subsurface demands time-consuming 3D acquisitions.

  10. Accelerating a 3D finite-difference wave propagation code by a factor of 50 and a spectral-element code by a factor of 25 using a cluster of GPU graphics cards

    NASA Astrophysics Data System (ADS)

    Komatitsch, Dimitri; Michéa, David; Erlebacher, Gordon; Göddeke, Dominik

    2010-05-01

    We first accelerate a three-dimensional finite-difference in the time domain (FDTD) wave propagation code by a factor of about 50 using Graphics Processing Unit (GPU) computing on a cheap NVIDIA graphics card with the CUDA programming language. We implement the code in CUDA in the case of the fully heterogeneous elastic wave equation. We also implement Convolution Perfectly Matched Layers (CPMLs) on the graphics card to efficiently absorb outgoing waves on the fictitious edges of the grid. We show that the code that runs on the graphics card gives the expected results by comparing our results to those obtained by running the same simulation on a classical processor core. The methodology that we present can be used for Maxwell's equations as well because their form is similar to that of the seismic wave equation written in velocity vector and stress tensor. We then implement a high-order finite-element (spectral-element) application, which performs the numerical simulation of seismic wave propagation resulting for instance from earthquakes at the scale of a continent or from active seismic acquisition experiments in the oil industry, on a cluster of NVIDIA Tesla graphics cards using the CUDA programming language and non blocking message passing based on MPI. We compare it to the implementation in C language and MPI on a classical cluster of CPU nodes. We use mesh coloring to efficiently handle summation operations over degrees of freedom on an unstructured mesh, and we exchange information between nodes using non blocking MPI messages. Using non-blocking communications allows us to overlap the communications across the network and the data transfer between the GPU card and the CPU node on which it is installed with calculations on that GPU card. We perform a number of numerical tests to validate the single-precision CUDA and MPI implementation and assess its accuracy. We then analyze performance measurements and in average we obtain a speedup of 20x to 25x.

  11. 3D light robotics

    NASA Astrophysics Data System (ADS)

    Glückstad, Jesper; Palima, Darwin; Villangca, Mark; Banas, Andrew

    2016-04-01

    As celebrated by the Nobel Prize 2014 in Chemistry light-based technologies can now overcome the diffraction barrier for imaging with nanoscopic resolution by so-called super-resolution microscopy1. However, interactive investigations coupled with advanced imaging modalities at these small scale domains gradually demand the development of a new generation of disruptive tools, not only for passively observing at nanoscopic scales, but also for actively reaching into and effectively handling constituents in this size domain. This intriguing mindset has recently led to the emergence of a novel research discipline that could potentially be able to offer the full packet needed for true "active nanoscopy" by use of so-called light-driven micro-robotics or Light Robotics in short.

  12. Lossy compression of hyperspectral images using shearlet transform and 3D SPECK

    NASA Astrophysics Data System (ADS)

    Karami, A.

    2015-10-01

    In this paper, a new lossy compression method for hyperspectral images (HSI) is introduced. HSI are considered as a 3D dataset with two dimensions in the spatial and one dimension in the spectral domain. In the proposed method, first 3D multidirectional anisotropic shearlet transform is applied to the HSI. Because, unlike traditional wavelets, shearlets are theoretically optimal in representing images with edges and other geometrical features. Second, soft thresholding method is applied to the shearlet transform coefficients and finally the modified coefficients are encoded using Three Dimensional- Set Partitioned Embedded bloCK (3D SPECK). Our simulation results show that the proposed method, in comparison with well-known approaches such as 3D SPECK (using 3D wavelet) and combined PCA and JPEG2000 algorithms, provides a higher SNR (signal to noise ratio) for any given compression ratio (CR). It is noteworthy to mention that the superiority of proposed method is distinguishable as the value of CR grows. In addition, the effect of proposed method on the spectral unmixing analysis is also evaluated.

  13. S-EMG signal compression based on domain transformation and spectral shape dynamic bit allocation

    PubMed Central

    2014-01-01

    Background Surface electromyographic (S-EMG) signal processing has been emerging in the past few years due to its non-invasive assessment of muscle function and structure and because of the fast growing rate of digital technology which brings about new solutions and applications. Factors such as sampling rate, quantization word length, number of channels and experiment duration can lead to a potentially large volume of data. Efficient transmission and/or storage of S-EMG signals are actually a research issue. That is the aim of this work. Methods This paper presents an algorithm for the data compression of surface electromyographic (S-EMG) signals recorded during isometric contractions protocol and during dynamic experimental protocols such as the cycling activity. The proposed algorithm is based on discrete wavelet transform to proceed spectral decomposition and de-correlation, on a dynamic bit allocation procedure to code the wavelets transformed coefficients, and on an entropy coding to minimize the remaining redundancy and to pack all data. The bit allocation scheme is based on mathematical decreasing spectral shape models, which indicates a shorter digital word length to code high frequency wavelets transformed coefficients. Four bit allocation spectral shape methods were implemented and compared: decreasing exponential spectral shape, decreasing linear spectral shape, decreasing square-root spectral shape and rotated hyperbolic tangent spectral shape. Results The proposed method is demonstrated and evaluated for an isometric protocol and for a dynamic protocol using a real S-EMG signal data bank. Objective performance evaluations metrics are presented. In addition, comparisons with other encoders proposed in scientific literature are shown. Conclusions The decreasing bit allocation shape applied to the quantized wavelet coefficients combined with arithmetic coding results is an efficient procedure. The performance comparisons of the proposed S-EMG data

  14. Intraoral 3D scanner

    NASA Astrophysics Data System (ADS)

    Kühmstedt, Peter; Bräuer-Burchardt, Christian; Munkelt, Christoph; Heinze, Matthias; Palme, Martin; Schmidt, Ingo; Hintersehr, Josef; Notni, Gunther

    2007-09-01

    Here a new set-up of a 3D-scanning system for CAD/CAM in dental industry is proposed. The system is designed for direct scanning of the dental preparations within the mouth. The measuring process is based on phase correlation technique in combination with fast fringe projection in a stereo arrangement. The novelty in the approach is characterized by the following features: A phase correlation between the phase values of the images of two cameras is used for the co-ordinate calculation. This works contrary to the usage of only phase values (phasogrammetry) or classical triangulation (phase values and camera image co-ordinate values) for the determination of the co-ordinates. The main advantage of the method is that the absolute value of the phase at each point does not directly determine the coordinate. Thus errors in the determination of the co-ordinates are prevented. Furthermore, using the epipolar geometry of the stereo-like arrangement the phase unwrapping problem of fringe analysis can be solved. The endoscope like measurement system contains one projection and two camera channels for illumination and observation of the object, respectively. The new system has a measurement field of nearly 25mm × 15mm. The user can measure two or three teeth at one time. So the system can by used for scanning of single tooth up to bridges preparations. In the paper the first realization of the intraoral scanner is described.

  15. 'Diamond' in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D, microscopic imager mosaic of a target area on a rock called 'Diamond Jenness' was taken after NASA's Mars Exploration Rover Opportunity ground into the surface with its rock abrasion tool for a second time.

    Opportunity has bored nearly a dozen holes into the inner walls of 'Endurance Crater.' On sols 177 and 178 (July 23 and July 24, 2004), the rover worked double-duty on Diamond Jenness. Surface debris and the bumpy shape of the rock resulted in a shallow and irregular hole, only about 2 millimeters (0.08 inch) deep. The final depth was not enough to remove all the bumps and leave a neat hole with a smooth floor. This extremely shallow depression was then examined by the rover's alpha particle X-ray spectrometer.

    On Sol 178, Opportunity's 'robotic rodent' dined on Diamond Jenness once again, grinding almost an additional 5 millimeters (about 0.2 inch). The rover then applied its Moessbauer spectrometer to the deepened hole. This double dose of Diamond Jenness enabled the science team to examine the rock at varying layers. Results from those grindings are currently being analyzed.

    The image mosaic is about 6 centimeters (2.4 inches) across.

  16. Prominent rocks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Many prominent rocks near the Sagan Memorial Station are featured in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. Wedge is at lower left; Shark, Half-Dome, and Pumpkin are at center. Flat Top, about four inches high, is at lower right. The horizon in the distance is one to two kilometers away.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  17. Radiative transfer with scattering for domain-decomposed 3D MHD simulations of cool stellar atmospheres. Numerical methods and application to the quiet, non-magnetic, surface of a solar-type star

    NASA Astrophysics Data System (ADS)

    Hayek, W.; Asplund, M.; Carlsson, M.; Trampedach, R.; Collet, R.; Gudiksen, B. V.; Hansteen, V. H.; Leenaarts, J.

    2010-07-01

    Aims: We present the implementation of a radiative transfer solver with coherent scattering in the new BIFROST code for radiative magneto-hydrodynamical (MHD) simulations of stellar surface convection. The code is fully parallelized using MPI domain decomposition, which allows for large grid sizes and improved resolution of hydrodynamical structures. We apply the code to simulate the surface granulation in a solar-type star, ignoring magnetic fields, and investigate the importance of coherent scattering for the atmospheric structure. Methods: A scattering term is added to the radiative transfer equation, requiring an iterative computation of the radiation field. We use a short-characteristics-based Gauss-Seidel acceleration scheme to compute radiative flux divergences for the energy equation. The effects of coherent scattering are tested by comparing the temperature stratification of three 3D time-dependent hydrodynamical atmosphere models of a solar-type star: without scattering, with continuum scattering only, and with both continuum and line scattering. Results: We show that continuum scattering does not have a significant impact on the photospheric temperature structure for a star like the Sun. Including scattering in line-blanketing, however, leads to a decrease of temperatures by about 350 K below log10 τ5000 ⪉ -4. The effect is opposite to that of 1D hydrostatic models in radiative equilibrium, where scattering reduces the cooling effect of strong LTE lines in the higher layers of the photosphere. Coherent line scattering also changes the temperature distribution in the high atmosphere, where we observe stronger fluctuations compared to a treatment of lines as true absorbers.

  18. Scoops3D: software to analyze 3D slope stability throughout a digital landscape

    USGS Publications Warehouse

    Reid, Mark E.; Christian, Sarah B.; Brien, Dianne L.; Henderson, Scott T.

    2015-01-01

    The computer program, Scoops3D, evaluates slope stability throughout a digital landscape represented by a digital elevation model (DEM). The program uses a three-dimensional (3D) method of columns approach to assess the stability of many (typically millions) potential landslides within a user-defined size range. For each potential landslide (or failure), Scoops3D assesses the stability of a rotational, spherical slip surface encompassing many DEM cells using a 3D version of either Bishop’s simplified method or the Ordinary (Fellenius) method of limit-equilibrium analysis. Scoops3D has several options for the user to systematically and efficiently search throughout an entire DEM, thereby incorporating the effects of complex surface topography. In a thorough search, each DEM cell is included in multiple potential failures, and Scoops3D records the lowest stability (factor of safety) for each DEM cell, as well as the size (volume or area) associated with each of these potential landslides. It also determines the least-stable potential failure for the entire DEM. The user has a variety of options for building a 3D domain, including layers or full 3D distributions of strength and pore-water pressures, simplistic earthquake loading, and unsaturated suction conditions. Results from Scoops3D can be readily incorporated into a geographic information system (GIS) or other visualization software. This manual includes information on the theoretical basis for the slope-stability analysis, requirements for constructing and searching a 3D domain, a detailed operational guide (including step-by-step instructions for using the graphical user interface [GUI] software, Scoops3D-i) and input/output file specifications, practical considerations for conducting an analysis, results of verification tests, and multiple examples illustrating the capabilities of Scoops3D. Easy-to-use software installation packages are available for the Windows or Macintosh operating systems; these packages

  19. Sub-micron resolution high-speed spectral domain optical coherence tomography in quality inspection for printed electronics

    NASA Astrophysics Data System (ADS)

    Czajkowski, J.; Lauri, J.; Sliz, R.; Fält, P.; Fabritius, T.; Myllylä, R.; Cense, B.

    2012-04-01

    We present the use of sub-micron resolution optical coherence tomography (OCT) in quality inspection for printed electronics. The device used in the study is based on a supercontinuum light source, Michelson interferometer and high-speed spectrometer. The spectrometer in the presented spectral-domain optical coherence tomography setup (SD-OCT) is centered at 600 nm and covers a 400 nm wide spectral region ranging from 400 nm to 800 nm. Spectra were acquired at a continuous rate of 140,000 per second. The full width at half maximum of the point spread function obtained from a Parylene C sample was 0:98 m. In addition to Parylene C layers, the applicability of sub-micron SD-OCT in printed electronics was studied using PET and epoxy covered solar cell, a printed RFID antenna and a screen-printed battery electrode. A commercial SD-OCT system was used for reference measurements.

  20. Simultaneous dual-band optical coherence tomography in the spectral domain for high resolution in vivo imaging.

    PubMed

    Cimalla, Peter; Walther, Julia; Mehner, Mirko; Cuevas, Maximiliano; Koch, Edmund

    2009-10-26

    Optical coherence tomography (OCT) in the spectral domain is demonstrated simultaneously at two wavelength bands centered at 800 nm and 1250 nm. A novel commercial supercontinuum laser is applied as a single low coherence broadband light source. The emission spectrum of the source is shaped by optical and spatial filtering in order to achieve an adequate double peak spectrum containing the wavelength bands 700 - 900 nm and 1100 - 1400 nm for dual-band OCT imaging and thus reducing the radiation exposure of the sample. Each wavelength band is analyzed with an individual spectrometer at an A-scan rate of about 12 kHz which enables real-time imaging for the examination of moving samples. A common path optical setup optimized for both spectral regions with a separate single fiber-based scanning unit was realized which facilitates flexible handling and easy access to the measurement area. The free-space axial resolutions were measured to be less than 4.5 microm and 7 microm at 800 nm and 1250 nm, respectively. Three-dimensional imaging ten times faster than previously reported with a signal-to-noise-ratio of above 90 dB is achieved simultaneously in both wavelength bands. Spectral domain dual-band OCT combines real-time imaging with high resolution at 800 nm and enhanced penetration depth at 1250 nm and therefore provides a well suited tool for in vivo vasodynamic measurements. Further, spatially resolved spectral features of the sample are obtained by means of comparing the backscattering properties at two different wavelength bands. The ability of dual-band OCT to enhance tissue contrast and the sensitivity of this imaging modality to wavelength-dependent sample birefringence is demonstrated.

  1. 3D steerable wavelets in practice.

    PubMed

    Chenouard, Nicolas; Unser, Michael

    2012-11-01

    We introduce a systematic and practical design for steerable wavelet frames in 3D. Our steerable wavelets are obtained by applying a 3D version of the generalized Riesz transform to a primary isotropic wavelet frame. The novel transform is self-reversible (tight frame) and its elementary constituents (Riesz wavelets) can be efficiently rotated in any 3D direction by forming appropriate linear combinations. Moreover, the basis functions at a given location can be linearly combined to design custom (and adaptive) steerable wavelets. The features of the proposed method are illustrated with the processing and analysis of 3D biomedical data. In particular, we show how those wavelets can be used to characterize directional patterns and to detect edges by means of a 3D monogenic analysis. We also propose a new inverse-problem formalism along with an optimization algorithm for reconstructing 3D images from a sparse set of wavelet-domain edges. The scheme results in high-quality image reconstructions which demonstrate the feature-reduction ability of the steerable wavelets as well as their potential for solving inverse problems.

  2. Fourier-based reconstruction for fully 3-D PET: optimization of interpolation parameters.

    PubMed

    Matej, Samuel; Kazantsev, Ivan G

    2006-07-01

    Fourier-based approaches for three-dimensional (3-D) reconstruction are based on the relationship between the 3-D Fourier transform (FT) of the volume and the two-dimensional (2-D) FT of a parallel-ray projection of the volume. The critical step in the Fourier-based methods is the estimation of the samples of the 3-D transform of the image from the samples of the 2-D transforms of the projections on the planes through the origin of Fourier space, and vice versa for forward-projection (reprojection). The Fourier-based approaches have the potential for very fast reconstruction, but their straightforward implementation might lead to unsatisfactory results if careful attention is not paid to interpolation and weighting functions. In our previous work, we have investigated optimal interpolation parameters for the Fourier-based forward and back-projectors for iterative image reconstruction. The optimized interpolation kernels were shown to provide excellent quality comparable to the ideal sinc interpolator. This work presents an optimization of interpolation parameters of the 3-D direct Fourier method with Fourier reprojection (3D-FRP) for fully 3-D positron emission tomography (PET) data with incomplete oblique projections. The reprojection step is needed for the estimation (from an initial image) of the missing portions of the oblique data. In the 3D-FRP implementation, we use the gridding interpolation strategy, combined with proper weighting approaches in the transform and image domains. We have found that while the 3-D reprojection step requires similar optimal interpolation parameters as found in our previous studies on Fourier-based iterative approaches, the optimal interpolation parameters for the main 3D-FRP reconstruction stage are quite different. Our experimental results confirm that for the optimal interpolation parameters a very good image accuracy can be achieved even without any extra spectral oversampling, which is a common practice to decrease errors

  3. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  4. Urbanisation and 3d Spatial - a Geometric Approach

    NASA Astrophysics Data System (ADS)

    Duncan, E. E.; Rahman, A. Abdul

    2013-09-01

    Urbanisation creates immense competition for space, this may be attributed to an increase in population owing to domestic and external tourism. Most cities are constantly exploring all avenues in maximising its limited space. Hence, urban or city authorities need to plan, expand and use such three dimensional (3D) space above, on and below the city space. Thus, difficulties in property ownership and the geometric representation of the 3D city space is a major challenge. This research, investigates the concept of representing a geometric topological 3D spatial model capable of representing 3D volume parcels for man-made constructions above and below the 3D surface volume parcel. A review of spatial data models suggests that the 3D TIN (TEN) model is significant and can be used as a unified model. The concepts, logical and physical models of 3D TIN for 3D volumes using tetrahedrons as the base geometry is presented and implemented to show man-made constructions above and below the surface parcel within a user friendly graphical interface. Concepts for 3D topology and 3D analysis are discussed. Simulations of this model for 3D cadastre are implemented. This model can be adopted by most countries to enhance and streamline geometric 3D property ownership for urban centres. 3D TIN concept for spatial modelling can be adopted for the LA_Spatial part of the Land Administration Domain Model (LADM) (ISO/TC211, 2012), this satisfies the concept of 3D volumes.

  5. A model of echolocation of multiple targets in 3D space from a single emission.

    PubMed

    Matsuo, I; Tani, J; Yano, M

    2001-07-01

    Bats, using frequency-modulated echolocation sounds, can capture a moving target in real 3D space. The process by which they are able to accomplish this, however, is not completely understood. This work offers and analyzes a model for description of one mechanism that may play a role in the echolocation process of real bats. This mechanism allows for the localization of targets in 3D space from the echoes produced by a single emission. It is impossible to locate multiple targets in 3D space by using only the delay time between an emission and the resulting echoes received at two points (i.e., two ears). To locate multiple targets in 3D space requires directional information for each target. The frequency of the spectral notch, which is the frequency corresponding to the minimum of the external ear's transfer function, provides a crucial cue for directional localization. The spectrum of the echoes from nearly equidistant targets includes spectral components of both the interference between the echoes and the interference resulting from the physical process of reception at the external ear. Thus, in order to extract the spectral component associated with the external ear, this component must first be distinguished from the spectral components associated with the interference of echoes from nearly equidistant targets. In the model presented, a computation that consists of the deconvolution of the spectrum is used to extract the external-ear-dependent component in the time domain. This model describes one mechanism that can be used to locate multiple targets in 3D space.

  6. SACR ADVance 3-D Cartesian Cloud Cover (SACR-ADV-3D3C) product

    DOE Data Explorer

    Meng Wang, Tami Toto, Eugene Clothiaux, Katia Lamer, Mariko Oue

    2017-03-08

    SACR-ADV-3D3C remaps the outputs of SACRCORR for cross-wind range-height indicator (CW-RHI) scans to a Cartesian grid and reports reflectivity CFAD and best estimate domain averaged cloud fraction. The final output is a single NetCDF file containing all aforementioned corrected radar moments remapped on a 3-D Cartesian grid, the SACR reflectivity CFAD, a profile of best estimate cloud fraction, a profile of maximum observable x-domain size (xmax), a profile time to horizontal distance estimate and a profile of minimum observable reflectivity (dBZmin).

  7. 3D Imaging by Mass Spectrometry: A New Frontier

    PubMed Central

    Seeley, Erin H.; Caprioli, Richard M.

    2012-01-01

    Summary Imaging mass spectrometry can generate three-dimensional volumes showing molecular distributions in an entire organ or animal through registration and stacking of serial tissue sections. Here we review the current state of 3D imaging mass spectrometry as well as provide insights and perspectives on the process of generating 3D mass spectral data along with a discussion of the process necessary to generate a 3D image volume. PMID:22276611

  8. 3D modeling to characterize lamina cribrosa surface and pore geometries using in vivo images from normal and glaucomatous eyes.

    PubMed

    Sredar, Nripun; Ivers, Kevin M; Queener, Hope M; Zouridakis, George; Porter, Jason

    2013-07-01

    En face adaptive optics scanning laser ophthalmoscope (AOSLO) images of the anterior lamina cribrosa surface (ALCS) represent a 2D projected view of a 3D laminar surface. Using spectral domain optical coherence tomography images acquired in living monkey eyes, a thin plate spline was used to model the ALCS in 3D. The 2D AOSLO images were registered and projected onto the 3D surface that was then tessellated into a triangular mesh to characterize differences in pore geometry between 2D and 3D images. Following 3D transformation of the anterior laminar surface in 11 normal eyes, mean pore area increased by 5.1 ± 2.0% with a minimal change in pore elongation (mean change = 0.0 ± 0.2%). These small changes were due to the relatively flat laminar surfaces inherent in normal eyes (mean radius of curvature = 3.0 ± 0.5 mm). The mean increase in pore area was larger following 3D transformation in 4 glaucomatous eyes (16.2 ± 6.0%) due to their more steeply curved laminar surfaces (mean radius of curvature = 1.3 ± 0.1 mm), while the change in pore elongation was comparable to that in normal eyes (-0.2 ± 2.0%). This 3D transformation and tessellation method can be used to better characterize and track 3D changes in laminar pore and surface geometries in glaucoma.

  9. Graphics processing unit-accelerated real-time compressive sensing spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Xu, Daguang; Huang, Yong; Kang, Jin U.

    2015-03-01

    In this paper, we systematically demonstrate two real-time CS SD OCT systems based on a conventional desktop having three GPUs. The first one takes fast Fourier transform (FFT) as the sensing technique and under-sampled linear wavenumber spectral sampling as input data, while the second one uses non-uniform fast Fourier transform (NUFFT) and under-sampled nonlinear wavenumber spectral sampling, respectively. The maximum reconstruction speed of 72k and 33.5k A-line/s were achieved for these two systems, respectively, with A-scan size 2048. It is >100 times faster than the C++ implementation and >400 times faster than the MATLAB implementation. Finally, we present real-time dispersion compensated image reconstruction for both systems.

  10. 3D face analysis for demographic biometrics

    SciTech Connect

    Tokola, Ryan A; Mikkilineni, Aravind K; Boehnen, Chris Bensing

    2015-01-01

    Despite being increasingly easy to acquire, 3D data is rarely used for face-based biometrics applications beyond identification. Recent work in image-based demographic biometrics has enjoyed much success, but these approaches suffer from the well-known limitations of 2D representations, particularly variations in illumination, texture, and pose, as well as a fundamental inability to describe 3D shape. This paper shows that simple 3D shape features in a face-based coordinate system are capable of representing many biometric attributes without problem-specific models or specialized domain knowledge. The same feature vector achieves impressive results for problems as diverse as age estimation, gender classification, and race classification.

  11. Spatial routing of optical beams through time-domain spatial-spectral filtering

    NASA Astrophysics Data System (ADS)

    Babbitt, W. R.; Mossberg, T. W.

    1995-04-01

    We propose a novel new method of temporal-waveform-controlled high-speed passive spatial routing of optical beams. The method provides for the redirection of optical signals contained within a single input beam into output directions that are specified entirely by temporal information encoded on the waveform of each incident signal. The routing is effected by means of deflection from spectrally structured spatial gratings that may be optically programmed into materials with or without intrinsic frequency selectivity.

  12. Irreducible 3D Radiative Transfer Effects in Multi-angle/Multi-spectral Radio-Polarimetric Signals (Not Noise!) from a Mixture of Clouds and Aerosol in a Single Large-Footprint Pixel

    NASA Astrophysics Data System (ADS)

    Davis, A. B.; Qu, Z.; Emde, C.; Xu, F.; Marshak, A.

    2013-12-01

    Although the Glory satellite mission failed at launch, the atmospheric observation strategy implemented in its Aerosol Polarization Sensor (APS) is alive and well since it is at least possible that another one will be built and launched. This strategy is based on APS's along-track scanning spectro-polarimetric measurement system that captures the three main Stokes vector elements (I,Q,U) at a large number (>200) viewing directions for 9 wavelengths emanating from a single pixel that is ~7 km in diameter at nadir and stretches into a ~7 x 20 km^2 ellipse at the most oblique views to be considered (~70 degrees). Two cloud cameras (CCs) were also onboard Glory to provide spatial context. If the relatively large APS footprint is cloud-free or fully-cloudy, then a 1D vector radiative transfer (RT) model is adequate for predicting the APS signals and, upon iteration over its input parameters, aerosol and cloud property retrievals are expected to be of high quality. And this level of accuracy is indeed required to make a real breakthrough in climate modeling where the radiative properties of aerosols and clouds remain one of the main sources of uncertainty. However, the CCs will often show that the APS's field-of-view is a spatially complex cloud scene, but where we are mostly interested in the ambient aerosols. Moreover, it is precisely these aerosols in contact with clouds that will influence their microphysical and optical properties, leading to the manifold indirect aerosol effects on the climate system that need to be far better understood in order to improve their representation in climate models. Therefore, the research presented here addresses the challenge of characterizing simultaneously aerosols and clouds in a single APS observation. Access to polarization can, at least in principle, be used to separate clouds and aerosols using the cloud-bow directions that will often be sampled by APS. In practice, however, we need to assess the extent of 3D polarized RT

  13. Full-range ultrahigh-resolution spectral-domain optical coherence tomography in 1.7 µm wavelength region for deep-penetration and high-resolution imaging of turbid tissues

    NASA Astrophysics Data System (ADS)

    Kawagoe, Hiroyuki; Yamanaka, Masahito; Makita, Shuichi; Yasuno, Yoshiaki; Nishizawa, Norihiko

    2016-12-01

    For the first time, we developed a full-range ultrahigh-resolution (UHR) spectral-domain optical coherence tomography (SD-OCT) technique working in the 1.7 µm wavelength region. This technique allowed high-resolution, deep-tissue imaging. By using a supercontinuum source operating at a wavelength of 1.7 µm, an axial resolution of 3.6 µm in a tissue specimen was achieved. To enhance the imaging depth of UHR-SD-OCT, we performed full-range OCT imaging based on a phase modulation method. We demonstrated the three-dimensional (3D) imaging of a mouse brain with the developed system, and specific structures in the mouse brain were clearly visualized at depths up to 1.7 mm.

  14. 3D Hydrodynamical and Radiative Transfer Modeling of Eta Carinae's Colliding Winds

    NASA Astrophysics Data System (ADS)

    Madura, Thomas Ignatius; Clementel, Nicola; Gull, Theodore R.; Kruip, Chael J. H.; Paardekooper, Jan-Pieter; Icke, Vincent

    2015-08-01

    We present the results of full 3D hydrodynamical and radiative transfer simulations of the colliding stellar winds in the massive binary system Eta Carinae (Clementel, Madura, et al. 2014, MNRAS, 443, 2475 and Clementel, Madura, et al. 2015, MNRAS, 447, 2445). We accomplish this by applying the SimpleX algorithm for 3D radiative transfer on an unstructured Voronoi-Delaunay grid to 3D smoothed particle hydrodynamics simulations of the binary colliding winds. We use SimpleX to obtain detailed ionization fractions of hydrogen and helium in 3D. We investigate several computational domain sizes and Luminous Blue Variable primary-star mass-loss rates. We show how the SimpleX simulations can be used to generate synthetic spectral data cubes for comparison to data obtained with the Hubble Space Telescope (HST)/Space Telescope Imaging Spectrograph as part of a multi-cycle program to map changes in Eta Carinae's spatially extended interacting wind structures across one binary cycle. Comparison of the HST observations to the SimpleX models can help lead to more accurate constraints on the orbital, stellar, and wind parameters of the Eta Carinae system, such as the LBV primary's mass-loss rate and the companion star's temperature and luminosity. We furthermore present new methods of visualizing and interacting with output from complex 3D numerical simulations, including 3D interactive graphics and 3D printing (Madura et al. 2015, arXiv:1503.00716). While we initially focus specifically on Eta Carinae, the methods employed can be applied to numerous other colliding wind (WR 140, WR 137, WR 19) and dusty ‘pinwheel’ (WR 112, WR 104, WR 98a) binary systems. Coupled with 3D hydrodynamical simulations, SimpleX simulations have the potential to help determine the regions where dust can form and survive in these unique objects.

  15. 3D Spectroscopy in Astronomy

    NASA Astrophysics Data System (ADS)

    Mediavilla, Evencio; Arribas, Santiago; Roth, Martin; Cepa-Nogué, Jordi; Sánchez, Francisco

    2011-09-01

    Preface; Acknowledgements; 1. Introductory review and technical approaches Martin M. Roth; 2. Observational procedures and data reduction James E. H. Turner; 3. 3D Spectroscopy instrumentation M. A. Bershady; 4. Analysis of 3D data Pierre Ferruit; 5. Science motivation for IFS and galactic studies F. Eisenhauer; 6. Extragalactic studies and future IFS science Luis Colina; 7. Tutorials: how to handle 3D spectroscopy data Sebastian F. Sánchez, Begona García-Lorenzo and Arlette Pécontal-Rousset.

  16. Spherical 3D isotropic wavelets

    NASA Astrophysics Data System (ADS)

    Lanusse, F.; Rassat, A.; Starck, J.-L.

    2012-04-01

    Context. Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D spherical Fourier-Bessel (SFB) analysis in spherical coordinates is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. Aims: The aim of this paper is to present a new formalism for a spherical 3D isotropic wavelet, i.e. one based on the SFB decomposition of a 3D field and accompany the formalism with a public code to perform wavelet transforms. Methods: We describe a new 3D isotropic spherical wavelet decomposition based on the undecimated wavelet transform (UWT) described in Starck et al. (2006). We also present a new fast discrete spherical Fourier-Bessel transform (DSFBT) based on both a discrete Bessel transform and the HEALPIX angular pixelisation scheme. We test the 3D wavelet transform and as a toy-application, apply a denoising algorithm in wavelet space to the Virgo large box cosmological simulations and find we can successfully remove noise without much loss to the large scale structure. Results: We have described a new spherical 3D isotropic wavelet transform, ideally suited to analyse and denoise future 3D spherical cosmological surveys, which uses a novel DSFBT. We illustrate its potential use for denoising using a toy model. All the algorithms presented in this paper are available for download as a public code called MRS3D at http://jstarck.free.fr/mrs3d.html

  17. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-04-14

    The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.  

  18. Time-domain and spectral properties of pulsars at 154 MHz

    NASA Astrophysics Data System (ADS)

    Bell, M. E.; Murphy, Tara; Johnston, S.; Kaplan, D. L.; Croft, S.; Hancock, P.; Callingham, J. R.; Zic, A.; Dobie, D.; Swiggum, J. K.; Rowlinson, A.; Hurley-Walker, N.; Offringa, A. R.; Bernardi, G.; Bowman, J. D.; Briggs, F.; Cappallo, R. J.; Deshpande, A. A.; Gaensler, B. M.; Greenhill, L. J.; Hazelton, B. J.; Johnston-Hollitt, M.; Lonsdale, C. J.; McWhirter, S. R.; Mitchell, D. A.; Morales, M. F.; Morgan, E.; Oberoi, D.; Ord, S. M.; Prabu, T.; Shankar, N. Udaya; Srivani, K. S.; Subrahmanyan, R.; Tingay, S. J.; Wayth, R. B.; Webster, R. L.; Williams, A.; Williams, C. L.

    2016-09-01

    We present 154 MHz Murchison Widefield Array imaging observations and variability information for a sample of pulsars. Over the declination range -80° < δ < 10°, we detect 17 known pulsars with mean flux density greater than 0.3 Jy. We explore the variability properties of this sample on time-scales of minutes to years. For three of these pulsars, PSR J0953+0755, PSR J0437-4715, and PSR J0630-2834, we observe interstellar scintillation and variability on time-scales of greater than 2 min. One further pulsar, PSR J0034-0721, showed significant variability, the physical origins of which are difficult to determine. The dynamic spectra for PSR J0953+0755 and PSR J0437-4715 show discrete time and frequency structure consistent with diffractive interstellar scintillation and we present the scintillation bandwidth and time-scales from these observations. The remaining pulsars within our sample were statistically non-variable. We also explore the spectral properties of this sample and find spectral curvature in pulsars PSR J0835-4510, PSR J1752-2806, and PSR J0437-4715.

  19. Pre-existing sensory biases in the spectral domain in frogs: empirical results and methodological considerations.

    PubMed

    Gerhardt, H C; Humfeld, Sarah C

    2013-02-01

    In many species of anurans, advertisement calls excite only one of the two inner-ear organs. One prediction of the pre-existing bias hypothesis is that signal innovations that additionally excite the "untapped" organ will be more behaviorally effective than normal calls. However, recent studies have shown that females of three species with single-peaked calls that stimulate only the basilar papilla (BP) preferred single-peaked synthetic calls with a frequency typical of conspecific calls to two-peaked calls that also stimulated the amphibian papilla (AP). We report that in spring peepers (Pseudacris crucifer) that also produce single-peaked calls, females did not show a preference in choices between single-peaked and two-peaked synthetic calls. Thus, the addition of energy exciting the AP had a neutral effect on signal attractiveness. Together, these results are unsupportive of the pre-existing bias hypothesis. An alternative hypothesis is that positive fitness consequences of responding to sounds providing extraordinary spectral stimulation are required for a novel call to become established as a mate-attracting signal. Testing these ideas requires a taxonomically broader examination of responses to sounds with novel spectral complexity, and attention to some methodological details will improve the comparability of such studies.

  20. Local normal vector field formulation for periodic scattering problems formulated in the spectral domain.

    PubMed

    van Beurden, M C; Setija, I D

    2017-02-01

    We present two adapted formulations, one tailored to isotropic media and one for general anisotropic media, of the normal vector field framework previously introduced to improve convergence near arbitrarily shaped material interfaces in spectral simulation methods for periodic scattering geometries. The adapted formulations enable the definition and generation of the normal vector fields to be confined to a region of prolongation that includes the material interfaces but is otherwise limited. This allows for a more flexible application of geometrical transformations like rotation and translation per scattering object in the unit cell. Moreover, these geometrical transformations enable a cut-and-connect strategy to compose general geometries from elementary building blocks. The entire framework gives rise to continuously parameterized geometries.

  1. The Spectral Flow for Dirac Operators on Compact Planar Domains with Local Boundary Conditions

    NASA Astrophysics Data System (ADS)

    Prokhorova, Marina

    2013-09-01

    Let Dt, {0≤slantt≤slant1} be a 1-parameter family of Dirac type operators on a two-dimensional disk with m - 1 holes. Suppose that all operators Dt have the same symbol, and that D1 is conjugate to D0 by a scalar gauge transformation. Suppose that all operators Dt are considered with the same elliptic local boundary condition. Our main result is a computation of the spectral flow for such a family of operators. The answer is obtained up to multiplication by an integer constant depending only on the number of holes in the disk. This constant is calculated explicitly for the case of the annulus (m = 2).

  2. A physical model eye with 3D resolution test targets for optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Hu, Zhixiong; Liu, Wenli; Hong, Baoyu; Hao, Bingtao; Wang, Lele; Li, Jiao

    2014-09-01

    Optical coherence tomography (OCT) has been widely employed as non-invasive 3D imaging diagnostic instrument, particularly in the field of ophthalmology. Although OCT has been approved for use in clinic in USA, Europe and Asia, international standardization of this technology is still in progress. Validation of OCT imaging capabilities is considered extremely important to ensure its effective use in clinical diagnoses. Phantom with appropriate test targets can assist evaluate and calibrate imaging performance of OCT at both installation and throughout lifetime of the instrument. In this paper, we design and fabricate a physical model eye with 3D resolution test targets to characterize OCT imaging performance. The model eye was fabricated with transparent resin to simulate realistic ophthalmic testing environment, and most key optical elements including cornea, lens and vitreous body were realized. The test targets which mimic USAF 1951 test chart were fabricated on the fundus of the model eye by 3D printing technology. Differing from traditional two dimensional USAF 1951 test chart, a group of patterns which have different thickness in depth were fabricated. By measuring the 3D test targets, axial resolution as well as lateral resolution of an OCT system can be evaluated at the same time with this model eye. To investigate this specialized model eye, it was measured by a scientific spectral domain OCT instrument and a clinical OCT system respectively. The results demonstrate that the model eye with 3D resolution test targets have the potential of qualitatively and quantitatively validating the performance of OCT systems.

  3. 3D World Building System

    ScienceCinema

    None

    2016-07-12

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  4. 3D Buckligami: Digital Matter

    NASA Astrophysics Data System (ADS)

    van Hecke, Martin; de Reus, Koen; Florijn, Bastiaan; Coulais, Corentin

    2014-03-01

    We present a class of elastic structures which exhibit collective buckling in 3D, and create these by a 3D printing/moulding technique. Our structures consist of cubic lattice of anisotropic unit cells, and we show that their mechanical properties are programmable via the orientation of these unit cells.

  5. 3D World Building System

    SciTech Connect

    2013-10-30

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  6. LLNL-Earth3D

    SciTech Connect

    2013-10-01

    Earth3D is a computer code designed to allow fast calculation of seismic rays and travel times through a 3D model of the Earth. LLNL is using this for earthquake location and global tomography efforts and such codes are of great interest to the Earth Science community.

  7. Market study: 3-D eyetracker

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A market study of a proposed version of a 3-D eyetracker for initial use at NASA's Ames Research Center was made. The commercialization potential of a simplified, less expensive 3-D eyetracker was ascertained. Primary focus on present and potential users of eyetrackers, as well as present and potential manufacturers has provided an effective means of analyzing the prospects for commercialization.

  8. 3D Radiative Transfer Effects in Multi-Angle/Multi-Spectral Radio-Polarimetric Signals from a Mixture of Clouds and Aerosols Viewed by a Non-Imaging Sensor

    NASA Technical Reports Server (NTRS)

    Davis, Anthony B.; Garay, Michael J.; Xu, Feng; Qu, Zheng; Emde, Claudia

    2013-01-01

    When observing a spatially complex mix of aerosols and clouds in a single relatively large field-of-view, nature entangles their signals non-linearly through polarized radiation transport processes that unfold in the 3D position and direction spaces. In contrast, any practical forward model in a retrieval algorithm will use only 1D vector radiative transfer (vRT) in a linear mixing technique. We assess the difference between the observed and predicted signals using synthetic data from a high-fidelity 3D vRT model with clouds generated using a Large Eddy Simulation model and an aerosol climatology. We find that this difference is signal--not noise--for the Aerosol Polarimetry Sensor (APS), an instrument developed by NASA. Moreover, the worst case scenario is also the most interesting case, namely, when the aerosol burden is large, hence hase the most impact on the cloud microphysics and dynamics. Based on our findings, we formulate a mitigation strategy for these unresolved cloud adjacency effects assuming that some spatial information is available about the structure of the clouds at higher resolution from "context" cameras, as was planned for NASA's ill-fated Glory mission that was to carry the APS but failed to reach orbit. Application to POLDER (POLarization and Directionality of Earth Reflectances) data from the period when PARASOL (Polarization and Anisotropy of Reflectances for Atmospheric Sciences coupled with Observations from a Lidar) was in the A-train is briefly discussed.

  9. 3D vision system assessment

    NASA Astrophysics Data System (ADS)

    Pezzaniti, J. Larry; Edmondson, Richard; Vaden, Justin; Hyatt, Bryan; Chenault, David B.; Kingston, David; Geulen, Vanilynmae; Newell, Scott; Pettijohn, Brad

    2009-02-01

    In this paper, we report on the development of a 3D vision system consisting of a flat panel stereoscopic display and auto-converging stereo camera and an assessment of the system's use for robotic driving, manipulation, and surveillance operations. The 3D vision system was integrated onto a Talon Robot and Operator Control Unit (OCU) such that direct comparisons of the performance of a number of test subjects using 2D and 3D vision systems were possible. A number of representative scenarios were developed to determine which tasks benefited most from the added depth perception and to understand when the 3D vision system hindered understanding of the scene. Two tests were conducted at Fort Leonard Wood, MO with noncommissioned officers ranked Staff Sergeant and Sergeant First Class. The scenarios; the test planning, approach and protocols; the data analysis; and the resulting performance assessment of the 3D vision system are reported.

  10. 3D printing in dentistry.

    PubMed

    Dawood, A; Marti Marti, B; Sauret-Jackson, V; Darwood, A

    2015-12-01

    3D printing has been hailed as a disruptive technology which will change manufacturing. Used in aerospace, defence, art and design, 3D printing is becoming a subject of great interest in surgery. The technology has a particular resonance with dentistry, and with advances in 3D imaging and modelling technologies such as cone beam computed tomography and intraoral scanning, and with the relatively long history of the use of CAD CAM technologies in dentistry, it will become of increasing importance. Uses of 3D printing include the production of drill guides for dental implants, the production of physical models for prosthodontics, orthodontics and surgery, the manufacture of dental, craniomaxillofacial and orthopaedic implants, and the fabrication of copings and frameworks for implant and dental restorations. This paper reviews the types of 3D printing technologies available and their various applications in dentistry and in maxillofacial surgery.

  11. PLOT3D user's manual

    NASA Technical Reports Server (NTRS)

    Walatka, Pamela P.; Buning, Pieter G.; Pierce, Larry; Elson, Patricia A.

    1990-01-01

    PLOT3D is a computer graphics program designed to visualize the grids and solutions of computational fluid dynamics. Seventy-four functions are available. Versions are available for many systems. PLOT3D can handle multiple grids with a million or more grid points, and can produce varieties of model renderings, such as wireframe or flat shaded. Output from PLOT3D can be used in animation programs. The first part of this manual is a tutorial that takes the reader, keystroke by keystroke, through a PLOT3D session. The second part of the manual contains reference chapters, including the helpfile, data file formats, advice on changing PLOT3D, and sample command files.

  12. High-speed and high-sensitivity parallel spectral-domain optical coherence tomography using a supercontinuum light source.

    PubMed

    Barrick, Jessica; Doblas, Ana; Gardner, Michael R; Sears, Patrick R; Ostrowski, Lawrence E; Oldenburg, Amy L

    2016-12-15

    The three most important metrics in optical coherence tomography (OCT) are resolution, speed, and sensitivity. Because there is a complex interplay between these metrics, no previous work has obtained the best performance in all three metrics simultaneously. We demonstrate that a high-power supercontinuum source, in combination with parallel spectral-domain OCT, achieves an unparalleled combination of resolution, speed, and sensitivity. This system captures cross-sectional images spanning 4  mm×0.5  mm at 1,024,000 lines/s with 2×14  μm resolution (axial×transverse) at a sensitivity of 113 dB. Imaging using the proposed system is demonstrated on highly differentiated human bronchial epithelial cells to capture and spatially localize ciliary dynamics.

  13. Improved phase sensitivity in spectral domain phase microscopy using line-field illumination and self phase-referencing

    PubMed Central

    Yaqoob, Zahid; Choi, Wonshik; Oh, Seungeun; Lue, Niyom; Park, Yongkeun; Fang-Yen, Christopher; Dasari, Ramachandra R.; Badizadegan, Kamran; Feld, Michael S.

    2010-01-01

    We report a quantitative phase microscope based on spectral domain optical coherence tomography and line-field illumination. The line illumination allows self phase-referencing method to reject common-mode phase noise. The quantitative phase microscope also features a separate reference arm, permitting the use of high numerical aperture (NA > 1) microscope objectives for high resolution phase measurement at multiple points along the line of illumination. We demonstrate that the path-length sensitivity of the instrument can be as good as 41 pm/Hz, which makes it suitable for nanometer scale study of cell motility. We present the detection of natural motions of cell surface and two-dimensional surface profiling of a HeLa cell. PMID:19550464

  14. Broadband frequency-domain near-infrared spectral tomography using a mode-locked Ti:sapphire laser

    PubMed Central

    Wang, Jia; Jiang, Shudong; Paulsen, Keith D.; Pogue, Brian W.

    2009-01-01

    Frequency-domain near-infrared (NIR) diffuse spectral tomography with a mode-locked Ti:sapphire laser is presented, providing tunable multiwavelength quantitative spectroscopy with maximal power for thick tissue imaging. The system was developed to show that intrinsically high stability can be achieved with many wavelengths in the NIR range, using a mode-locked signal of 80 MHz with heterodyned lock-in detection. The effect of cumulative noise from multiple wavelengths of data on the reconstruction process was studied, and it was shown that inclusion of more wavelengths can reduce skew in the noise distribution. This normalization of the data variance then minimizes errors in estimation of chromophore concentrations. Simulations and tissue phantom experiments were used to quantify this improvement in image accuracy for recovery of tissue hemoglobin and oxygen saturation. PMID:19340109

  15. Simultaneous Confocal Scanning Laser Ophthalmoscopy Combined with High-Resolution Spectral-Domain Optical Coherence Tomography: A Review

    PubMed Central

    Castro Lima, Verônica; Rodrigues, Eduardo B.; Nunes, Renata P.; Sallum, Juliana F.; Farah, Michel E.; Meyer, Carsten H.

    2011-01-01

    We aimed to evaluate technical aspects and the clinical relevance of a simultaneous confocal scanning laser ophthalmoscope and a high-speed, high-resolution, spectral-domain optical coherence tomography (SDOCT) device for retinal imaging. The principle of confocal scanning laser imaging provides a high resolution of retinal and choroidal vasculature with low light exposure. Enhanced contrast, details, and image sharpness are generated using confocality. The real-time SDOCT provides a new level of accuracy for assessment of the angiographic and morphological correlation. The combined system allows for simultaneous recordings of topographic and tomographic images with accurate correlation between them. Also it can provide simultaneous multimodal imaging of retinal pathologies, such as fluorescein and indocyanine green angiographies, infrared and blue reflectance (red-free) images, fundus autofluorescence images, and OCT scans (Spectralis HRA + OCT; Heidelberg Engineering, Heidelberg, Germany). The combination of various macular diagnostic tools can lead to a better understanding and improved knowledge of macular diseases. PMID:22132313

  16. Three-dimensional segmentation and reconstruction of the retinal vasculature from spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Guimarães, Pedro; Rodrigues, Pedro; Celorico, Dirce; Serranho, Pedro; Bernardes, Rui

    2015-01-01

    We reconstruct the three-dimensional shape and location of the retinal vascular network from commercial spectral-domain (SD) optical coherence tomography (OCT) data. The two-dimensional location of retinal vascular network on the eye fundus is obtained through support vector machines classification of properly defined fundus images from OCT data, taking advantage of the fact that on standard SD-OCT, the incident light beam is absorbed by hemoglobin, creating a shadow on the OCT signal below each perfused vessel. The depth-wise location of the vessel is obtained as the beginning of the shadow. The classification of crossovers and bifurcations within the vascular network is also addressed. We illustrate the feasibility of the method in terms of vessel caliber estimation and the accuracy of bifurcations and crossovers classification.

  17. An anomaly detection approach for the identification of DME patients using spectral domain optical coherence tomography images.

    PubMed

    Sidibé, Désiré; Sankar, Shrinivasan; Lemaître, Guillaume; Rastgoo, Mojdeh; Massich, Joan; Cheung, Carol Y; Tan, Gavin S W; Milea, Dan; Lamoureux, Ecosse; Wong, Tien Y; Mériaudeau, Fabrice

    2017-02-01

    This paper proposes a method for automatic classification of spectral domain OCT data for the identification of patients with retinal diseases such as Diabetic Macular Edema (DME). We address this issue as an anomaly detection problem and propose a method that not only allows the classification of the OCT volume, but also allows the identification of the individual diseased B-scans inside the volume. Our approach is based on modeling the appearance of normal OCT images with a Gaussian Mixture Model (GMM) and detecting abnormal OCT images as outliers. The classification of an OCT volume is based on the number of detected outliers. Experimental results with two different datasets show that the proposed method achieves a sensitivity and a specificity of 80% and 93% on the first dataset, and 100% and 80% on the second one. Moreover, the experiments show that the proposed method achieves better classification performance than other recently published works.

  18. Noninvasive in vivo structural and vascular imaging of human oral tissues with spectral domain optical coherence tomography

    PubMed Central

    Davoudi, Bahar; Lindenmaier, Andras; Standish, Beau A.; Allo, Ghassan; Bizheva, Kostadinka; Vitkin, Alex

    2012-01-01

    A spectral domain optical coherence tomography (SD-OCT) system and an oral imaging probe have been developed to visualize the microstructural morphology and microvasculature in the human oral cavity. Structural OCT images of ex vivo pig oral tissues with the histology of the same sites were acquired and compared for correlations. Structural in vivo OCT images of healthy human tissue as well as a pathologic site (ulcer) were obtained and analyzed based on the results of the ex vivo pig study, drawing on the similarity between human and swine oral tissues. In vivo Doppler and speckle variance OCT images of the oral cavity in human volunteers were also acquired, to demonstrate the feasibility of microvascular imaging of healthy and pathologic (scar) oral tissue. PMID:22567578

  19. Intrasurgical Human Retinal Imaging With Manual Instrument Tracking Using a Microscope-Integrated Spectral-Domain Optical Coherence Tomography Device

    PubMed Central

    Hahn, Paul; Carrasco-Zevallos, Oscar; Cunefare, David; Migacz, Justin; Farsiu, Sina; Izatt, Joseph A.; Toth, Cynthia A.

    2015-01-01

    Purpose: To characterize the first in-human intraoperative imaging using a custom prototype spectral-domain microscope-integrated optical coherence tomography (MIOCT) device during vitreoretinal surgery with instruments in the eye. Methods: Under institutional review board approval for a prospective intraoperative study, MIOCT images were obtained at surgical pauses with instruments held static in the vitreous cavity and then concurrently with surgical maneuvers. Postoperatively, MIOCT images obtained at surgical pauses were compared with images obtained with a high-resolution handheld spectral-domain OCT (HHOCT) system with objective endpoints, including acquisition of images acceptable for analysis and identification of predefined macular morphologic or pathologic features. Results: Human MIOCT images were successfully obtained before incision and during pauses in surgical maneuvers. MIOCT imaging confirmed preoperative diagnoses, such as epiretinal membrane, full-thickness macular hole, and vitreomacular traction and demonstrated successful achievement of surgical goals. MIOCT and HHOCT images obtained at surgical pauses in two cohorts of five patients were comparable with greater than or equal to 80% correlation in 80% of patients. Real-time video-imaging concurrent with surgical manipulations enabled, for the first time using this device, visualization of dynamic instrument-retina interaction with targeted OCT tracking. Conclusion: MIOCT is successful for imaging at surgical pauses and for real-time image guidance with implementation of targeted OCT tracking. Even faster acquisition speeds are currently being developed with incorporation of a swept-source MIOCT engine. Further refinements and investigations will be directed toward continued integration for real-time volumetric imaging of surgical maneuvers. Translational Relevance: Ongoing development of seamless MIOCT systems will likely transform surgical visualization, approaches, and decision-making. PMID

  20. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  1. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  2. Spectral-domain low-coherence interferometry for phase-sensitive measurement of Faraday rotation at multiple depths.

    PubMed

    Yeh, Yi-Jou; Black, Adam J; Akkin, Taner

    2013-10-10

    We describe a method for differential phase measurement of Faraday rotation from multiple depth locations simultaneously. A polarization-maintaining fiber-based spectral-domain interferometer that utilizes a low-coherent light source and a single camera is developed. Light decorrelated by the orthogonal channels of the fiber is launched on a sample as two oppositely polarized circular states. These states reflect from sample surfaces and interfere with the corresponding states of the reference arm. A custom spectrometer, which is designed to simplify camera alignment, separates the orthogonal channels and records the interference-related oscillations on both spectra. Inverse Fourier transform of the spectral oscillations in k-space yields complex depth profiles, whose amplitudes and phase difference are related to reflectivity and Faraday rotation within the sample, respectively. Information along a full depth profile is produced at the camera speed without performing an axial scan for a multisurface sample. System sensitivity for the Faraday rotation measurement is 0.86 min of arc. Verdet constants of clear liquids and turbid media are measured at 687 nm.

  3. High precision computing with charge domain devices and a pseudo-spectral method therefor

    NASA Technical Reports Server (NTRS)

    Barhen, Jacob (Inventor); Toomarian, Nikzad (Inventor); Fijany, Amir (Inventor); Zak, Michail (Inventor)

    1997-01-01

    The present invention enhances the bit resolution of a CCD/CID MVM processor by storing each bit of each matrix element as a separate CCD charge packet. The bits of each input vector are separately multiplied by each bit of each matrix element in massive parallelism and the resulting products are combined appropriately to synthesize the correct product. In another aspect of the invention, such arrays are employed in a pseudo-spectral method of the invention, in which partial differential equations are solved by expressing each derivative analytically as matrices, and the state function is updated at each computation cycle by multiplying it by the matrices. The matrices are treated as synaptic arrays of a neural network and the state function vector elements are treated as neurons. In a further aspect of the invention, moving target detection is performed by driving the soliton equation with a vector of detector outputs. The neural architecture consists of two synaptic arrays corresponding to the two differential terms of the soliton-equation and an adder connected to the output thereof and to the output of the detector array to drive the soliton equation.

  4. Optical characterization of agricultural pest insects: a methodological study in the spectral and time domains

    NASA Astrophysics Data System (ADS)

    Li, Y. Y.; Zhang, H.; Duan, Z.; Lian, M.; Zhao, G. Y.; Sun, X. H.; Hu, J. D.; Gao, L. N.; Feng, H. Q.; Svanberg, S.

    2016-08-01

    Identification of agricultural pest insects is an important aspect in insect research and agricultural monitoring. We have performed a methodological study of how spectroscopic techniques and wing-beat frequency analysis might provide relevant information. An optical system based on the combination of close-range remote sensing and reflectance spectroscopy was developed to study the optical characteristics of different flying insects, collected in Southern China. The results demonstrate that the combination of wing-beat frequency assessment and reflectance spectral analysis has the potential to successfully differentiate between insect species. Further, studies of spectroscopic characteristics of fixed specimen of insects, also from Central China, showed the possibility of refined agricultural pest identification. Here, in addition to reflectance recordings also laser-induced fluorescence spectra were investigated for all the species of insects under study and found to provide complementary information to optically distinguish insects. In order to prove the practicality of the techniques explored, clearly fieldwork aiming at elucidating the variability of parameters, even within species, must be performed.

  5. Standard resolution spectral domain optical coherence tomography in clinical ophthalmic imaging

    NASA Astrophysics Data System (ADS)

    Szkulmowska, Anna; Cyganek, Marta; Targowski, Piotr; Kowalczyk, Andrzej; Kaluzny, Jakub J.; Wojtkowski, Maciej; Fujimoto, James G.

    2005-04-01

    In this study we show clinical application of Spectral Optical Coherence Tomography (SOCT), which enables operation with 40 times higher speed than commercial Stratus OCT instrument. Using high speed SOCT instrument it is possible to collect more information and increase the quality of reconstructed cross-sectional retinal images. Two generations of compact and portable clinical SOCT instruments were constructed in Medical Physics Group at Nicolaus Copernicus University in Poland. The first SOCT instrument is a low-cost system operating with standard, 12 micrometer axial resolution and the second is high resolution system using combined superluminescent diodes light source, which enables imaging with 4.8 micrometer axial resolution. Both instruments have worked in Ophthalmology Clinic of Collegium Medicum in Bydgoszcz. During the study we have examined 44 patients with different pathologies of the retina including: Central Serous Chorioretinopathy (CSC), Choroidal Neovascularization (CNV), Pigment Epithelial Detachment (PED), Macular Hole, Epiretinal Membrane, Outer Retinal Infarction etc. All these pathologies were first diagnosed by classical methods (like fundus camera imaging and angiography) and then examined with the aid of SOCT system. In this contribution we present examples of SOCT cross-sectional retinal imaging of pathologic eyes measured with standard resolution. We also compare cross-sectional images of pathology obtained by standard and high resolution systems.

  6. Unassisted 3D camera calibration

    NASA Astrophysics Data System (ADS)

    Atanassov, Kalin; Ramachandra, Vikas; Nash, James; Goma, Sergio R.

    2012-03-01

    With the rapid growth of 3D technology, 3D image capture has become a critical part of the 3D feature set on mobile phones. 3D image quality is affected by the scene geometry as well as on-the-device processing. An automatic 3D system usually assumes known camera poses accomplished by factory calibration using a special chart. In real life settings, pose parameters estimated by factory calibration can be negatively impacted by movements of the lens barrel due to shaking, focusing, or camera drop. If any of these factors displaces the optical axes of either or both cameras, vertical disparity might exceed the maximum tolerable margin and the 3D user may experience eye strain or headaches. To make 3D capture more practical, one needs to consider unassisted (on arbitrary scenes) calibration. In this paper, we propose an algorithm that relies on detection and matching of keypoints between left and right images. Frames containing erroneous matches, along with frames with insufficiently rich keypoint constellations, are detected and discarded. Roll, pitch yaw , and scale differences between left and right frames are then estimated. The algorithm performance is evaluated in terms of the remaining vertical disparity as compared to the maximum tolerable vertical disparity.

  7. Model-based 3D SAR reconstruction

    NASA Astrophysics Data System (ADS)

    Knight, Chad; Gunther, Jake; Moon, Todd

    2014-06-01

    Three dimensional scene reconstruction with synthetic aperture radar (SAR) is desirable for target recognition and improved scene interpretability. The vertical aperture, which is critical to reconstruct 3D SAR scenes, is almost always sparsely sampled due to practical limitations, which creates an underdetermined problem. This papers explores 3D scene reconstruction using a convex model-based approach. The approach developed is demonstrated on 3D scenes, but can be extended to SAR reconstruction of sparsely sampled signals in the spatial and, or, frequency domains. The model-based approach enables knowledge-aided image formation (KAIF) by incorporating spatial, aspect, and sparsity magnitude terms into the image reconstruction. The incorporation of these terms, which are based on prior scene knowledge, will demonstrate improved results compared to traditional image formation algorithms. The SAR image formation problem is formulated as a second order cone program (SOCP) and the results are demonstrated on 3D scenes using simulated data and data from the GOTCHA data collect.1 The model-based results are contrasted against traditional backprojected images.

  8. 3D Scan Systems Integration

    DTIC Science & Technology

    2007-11-02

    AGENCY USE ONLY (Leave Blank) 2. REPORT DATE 5 Feb 98 4. TITLE AND SUBTITLE 3D Scan Systems Integration REPORT TYPE AND DATES COVERED...2-89) Prescribed by ANSI Std. Z39-1 298-102 [ EDO QUALITY W3PECTEDI DLA-ARN Final Report for US Defense Logistics Agency on DDFG-T2/P3: 3D...SCAN SYSTEMS INTEGRATION Contract Number SPO100-95-D-1014 Contractor Ohio University Delivery Order # 0001 Delivery Order Title 3D Scan Systems

  9. Spectral and spatial nondestructive examination of dielectric materials with THz time domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Beckmann, J.; von Chrzanowski, L. S.; Fratzscher, D.; Ewert, U.

    2012-05-01

    A time domain spectrometer T-ray 2000® operating in the range of 0.2-2 THz was used for Time of Flight measurements. A series of ethanol water mixtures from 10% to 90% were produced subsequently filled in polystyrene cells and analyzed in the T-ray 2000 TDS system in the reflection mode. The reflectivity of the material liquid interface is strongly influenced by the ethanol concentration in water. The reciprocal reflection coefficient of the material liquid interface was found to be a useful discriminating feature for further Probably of Detection calculations which can be used for the performance evaluation of potential THz bottle scanners. THz pulse echo (PE) measurements were performed in comparison to the established ultra sound PE technique for flaw detection of plastics. Synthetic aperture reconstructions were applied for simulated data to reconstruct the flaw shape. The results were compared with B-scan images of a high density polyethylene (HDPE) test cylinder. Existing restrictions on the quality of the back projected images and limits of the existing model are discussed in detail.

  10. Double-difference relocations and spectral ratio analysis of volcanic seismic events in the Mount St. Helens crater using a 3D velocity model suggest slip events under the new dome with constant stress-drop scaling.

    NASA Astrophysics Data System (ADS)

    Harrington, R. M.; Kwiatek, G.; Moran, S. C.

    2014-12-01

    Shallow low frequency seismic events are common features associated with restless and erupting volcanoes. The physical mechanisms generating their characteristic low frequency, and often extended duration signals remain poorly understood. Here we present new double-difference relocations and spectral scaling of a group of ~400 shallow low-frequency seismic events occurring within the Mount St. Helens edifice during its 2004-2008 dome-building eruption, as recorded by a temporary seismic array for a month within the crater in 2006. Relocation results suggest that the majority of earthquakes occurred in the center of the crater close to the vent at depths < 500 m, with some events potentially locating under the new dome but ~200-300m southwest of the vent. Low-frequency events exhibit moment-corner frequency scaling roughly consistent with a constant static stress-drop, similar to tectonic earthquakes occurring elsewhere in shallow crustal faults. The scaling suggests that the ~400 events result from stick-slip behavior, and that the low frequency character of the waveforms may result from a combination of path effects and slow rupture speeds. For relocation, we divide the 400 events into eight families based on waveform similarity, and use a subset of nearly 40 earthquakes with clear first arrivals ranging in moment magnitude from 0.4 - 1.8 to calculate hypocenters. We then relocate these events using a double-difference method with a three-dimensional velocity model of the edifice from Waite and Moran (2009). The relocated events are then used to estimate source parameters of the remaining earthquakes via a spectral ratio technique. Spectral corner frequency estimations based on this spectral ratio approach produce stress-drop values of ~1 MPa assuming a shear-wave velocity of 1500 m/s. The estimations also indicate a constant stress-drop scaling for all events, with two event families having lower estimated stress drops of ~0.1 MPa. While localized lithological

  11. 3D polymer scaffold arrays.

    PubMed

    Simon, Carl G; Yang, Yanyin; Dorsey, Shauna M; Ramalingam, Murugan; Chatterjee, Kaushik

    2011-01-01

    We have developed a combinatorial platform for fabricating tissue scaffold arrays that can be used for screening cell-material interactions. Traditional research involves preparing samples one at a time for characterization and testing. Combinatorial and high-throughput (CHT) methods lower the cost of research by reducing the amount of time and material required for experiments by combining many samples into miniaturized specimens. In order to help accelerate biomaterials research, many new CHT methods have been developed for screening cell-material interactions where materials are presented to cells as a 2D film or surface. However, biomaterials are frequently used to fabricate 3D scaffolds, cells exist in vivo in a 3D environment and cells cultured in a 3D environment in vitro typically behave more physiologically than those cultured on a 2D surface. Thus, we have developed a platform for fabricating tissue scaffold libraries where biomaterials can be presented to cells in a 3D format.

  12. Autofocus for 3D imaging

    NASA Astrophysics Data System (ADS)

    Lee-Elkin, Forest

    2008-04-01

    Three dimensional (3D) autofocus remains a significant challenge for the development of practical 3D multipass radar imaging. The current 2D radar autofocus methods are not readily extendable across sensor passes. We propose a general framework that allows a class of data adaptive solutions for 3D auto-focus across passes with minimal constraints on the scene contents. The key enabling assumption is that portions of the scene are sparse in elevation which reduces the number of free variables and results in a system that is simultaneously solved for scatterer heights and autofocus parameters. The proposed method extends 2-pass interferometric synthetic aperture radar (IFSAR) methods to an arbitrary number of passes allowing the consideration of scattering from multiple height locations. A specific case from the proposed autofocus framework is solved and demonstrates autofocus and coherent multipass 3D estimation across the 8 passes of the "Gotcha Volumetric SAR Data Set" X-Band radar data.

  13. Combinatorial 3D Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2015-03-01

    We present a class of elastic structures which exhibit 3D-folding motion. Our structures consist of cubic lattices of anisotropic unit cells that can be tiled in a complex combinatorial fashion. We design and 3d-print this complex ordered mechanism, in which we combine elastic hinges and defects to tailor the mechanics of the material. Finally, we use this large design space to encode smart functionalities such as surface patterning and multistability.

  14. Light field display and 3D image reconstruction

    NASA Astrophysics Data System (ADS)

    Iwane, Toru

    2016-06-01

    Light field optics and its applications become rather popular in these days. With light field optics or light field thesis, real 3D space can be described in 2D plane as 4D data, which we call as light field data. This process can be divided in two procedures. First, real3D scene is optically reduced with imaging lens. Second, this optically reduced 3D image is encoded into light field data. In later procedure we can say that 3D information is encoded onto a plane as 2D data by lens array plate. This transformation is reversible and acquired light field data can be decoded again into 3D image with the arrayed lens plate. "Refocusing" (focusing image on your favorite point after taking a picture), light-field camera's most popular function, is some kind of sectioning process from encoded 3D data (light field data) to 2D image. In this paper at first I show our actual light field camera and our 3D display using acquired and computer-simulated light field data, on which real 3D image is reconstructed. In second I explain our data processing method whose arithmetic operation is performed not in Fourier domain but in real domain. Then our 3D display system is characterized by a few features; reconstructed image is of finer resolutions than density of arrayed lenses and it is not necessary to adjust lens array plate to flat display on which light field data is displayed.

  15. Optical microcavity scanning 3D tomography.

    PubMed

    Di Donato, Andrea; Criante, Luigino; LoTurco, Sara; Farina, Marco

    2014-10-01

    A scanning optical microcavity is exploited to achieve lens-free 3D tomography of microfluidic channels. The microcavity, powered by a low-coherence source, is realized by approaching a cleaved fiber to few tens of micrometers over the sample. The interference of scattered waves inside the cavity shapes the transverse field distribution by focusing the beam and overcoming the diffraction limit due to the optical-fiber numerical aperture. The focusing effect is also preserved in the inner layers of the sample, allowing optical 3D tomography. Analysis of microfluidic channels was demonstrated through this noninvasive technique. Although the experimental setup recalls the well-known fiber-optic Fourier-domain common-path optical coherence tomography, the proposed method has intrinsic characteristics that distinguish it from the former one.

  16. Azimuthally Anisotropic 3D Velocity Continuation

    DOE PAGES

    Burnett, William; Fomel, Sergey

    2011-01-01

    We extend time-domain velocity continuation to the zero-offset 3D azimuthally anisotropic case. Velocity continuation describes how a seismic image changes given a change in migration velocity. This description turns out to be of a wave propagation process, in which images change along a velocity axis. In the anisotropic case, the velocity model is multiparameter. Therefore, anisotropic image propagation is multidimensional. We use a three-parameter slowness model, which is related to azimuthal variations in velocity, as well as their principal directions. This information is useful for fracture and reservoir characterization from seismic data. We provide synthetic diffraction imaging examples to illustratemore » the concept and potential applications of azimuthal velocity continuation and to analyze the impulse response of the 3D velocity continuation operator.« less

  17. Complex Resistivity 3D Imaging for Ground Reinforcement Site

    NASA Astrophysics Data System (ADS)

    Son, J.; Kim, J.; Park, S.

    2012-12-01

    Induced polarization (IP) method is used for mineral exploration and generally classified into two categories, time and frequency domain method. IP method in frequency domain measures amplitude and absolute phase to the transmitted currents, and is often called spectral induced polarization (SIP) when measurement is made for the wide-band frequencies. Our research group has been studying the modeling and inversion algorithms of complex resistivity method since several years ago and recently started to apply this method for various field applications. We already completed the development of 2/3D modeling and inversion program and developing another algorithm to use wide-band data altogether. Until now complex resistivity (CR) method was mainly used for the surface or tomographic survey of mineral exploration. Through the experience, we can find that the resistivity section from CR method is very similar with that of conventional resistivity method. Interpretation of the phase section is generally well matched with the geological information of survey area. But because most of survey area has very touch and complex terrain, 2D survey and interpretation are used generally. In this study, the case study of 3D CR survey conducted for the site where ground reinforcement was done to prevent the subsidence will be introduced. Data was acquired with the Zeta system, the complex resistivity measurement system produced by Zonge Co. using 8 frequencies from 0.125 to 16 Hz. 2D survey was conducted for total 6 lines with 5 m dipole spacing and 20 electrodes. Line length is 95 meter for every line. Among these 8 frequency data, data below 1 Hz was used considering its quality. With the 6 line data, 3D inversion was conducted. Firstly 2D interpretation was made with acquired data and its results were compared with those of resistivity survey. Resulting resistivity image sections of CR and resistivity method were very similar. Anomalies in phase image section showed good agreement

  18. From 3D view to 3D print

    NASA Astrophysics Data System (ADS)

    Dima, M.; Farisato, G.; Bergomi, M.; Viotto, V.; Magrin, D.; Greggio, D.; Farinato, J.; Marafatto, L.; Ragazzoni, R.; Piazza, D.

    2014-08-01

    In the last few years 3D printing is getting more and more popular and used in many fields going from manufacturing to industrial design, architecture, medical support and aerospace. 3D printing is an evolution of bi-dimensional printing, which allows to obtain a solid object from a 3D model, realized with a 3D modelling software. The final product is obtained using an additive process, in which successive layers of material are laid down one over the other. A 3D printer allows to realize, in a simple way, very complex shapes, which would be quite difficult to be produced with dedicated conventional facilities. Thanks to the fact that the 3D printing is obtained superposing one layer to the others, it doesn't need any particular work flow and it is sufficient to simply draw the model and send it to print. Many different kinds of 3D printers exist based on the technology and material used for layer deposition. A common material used by the toner is ABS plastics, which is a light and rigid thermoplastic polymer, whose peculiar mechanical properties make it diffusely used in several fields, like pipes production and cars interiors manufacturing. I used this technology to create a 1:1 scale model of the telescope which is the hardware core of the space small mission CHEOPS (CHaracterising ExOPlanets Satellite) by ESA, which aims to characterize EXOplanets via transits observations. The telescope has a Ritchey-Chrétien configuration with a 30cm aperture and the launch is foreseen in 2017. In this paper, I present the different phases for the realization of such a model, focusing onto pros and cons of this kind of technology. For example, because of the finite printable volume (10×10×12 inches in the x, y and z directions respectively), it has been necessary to split the largest parts of the instrument in smaller components to be then reassembled and post-processed. A further issue is the resolution of the printed material, which is expressed in terms of layers

  19. Reproducibility of Spectral Domain Optical Coherence Tomography Retinal Thickness Measurements and Conversion to Equivalent Time Domain Metrics in Diabetic Macular Edema

    PubMed Central

    Bressler, Susan B.; Edwards, Allison R.; Chalam, Kakarla V.; Bressler, Neil M.; Glassman, Adam R.; Jaffe, Glenn J.; Melia, Michele; Saggau, David D.; Plous, Oren Z.

    2014-01-01

    Importance Advances in retinal imaging have led to the development of optical coherence tomography (OCT) instruments that incorporate spectral domain (SD) technology. Understanding measurement variability and relationships between retinal thickness measurements obtained on different machines is critical for proper use in clinical trials and clinical settings. Objectives Evaluate reproducibility of retinal thickness measurements from OCT images obtained by time domain (TD) (Zeiss Stratus) and SD (Zeiss Cirrus and Heidelberg Spectralis) instruments and formulate equations to convert retinal thickness measurements from SD-OCT to equivalent values on TD-OCT. Design Cross-sectional observational study. Each study eye underwent two replicate Stratus scans followed by two replicate Cirrus or Spectralis (real time image registration utilized) scans centered on the fovea. Setting Private and institutional practices Participants Diabetic persons with at least one eye with central-involved diabetic macular edema (DME), defined as Stratus central subfield thickness (CST)≥250μm. An additional normative cohort, individuals with diabetes but without DME, was enrolled. Main Outcome Measure(s) OCT CST and macular volume Results The Bland-Altman coefficient of repeatability for relative change in CST (the degree of change that could be expected from measurement variability) was lower on Spectralis compared with Stratus and Cirrus scans (7%, 12–15%, and 14%, respectively). For each cohort, the initial Stratus CST was within 10% of the replicate Stratus measurement 92% of the time; the conversion equations predicted a Stratus CST within 10% of the observed thickness 86% and 89% of the time for Stratus/Cirrus and Stratus/Spectralis groups, respectively. The Bland-Altman limits of agreement for relative change in CST between machines (the degree of change that could be expected from measurement variability, combined within and between instrument variability) were 21% for Cirrus and

  20. 2D time domain spectral phase encoding/wavelength hopping coherent DPSK-OCDMA system using fiber Bragg gratings and phase modulator

    NASA Astrophysics Data System (ADS)

    Gao, Zhensen; Dai, Bo; Wang, Xu; Kataoka, Nobuyuki; Wada, Naoya

    2010-12-01

    We propose and experimentally demonstrate a reconfigurable two-dimensional (temporal-spectral) time domain spectral phase encoding (SPE) scheme for coherent optical code-division-multiple-access (OCDMA) application. 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. 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. A Fiber Bragg Gratings array is used for generating the two-dimensional wavelength hopping pattern while the high speed phase modulator is used for generating the spectral phase pattern. The proposed scheme can enable simultaneous generation of the time domain spectral phase encoding and DPSK data modulation using only a single phase modulator. In the experiment, the two-dimensional SPE codes have been generated and modulated with 2.5-Gb/s DPSK data using a single phase modulator. Transmission of the 2.5-Gb/s DPSK data over 49km fiber with BER<10-9 has been demonstrated successfully. The proposed scheme exhibits the potential to simplify the architecture and improve the security of the OCDMA system.

  1. 3D Face modeling using the multi-deformable method.

    PubMed

    Hwang, Jinkyu; Yu, Sunjin; Kim, Joongrock; Lee, Sangyoun

    2012-09-25

    In this paper, we focus on the problem of the accuracy performance of 3D face modeling techniques using corresponding features in multiple views, which is quite sensitive to feature extraction errors. To solve the problem, we adopt a statistical model-based 3D face modeling approach in a mirror system consisting of two mirrors and a camera. The overall procedure of our 3D facial modeling method has two primary steps: 3D facial shape estimation using a multiple 3D face deformable model and texture mapping using seamless cloning that is a type of gradient-domain blending. To evaluate our method's performance, we generate 3D faces of 30 individuals and then carry out two tests: accuracy test and robustness test. Our method shows not only highly accurate 3D face shape results when compared with the ground truth, but also robustness to feature extraction errors. Moreover, 3D face rendering results intuitively show that our method is more robust to feature extraction errors than other 3D face modeling methods. An additional contribution of our method is that a wide range of face textures can be acquired by the mirror system. By using this texture map, we generate realistic 3D face for individuals at the end of the paper.

  2. YouDash3D: exploring stereoscopic 3D gaming for 3D movie theaters

    NASA Astrophysics Data System (ADS)

    Schild, Jonas; Seele, Sven; Masuch, Maic

    2012-03-01

    Along with the success of the digitally revived stereoscopic cinema, events beyond 3D movies become attractive for movie theater operators, i.e. interactive 3D games. In this paper, we present a case that explores possible challenges and solutions for interactive 3D games to be played by a movie theater audience. We analyze the setting and showcase current issues related to lighting and interaction. Our second focus is to provide gameplay mechanics that make special use of stereoscopy, especially depth-based game design. Based on these results, we present YouDash3D, a game prototype that explores public stereoscopic gameplay in a reduced kiosk setup. It features live 3D HD video stream of a professional stereo camera rig rendered in a real-time game scene. We use the effect to place the stereoscopic effigies of players into the digital game. The game showcases how stereoscopic vision can provide for a novel depth-based game mechanic. Projected trigger zones and distributed clusters of the audience video allow for easy adaptation to larger audiences and 3D movie theater gaming.

  3. Speaking Volumes About 3-D

    NASA Technical Reports Server (NTRS)

    2002-01-01

    In 1999, Genex submitted a proposal to Stennis Space Center for a volumetric 3-D display technique that would provide multiple users with a 360-degree perspective to simultaneously view and analyze 3-D data. The futuristic capabilities of the VolumeViewer(R) have offered tremendous benefits to commercial users in the fields of medicine and surgery, air traffic control, pilot training and education, computer-aided design/computer-aided manufacturing, and military/battlefield management. The technology has also helped NASA to better analyze and assess the various data collected by its satellite and spacecraft sensors. Genex capitalized on its success with Stennis by introducing two separate products to the commercial market that incorporate key elements of the 3-D display technology designed under an SBIR contract. The company Rainbow 3D(R) imaging camera is a novel, three-dimensional surface profile measurement system that can obtain a full-frame 3-D image in less than 1 second. The third product is the 360-degree OmniEye(R) video system. Ideal for intrusion detection, surveillance, and situation management, this unique camera system offers a continuous, panoramic view of a scene in real time.

  4. A 3-D chimera grid embedding technique

    NASA Technical Reports Server (NTRS)

    Benek, J. A.; Buning, P. G.; Steger, J. L.

    1985-01-01

    A three-dimensional (3-D) chimera grid-embedding technique is described. The technique simplifies the construction of computational grids about complex geometries. The method subdivides the physical domain into regions which can accommodate easily generated grids. Communication among the grids is accomplished by interpolation of the dependent variables at grid boundaries. The procedures for constructing the composite mesh and the associated data structures are described. The method is demonstrated by solution of the Euler equations for the transonic flow about a wing/body, wing/body/tail, and a configuration of three ellipsoidal bodies.

  5. Macrophage podosomes go 3D.

    PubMed

    Van Goethem, Emeline; Guiet, Romain; Balor, Stéphanie; Charrière, Guillaume M; Poincloux, Renaud; Labrousse, Arnaud; Maridonneau-Parini, Isabelle; Le Cabec, Véronique

    2011-01-01

    Macrophage tissue infiltration is a critical step in the immune response against microorganisms and is also associated with disease progression in chronic inflammation and cancer. Macrophages are constitutively equipped with specialized structures called podosomes dedicated to extracellular matrix (ECM) degradation. We recently reported that these structures play a critical role in trans-matrix mesenchymal migration mode, a protease-dependent mechanism. Podosome molecular components and their ECM-degrading activity have been extensively studied in two dimensions (2D), but yet very little is known about their fate in three-dimensional (3D) environments. Therefore, localization of podosome markers and proteolytic activity were carefully examined in human macrophages performing mesenchymal migration. Using our gelled collagen I 3D matrix model to obligate human macrophages to perform mesenchymal migration, classical podosome markers including talin, paxillin, vinculin, gelsolin, cortactin were found to accumulate at the tip of F-actin-rich cell protrusions together with β1 integrin and CD44 but not β2 integrin. Macrophage proteolytic activity was observed at podosome-like protrusion sites using confocal fluorescence microscopy and electron microscopy. The formation of migration tunnels by macrophages inside the matrix was accomplished by degradation, engulfment and mechanic compaction of the matrix. In addition, videomicroscopy revealed that 3D F-actin-rich protrusions of migrating macrophages were as dynamic as their 2D counterparts. Overall, the specifications of 3D podosomes resembled those of 2D podosome rosettes rather than those of individual podosomes. This observation was further supported by the aspect of 3D podosomes in fibroblasts expressing Hck, a master regulator of podosome rosettes in macrophages. In conclusion, human macrophage podosomes go 3D and take the shape of spherical podosome rosettes when the cells perform mesenchymal migration. This work

  6. 3D Printed Bionic Nanodevices.

    PubMed

    Kong, Yong Lin; Gupta, Maneesh K; Johnson, Blake N; McAlpine, Michael C

    2016-06-01

    The ability to three-dimensionally interweave biological and functional materials could enable the creation of bionic devices possessing unique and compelling geometries, properties, and functionalities. Indeed, interfacing high performance active devices with biology could impact a variety of fields, including regenerative bioelectronic medicines, smart prosthetics, medical robotics, and human-machine interfaces. Biology, from the molecular scale of DNA and proteins, to the macroscopic scale of tissues and organs, is three-dimensional, often soft and stretchable, and temperature sensitive. This renders most biological platforms incompatible with the fabrication and materials processing methods that have been developed and optimized for functional electronics, which are typically planar, rigid and brittle. A number of strategies have been developed to overcome these dichotomies. One particularly novel approach is the use of extrusion-based multi-material 3D printing, which is an additive manufacturing technology that offers a freeform fabrication strategy. This approach addresses the dichotomies presented above by (1) using 3D printing and imaging for customized, hierarchical, and interwoven device architectures; (2) employing nanotechnology as an enabling route for introducing high performance materials, with the potential for exhibiting properties not found in the bulk; and (3) 3D printing a range of soft and nanoscale materials to enable the integration of a diverse palette of high quality functional nanomaterials with biology. Further, 3D printing is a multi-scale platform, allowing for the incorporation of functional nanoscale inks, the printing of microscale features, and ultimately the creation of macroscale devices. This blending of 3D printing, novel nanomaterial properties, and 'living' platforms may enable next-generation bionic systems. In this review, we highlight this synergistic integration of the unique properties of nanomaterials with the

  7. A colour image reproduction framework for 3D colour printing

    NASA Astrophysics Data System (ADS)

    Xiao, Kaida; Sohiab, Ali; Sun, Pei-li; Yates, Julian M.; Li, Changjun; Wuerger, Sophie

    2016-10-01

    In this paper, the current technologies in full colour 3D printing technology were introduced. A framework of colour image reproduction process for 3D colour printing is proposed. A special focus was put on colour management for 3D printed objects. Two approaches, colorimetric colour reproduction and spectral based colour reproduction are proposed in order to faithfully reproduce colours in 3D objects. Two key studies, colour reproduction for soft tissue prostheses and colour uniformity correction across different orientations are described subsequently. Results are clear shown that applying proposed colour image reproduction framework, performance of colour reproduction can be significantly enhanced. With post colour corrections, a further improvement in colour process are achieved for 3D printed objects.

  8. Petal, terrain & airbags - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Portions of the lander's deflated airbags and a petal are at the lower area of this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. The metallic object at lower right is part of the lander's low-gain antenna. This image is part of a 3D 'monster

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  9. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2004-04-05

    This project consists of two activities. Task A, Simulations and Measurements, combines all the material model development and associated numerical work with the materials-oriented experimental activities. The goal of this effort is to provide an improved understanding of dynamic material properties and to provide accurate numerical representations of those properties for use in analysis codes. Task B, ALE3D Development, involves general development activities in the ALE3D code with the focus of improving simulation capabilities for problems of mutual interest to DoD and DOE. Emphasis is on problems involving multi-phase flow, blast loading of structures and system safety/vulnerability studies.

  10. Vel-IO 3D: A tool for 3D velocity model construction, optimization and time-depth conversion in 3D geological modeling workflow

    NASA Astrophysics Data System (ADS)

    Maesano, Francesco E.; D'Ambrogi, Chiara

    2017-02-01

    We present Vel-IO 3D, a tool for 3D velocity model creation and time-depth conversion, as part of a workflow for 3D model building. The workflow addresses the management of large subsurface dataset, mainly seismic lines and well logs, and the construction of a 3D velocity model able to describe the variation of the velocity parameters related to strong facies and thickness variability and to high structural complexity. Although it is applicable in many geological contexts (e.g. foreland basins, large intermountain basins), it is particularly suitable in wide flat regions, where subsurface structures have no surface expression. The Vel-IO 3D tool is composed by three scripts, written in Python 2.7.11, that automate i) the 3D instantaneous velocity model building, ii) the velocity model optimization, iii) the time-depth conversion. They determine a 3D geological model that is consistent with the primary geological constraints (e.g. depth of the markers on wells). The proposed workflow and the Vel-IO 3D tool have been tested, during the EU funded Project GeoMol, by the construction of the 3D geological model of a flat region, 5700 km2 in area, located in the central part of the Po Plain. The final 3D model showed the efficiency of the workflow and Vel-IO 3D tool in the management of large amount of data both in time and depth domain. A 4 layer-cake velocity model has been applied to a several thousand (5000-13,000 m) thick succession, with 15 horizons from Triassic up to Pleistocene, complicated by a Mesozoic extensional tectonics and by buried thrusts related to Southern Alps and Northern Apennines.

  11. Dynamic virtual optical network embedding in spectral and spatial domains over elastic optical networks with multicore fibers

    NASA Astrophysics Data System (ADS)

    Zhu, Ruijie; Zhao, Yongli; Yang, Hui; Tan, Yuanlong; Chen, Haoran; Zhang, Jie; Jue, Jason P.

    2016-08-01

    Network virtualization can eradicate the ossification of the infrastructure and stimulate innovation of new network architectures and applications. Elastic optical networks (EONs) are ideal substrate networks for provisioning flexible virtual optical network (VON) services. However, as network traffic continues to increase exponentially, the capacity of EONs will reach the physical limitation soon. To further increase network flexibility and capacity, the concept of EONs is extended into the spatial domain. How to map the VON onto substrate networks by thoroughly using the spectral and spatial resources is extremely important. This process is called VON embedding (VONE).Considering the two kinds of resources at the same time during the embedding process, we propose two VONE algorithms, the adjacent link embedding algorithm (ALEA) and the remote link embedding algorithm (RLEA). First, we introduce a model to solve the VONE problem. Then we design the embedding ability measurement of network elements. Based on the network elements' embedding ability, two VONE algorithms were proposed. Simulation results show that the proposed VONE algorithms could achieve better performance than the baseline algorithm in terms of blocking probability and revenue-to-cost ratio.

  12. Imaging site-specific peptide-targeting in tumor tissues using spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Ma, Lixin; Zhang, Miao; Yu, Ping

    2011-03-01

    We report imaging studies on site-specific peptide-targeting in tumor tissues using newly developed optical peptide probes and spectral-domain optical coherence tomography (SD-OCT). The system used two broadband superluminescent light emission diodes with different central wavelengths. An electro-optic modulation in the reference beam was used to get full-range deep imaging inside tumor tissues. The optical probes were based on Bombesin (BBN) that is a fourteen amino acid peptide. BBN has high binding affinity to gastrin-releasing peptide (GRP) receptors overexpressed on several human cancer cell lines. Fluorescence BBN probes were developed by conjugating the last eight residues of BBN, -Q-W-A-V-G-H-L-M-(NH2), with Alexa Flour 680 or Alexa Fluor 750 dye molecules via amino acid linker -G-G-G. The SD-OCT imaging can identify normal tissue and tumor tissue through the difference in scattering coefficient, and trace the BBN conjugate probes through the absorption of the dye molecules using the twowavelength algorithm. We performed the specific uptake and receptor-blocking experiments of the optical BBN probes in severely compromised immunodeficient mouse model bearing human PC-3 prostate tumor xenografts. Tumor and muscle tissues were collected and used for SD-OCT imaging. The SD-OCT images showed fluorescence traces of the BBN probes in the peptide-targeted tumor tissues. Our results demonstrated that SD-OCT is a potential tool for preclinical and clinical early cancer detection.

  13. Ultrahigh resolution endoscopic spectral domain optical coherence tomography with a tiny rotary probe driven by a hollow ultrasonic motor

    NASA Astrophysics Data System (ADS)

    Zhang, Ning; Chen, Tianyuan; Huo, Tiancheng; Wang, Chengming; Zheng, Jing-gao; Zhou, Tieying; Xue, Ping

    2013-03-01

    This paper proposes a novel rotary endoscopic probe for spectral-domain optical coherence tomography (SD-OCT). The probe with a large N.A. objective lens is driven by an ultra-small hollow rectangular ultrasonic motor for circular scanning. Compared to the conventional driven techniques, the hollow ultrasonic motor enables the fiber to pass through its inside. Therefore the fiber, the objective lens and the motor are all at the same side. This enables 360 degree unobstructed imaging without any shadow resulted from power wire as in the conventional motor-driven endoscopic OCT. Moreover, it shortens the length of the rigid tip and enhances the flexibility of the probe. Meanwhile, the ultrasonic motor is robust, simple, quiet and of high torque, very suitable for OCT endoscopic probe. The side length of the motor is 0.7 mm with 5mm in length. The outer diameter of the probe is 1.5mm. A significant improvement in the lateral resolution is demonstrated due to the novel design of the objective lens. A right-angle lens is utilized instead of the traditional right-angle prism as the last optics close to the sample, leading to a reduction of the working distance and an enlargement of the N.A. of the objective lens. It is demonstrated that the endoscopic SD-OCT system achieves an axial resolution of ~7μm, a lateral resolution of ~6μm and a SNR of ~96dB.

  14. Direct visualization of tear film on soft contact lens using ultra-high resolution spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Wang, Jianhua; Jiao, Shuliang; Ruggeri, Marco; Wehbe, Hassan M.

    2008-02-01

    The integrity of the tear film on the surface of contact lenses is essential to maintaining visual clarity and the overall health of the superficial structures of the eye (cornea and conjunctiva) for contact lens wearers. It is very critical to evaluate pre- and post-lens tear films in contact lens practice to make sure the lens is properly fitted. Improper lens fitting may cause ocular discomfort, visual distortion and ocular infection. It is very often for soft contact lens wearers to experience dry eye, especially in the afternoon after wearing the lens for a period of time. Dry eye has been a common cause of contact lens drop-off. There is currently no method available to directly visualize the tears on and underneath the contact lens in situ on human eye, mainly due to the extremely difficulty in imaging the micrometer-thin tear layer. An ultra-high resolution spectral domain optical coherence tomography has been developed with a telecentric light delivery system mounted with a slit-lamp. The system has a 3 micrometer depth resolution with a scan width up to 15 mm. The system was used to image soft contact lenses on the human eye. For the first time to our knowledge, tear films on the center and edge of the soft contact lens were directly visualized in vivo.

  15. GPU-accelerated non-uniform fast Fourier transform-based compressive sensing spectral domain optical coherence tomography.

    PubMed

    Xu, Daguang; Huang, Yong; Kang, Jin U

    2014-06-16

    We implemented the graphics processing unit (GPU) accelerated compressive sensing (CS) non-uniform in k-space spectral domain optical coherence tomography (SD OCT). Kaiser-Bessel (KB) function and Gaussian function are used independently as the convolution kernel in the gridding-based non-uniform fast Fourier transform (NUFFT) algorithm with different oversampling ratios and kernel widths. Our implementation is compared with the GPU-accelerated modified non-uniform discrete Fourier transform (MNUDFT) matrix-based CS SD OCT and the GPU-accelerated fast Fourier transform (FFT)-based CS SD OCT. It was found that our implementation has comparable performance to the GPU-accelerated MNUDFT-based CS SD OCT in terms of image quality while providing more than 5 times speed enhancement. When compared to the GPU-accelerated FFT based-CS SD OCT, it shows smaller background noise and less side lobes while eliminating the need for the cumbersome k-space grid filling and the k-linear calibration procedure. Finally, we demonstrated that by using a conventional desktop computer architecture having three GPUs, real-time B-mode imaging can be obtained in excess of 30 fps for the GPU-accelerated NUFFT based CS SD OCT with frame size 2048(axial) × 1,000(lateral).

  16. Combined analysis of whole human blood parameters by Raman spectroscopy and spectral-domain low-coherence interferometry

    NASA Astrophysics Data System (ADS)

    Gnyba, M.; Wróbel, M. S.; Karpienko, K.; Milewska, D.; Jedrzejewska-Szczerska, M.

    2015-07-01

    In this article the simultaneous investigation of blood parameters by complementary optical methods, Raman spectroscopy and spectral-domain low-coherence interferometry, is presented. Thus, the mutual relationship between chemical and physical properties may be investigated, because low-coherence interferometry measures optical properties of the investigated object, while Raman spectroscopy gives information about its molecular composition. A series of in-vitro measurements were carried out to assess sufficient accuracy for monitoring of blood parameters. A vast number of blood samples with various hematological parameters, collected from different donors, were measured in order to achieve a statistical significance of results and validation of the methods. Preliminary results indicate the benefits in combination of presented complementary methods and form the basis for development of a multimodal system for rapid and accurate optical determination of selected parameters in whole human blood. Future development of optical systems and multivariate calibration models are planned to extend the number of detected blood parameters and provide a robust quantitative multi-component analysis.

  17. The use of handheld spectral domain optical coherence tomography in pediatric ophthalmology practice: Our experience of 975 infants and children

    PubMed Central

    Mallipatna, Ashwin; Vinekar, Anand; Jayadev, Chaitra; Dabir, Supriya; Sivakumar, Munsusamy; Krishnan, Narasimha; Mehta, Pooja; Berendschot, Tos; Yadav, Naresh Kumar

    2015-01-01

    Purpose: Optical coherence tomography (OCT) is an important imaging tool assessing retinal architecture. In this article, we report a single centers experience of using handheld spectral domain (SD)-OCT in a pediatric population using the Envisu 2300 (Bioptigen Inc., Research Triangle Park, NC, USA). Methods: We studied SD-OCT images from 975 patients imaged from January 2011 to December 2014. The variety of cases that underwent an SD-OCT was analyzed. Cases examples from different case scenarios were selected to showcase unique examples of many diseases. Results: Three hundred and sixty-eight infants (37.7%) were imaged for retinopathy of prematurity, 362 children (37.1%) underwent the test for evaluation of suboptimal vision or an unexplained vision loss, 126 children (12.9%) for evaluation of nystagmus or night blindness, 54 children (5.5%) for an intraocular tumor or a mass lesion such as retinoblastoma, and 65 children (6.7%) for other diseases of the pediatric retina. The unique findings in the retinal morphology seen with some of these diseases are discussed. Conclusion: The handheld SD-OCT is useful in the evaluation of the pediatric retinal diseases. The test is useful in the assessment of vision development in premature children, evaluation of unexplained vision loss and amblyopia, nystagmus and night blindness, and intraocular tumors (including retinoblastoma). PMID:26458476

  18. The Effect of Optic Disc Center Displacement on Retinal Nerve Fiber Layer Measurement Determined by Spectral Domain Optical Coherence Tomography

    PubMed Central

    Uhm, Ki Bang; Sung, Kyung Rim; Kang, Min Ho; Cho, Hee Yoon; Seong, Mincheol

    2016-01-01

    Purpose To investigate the effect of optic disc center displacement on retinal nerve fiber layer (RNFL) measurement determined by spectral domain optical coherence tomography (SD-OCT). Methods The optic disc center was manipulated at 1-pixel intervals in horizontal, vertical, and diagonal directions. According to the manipulated optic disc center location, the RNFL thickness data were resampled: (1) at a 3.46-mm diameter circle; and (2) between a 2.5-mm diameter circle and 5.4-mm square. Error was calculated between the original and resampled RNFL measurements. The tolerable error threshold of the optic disc center displacement was determined by considering test-retest variability of SD-OCT. The unreliable zone was defined as an area with 10% or more variability. Results The maximum tolerable error thresholds of optic disc center displacement on the RNFL thickness map were distributed from 0.042 to 0.09 mm in 8 directions. The threshold shape was vertically elongated. Clinically important unreliable zones were located: (1) at superior and inferior region in the vertical displacement; (2) at inferotemporal region in the horizontal displacement, and (3) at superotemporal or inferotemporal region in the diagonal displacement. The unreliable zone pattern and threshold limit varied according to the direction of optic disc displacement. Conclusions Optic disc center displacement had a considerable impact on whole RNFL thickness measurements. Understanding the effect of optic disc center displacement could contribute to reliable RNFL measurements. PMID:27783663

  19. Blood flowing state analysis in outflow tract of chick embryonic heart based on spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zhao, Yuqian; Suo, Yanyan; Liang, Chengbo; Ma, Zhenhe

    2016-03-01

    The cardiac development is a complicated process affected by genetic and environmental factors. Wall shear stress (WSS) and periodic stress (WPS) are the components which have been proved to influence the morphogenesis during early stages of cardiac development. The vessel wall will be deformed by the blood pressure and produce natural elastic force acting on the blood. Because blood flowing in different flow state and show different characteristics of fluid, which influence the calculation of WSS and WPS directly, it is necessary to study the blood flow state. In this paper, we introduce a method to quantify the blood flowing state of early stage chick embryonic heart based on high speed spectral domain optical coherence tomography (SDOCT).4D (x,y,z,t) scan was performed on the outflow tract (OFT) of HH18 (~3 days of incubation) chick embryonic heart. By processing the structural image, the geometric parameters were obtained. Blood flow velocity distribution in the OFT were calculated by Doppler OCT method. Hemodynamic parameters were obtained at different times during the cardiac cycle used biofluid mechanics theory, such as Reynolds number and Womersley number.

  20. Effect of Hydroxychloroquine on the Retinal Layers: A Quantitative Evaluation with Spectral-Domain Optical Coherence Tomography

    PubMed Central

    Gurler, Bulent; Yildirim, Aydin; Goker, Hasan; Pehlevan, Hatice Seval

    2016-01-01

    Purpose. To evaluate the effect of hydroxychloroquine on retinal pigment epithelium- (RPE-) Bruch's membrane complex, photoreceptor outer segment, and macular ganglion cell-inner plexiform layer (GCIPL) thicknesses using spectral-domain optical coherence tomography (SD-OCT). Methods. In this prospective case-control study, 51 eyes of 51 hydroxychloroquine patients and 30 eyes of 30 healthy subjects were included. High-quality images were obtained using a Cirrus HD-OCT with 5-line raster mode; the photoreceptor inner segment (IS) and outer segment (OS), sum of the segments (IS + OS), and RPE-Bruch's membrane complex were analyzed. Results. The thicknesses of the IS + OS and OS layers were significantly lower in the hydroxychloroquine subjects compared to the control subjects (P < 0.05). RPE-Bruch's membrane complex thicknesses were significantly higher in the hydroxychloroquine subjects than for those of the control subjects (P < 0.05). The minimum and temporal-inferior macular GCIPL thicknesses were significantly different between the patients with hydroxychloroquine use and the control subjects (P = 0.04 and P = 0.03, resp.). Conclusions. The foveal photoreceptor OS thinning, loss of GCIPL, and RPE-Bruch's membrane thickening were detected in patients with hydroxychloroquine therapy. This quantitative approach using SD-OCT images may have important implications to use as an early indicator of retinal toxicity without any visible signs of hydroxychloroquine retinopathy. PMID:27656292

  1. Evaluation of Corneal Epithelial Healing Under Contact Lens with Spectral-Domain Anterior Segment Optical Coherence Tomography (SD-OCT)

    PubMed Central

    Pang, Claudine E; M, Vanathi; Tan, Donald T.H; Mehta, Jodhbir S

    2011-01-01

    Purpose: To describe a novel technique of using Spectral-domain (SD) anterior segment optical coherence tomography (SD-OCT) in the evaluation of corneal epithelial healing under a therapeutic contact lens (TCL) after lamellar keratoplasty and Epi-LASIK procedures. Design: Prospective, non-comparative, observational case series. Methods: Ten eyes of eight patients undergoing lamellar corneal transplantation and Epi-LASIK procedures at the Singapore National Eye Centre were included in the study. Ultra-high resolution SD-OCT scans of the cornea with a TCL in-situ were performed sequentially on the first, third and fifth day after procedure, with the RTVue (Optovue, Inc, Fremont, CA, USA), and the image findings were correlated with the clinical picture. Complete epithelial healing was verified with removal of TCL and fluorescein staining. Results: 5 eyes underwent Descemet’s stripping automated endothelial keratoplasty (DSAEK), 1 eye underwent deep anterior lamellar keratoplasty (DALK) and 4 eyes underwent Epi-LASIK. All eyes had complete epithelial healing with TCL in-situ by the third post-operative day. SD-OCT images were able to demonstrate the epithelial layer distinctly under the TCL in all cases. Conclusions: SD-OCT is a valuable imaging tool for monitoring the progression of epithelial healing with TCL in situ in patients following corneal surgical procedures. PMID:21686324

  2. Spectral-domain optical coherence tomography in subjects over 60 years of age, and its implications for designing clinical trials

    PubMed Central

    Caramoy, Albert; Foerster, Jonathan; Allakhiarova, Elvira; Hoyng, Carel B; Dröge, Katharina; Kirchhof, Bernd; Fauser, Sascha

    2012-01-01

    Aims To study the variability of central retinal thickness (CRT), its concordance to the fellow eye, and the implications for designing future clinical trials using spectral-domain optical coherence tomography (SD-OCT). Methods Cross-sectional retrospective analysis of European Genetic Database. 632 eyes of 316 subjects over 60 years of age without macular pathology were examined using SD-OCT. Results Mean CRT was 280.22 µm and 281.02 µm for the right and left eyes, respectively. There was a strong concordance for all measured values between right and left eyes. Men had significantly thicker CRT than women. Variation up to 23 µm difference between both eyes was seen. To detect a change of at least 30 µm in CRT, a sample size of 90 or 176 per group is needed for a single-arm or double-arm study, respectively (α=0.05, power=0.80, no loss to follow up, assuming SD in future studies=100 µm). Conclusions Clinical trials using CRT as an endpoint are feasible in terms of sample size needed. PMID:22863948

  3. In vivo tear film thickness measurement and tear film dynamics visualization using spectral domain OCT and an efficient delay estimator

    NASA Astrophysics Data System (ADS)

    Aranha dos Santos, Valentin; Schmetterer, Leopold; Gröschl, Martin; Garhofer, Gerhard; Werkmeister, René M.

    2016-03-01

    Dry eye syndrome is a highly prevalent disease of the ocular surface characterized by an instability of the tear film. Traditional methods used for the evaluation of tear film stability are invasive or show limited repeatability. Here we propose a new noninvasive approach to measure tear film thickness using an efficient delay estimator and ultrahigh resolution spectral domain OCT. Silicon wafer phantoms with layers of known thickness and group index were used to validate the estimator-based thickness measurement. A theoretical analysis of the fundamental limit of the precision of the estimator is presented and the analytical expression of the Cramér-Rao lower bound (CRLB), which is the minimum variance that may be achieved by any unbiased estimator, is derived. The performance of the estimator against noise was investigated using simulations. We found that the proposed estimator reaches the CRLB associated with the OCT amplitude signal. The technique was applied in vivo in healthy subjects and dry eye patients. Series of tear film thickness maps were generated, allowing for the visualization of tear film dynamics. Our results show that the central tear film thickness precisely measured in vivo with a coefficient of variation of about 0.65% and that repeatable tear film dynamics can be observed. The presented method has the potential of being an alternative to breakup time measurements (BUT) and could be used in clinical setting to study patients with dry eye disease and monitor their treatments.

  4. Assessment of the Optic Disc Morphology Using Spectral-Domain Optical Coherence Tomography and Scanning Laser Ophthalmoscopy

    PubMed Central

    Calvo, Pilar; Ferreras, Antonio; Abadia, Beatriz; Ara, Mirian; Figus, Michele; Pablo, Luis E.; Frezzotti, Paolo

    2014-01-01

    Objective. To compare the equivalent optic nerve head (OHN) parameters obtained with confocal scanning laser ophthalmoscopy (HRT3) and spectral-domain optical coherence tomography (OCT) in healthy and glaucoma patients. Methods. One hundred and eighty-two consecutive healthy subjects and 156 patients with open-angle glaucoma were divided into 2 groups according to intraocular pressure and visual field outcomes. All participants underwent imaging of the ONH with the HRT3 and the Cirrus OCT. The ONH parameters and the receiver operating characteristic (ROC) curves were compared between both groups. Results. Mean age did not differ between the normal and glaucoma groups (59.55 ± 9.7 years and 61.05 ± 9.4 years, resp.; P = 0.15). Rim area, average cup-to-disc (C/D) ratio, vertical C/D ratio, and cup volume were different between both instruments (P < 0.001). All equivalent ONH parameters, except disc area, were different between both groups (P < 0.001). The best areas under the ROC curve were observed for vertical C/D ratio (0.980 for OCT and 0.942 for HRT3; P = 0.11). Sensitivities at 95% fixed-specificities of OCT parameters were higher than those of HRT3. Conclusions. Equivalent ONH parameters of Cirrus OCT and HRT3 are different and cannot be used interchangeably. ONH parameters measured with OCT yielded a slightly better diagnostic performance. PMID:25110668

  5. Relationship between Spectral-Domain Optical Coherence Tomography and Standard Automated Perimetry in Healthy and Glaucoma Patients

    PubMed Central

    Abadia, Beatriz; Ara, Mirian; Ferrandez, Blanca; Otin, Sofia; Frezzotti, Paolo; Pablo, Luis E.

    2014-01-01

    Objective. To evaluate the relationship between spectral-domain optical coherence tomography (OCT) and standard automated perimetry (SAP) in healthy and glaucoma individuals. Methods. The sample comprised 338 individuals divided into 2 groups according to intraocular pressure and visual field outcomes. All participants underwent a reliable SAP and imaging of the optic nerve head with the Cirrus OCT. Pearson correlations were calculated between threshold sensitivity values of SAP (converted to linear scale) and OCT parameters. Results. Mean age did not differ between the control and glaucoma groups (59.55 ± 9.7 years and 61.05 ± 9.4 years, resp.; P = 0.15). Significant differences were found for the threshold sensitivities at each of the 52 points evaluated with SAP (P < 0.001) and the peripapillary retinal nerve fiber layer (RNFL) thicknesses, except at 3 and 9 clock-hour positions between both groups. Mild to moderate correlations (ranging between 0.286 and 0.593; P < 0.001) were observed between SAP and most OCT parameters in the glaucoma group. The strongest correlations were found between the inferior RNFL thickness and the superior hemifield points. The healthy group showed lower and weaker correlations than the glaucoma group. Conclusions. Peripapillary RNFL thickness measured with Cirrus OCT showed mild to moderate correlations with SAP in glaucoma patients. PMID:25028657

  6. Comparison of Very High-Frequency Ultrasound and Spectral-Domain Optical Coherence Tomography Corneal and Epithelial Thickness Maps

    PubMed Central

    Urs, Raksha; Lloyd, Harriet O.; Reinstein, Dan Z.; Silverman, Ronald H.

    2015-01-01

    Purpose To compare measurements of corneal thickness (CT) and epithelial thickness (ET) in maps obtained by the RTVue spectral domain optical coherence tomography (SD-OCT) system with those obtained from the Artemis 2 immersion arc-scanning very high-frequency ultrasound system. Setting Department of Ophthalmology of the Columbia University Medical Center Design A method-comparison study design to examine the agreement between two systems for measurement and mapping of CT and ET. Methods Both eyes of 12 normal volunteers were scanned with RTVue followed by Artemis and then by repeated RTVue. For each map, the minimum CT and mean values of CT and ET in the 3 mm radius zone and in 0.5 mm-wide concentric annuli of up to 3 mm radius around the corneal vertex were determined. Results The CT values from both devices were highly correlated and in the 3-mm radius zone (R>0.96) they were not statistically significantly different. There was no statistically significant change in ET or CT in RTVue measurements made before versus after immersion ultrasound. While highly correlated (R>0.76), RTVue ET values were systematically thinner (1.7 ± 2.1 µm) than Artemis 2 measurements (p<0.01) in the 3 mm radius zone. Conclusions Artemis and RTVue CT measurements in the 3 mm radius zone are equivalent in normal eyes. While correlated, Artemis ET measurements were systemically thicker than RTVue values. PMID:26948783

  7. (abstract) 3D Electromagnetic Plasma Particle Simulations

    NASA Technical Reports Server (NTRS)

    Wang, J.; Liewer, P. C.; Lyster, P.; Decyk, V. K.

    1993-01-01

    A 3D electromagnetic plasma particle-in-cell code has been developed using the General Concurrent PIC algorithm. The GCPIC algorithm uses a domain decomposition to divide the computation among the processors. Particles must be exchanged between processors as they move. The efficiencies for 1-, 2-, and 3-dimensional partitions of the three dimensional domain are compared, and the algorithm is found to be very efficient even when a large fraction (e.g., 30%) of the particles must be exchanged at every time step. This PIC code has been used to perform simulations of a variety of space plasma physics problems. Results of three applications will be discussed: 1) plasma disturbances induced by moving conducting bodies in a magnetized plasma; 2) plasma plume interactions; and 3) solar wind termination shock.

  8. The World of 3-D.

    ERIC Educational Resources Information Center

    Mayshark, Robin K.

    1991-01-01

    Students explore three-dimensional properties by creating red and green wall decorations related to Christmas. Students examine why images seem to vibrate when red and green pieces are small and close together. Instructions to conduct the activity and construct 3-D glasses are given. (MDH)

  9. 3D Printing: Exploring Capabilities

    ERIC Educational Resources Information Center

    Samuels, Kyle; Flowers, Jim

    2015-01-01

    As 3D printers become more affordable, schools are using them in increasing numbers. They fit well with the emphasis on product design in technology and engineering education, allowing students to create high-fidelity physical models to see and test different iterations in their product designs. They may also help students to "think in three…

  10. SNL3dFace

    SciTech Connect

    Russ, Trina; Koch, Mark; Koudelka, Melissa; Peters, Ralph; Little, Charles; Boehnen, Chris; Peters, Tanya

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial features of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.

  11. Making Inexpensive 3-D Models

    ERIC Educational Resources Information Center

    Manos, Harry

    2016-01-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the "TPT" theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity…

  12. Estimation of Soil Moisture Content from the Spectral Reflectance of Bare Soils in the 0.4–2.5 μm Domain

    PubMed Central

    Fabre, Sophie; Briottet, Xavier; Lesaignoux, Audrey

    2015-01-01

    This work aims to compare the performance of new methods to estimate the Soil Moisture Content (SMC) of bare soils from their spectral signatures in the reflective domain (0.4–2.5 μm) in comparison with widely used spectral indices like Normalized Soil Moisture Index (NSMI) and Water Index SOIL (WISOIL). Indeed, these reference spectral indices use wavelengths located in the water vapour absorption bands and their performance are thus very sensitive to the quality of the atmospheric compensation. To reduce these limitations, two new spectral indices are proposed which wavelengths are defined using the determination matrix tool by taking into account the atmospheric transmission: Normalized Index of Nswir domain for Smc estimatiOn from Linear correlation (NINSOL) and Normalized Index of Nswir domain for Smc estimatiOn from Non linear correlation (NINSON). These spectral indices are completed by two new methods based on the global shape of the soil spectral signatures. These methods are the Inverse Soil semi-Empirical Reflectance model (ISER), using the inversion of an existing empirical soil model simulating the soil spectral reflectance according to soil moisture content for a given soil class, and the convex envelope model, linking the area between the envelope and the spectral signature to the SMC. All these methods are compared using a reference database built with 32 soil samples and composed of 190 spectral signatures with five or six soil moisture contents. Half of the database is used for the calibration stage and the remaining to evaluate the performance of the SMC estimation methods. The results show that the four new methods lead to similar or better performance than the one obtained by the reference indices. The RMSE is ranging from 3.8% to 6.2% and the coefficient of determination R2 varies between 0.74 and 0.91 with the best performance obtained with the ISER model. In a second step, simulated spectral radiances at the sensor level are used to

  13. Estimation of soil moisture content from the spectral reflectance of bare soils in the 0.4-2.5 µm domain.

    PubMed

    Fabre, Sophie; Briottet, Xavier; Lesaignoux, Audrey

    2015-02-02

    This work aims to compare the performance of new methods to estimate the Soil Moisture Content (SMC) of bare soils from their spectral signatures in the reflective domain (0.4-2.5 µm) in comparison with widely used spectral indices like Normalized Soil Moisture Index (NSMI) and Water Index SOIL (WISOIL). Indeed, these reference spectral indices use wavelengths located in the water vapour absorption bands and their performance are thus very sensitive to the quality of the atmospheric compensation. To reduce these limitations, two new spectral indices are proposed which wavelengths are defined using the determination matrix tool by taking into account the atmospheric transmission: Normalized Index of Nswir domain for Smc estimatiOn from Linear correlation (NINSOL) and Normalized Index of Nswir domain for Smc estimatiOn from Non linear correlation (NINSON). These spectral indices are completed by two new methods based on the global shape of the soil spectral signatures. These methods are the Inverse Soil semi-Empirical Reflectance model (ISER), using the inversion of an existing empirical soil model simulating the soil spectral reflectance according to soil moisture content for a given soil class, and the convex envelope model, linking the area between the envelope and the spectral signature to the SMC. All these methods are compared using a reference database built with 32 soil samples and composed of 190 spectral signatures with five or six soil moisture contents. Half of the database is used for the calibration stage and the remaining to evaluate the performance of the SMC estimation methods. The results show that the four new methods lead to similar or better performance than the one obtained by the reference indices. The RMSE is ranging from 3.8% to 6.2% and the coefficient of determination R2 varies between 0.74 and 0.91 with the best performance obtained with the ISER model. In a second step, simulated spectral radiances at the sensor level are used to analyse

  14. 3D Imaging with Holographic Tomography

    NASA Astrophysics Data System (ADS)

    Sheppard, Colin J. R.; Kou, Shan Shan

    2010-04-01

    There are two main types of tomography that enable the 3D internal structures of objects to be reconstructed from scattered data. The commonly known computerized tomography (CT) give good results in the x-ray wavelength range where the filtered back-projection theorem and Radon transform can be used. These techniques rely on the Fourier projection-slice theorem where rays are considered to propagate straight through the object. Another type of tomography called `diffraction tomography' applies in applications in optics and acoustics where diffraction and scattering effects must be taken into account. The latter proves to be a more difficult problem, as light no longer travels straight through the sample. Holographic tomography is a popular way of performing diffraction tomography and there has been active experimental research on reconstructing complex refractive index data using this approach recently. However, there are two distinct ways of doing tomography: either by rotation of the objec