Science.gov

Sample records for 3d spectral domain

  1. Volumetric (3D) compressive sensing spectral domain optical coherence tomography

    PubMed Central

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

    2014-01-01

    In this work, we proposed a novel three-dimensional compressive sensing (CS) approach for spectral domain optical coherence tomography (SD OCT) volumetric image acquisition and reconstruction. Instead of taking a spectral volume whose size is the same as that of the volumetric image, our method uses a sub set of the original spectral volume that is under-sampled in all three dimensions, which reduces the amount of spectral measurements to less than 20% of that required by the Shan-non/Nyquist theory. The 3D image is recovered from the under-sampled spectral data dimension-by-dimension using the proposed three-step CS reconstruction strategy. Experimental results show that our method can significantly reduce the sampling rate required for a volumetric SD OCT image while preserving the image quality. PMID:25426320

  2. Volumetric (3D) compressive sensing spectral domain optical coherence tomography.

    PubMed

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

    2014-11-01

    In this work, we proposed a novel three-dimensional compressive sensing (CS) approach for spectral domain optical coherence tomography (SD OCT) volumetric image acquisition and reconstruction. Instead of taking a spectral volume whose size is the same as that of the volumetric image, our method uses a sub set of the original spectral volume that is under-sampled in all three dimensions, which reduces the amount of spectral measurements to less than 20% of that required by the Shan-non/Nyquist theory. The 3D image is recovered from the under-sampled spectral data dimension-by-dimension using the proposed three-step CS reconstruction strategy. Experimental results show that our method can significantly reduce the sampling rate required for a volumetric SD OCT image while preserving the image quality.

  3. 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.

  4. 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).

  5. 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.

  6. 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.

  7. 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.

  8. 3D refraction correction and extraction of clinical parameters from spectral domain optical coherence tomography of the cornea.

    PubMed

    Zhao, Mingtao; Kuo, Anthony N; Izatt, Joseph A

    2010-04-26

    Capable of three-dimensional imaging of the cornea with micrometer-scale resolution, spectral domain-optical coherence tomography (SDOCT) offers potential advantages over Placido ring and Scheimpflug photography based systems for accurate extraction of quantitative keratometric parameters. In this work, an SDOCT scanning protocol and motion correction algorithm were implemented to minimize the effects of patient motion during data acquisition. Procedures are described for correction of image data artifacts resulting from 3D refraction of SDOCT light in the cornea and from non-idealities of the scanning system geometry performed as a pre-requisite for accurate parameter extraction. Zernike polynomial 3D reconstruction and a recursive half searching algorithm (RHSA) were implemented to extract clinical keratometric parameters including anterior and posterior radii of curvature, central cornea optical power, central corneal thickness, and thickness maps of the cornea. Accuracy and repeatability of the extracted parameters obtained using a commercial 859nm SDOCT retinal imaging system with a corneal adapter were assessed using a rigid gas permeable (RGP) contact lens as a phantom target. Extraction of these parameters was performed in vivo in 3 patients and compared to commercial Placido topography and Scheimpflug photography systems. The repeatability of SDOCT central corneal power measured in vivo was 0.18 Diopters, and the difference observed between the systems averaged 0.1 Diopters between SDOCT and Scheimpflug photography, and 0.6 Diopters between SDOCT and Placido topography.

  9. 3D spatial resolution and spectral resolution of interferometric 3D imaging spectrometry.

    PubMed

    Obara, Masaki; Yoshimori, Kyu

    2016-04-01

    Recently developed interferometric 3D imaging spectrometry (J. Opt. Soc. Am A18, 765 [2001]1084-7529JOAOD610.1364/JOSAA.18.000765) enables obtainment of the spectral information and 3D spatial information for incoherently illuminated or self-luminous object simultaneously. Using this method, we can obtain multispectral components of complex holograms, which correspond directly to the phase distribution of the wavefronts propagated from the polychromatic object. This paper focuses on the analysis of spectral resolution and 3D spatial resolution in interferometric 3D imaging spectrometry. Our analysis is based on a novel analytical impulse response function defined over four-dimensional space. We found that the experimental results agree well with the theoretical prediction. This work also suggests a new criterion and estimate method regarding 3D spatial resolution of digital holography. PMID:27139648

  10. Spectral ladar: towards active 3D multispectral imaging

    NASA Astrophysics Data System (ADS)

    Powers, Michael A.; Davis, Christopher C.

    2010-04-01

    In this paper we present our Spectral LADAR concept, an augmented implementation of traditional LADAR. This sensor uses a polychromatic source to obtain range-resolved 3D spectral images which are used to identify objects based on combined spatial and spectral features, resolving positions in three dimensions and up to hundreds of meters in distance. We report on a proof-of-concept Spectral LADAR demonstrator that generates spectral point clouds from static scenes. The demonstrator transmits nanosecond supercontinuum pulses generated in a photonic crystal fiber. Currently we use a rapidly tuned receiver with a high-speed InGaAs APD for 25 spectral bands with the future expectation of implementing a linear APD array spectrograph. Each spectral band is independently range resolved with multiple return pulse recognition. This is a critical feature, enabling simultaneous spectral and spatial unmixing of partially obscured objects when not achievable using image fusion of monochromatic LADAR and passive spectral imagers. This enables higher identification confidence in highly cluttered environments such as forested or urban areas (e.g. vehicles behind camouflage or foliage). These environments present challenges for situational awareness and robotic perception which can benefit from the unique attributes of Spectral LADAR. Results from this demonstrator unit are presented for scenes typical of military operations and characterize the operation of the device. The results are discussed here in the context of autonomous vehicle navigation and target recognition.

  11. 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.

  12. Registration of 3D spectral OCT volumes using 3D SIFT feature point matching

    NASA Astrophysics Data System (ADS)

    Niemeijer, Meindert; Garvin, Mona K.; Lee, Kyungmoo; van Ginneken, Bram; Abràmoff, Michael D.; Sonka, Milan

    2009-02-01

    The recent introduction of next generation spectral OCT scanners has enabled routine acquisition of high resolution, 3D cross-sectional volumetric images of the retina. 3D OCT is used in the detection and management of serious eye diseases such as glaucoma and age-related macular degeneration. For follow-up studies, image registration is a vital tool to enable more precise, quantitative comparison of disease states. This work presents a registration method based on a recently introduced extension of the 2D Scale-Invariant Feature Transform (SIFT) framework1 to 3D.2 The SIFT feature extractor locates minima and maxima in the difference of Gaussian scale space to find salient feature points. It then uses histograms of the local gradient directions around each found extremum in 3D to characterize them in a 4096 element feature vector. Matching points are found by comparing the distance between feature vectors. We apply this method to the rigid registration of optic nerve head- (ONH) and macula-centered 3D OCT scans of the same patient that have only limited overlap. Three OCT data set pairs with known deformation were used for quantitative assessment of the method's robustness and accuracy when deformations of rotation and scaling were considered. Three-dimensional registration accuracy of 2.0+/-3.3 voxels was observed. The accuracy was assessed as average voxel distance error in N=1572 matched locations. The registration method was applied to 12 3D OCT scans (200 x 200 x 1024 voxels) of 6 normal eyes imaged in vivo to demonstrate the clinical utility and robustness of the method in a real-world environment.

  13. Navier-Stokes equations in 3D thin domains with Navier friction boundary condition

    NASA Astrophysics Data System (ADS)

    Hu, Changbing

    In this article we study the 3D Navier-Stokes equations with Navier friction boundary condition in thin domains. We prove the global existence of strong solutions to the 3D Navier-Stokes equations when the initial data and external forces are in large sets as the thickness of the domain is small. We generalize the techniques developed to study the 3D Navier-Stokes equations in thin domains, see [G. Raugel, G. Sell, Navier-Stokes equations on thin 3D domains I: Global attractors and global regularity of solutions, J. Amer. Math. Soc. 6 (1993) 503-568; G. Raugel, G. Sell, Navier-Stokes equations on thin 3D domains II: Global regularity of spatially periodic conditions, in: Nonlinear Partial Differential Equations and Their Application, College de France Seminar, vol. XI, Longman, Harlow, 1994, pp. 205-247; R. Temam, M. Ziane, Navier-Stokes equations in three-dimensional thin domains with various boundary conditions, Adv. Differential Equations 1 (1996) 499-546; R. Temam, M. Ziane, Navier-Stokes equations in thin spherical shells, in: Optimization Methods in Partial Differential Equations, in: Contemp. Math., vol. 209, Amer. Math. Soc., Providence, RI, 1996, pp. 281-314], to the Navier friction boundary condition by introducing a new average operator M in the thin direction according to the spectral decomposition of the Stokes operator A. Our analysis hinges on the refined investigation of the eigenvalue problem corresponding to the Stokes operator A with Navier friction boundary condition.

  14. Spectral Domain Phase Microscopy

    NASA Astrophysics Data System (ADS)

    Hendargo, Hansford C.; Ellerbee, Audrey K.; Izatt, Joseph A.

    Spectral domain phase microscopy (SDPM) is a functional extension of optical coherence tomography (OCT) using common-path interferometry to produce phase-referenced images of dynamic samples. Like OCT, axial resolution in SDPM is determined by the source coherence length, while lateral resolution is limited by diffraction in the microscope optics. However, the quantitative phase information SDPM generates is sensitive to nanometer-scale displacements of scattering structures. The use of a common-path optical geometry yields an imaging system with high phase stability. Due to coherence gating, SDPM can achieve full depth discrimination, allowing for independent motion resolution of subcellular structures throughout the sample volume. Here we review the basic theory of OCT and SDPM along with applications of SDPM in cellular imaging to measure topology, Doppler flow in single-celled organisms, time-resolved motions, rheological information of the cytoskeleton, and optical signaling of neural activation. Phase imaging limitations, artifacts, and sensitivity considerations are discussed.

  15. Coverage Assessment and Target Tracking in 3D Domains

    PubMed Central

    Boudriga, Noureddine; Hamdi, Mohamed; Iyengar, Sitharama

    2011-01-01

    Recent advances in integrated electronic devices motivated the use of Wireless Sensor Networks (WSNs) in many applications including domain surveillance and mobile target tracking, where a number of sensors are scattered within a sensitive region to detect the presence of intruders and forward related events to some analysis center(s). Obviously, sensor deployment should guarantee an optimal event detection rate and should reduce coverage holes. Most of the coverage control approaches proposed in the literature deal with two-dimensional zones and do not develop strategies to handle coverage in three-dimensional domains, which is becoming a requirement for many applications including water monitoring, indoor surveillance, and projectile tracking. This paper proposes efficient techniques to detect coverage holes in a 3D domain using a finite set of sensors, repair the holes, and track hostile targets. To this end, we use the concepts of Voronoi tessellation, Vietoris complex, and retract by deformation. We show in particular that, through a set of iterative transformations of the Vietoris complex corresponding to the deployed sensors, the number of coverage holes can be computed with a low complexity. Mobility strategies are also proposed to repair holes by moving appropriately sensors towards the uncovered zones. The tracking objective is to set a non-uniform WSN coverage within the monitored domain to allow detecting the target(s) by the set of sensors. We show, in particular, how the proposed algorithms adapt to cope with obstacles. Simulation experiments are carried out to analyze the efficiency of the proposed models. To our knowledge, repairing and tracking is addressed for the first time in 3D spaces with different sensor coverage schemes. PMID:22163733

  16. 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.

  17. Spectral Element Modeling of 3D Site Effects in the Alpine Valley of Grenoble, France.

    NASA Astrophysics Data System (ADS)

    Chaljub, E.; Cornou, C.; Gueguen, P.; Causse, M.; Komatitsch, D.

    2004-12-01

    Sitting on top of a 3D Y-shaped basin filled mostly with late quaternary deposits, the city of Grenoble (French Alps) is subject to strong amplification of seismic motion (see the SISMOVALP web site). In order to assess the magnitude and 3D complexity of these site effects, we propose a spectral element modeling approach previously applied to the prediction of strong ground motion in the Los Angeles sedimentary basin (Komatitstch et al., 2004). The spectral element method naturally accounts for depth variations of the free surface and of internal interfaces, such as the contact between the sediments and the bedrock. It is also well suited to model the propagation of surface waves generated at the basin edges. The 3D spectral element mesh honors the stiff surface topography of the mountains surrounding the city, as well as the bedrock depth obtained from extensive gravimetric measurements. In the basin, we use a generic 1D velocity model derived from geophysical measurements performed in a deep borehole that reached the substratum at 550 m depth in 1999. Results and comparison to data are shown in the time and frequency domain for small-size (Mw=2.5 and Mw=3.5) local events recorded in the past years. Then, a Mw=5.5 strike-slip event is simulated on the eastern border of the basin along the Belledonne fault, and the results are compared to those obtained by the method of Empirical Green Functions. References: http://www-lgit.obs.ujf-grenoble.fr/sismovalp/ Simulations of ground motion in the Los Angeles basin based upon the spectral- element method, Dimitri Komatitsch, Qinya Liu, Jeroen Tromp, Peter Süss, Christiane Stidham and John H. Shaw, Bulletin of the Seismological Society of America, vol. 94, p 187-206 (2004).

  18. 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

  19. 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.

  20. 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.

  1. Time domain topology optimization of 3D nanophotonic devices

    NASA Astrophysics Data System (ADS)

    Elesin, Y.; Lazarov, B. S.; Jensen, J. S.; Sigmund, O.

    2014-02-01

    We present an efficient parallel topology optimization framework for design of large scale 3D nanophotonic devices. The code shows excellent scalability and is demonstrated for optimization of broadband frequency splitter, waveguide intersection, photonic crystal-based waveguide and nanowire-based waveguide. The obtained results are compared to simplified 2D studies and we demonstrate that 3D topology optimization may lead to significant performance improvements.

  2. 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.

  3. Dual-color 3D superresolution microscopy by combined spectral-demixing and biplane imaging.

    PubMed

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

    2015-07-01

    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.

  4. Multivariate statistical analysis as a tool for the segmentation of 3D spectral data.

    PubMed

    Lucas, G; Burdet, P; Cantoni, M; Hébert, C

    2013-01-01

    Acquisition of three-dimensional (3D) spectral data is nowadays common using many different microanalytical techniques. In order to proceed to the 3D reconstruction, data processing is necessary not only to deal with noisy acquisitions but also to segment the data in term of chemical composition. In this article, we demonstrate the value of multivariate statistical analysis (MSA) methods for this purpose, allowing fast and reliable results. Using scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX) coupled with a focused ion beam (FIB), a stack of spectrum images have been acquired on a sample produced by laser welding of a nickel-titanium wire and a stainless steel wire presenting a complex microstructure. These data have been analyzed using principal component analysis (PCA) and factor rotations. PCA allows to significantly improve the overall quality of the data, but produces abstract components. Here it is shown that rotated components can be used without prior knowledge of the sample to help the interpretation of the data, obtaining quickly qualitative mappings representative of elements or compounds found in the material. Such abundance maps can then be used to plot scatter diagrams and interactively identify the different domains in presence by defining clusters of voxels having similar compositions. Identified voxels are advantageously overlaid on secondary electron (SE) images with higher resolution in order to refine the segmentation. The 3D reconstruction can then be performed using available commercial softwares on the basis of the provided segmentation. To asses the quality of the segmentation, the results have been compared to an EDX quantification performed on the same data. PMID:24035679

  5. 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.

  6. 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.

  7. 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.

  8. Oxygen spectral line synthesis: 3D non-LTE with CO5BOLD hydrodynamical model atmospheres.

    NASA Astrophysics Data System (ADS)

    Prakapavičius, D.; Steffen, M.; Kučinskas, A.; Ludwig, H.-G.; Freytag, B.; Caffau, E.; Cayrel, R.

    In this work we present first results of our current project aimed at combining the 3D hydrodynamical stellar atmosphere approach with non-LTE (NLTE) spectral line synthesis for a number of key chemical species. We carried out a full 3D-NLTE spectrum synthesis of the oxygen IR 777 nm triplet, using a modified and improved version of our NLTE3D package to calculate departure coefficients for the atomic levels of oxygen in a CO5BOLD 3D hydrodynamical solar model atmosphere. Spectral line synthesis was subsequently performed with the Linfor3D code. In agreement with previous studies, we find that the lines of the oxygen triplet produce deeper cores under NLTE conditions, due to the diminished line source function in the line forming region. This means that the solar oxygen IR 777 nm lines should be stronger in NLTE, leading to negative 3D NLTE-LTE abundance corrections. Qualitatively this result would support previous claims for a relatively low solar oxygen abundance. Finally, we outline several further steps that need to be taken in order to improve the physical realism and numerical accuracy of our current 3D-NLTE calculations.

  9. A Spectral Element Ocean Model on the Cray T3D: the interannual variability of the Mediterranean Sea general circulation

    NASA Astrophysics Data System (ADS)

    Molcard, A. J.; Pinardi, N.; Ansaloni, R.

    A new numerical model, SEOM (Spectral Element Ocean Model, (Iskandarani et al, 1994)), has been implemented in the Mediterranean Sea. Spectral element methods combine the geometric flexibility of finite element techniques with the rapid convergence rate of spectral schemes. The current version solves the shallow water equations with a fifth (or sixth) order accuracy spectral scheme and about 50.000 nodes. The domain decomposition philosophy makes it possible to exploit the power of parallel machines. The original MIMD master/slave version of SEOM, written in F90 and PVM, has been ported to the Cray T3D. When critical for performance, Cray specific high-performance one-sided communication routines (SHMEM) have been adopted to fully exploit the Cray T3D interprocessor network. Tests performed with highly unstructured and irregular grid, on up to 128 processors, show an almost linear scalability even with unoptimized domain decomposition techniques. Results from various case studies on the Mediterranean Sea are shown, involving realistic coastline geometry, and monthly mean 1000mb winds from the ECMWF's atmospheric model operational analysis from the period January 1987 to December 1994. The simulation results show that variability in the wind forcing considerably affect the circulation dynamics of the Mediterranean Sea.

  10. 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

  11. 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

  12. Efficient 2D and 3D multiparameters frequency-domain full waveform inversion (Invited)

    NASA Astrophysics Data System (ADS)

    Virieux, J.; Operto, S.; Ribodetti, A.; Ben Hadj Ali, H.; Brossier, R.; Etienne, V.; Gholami, Y.; Hu, G.; Jia, Y.; Pageot, D.; Prieux, V.

    2010-12-01

    but this technique requests too much core memory for present-day computers and suffers from a too limited scalability to tackle large-scale acoustic problems and 3D elastic FWI. We rely on other strategies such as iterative methods, hybrid methods (including a domain decomposition mixing a direct solver inside each subdomain and an iterative solver for boundary unknowns between subdomains) or extraction of monochromatic solutions from a 3D time-marching modeling based on finite-difference methods or spectral element methods or discontinuous Galerkin methods. Because of the computational burden resulting from multisource modelling a significant effort is asked for each source, an additional strategy based on source assembling with random phase encoding as proposed initially for the global Earth is now used in migration and FWI for crustal imaging: cross-talk noise between assembled sources is mitigated efficiently by using random phase encoding. Few synthetic examples will show that we can afford performing 3D FWI for acoustic and elastic 3D crustal FWI imaging with available computer resources. What is the most efficient tool for 3D (an-)elastic FWI: a time formulation or a frequency formulation of the inverse problem. This is still an open question.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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 34s down to 11s. 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.

  14. Spectral/Fourier Domain Optical Coherence Tomography

    NASA Astrophysics Data System (ADS)

    de Boer, Johannes F.

    Optical coherence tomography is a low-coherence interferometric method for imaging of biological tissue [1, 2]. For more than a decade after its inception between 1988 and 1991, the dominant implementation has been time domain OCT (TD-OCT), in which the length of a reference arm is rapidly scanned. The first spectral or Fourier domain OCT (SD/FD-OCT) implementation was reported in 1995 [3]. In SD-OCT the reference arm is kept stationary, and the depth information is obtained by a Fourier transform of the spectrally resolved interference fringes in the detection arm of a Michelson interferometer. This approach has provided a significant advantage in signal-to-noise ratio (SNR), which despite reports as early as 1997 [4, 5] has taken about half a decade to be recognized fully by the OCT community in 2003 [6-8]. The first demonstration of SD-OCT for in vivo retinal imaging in 2002 [9] was followed by a full realization of the sensitivity advantage by video rate in vivo retinal imaging [10], including high-speed 3-D volumetric imaging [11], ultrahigh-resolution video rate imaging [12, 13], and Doppler blood flow determination in the human retina [14, 15]. The superior sensitivity of SD-OCT, combined with the lack of need for a fast mechanical scanning mechanism, has opened up the possibility of much faster scanning without loss of image quality and provided a paradigm shift from point sampling to volumetric mapping of biological tissue in vivo. The technology has been particularly promising for ophthalmology [16, 17]. In this chapter, the principles and system design considerations of SD-OCT will be discussed in more detail.

  15. 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.

  16. 3D reconstruction of coronary arteries using frequency domain optical coherence tomography images and biplane angiography.

    PubMed

    Athanasiou, L S; Bourantas, C V; Siogkas, P K; Sakellarios, A I; Exarchos, T P; Naka, K K; Papafaklis, M I; Michalis, L K; Prati, F; Fotiadis, D I

    2012-01-01

    The aim of this study is to describe a new method for three-dimensional (3D) reconstruction of coronary arteries using Frequency Domain Optical Coherence Tomography (FD-OCT) images. The rationale is to fuse the information about the curvature of the artery, derived from biplane angiographies, with the information regarding the lumen wall, which is produced from the FD-OCT examination. The method is based on a three step approach. In the first step the lumen borders in FD-OCT images are detected. In the second step a 3D curve is produced using the center line of the vessel from the two biplane projections. Finally in the third step the detected lumen borders are placed perpendicularly onto the path based on the centroid of each lumen border. The result is a 3D reconstructed artery produced by all the lumen borders of the FD-OCT pullback representing the 3D arterial geometry of the vessel.

  17. The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins.

    PubMed

    Girdlestone, Christopher; Hayward, Steven

    2016-01-01

    DynDom3D is a program for the analysis of domain movements in multimeric proteins. Its inputs are two structure files that indicate a possible domain movement, but the onus has been on the user to process the files so that there is the necessary one-to-one equivalence between atoms in the two atom lists. This is often a prohibitive task to carry out manually, which has limited the application of DynDom3D. Here we report on a webserver with a preprocessor that automatically creates an equivalence between atoms using sequence alignment methods. The processed structure files are passed to DynDom3D and the results are presented on a webpage that includes molecular graphics for easy visualization. PMID:26540459

  18. 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

  19. 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.

  20. Global regular solutions for the 3D Zakharov-Kuznetsov equation posed on unbounded domains

    NASA Astrophysics Data System (ADS)

    Larkin, N. A.

    2015-09-01

    An initial-boundary value problem for the 3D Zakharov-Kuznetsov equation posed on unbounded domains is considered. Existence and uniqueness of a global regular solution as well as exponential decay of the H2-norm for small initial data are proven.

  1. 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

  2. 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.

  3. 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. PMID:27140495

  4. In Vivo 3D Meibography of the Human Eyelid Using Real Time Imaging Fourier-Domain OCT

    PubMed Central

    Hwang, Ho Sik; Shin, Jun Geun; Lee, Byeong Ha; Eom, Tae Joong; Joo, Choun-Ki

    2013-01-01

    Recently, we reported obtaining tomograms of meibomian glands from healthy volunteers using commercial anterior segment optical coherence tomography (AS-OCT), which is widely employed in clinics for examination of the anterior segment. However, we could not create 3D images of the meibomian glands, because the commercial OCT does not have a 3D reconstruction function. In this study we report the creation of 3D images of the meibomian glands by reconstructing the tomograms of these glands using high speed Fourier-Domain OCT (FD-OCT) developed in our laboratory. This research was jointly undertaken at the Department of Ophthalmology, Seoul St. Mary's Hospital (Seoul, Korea) and the Advanced Photonics Research Institute of Gwangju Institute of Science and Technology (Gwangju, Korea) with two healthy volunteers and seven patients with meibomian gland dysfunction. A real time imaging FD-OCT system based on a high-speed wavelength swept laser was developed that had a spectral bandwidth of 100 nm at the 1310 nm center wavelength. The axial resolution was 5 µm and the lateral resolution was 13 µm in air. Using this device, the meibomian glands of nine subjects were examined. A series of tomograms from the upper eyelid measuring 5 mm (from left to right, B-scan) × 2 mm (from upper part to lower part, C-scan) were collected. Three-D images of the meibomian glands were then reconstructed using 3D “data visualization, analysis, and modeling software”. Established infrared meibography was also performed for comparison. The 3D images of healthy subjects clearly showed the meibomian glands, which looked similar to bunches of grapes. These results were consistent with previous infrared meibography results. The meibomian glands were parallel to each other, and the saccular acini were clearly visible. Here we report the successful production of 3D images of human meibomian glands by reconstructing tomograms of these glands with high speed FD-OCT. PMID:23805297

  5. In Vivo 3D Meibography of the Human Eyelid Using Real Time Imaging Fourier-Domain OCT.

    PubMed

    Hwang, Ho Sik; Shin, Jun Geun; Lee, Byeong Ha; Eom, Tae Joong; Joo, Choun-Ki

    2013-01-01

    Recently, we reported obtaining tomograms of meibomian glands from healthy volunteers using commercial anterior segment optical coherence tomography (AS-OCT), which is widely employed in clinics for examination of the anterior segment. However, we could not create 3D images of the meibomian glands, because the commercial OCT does not have a 3D reconstruction function. In this study we report the creation of 3D images of the meibomian glands by reconstructing the tomograms of these glands using high speed Fourier-Domain OCT (FD-OCT) developed in our laboratory. This research was jointly undertaken at the Department of Ophthalmology, Seoul St. Mary's Hospital (Seoul, Korea) and the Advanced Photonics Research Institute of Gwangju Institute of Science and Technology (Gwangju, Korea) with two healthy volunteers and seven patients with meibomian gland dysfunction. A real time imaging FD-OCT system based on a high-speed wavelength swept laser was developed that had a spectral bandwidth of 100 nm at the 1310 nm center wavelength. The axial resolution was 5 µm and the lateral resolution was 13 µm in air. Using this device, the meibomian glands of nine subjects were examined. A series of tomograms from the upper eyelid measuring 5 mm (from left to right, B-scan) × 2 mm (from upper part to lower part, C-scan) were collected. Three-D images of the meibomian glands were then reconstructed using 3D "data visualization, analysis, and modeling software". Established infrared meibography was also performed for comparison. The 3D images of healthy subjects clearly showed the meibomian glands, which looked similar to bunches of grapes. These results were consistent with previous infrared meibography results. The meibomian glands were parallel to each other, and the saccular acini were clearly visible. Here we report the successful production of 3D images of human meibomian glands by reconstructing tomograms of these glands with high speed FD-OCT.

  6. 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.

  7. 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.

  8. 3D time-domain airborne EM modeling for an arbitrarily anisotropic earth

    NASA Astrophysics Data System (ADS)

    Yin, Changchun; Qi, Yanfu; Liu, Yunhe

    2016-08-01

    Time-domain airborne EM data is currently interpreted based on an isotropic model. Sometimes, it can be problematic when working in the region with distinct dipping stratifications. In this paper, we simulate the 3D time-domain airborne EM responses over an arbitrarily anisotropic earth with topography by edge-based finite-element method. Tetrahedral meshes are used to describe the abnormal bodies with complicated shapes. We further adopt the Backward Euler scheme to discretize the time-domain diffusion equation for electric field, obtaining an unconditionally stable linear equations system. We verify the accuracy of our 3D algorithm by comparing with 1D solutions for an anisotropic half-space. Then, we switch attentions to effects of anisotropic media on the strengths and the diffusion patterns of time-domain airborne EM responses. For numerical experiments, we adopt three typical anisotropic models: 1) an anisotropic anomalous body embedded in an isotropic half-space; 2) an isotropic anomalous body embedded in an anisotropic half-space; 3) an anisotropic half-space with topography. The modeling results show that the electric anisotropy of the subsurface media has big effects on both the strengths and the distribution patterns of time-domain airborne EM responses; this effect needs to be taken into account when interpreting ATEM data in areas with distinct anisotropy.

  9. 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

  10. 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. PMID:27040943

  11. Crystal structure of human glyoxalase I--evidence for gene duplication and 3D domain swapping.

    PubMed Central

    Cameron, A D; Olin, B; Ridderström, M; Mannervik, B; Jones, T A

    1997-01-01

    The zinc metalloenzyme glyoxalase I catalyses the glutathione-dependent inactivation of toxic methylglyoxal. The structure of the dimeric human enzyme in complex with S-benzyl-glutathione has been determined by multiple isomorphous replacement (MIR) and refined at 2.2 A resolution. Each monomer consists of two domains. Despite only low sequence homology between them, these domains are structurally equivalent and appear to have arisen by a gene duplication. On the other hand, there is no structural homology to the 'glutathione binding domain' found in other glutathione-linked proteins. 3D domain swapping of the N- and C-terminal domains has resulted in the active site being situated in the dimer interface, with the inhibitor and essential zinc ion interacting with side chains from both subunits. Two structurally equivalent residues from each domain contribute to a square pyramidal coordination of the zinc ion, rarely seen in zinc enzymes. Comparison of glyoxalase I with other known structures shows the enzyme to belong to a new structural family which includes the Fe2+-dependent dihydroxybiphenyl dioxygenase and the bleomycin resistance protein. This structural family appears to allow members to form with or without domain swapping. PMID:9218781

  12. 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.

  13. 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.

  14. 3D Laplace-domain full waveform inversion using a single GPU card

    NASA Astrophysics Data System (ADS)

    Shin, Jungkyun; Ha, Wansoo; Jun, Hyunggu; Min, Dong-Joo; Shin, Changsoo

    2014-06-01

    The Laplace-domain full waveform inversion is an efficient long-wavelength velocity estimation method for seismic datasets lacking low-frequency components. However, to invert a 3D velocity model, a large cluster of CPU cores have commonly been required to overcome the extremely long computing time caused by a large impedance matrix and a number of source positions. In this study, a workstation with a single GPU card (NVIDIA GTX 580) is successfully used for the 3D Laplace-domain full waveform inversion rather than a large cluster of CPU cores. To exploit a GPU for our inversion algorithm, the routine for the iterative matrix solver is ported to the CUDA programming language for forward and backward modeling parts with minimized modification of the remaining parts, which were originally written in Fortran 90. Using a uniformly structured grid set, nonzero values in the sparse impedance matrix can be arranged according to certain rules, which efficiently parallelize the preconditioned conjugate gradient method for a number of threads contained in the GPU card. We perform a numerical experiment to verify the accuracy of a floating point operation performed by a GPU to calculate the Laplace-domain wavefield. We also measure the efficiencies of the original CPU and modified GPU programs using a cluster of CPU cores and a workstation with a GPU card, respectively. Through the analysis, the parallelized inversion code for a GPU achieves the speedup of 14.7-24.6x compared to a CPU-based serial code depending on the degrees of freedom of the impedance matrix. Finally, the practicality of the proposed algorithm is examined by inverting a 3D long-wavelength velocity model using wide azimuth real datasets in 3.7 days.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 3D seismic data reconstruction based on complex-valued curvelet transform in frequency domain

    NASA Astrophysics Data System (ADS)

    Zhang, Hua; Chen, Xiaohong; Li, Hongxing

    2015-02-01

    Traditional seismic data sampling must follow the Nyquist Sampling Theorem. However, the field data acquisition may not meet the sampling criteria due to missing traces or limits in exploration cost, causing a prestack data reconstruction problem. Recently researchers have proposed many useful methods to regularize the seismic data. In this paper, a 3D seismic data reconstruction method based on the Projections Onto Convex Sets (POCS) algorithm and a complex-valued curvelet transform (CCT) has been introduced in the frequency domain. In order to improve reconstruction efficiency and reduce the computation time, the seismic data are transformed from the t-x-y domain to the f-x-y domain and the data reconstruction is processed for every frequency slice during the reconstruction process. The selection threshold parameter is important for reconstruction efficiency for each iteration, therefore an exponential square root decreased (ESRD) threshold is proposed. The experimental results show that the ESRD threshold can greatly reduce iterations and improve reconstruction efficiency compared to the other thresholds for the same reconstruction result. We also analyze the antinoise ability of the CCT-based POCS reconstruction method. The example studies on synthetic and real marine seismic data showed that our proposed method is more efficient and applicable.

  20. 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.

  1. Global regularity to the 3D MHD equations with large initial data in bounded domains

    NASA Astrophysics Data System (ADS)

    Yu, Haibo

    2016-08-01

    This paper considers the global regularity to the 3D incompressible MHD equations with large initial data in bounded domains. Let μ, ν, u, and b denote the viscosity coefficient, magnetic diffusivity, velocity field, and magnetic field, respectively. We construct new systems for (u - b) and (u + b) to overcome the difficulties caused by the large initial data. It is shown that ↑" separators=" ( u , b ) ↑ H 1 is globally bounded as long as ↑" separators=" ( u0 - b 0 ) ↑ H 1 + |" separators=" μ - ν | ( μ + ν ) - 1 or ↑" separators=" ( u0 + b 0 ) ↑ H 1 + |" separators=" μ - ν | ( μ + ν ) - 1 is sufficiently small, which indicates that the Navier-Stokes equations can be regularized by the magnetic field.

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

    PubMed

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

    2015-01-01

    Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and extremely dynamic. This review presents the most recent advances in topological domains' organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. CTCF protein appears as a central factor of these two organization levels having either a strong insulating role at TAD borders, or a weaker architectural role in chromatin loop formation. TAD borders directly impact on chromatin dynamics by restricting contacts within specific genomic portions thus confining chromatin loop formation within TADs. We discuss how sub-TAD chromatin dynamics, constrained into a recently described statistical helix conformation, can produce functional interactions by contact stabilization. PMID:26226004

  3. 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).

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

    NASA Astrophysics Data System (ADS)

    Maceira, M.; Rowe, C. A.; Allen, R. M.; Obrebski, M. J.

    2010-12-01

    As seismic instrumentation, data storage and dissemination and computational power improve, seismic velocity models attempt to resolve smaller structures and cover larger areas. However, it is unclear how accurate these velocity models are and, while the best models available are used for event determination, it is difficult to put uncertainties on seismic event parameters. Model validation is typically done using resolution tests that assume the imaging theory used is accurate and thus only considers the impact of the data coverage on resolution. We present the results of a more rigorous approach to model validation via full three-dimensional waveform propagation using Spectral Element Methods (SEM). This approach makes no assumptions about the theory used to generate the models but require substantial computational resources. We first validate 3D tomographic models for the Western USA generated using both ray-theoretical and finite-frequency methods. The Dynamic North America (DNA) Models of P- and S- velocity structure (DNA09-P and DNA09-S) use teleseismic body-wave traveltime residuals recorded at over 800 seismic stations provided by the Earthscope USArray and regional seismic networks. We performed systematic computations of synthetics for the dataset used to generate the DNA models. Direct comparison of these synthetic seismograms to the actual observations allows us to accurately assess and validate the models. Implementation of the method for a densely instrumented region such as that covered by the DNA model provides a useful testbed for the validation methods that we will subsequently apply to other, more challenging study areas.

  5. An Automatic 3D Mesh Generation Method for Domains with Multiple Materials.

    PubMed

    Zhang, Yongjie; Hughes, Thomas J R; Bajaj, Chandrajit L

    2010-01-01

    This paper describes an automatic and efficient approach to construct unstructured tetrahedral and hexahedral meshes for a composite domain made up of heterogeneous materials. The boundaries of these material regions form non-manifold surfaces. In earlier papers, we developed an octree-based isocontouring method to construct unstructured 3D meshes for a single-material (homogeneous) domain with manifold boundary. In this paper, we introduce the notion of a material change edge and use it to identify the interface between two or several different materials. A novel method to calculate the minimizer point for a cell shared by more than two materials is provided, which forms a non-manifold node on the boundary. We then mesh all the material regions simultaneously and automatically while conforming to their boundaries directly from volumetric data. Both material change edges and interior edges are analyzed to construct tetrahedral meshes, and interior grid points are analyzed for proper hexahedral mesh construction. Finally, edge-contraction and smoothing methods are used to improve the quality of tetrahedral meshes, and a combination of pillowing, geometric flow and optimization techniques is used for hexahedral mesh quality improvement. The shrink set of pillowing schemes is defined automatically as the boundary of each material region. Several application results of our multi-material mesh generation method are also provided. PMID:20161555

  6. 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.

  7. 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.

  8. Modified block-matching 3-D filter in Laplacian pyramid domain for speckle reduction

    NASA Astrophysics Data System (ADS)

    Wen, Donghai; Jiang, Yuesong; Zhang, Yanzhong; He, Yuntao; Hua, Houqiang; Yu, Rong; Wu, Xiaofang; Gao, Qian

    2014-07-01

    The Laplacian pyramid-based block-matching 3-D filtering (BM3D) is proposed (LPBM3D) for despeckling the speckle image. For BM3D in each pyramid layer, the criterion used to collect blocks in the 3-D groups to the actual data statistics is devised. An adaptive wavelet thresholding operator that depends on both noise level and signal characteristics is proposed. The performance of the proposed LPBM3D method has been compared with the state-of-the-art methods, including the recently proposed nonlocal mean (NLM) and BM3D method. Experimental results show that the visual quality and evaluation indexes outperform the other methods with no edge preservation. The proposed algorithm effectively realizes both despeckling and edge preservation.

  9. 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. PMID:27046601

  10. Automated multimodality concurrent classification for segmenting vessels in 3D spectral OCT and color fundus images

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

    Segmenting vessels in spectral-domain optical coherence tomography (SD-OCT) volumes is particularly challenging in the region near and inside the neural canal opening (NCO). Furthermore, accurately segmenting them in color fundus photographs also presents a challenge near the projected NCO. However, both modalities also provide complementary information to help indicate vessels, such as a better NCO contrast from the NCO-aimed OCT projection image and a better vessel contrast inside the NCO from fundus photographs. We thus present a novel multimodal automated classification approach for simultaneously segmenting vessels in SD-OCT volumes and fundus photographs, with a particular focus on better segmenting vessels near and inside the NCO by using a combination of their complementary features. In particular, in each SD-OCT volume, the algorithm pre-segments the NCO using a graph-theoretic approach and then applies oriented Gabor wavelets with oriented NCO-based templates to generate OCT image features. After fundus-to-OCT registration, the fundus image features are computed using Gaussian filter banks and combined with OCT image features. A k-NN classifier is trained on 5 and tested on 10 randomly chosen independent image pairs of SD-OCT volumes and fundus images from 15 subjects with glaucoma. Using ROC analysis, we demonstrate an improvement over two closest previous works performed in single modal SD-OCT volumes with an area under the curve (AUC) of 0.87 (0.81 for our and 0.72 for Niemeijer's single modal approach) in the region around the NCO and 0.90 outside the NCO (0.84 for our and 0.81 for Niemeijer's single modal approach).

  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. Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.

    PubMed

    Lees, Jonathan; Yeats, Corin; Perkins, James; Sillitoe, Ian; Rentzsch, Robert; Dessailly, Benoit H; Orengo, Christine

    2012-01-01

    Gene3D http://gene3d.biochem.ucl.ac.uk is a comprehensive database of protein domain assignments for sequences from the major sequence databases. Domains are directly mapped from structures in the CATH database or predicted using a library of representative profile HMMs derived from CATH superfamilies. As previously described, Gene3D integrates many other protein family and function databases. These facilitate complex associations of molecular function, structure and evolution. Gene3D now includes a domain functional family (FunFam) level below the homologous superfamily level assignments. Additions have also been made to the interaction data. More significantly, to help with the visualization and interpretation of multi-genome scale data sets, we have developed a new, revamped website. Searching has been simplified with more sophisticated filtering of results, along with new tools based on Cytoscape Web, for visualizing protein-protein interaction networks, differences in domain composition between genomes and the taxonomic distribution of individual superfamilies.

  13. 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.

  14. 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

    2016-01-01

    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

  15. 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.

  16. 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

  17. STEMS3D: An X-ray spectral model for magnetar persistent radiations

    NASA Astrophysics Data System (ADS)

    Gogus, Ersin; Weng, Shan-Shan

    2016-07-01

    Anomalous X-ray pulsars and soft gamma-ray repeaters are recognized as the most promising magnetar candidates, as indicated by their energetic bursts and rapid spin-downs. It is expected that the strong magnetic field leaves distinctive imprints on the emergent radiation both by affecting the radiative processes in atmospheres of magnetars and by scattering in the upper magnetospheres. We construct a self-consistent physical model that incorporates emission from the magnetar surface and its reprocessing in the three-dimensional twisted magnetosphere using a Monte Carlo technique. The synthetic spectra are characterized by four parameters: surface temperature kT, surface magnetic field strength B, magnetospheric twist angle Δφ, and the normalized electron velocity β. We also create a tabular model (STEMS3D) and apply it to X-ray spectra of magnetars.

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

    PubMed

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

    2015-03-11

    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

  19. 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

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

    PubMed

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

    2015-03-11

    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.

  1. 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.

  2. Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture.

    PubMed

    Matharu, Navneet K; Ahanger, Sajad H

    2015-09-01

    The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress.

  3. Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture

    PubMed Central

    Matharu, Navneet K.; Ahanger, Sajad H.

    2015-01-01

    The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress. PMID:26340639

  4. Modulated Magnetic Nanowires for Controlling Domain Wall Motion: Toward 3D Magnetic Memories.

    PubMed

    Ivanov, Yurii P; Chuvilin, Andrey; Lopatin, Sergei; Kosel, Jurgen

    2016-05-24

    Cylindrical magnetic nanowires are attractive materials for next generation data storage devices owing to the theoretically achievable high domain wall velocity and their efficient fabrication in highly dense arrays. In order to obtain control over domain wall motion, reliable and well-defined pinning sites are required. Here, we show that modulated nanowires consisting of alternating nickel and cobalt sections facilitate efficient domain wall pinning at the interfaces of those sections. By combining electron holography with micromagnetic simulations, the pinning effect can be explained by the interaction of the stray fields generated at the interface and the domain wall. Utilizing a modified differential phase contrast imaging, we visualized the pinned domain wall with a high resolution, revealing its three-dimensional vortex structure with the previously predicted Bloch point at its center. These findings suggest the potential of modulated nanowires for the development of high-density, three-dimensional data storage devices. PMID:27138460

  5. Modulated Magnetic Nanowires for Controlling Domain Wall Motion: Toward 3D Magnetic Memories.

    PubMed

    Ivanov, Yurii P; Chuvilin, Andrey; Lopatin, Sergei; Kosel, Jurgen

    2016-05-24

    Cylindrical magnetic nanowires are attractive materials for next generation data storage devices owing to the theoretically achievable high domain wall velocity and their efficient fabrication in highly dense arrays. In order to obtain control over domain wall motion, reliable and well-defined pinning sites are required. Here, we show that modulated nanowires consisting of alternating nickel and cobalt sections facilitate efficient domain wall pinning at the interfaces of those sections. By combining electron holography with micromagnetic simulations, the pinning effect can be explained by the interaction of the stray fields generated at the interface and the domain wall. Utilizing a modified differential phase contrast imaging, we visualized the pinned domain wall with a high resolution, revealing its three-dimensional vortex structure with the previously predicted Bloch point at its center. These findings suggest the potential of modulated nanowires for the development of high-density, three-dimensional data storage devices.

  6. 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.

  7. A Fourier rebinning algorithm incorporating spectral transfer efficiency for 3D PET.

    PubMed

    Tanaka, E; Amo, Y

    1998-04-01

    This paper presents a Fourier rebinning algorithm for three-dimensional image reconstruction in PET that incorporates the concept of spectral transfer function. It suggests the need for discarding low-frequency components in the rebinning. It also includes the correction for rebinning efficiency which was evaluated by simulations as a function of oblique angle of projections. The performance was optimized by high-pass filters and axial smoothing. The algorithm yields satisfactory images with negligible axial cross-talk for a maximum oblique angle up to 26.6 degrees. The statistical noise was evaluated in terms of 'noise equivalent number of oblique angles', and reasonable results were obtained in view of the theoretical expectation. Ring artefacts due to noise are negligibly small.

  8. Calibration and optimization of 3D digital breast tomosynthesis guided near infrared spectral tomography

    PubMed Central

    Michaelsen, Kelly E.; Krishnaswamy, Venkataramanan; Shi, Linxi; Vedantham, Srinivasan; Poplack, Steven P.; Karellas, Andrew; Pogue, Brian W.; Paulsen, Keith D.

    2015-01-01

    Calibration of a three-dimensional multimodal digital breast tomosynthesis (DBT) x-ray and non-fiber based near infrared spectral tomography (NIRST) system is challenging but essential for clinical studies. Phantom imaging results yielded linear contrast recovery of total hemoglobin (HbT) concentration for cylindrical inclusions of 15 mm, 10 mm and 7 mm with a 3.5% decrease in the HbT estimate for each 1 cm increase in inclusion depth. A clinical exam of a patient’s breast containing both benign and malignant lesions was successfully imaged, with greater HbT was found in the malignancy relative to the benign abnormality and fibroglandular regions (11 μM vs. 9.5 μM). Tools developed improved imaging system characterization and optimization of signal quality, which will ultimately improve patient selection and subsequent clinical trial results. PMID:26713210

  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. 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

  11. 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.

  12. Ultrahigh resolution spectral/Fourier domain OCT systems for retinal imaging applications

    NASA Astrophysics Data System (ADS)

    Srinivasan, V. J.; Wojtkowski, M.; Witkin, A.; Monson, B.; Duker, J. S.; Schuman, J. S.; Shidlovski, V.; Yakubovich, S.; Fujimoto, J. G.

    2006-02-01

    In this manuscript we describe the design and optimization of ultrahigh resolution spectral/Fourier domain OCT systems for three applications in retinal imaging: imaging of the normal retina, three-dimensional (3D) imaging of retinal pathologies, and 3D imaging of the rodent retina. Seven spectrometer configurations were tested for resolution and sensitivity drop with depth, and CCD pixel crosstalk was characterized. The human retina was imaged in vivo with five different axial resolutions between 2 and 10 microns, and with three different transverse resolutions. Information from these experiments enabled the optimization of OCT systems for the above applications. Results include clinical 3D data of retinal pathologies, high quality cross-sectional images of the normal retina with different axial and transverse resolutions and 3D data from the rat and mouse retinas. Factors affecting the sensitivity fall-off are discussed and theoretical predictions are compared with experimental measurements. Different retinal imaging applications necessitate different system designs, depending on the requirements of speed, axial resolution, axial measurement range, transverse resolution, and field of view. While axial resolution is the dominant factor in image quality, a smaller transverse spot size can reduce speckle size and improve contrast at boundaries such as the boundary between the ganglion cell layer and the inner plexiform layer. The effect of reducing the transverse spot size is most pronounced in images with 5-10 um axial resolution. In addition, we characterize all factors responsible for the sensitivity drop with depth in spectral/Fourier domain OCT.

  13. Schur-decomposition for 3D matrix equations and its application in solving radiative discrete ordinates equations discretized by Chebyshev collocation spectral method

    SciTech Connect

    Li Benwen Tian Shuai; Sun Yasong; Hu, Zhang-Mao

    2010-02-20

    The Schur-decomposition for three-dimensional matrix equations is developed and used to directly solve the radiative discrete ordinates equations which are discretized by Chebyshev collocation spectral method. Three methods, say, the spectral methods based on 2D and 3D matrix equation solvers individually, and the standard discrete ordinates method, are presented. The numerical results show the good accuracy of spectral method based on direct solvers. The CPU time cost comparisons against the resolutions between these three methods are made using MATLAB and FORTRAN 95 computer languages separately. The results show that the CPU time cost of Chebyshev collocation spectral method with 3D Schur-decomposition solver is the least, and almost only one thirtieth to one fiftieth CPU time is needed when using the spectral method with 3D Schur-decomposition solver compared with the standard discrete ordinates method.

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

    PubMed Central

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

    2015-01-01

    Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and extremely dynamic. This review presents the most recent advances in topological domains’ organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. CTCF protein appears as a central factor of these two organization levels having either a strong insulating role at TAD borders, or a weaker architectural role in chromatin loop formation. TAD borders directly impact on chromatin dynamics by restricting contacts within specific genomic portions thus confining chromatin loop formation within TADs. We discuss how sub-TAD chromatin dynamics, constrained into a recently described statistical helix conformation, can produce functional interactions by contact stabilization. PMID:26226004

  15. 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.

  16. Laplace-domain wave-equation modeling and full waveform inversion in 3D isotropic elastic media

    NASA Astrophysics Data System (ADS)

    Son, Woohyun; Pyun, Sukjoon; Shin, Changsoo; Kim, Han-Joon

    2014-06-01

    The 3D elastic problem has not been widely studied because of the computational burden. Over the past few years, 3D elastic full waveform inversion (FWI) techniques in the time and frequency domains have been proposed by some researchers based on developments in computer science. However, these techniques still have the non-uniqueness and high nonlinearity problems. In this paper, we propose a 3D elastic FWI algorithm in the Laplace domain that can mitigate these problems. To efficiently solve the impedance matrix, we adopt a first-order absorbing boundary condition that results in a symmetric system. A conjugate gradient (CG) solver can be used because the Laplace-domain wave equation is naturally positive definite. We apply the Jacobi preconditioner to increase the convergence speed. We identify the permissible range of Laplace damping constants through dispersion analysis and accuracy tests. We perform the Laplace-domain FWI based on a logarithmic objective function, and the inversion examples are designed for a land setting, which means that the source is vertically excited and multi-component data are considered. The inversion results indicate that the inversion that uses only the vertical component performs slightly better than the multi-component inversion. This unexpected result is obtained partly because we use a vertically polarized source. We analyze the residuals and Frechet derivatives for each component to examine the characteristics of the Laplace-domain multi-component FWI. The results indicate that the residuals and Frechet derivatives for the horizontal component have a singularity problem. The numerical examples demonstrate that the singularity problem is related to the directivity of the displacement and to taking the logarithm of Laplace-domain wave fields. To avoid this singularity problem, we use a simple method that excludes the data near the singular region. Although we can use either simultaneous or sequential strategies to invert the

  17. Efficient spectral and pseudospectral algorithms for 3D simulations of whistler-mode waves in a plasma

    SciTech Connect

    Gumerov, Nail A.; Karavaev, Alexey V.; Surjalal Sharma, A.; Shao Xi; Papadopoulos, Konstantinos D.

    2011-04-01

    Efficient spectral and pseudospectral algorithms for simulation of linear and nonlinear 3D whistler waves in a cold electron plasma are developed. These algorithms are applied to the simulation of whistler waves generated by loop antennas and spheromak-like stationary waves of considerable amplitude. The algorithms are linearly stable and show good stability properties for computations of nonlinear waves over tens of thousands of time steps. Additional speedups by factors of 10-20 (comparing single core CPU and one GPU) are achieved by using graphics processors (GPUs), which enable efficient numerical simulation of the wave propagation on relatively high resolution meshes (tens of millions nodes) in personal computing environment. Comparisons of the numerical results with analytical solutions and experiments show good agreement. The limitations of the codes and the performance of the GPU computing are discussed.

  18. [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. PMID:26422942

  19. 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.

  20. 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.

  1. 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.

    PubMed

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

    2016-02-23

    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.

  2. Sequence-structure signals of 3D domain swapping in proteins.

    PubMed

    Dehouck, Yves; Biot, Christophe; Gilis, Dimitri; Kwasigroch, Jean Marc; Rooman, Marianne

    2003-07-25

    Three-dimensional domain swapping occurs when two or more identical proteins exchange identical parts of their structure to generate an oligomeric unit. It affects proteins with diverse sequences and structures, and is expected to play important roles in evolution, functional regulation and even conformational diseases. Here, we search for traces of domain swapping in the protein sequence, by means of algorithms that predict the structure and stability of proteins using database-derived potentials. Regions whose sequences are not optimal with regard to the stability of the native structure, or showing marked intrinsic preferences for non-native conformations in absence of tertiary interactions are detected in most domain-swapping proteins. These regions are often located in areas crucial in the swapping process and are likely to influence it on a kinetic or thermodynamic level. In addition, cation-pi interactions are frequently observed to zip up the edges of the interface between intertwined chains or to involve hinge loop residues, thereby modulating stability. We end by proposing a set of mutations altering the swapping propensities, whose experimental characterization would contribute to refine our in silico derived hypotheses.

  3. Multivariate analysis of X-ray, ion and electron spectral images: from surface to 3D materials characterization.

    SciTech Connect

    Kotula, Paul Gabriel; Keenan, Michael Robert

    2005-02-01

    Spectral imaging where a complete spectrum is collected from each of a series of spatial locations (1D lines, 2D images or 3D volumes) is now available on a wide range of analytical tools - from electron and x-ray to ion beam instruments. With this capability to collect extremely large spectral images comes the need for automated data analysis tools that can rapidly and without bias reduce a large number of raw spectra to a compact, chemically relevant, and easily interpreted representation. It is clear that manual interrogation of individual spectra is impractical even for very small spectral images (< 5000 spectra). More typical spectral images can contain tens of thousands to millions of spectra, which given the constraint of acquisition time may contain between 5 and 300 counts per 1000-channel spectrum. Conventional manual approaches to spectral image analysis such as summing spectra from regions or constructing x-ray maps are prone to bias and possibly error. One way to comprehensively analyze spectral image data, which has been automated, is to utilize an unsupervised self-modeling multivariate statistical analysis method such as multivariate curve resolution (MCR). This approach has proven capable of solving a wide range of analytical problems based upon the counting of x-rays (SEM/STEM-EDX, XRF, PIXE), electrons (EELS, XPS) and ions (TOF-SIMS). As an example of the MCR approach, a STEM x-ray spectral image from a ZrB2-SiC composite was acquired and analyzed. The data were generated in a FEI Tecnai F30-ST TEM/STEM operated at 300kV, equipped with an EDAX SUTW x-ray detector. The spectral image was acquired with the TIA software on the STEM at 128 by 128 pixels (12nm/pixel) for 100msec dwell per pixel (total acquisition time was 30 minutes) with a probe of approximately the same size as each pixel. Each spectrum in the image had, on average, 500 counts. The calculation took 5 seconds on a PC workstation with dual 2.4GHz PentiumIV Xeon processors and 2Gbytes

  4. Intensity-based quantification of fast retinal blood flow in 3D via high resolution resonant Doppler spectral OCT

    NASA Astrophysics Data System (ADS)

    Michaely, R.; Bachmann, A. H.; Villiger, M. L.; Blatter, C.; Lasser, T.; Leitgeb, R. A.

    2007-07-01

    Resonant Doppler Fourier Domain Optical Coherence Tomography is a functional imaging modality for quantifying fast tissue flow. The method profits from the effect of interference fringe blurring in spectrometer-based FDOCT in the presence of sample motion. If the reference path length is changed in resonance with the Doppler frequency of the sample flow the signals of resting structures will be suppressed whereas the signals of blood flow are enhanced. This allows for an easy extraction of vascularization structure. 3D images of blood vessels at the human optic nerve head are obtained with high axial resolution of 8 μm in air and an imaging speed of 17.400 depth profiles per second. An electro-optic modulator allows controlled reference phase shifting during camera integration. A differential approach is presented for the quantification of fast flows that are un-accessible via standard phase sensitive Doppler analysis. Flow velocity analysis extracts only the axial component which is dependent on the orientation of the vessel with respect to the optical axis. 3D information of the segmented vessel structure is readily used to obtain the flow velocity vectors along the individual vessels and to calculate the true angle-corrected flow speed.

  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. Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain

    PubMed Central

    Sonka, Milan; Abramoff, Michael D.

    2013-01-01

    In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR. PMID:24222760

  7. Integrated ray tracing simulation of annual variation of spectral bio-signatures from cloud free 3D optical Earth model

    NASA Astrophysics Data System (ADS)

    Ryu, Dongok; Kim, Sug-Whan; Kim, Dae Wook; Lee, Jae-Min; Lee, Hanshin; Park, Won Hyun; Seong, Sehyun; Ham, Sun-Jeong

    2010-09-01

    Understanding the Earth spectral bio-signatures provides an important reference datum for accurate de-convolution of collapsed spectral signals from potential earth-like planets of other star systems. This study presents a new ray tracing computation method including an improved 3D optical earth model constructed with the coastal line and vegetation distribution data from the Global Ecological Zone (GEZ) map. Using non-Lambertian bidirectional scattering distribution function (BSDF) models, the input earth surface model is characterized with three different scattering properties and their annual variations depending on monthly changes in vegetation distribution, sea ice coverage and illumination angle. The input atmosphere model consists of one layer with Rayleigh scattering model from the sea level to 100 km in altitude and its radiative transfer characteristics is computed for four seasons using the SMART codes. The ocean scattering model is a combination of sun-glint scattering and Lambertian scattering models. The land surface scattering is defined with the semi empirical parametric kernel method used for MODIS and POLDER missions. These three component models were integrated into the final Earth model that was then incorporated into the in-house built integrated ray tracing (IRT) model capable of computing both spectral imaging and radiative transfer performance of a hypothetical space instrument as it observes the Earth from its designated orbit. The IRT model simulation inputs include variation in earth orientation, illuminated phases, and seasonal sea ice and vegetation distribution. The trial simulation runs result in the annual variations in phase dependent disk averaged spectra (DAS) and its associated bio-signatures such as NDVI. The full computational details are presented together with the resulting annual variation in DAS and its associated bio-signatures.

  8. Controlling integrin specificity and stem cell differentiation in 2-D and 3-D environments through regulation of fibronectin domain stability

    PubMed Central

    Martino, Mikaël M.; Mochizuki, Mayumi; Rothenfluh, Dominique A.; Rempel, Sandra A.; Hubbell, Jeffrey A.; Barker, Thomas H.

    2009-01-01

    The extracellular matrix (ECM) exerts powerful control over many cellular phenomena, including stem cell differentiation. As such, design and modulation of ECM analogs to ligate specific integrin is a promising approach to control cellular processes in vitro and in vivo for regenerative medicine strategies. Although fibronectin (FN), a crucial ECM protein in tissue development and repair, and its RGD peptide are widely used for cell adhesion, the promiscuity with which they engage integrins leads to difficulty in control of receptor-specific interactions. Recent simulations of force-mediated unfolding of FN domains and sequences analysis of human versus mouse FN suggest that the structural stability of the FN’s central cell-binding domains (FN III9-10) affects its integrin specificity. Through production of FN III9-10 variants with variable stabilities, we obtained ligands that present different specificities for the integrin α5β1 and that can be covalently linked into fibrin matrices. Here, we demonstrate the capacity of α5β1 integrin-specific engagement to influence human mesenchymal stem cell (MSC) behavior in 2D and 3D environments. Our data indicate that α5β1 has an important role in the control of MSC osteogenic differentiation. FN fragments with increased specificity for α5β1 versus αvβ3 results in significantly enhanced osteogenic differentiation of MSCs in 2D and in a clinically relevant 3D fibrin matrix system, although attachment/spreading and proliferation were comparable with that on full-length FN. This work shows how integrin-dependant cellular interactions with the ECM can be engineered to control stem cell fate, within a system appropriate for both 3D cell culture and tissue engineering. PMID:19027948

  9. Dialog-Based 3D-Image Recognition Using a Domain Ontology

    NASA Astrophysics Data System (ADS)

    Hois, Joana; Wünstel, Michael; Bateman, John A.; Röfer, Thomas

    The combination of vision and speech, together with the resulting necessity for formal representations, builds a central component of an autonomous system. A robot that is supposed to navigate autonomously through space must be able to perceive its environment as automatically as possible. But each recognition system has its own inherent limits. Especially a robot whose task is to navigate through unknown terrain has to deal with unidentified or even unknown objects, thus compounding the recognition problem still further. The system described in this paper takes this into account by trying to identify objects based on their functionality where possible. To handle cases where recognition is insufficient, we examine here two further strategies: on the one hand, the linguistic reference and labeling of the unidentified objects and, on the other hand, ontological deduction. This approach then connects the probabilistic area of object recognition with the logical area of formal reasoning. In order to support formal reasoning, additional relational scene information has to be supplied by the recognition system. Moreover, for a sound ontological basis for these reasoning tasks, it is necessary to define a domain ontology that provides for the representation of real-world objects and their corresponding spatial relations in linguistic and physical respects. Physical spatial relations and objects are measured by the visual system, whereas linguistic spatial relations and objects are required for interactions with a user.

  10. The 3D structure of Kaposi sarcoma herpesvirus LANA C-terminal domain bound to DNA

    PubMed Central

    Hellert, Jan; Weidner-Glunde, Magdalena; Krausze, Joern; Lünsdorf, Heinrich; Ritter, Christiane; Schulz, Thomas F.; Lührs, Thorsten

    2015-01-01

    Kaposi sarcoma herpesvirus (KSHV) persists as a latent nuclear episome in dividing host cells. This episome is tethered to host chromatin to ensure proper segregation during mitosis. For duplication of the latent genome, the cellular replication machinery is recruited. Both of these functions rely on the constitutively expressed latency-associated nuclear antigen (LANA) of the virus. Here, we report the crystal structure of the KSHV LANA DNA-binding domain (DBD) in complex with its high-affinity viral target DNA, LANA binding site 1 (LBS1), at 2.9 Å resolution. In contrast to homologous proteins such as Epstein-Barr virus nuclear antigen 1 (EBNA-1) of the related γ-herpesvirus Epstein-Barr virus, specific DNA recognition by LANA is highly asymmetric. In addition to solving the crystal structure, we found that apart from the two known LANA binding sites, LBS1 and LBS2, LANA also binds to a novel site, denoted LBS3. All three sites are located in a region of the KSHV terminal repeat subunit previously recognized as a minimal replicator. Moreover, we show that the LANA DBD can coat DNA of arbitrary sequence by virtue of a characteristic lysine patch, which is absent in EBNA-1 of the Epstein-Barr virus. Likely, these higher-order assemblies involve the self-association of LANA into supermolecular spirals. One such spiral assembly was solved as a crystal structure of 3.7 Å resolution in the absence of DNA. On the basis of our data, we propose a model for the controlled nucleation of higher-order LANA oligomers that might contribute to the characteristic subnuclear KSHV microdomains (“LANA speckles”), a hallmark of KSHV latency. PMID:25947153

  11. 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.

  12. Spectral domain optical coherence tomography and microperimetry in foveal hypoplasia.

    PubMed

    Pal, Swakshyar Saumya; Gella, Laxmi; Sharma, Tarun; Raman, Rajiv

    2011-01-01

    A case of foveal hypoplasia associated with ocular albinism with anatomic and functional changes by various techniques using spectral domain optical coherence tomography (SD-OCT), microperimeter and confocal scanning laser ophthalmoscope is described. This case highlights the importance of microperimeter in detecting the functional abnormalities of vision and SD-OCT in identifying the retinal laminar abnormalities in foveal hypoplasia. PMID:22011499

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. Noninvasive quantification of in vitro osteoblastic differentiation in 3D engineered tissue constructs using spectral ultrasound imaging.

    PubMed

    Gudur, Madhu Sudhan Reddy; Rao, Rameshwar R; Peterson, Alexis W; Caldwell, David J; Stegemann, Jan P; Deng, Cheri X

    2014-01-01

    Non-destructive monitoring of engineered tissues is needed for translation of these products from the lab to the clinic. In this study, non-invasive, high resolution spectral ultrasound imaging (SUSI) was used to monitor the differentiation of MC3T3 pre-osteoblasts seeded within collagen hydrogels. SUSI was used to measure the diameter, concentration and acoustic attenuation of scatterers within such constructs cultured in either control or osteogenic medium over 21 days. Conventional biochemical assays were used on parallel samples to determine DNA content and calcium deposition. Construct volume and morphology were accurately imaged using ultrasound. Cell diameter was estimated to be approximately 12.5-15.5 µm using SUSI, which corresponded well to measurements of fluorescently stained cells. The total number of cells per construct assessed by quantitation of DNA content decreased from 5.6±2.4×10(4) at day 1 to 0.9±0.2×10(4) at day 21. SUSI estimation of the equivalent number of acoustic scatters showed a similar decreasing trend, except at day 21 in the osteogenic samples, which showed a marked increase in both scatterer number and acoustic impedance, suggestive of mineral deposition by the differentiating MC3T3 cells. Estimation of calcium content by SUSI was 41.7±11.4 µg/ml, which agreed well with the biochemical measurement of 38.7±16.7 µg/ml. Color coded maps of parameter values were overlaid on B-mode images to show spatiotemporal changes in cell diameter and calcium deposition. This study demonstrates the use of non-destructive ultrasound imaging to provide quantitative information on the number and differentiated state of cells embedded within 3D engineered constructs, and therefore presents a valuable tool for longitudinal monitoring of engineered tissue development.

  18. Hinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C.

    PubMed

    Orlikowska, Marta; Jankowska, Elżbieta; Kołodziejczyk, Robert; Jaskólski, Mariusz; Szymańska, Aneta

    2011-02-01

    Cystatins are natural inhibitors of cysteine proteases, enzymes that are widely distributed in animals, plants, and microorganisms. Human cystatin C (hCC) has been also recognized as an aggregating protein directly involved in the formation of pathological amyloid fibrils, and these amyloidogenic properties greatly increase in a naturally occurring L68Q hCC variant. For a long time only dimeric structure of wild-type hCC has been known. The dimer is created through 3D domain swapping process, in which two parts of the cystatin structure become separated from each other and next exchanged between two molecules. Important role in the domain swapping plays the L1 loop, which connects the exchanging segments and, upon dimerization, transforms from a β-turn into a part of a long β-strand. In the very recently published first monomeric structure of human cystatin C (hCC-stab1), dimerization was abrogated due to clasping of the β-strands from the swapping domains by an engineered disulfide bridge. We have designed and constructed another mutated cystatin C with the smallest possible structural intervention, that is a single-point mutation replacing hydrophobic V57 from the L1 loop by polar asparagine, known as a stabilizer of a β-turn motif. V57N hCC mutant occurred to be stable in its monomeric form and crystallized as a monomer, revealing typical cystatin fold with a five-stranded antiparallel β-sheet wrapped around an α-helix. Here we report a 2.04 Å resolution crystal structure of V57N hCC and discuss the architecture of the protein in comparison to chicken cystatin, hCC-stab1 and dimeric hCC.

  19. Hinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C.

    PubMed

    Orlikowska, Marta; Jankowska, Elżbieta; Kołodziejczyk, Robert; Jaskólski, Mariusz; Szymańska, Aneta

    2011-02-01

    Cystatins are natural inhibitors of cysteine proteases, enzymes that are widely distributed in animals, plants, and microorganisms. Human cystatin C (hCC) has been also recognized as an aggregating protein directly involved in the formation of pathological amyloid fibrils, and these amyloidogenic properties greatly increase in a naturally occurring L68Q hCC variant. For a long time only dimeric structure of wild-type hCC has been known. The dimer is created through 3D domain swapping process, in which two parts of the cystatin structure become separated from each other and next exchanged between two molecules. Important role in the domain swapping plays the L1 loop, which connects the exchanging segments and, upon dimerization, transforms from a β-turn into a part of a long β-strand. In the very recently published first monomeric structure of human cystatin C (hCC-stab1), dimerization was abrogated due to clasping of the β-strands from the swapping domains by an engineered disulfide bridge. We have designed and constructed another mutated cystatin C with the smallest possible structural intervention, that is a single-point mutation replacing hydrophobic V57 from the L1 loop by polar asparagine, known as a stabilizer of a β-turn motif. V57N hCC mutant occurred to be stable in its monomeric form and crystallized as a monomer, revealing typical cystatin fold with a five-stranded antiparallel β-sheet wrapped around an α-helix. Here we report a 2.04 Å resolution crystal structure of V57N hCC and discuss the architecture of the protein in comparison to chicken cystatin, hCC-stab1 and dimeric hCC. PMID:21074623

  20. 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.

  1. 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

  2. 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. PMID:20588552

  3. Imaging tamoxifen retinopathy using spectral-domain optical coherence tomography

    PubMed Central

    Caramoy, Albert; Scholz, Paula; Fauser, Sascha; Kirchhof, Bernd

    2011-01-01

    A case of tamoxifen retinopathy examined with spectral-domain optical coherence tomography (SD-OCT) is presented. The typical refractile deposits are located between ganglion cell layer and inner plexiform layer in SD-OCT. A defect on the outer retinal layer with disruption of the photoreceptor layer with sharp edges is seen. The still attached posterior hyaloids gives evidence of other pathomechanism involved in the outer retinal defect than that of macular hole, as suggested in the literature.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Compressive sensing spectral domain optical coherence tomography with dispersion compensation

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    In this paper, we describe a novel CS method that incorporates dispersion compensation into the CS reconstruction of spectral domain OCT (SD OCT) signal. We show that A-scans with dispersion compensation can be obtained by multiplying the dispersion correcting term to the undersampled linear-in-wavenumber spectral data before the CS reconstruction. We also implemented fast CS reconstruction by taking the advantage of fast Fourier transform (FFT). The matrix-vector multiplication commonly used in the CS reconstruction is implemented by a two-step procedure. Compared to the CS reconstruction with matrix multiplication, our method can obtain dispersion compensated A-scan at least 5 times faster. Experimental results show that the proposed method can achieve high quality image with dispersion compensation.

  9. Spectral and lifetime domain measurements of rat brain tumours

    NASA Astrophysics Data System (ADS)

    Abi Haidar, D.; Leh, B.; Allaoua, K.; Genoux, A.; Siebert, R.; Steffenhagen, M.; Peyrot, D.; Sandeau, N.; Vever-Bizet, C.; Bourg-Heckly, G.; Chebbi, I.; Collado-Hilly, M.

    2012-02-01

    During glioblastoma surgery, delineation of the brain tumour margins remains difficult especially since infiltrated and normal tissues have the same visual appearance. This problematic constitutes our research interest. We developed a fibre-optical fluorescence probe for spectroscopic and time domain measurements. First measurements of endogenous tissue fluorescence were performed on fresh and fixed rat tumour brain slices. Spectral characteristics, fluorescence redox ratios and fluorescence lifetime measurements were analysed. Fluorescence information collected from both, lifetime and spectroscopic experiments, appeared promising for tumour tissue discrimination. Two photon measurements were performed on the same fixed tissue. Different wavelengths are used to acquire two-photon excitation-fluorescence of tumorous and healthy sites.

  10. Numerical dispersion, stability, and phase-speed for 3D time-domain finite-difference seismic wave propagation algorithms

    NASA Astrophysics Data System (ADS)

    Haney, M. M.; Aldridge, D. F.; Symons, N. P.

    2005-12-01

    Numerical solution of partial differential equations by explicit, time-domain, finite-difference (FD) methods entails approximating temporal and spatial derivatives by discrete function differences. Thus, the solution of the difference equation will not be identical to the solution of the underlying differential equation. Solution accuracy degrades if temporal and spatial gridding intervals are too large. Overly coarse spatial gridding leads to spurious artifacts in the calculated results referred to as numerical dispersion, whereas coarse temporal sampling may produce numerical instability (manifest as unbounded growth in the calculations as FD timestepping proceeds). Quantitative conditions for minimizing dispersion and avoiding instability are developed by deriving the dispersion relation appropriate for the discrete difference equation (or coupled system of difference equations) under examination. A dispersion relation appropriate for FD solution of the 3D velocity-stress system of isotropic elastodynamics, on staggered temporal and spatial grids, is developed. The relation applies to either compressional or shear wave propagation, and reduces to the proper form for acoustic propagation in the limit of vanishing shear modulus. A stability condition and a plane-wave phase-speed formula follow as consequences of the dispersion relation. The mathematical procedure utilized for the derivation is a modern variant of classical von Neumann analysis, and involves a 4D discrete space/time Fourier transform of the nine, coupled, FD updating formulae for particle velocity vector and stress tensor components. The method is generalized to seismic wave propagation within anelastic and poroelastic media, as well as sound wave propagation within a uniformly-moving atmosphere. A significant extension of the approach yields a stability condition for wave propagation across an interface between dissimilar media with strong material contrast (e.g., the earth's surface, the seabed

  11. 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

  12. The spectral-domain approach for microwave integrated circuits

    NASA Astrophysics Data System (ADS)

    Jansen, R. H.

    1985-10-01

    A survey is given of the so-called spectral-domain approach, an analytical and numerical technique particularly suited for the solution of boundary-value problems in microwave and millimeter-wave integrated circuits. The mathematical formulation of the analytical part of this approach is described in a generalized notation for two- and three-dimensional strip- and slot-type fields. In a similar way, the numerical part of the technique is treated, keeping always in touch with the mathematical and physical background, as well as with the respective microwave applications. A discussion of different specific aspects of the approach is presented, and outlines are provided of the peculiarities of shielded-, covered-, and open-type problems. A brief review of the progress achieved in the last decade (1975-1984) follows. The survey closes with considerations on numerical efficiency, demonstrating that spectral-domain computations can by speeded up remarkably by analytical preprocessing. The presented material is based on ten years of active involvement by the author in the field and reveals a variety of contributions by West German researchers previously not known to the international microwave community.

  13. Adaptive compressed sensing for spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Wang, Yi; Chen, Xiaodong; Wang, Ting; Li, Hongxiao; Yu, Daoyin

    2014-03-01

    Spectral-domain optical coherence tomography (SD-OCT) is a non-contact and non-invasive method for measuring the change of biological tissues caused by pathological changes of body. CCD with huge number of pixels is usually used in SD-OCT to increase the detecting depth, thus enhancing the hardness of data transmission and storage. The usage of compressed sensing (CS) in SD-OCT is able to reduce the trouble of large data transfer and storage, thus eliminating the complexity of processing system. The traditional CS uses the same sampling model for SD-OCT images of different tissue, leading to reconstruction images with different quality. We proposed a CS with adaptive sampling model. The new model is based on uniform sampling model, and the interference spectral of SD-OCT is considered to adjust the local sampling ratio. Compared with traditional CS, adaptive CS can modify the sampling model for images of different tissue according to different interference spectral, getting reconstruction images with high quality without changing sampling model.

  14. 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.

  15. 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…

  16. 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

  17. Interference enhancement in spectral domain interferometric measurements on transparent plate.

    PubMed

    Zhang, Ke; Tao, Li; Cheng, Wenkai; Liu, Jianhua; Chen, Zhongping

    2014-09-10

    In spectral domain interferometry, the interference signal generated by directly reflected waves from the two surfaces of a sample plate under test is greatly enhanced by the blockage of those light waves reflected by the two arm mirrors in the Michelson interferometer. This sample surface-reflected interference signal, being the optical path length of the plate, is therefore identifiable directly from the Fourier-transformed interference spectrum. Consequently, the group refractive index and physical thickness of the plate can be obtained simultaneously without any prior information of them. Moreover, subsequent in situ angular scanning on the interference spectra helps to retrieve the wavelength-dependent phase refractive index and first-order dispersion. The order of magnitude of the relative error for the group refractive index is 10(-4), while that for the phase refractive index and the physical thickness is 10(-3).

  18. Shift-multiplexing complex spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Huang, Haochong; Jiang, Zhuqing; Wang, Dayong; Cai, Wenyuan; Man, Tianlong; Wang, Zhe; Panezai, Spozmai

    2014-01-01

    We propose and experimentally demonstrate a shift-multiplexing complex spectral-domain optical coherence tomography (shift-multiplexing CSD-OCT) method, in which the maximum detection depth of SD-OCT can be greatly extended by incorporating the shift-multiplexing of detection positions with CSD-OCT. The tomographic imaging with twofold or threefold microscopic slides as the target sample is performed. The experimental results show that the tomographic imaging with more uniform brightness and clarity for the different depth regions in a thick sample can be achieved by the shift-multiplexing CSD-OCT system. In particular, even while the sample's depth is beyond the maximum imaging depth of CSD-OCT system, the tomographic imaging of this sample can still be realized by using the shift-multiplexing CSD-OCT method without the need for any replacement of the equipment, such as high spectral capacity grating or high resolution of CCD. The shift-multiplexing CSD-OCT system can perform the imaging with the optimization and less reduction of sensitivity for the deeper detection position in the sample.

  19. 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.

  20. Reconstruction for time-domain in vivo EPR 3D multigradient oximetric imaging--a parallel processing perspective.

    PubMed

    Dharmaraj, Christopher D; Thadikonda, Kishan; Fletcher, Anthony R; Doan, Phuc N; Devasahayam, Nallathamby; Matsumoto, Shingo; Johnson, Calvin A; Cook, John A; Mitchell, James B; Subramanian, Sankaran; Krishna, Murali C

    2009-01-01

    Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23 x 23 x 23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time.

  1. Three-beam spectral-domain optical coherence tomography for retinal imaging.

    PubMed

    Suehira, Nobuhito; Ooto, Sotaro; Hangai, Masanori; Matsumoto, Kazuhiro; Tomatsu, Nobuhiro; Yuasa, Takashi; Yamada, Kazuro; Yoshimura, Nagahisa

    2012-10-01

    A three-beam spectral domain optical coherence tomography system (OCT) whose center wavelength is 840 nm was developed. The three beams focus on fundus 3.1 mm apart from each other and are detected by a single line sensor. The distance between the beams is fixed and the beams scan a total area of 10×10  mm² while keeping this separation during three-dimensional (3-D) measurement. The line rate of the sensor is 70 kHz, therefore the total speed is equivalent to 210k A-scans per second in this system. A 1000(x)×500(z)×250(y) voxel volumetric 3D OCT data set can be acquired within 2 s. Images of a model eye, a healthy human eye and a diseased eye taken by this system are shown and evaluated. The image quality of one B-Scan is as good as an image from a single-beam OCT. Adjustment among the beams is solved by additional signal processing using a model eye. A multi-beam OCT has the potential not only for high speed imaging but also functional imaging although problems such as compensation among the beams and motion artifacts must be solved. PMID:23224000

  2. 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.

  3. Diffractive centrosymmetric 3D-transmission phase gratings positioned at the image plane of optical systems transform lightlike 4D-WORLD as tunable resonators into spectral metrics...

    NASA Astrophysics Data System (ADS)

    Lauinger, Norbert

    1999-08-01

    Diffractive 3D phase gratings of spherical scatterers dense in hexagonal packing geometry represent adaptively tunable 4D-spatiotemporal filters with trichromatic resonance in visible spectrum. They are described in the (lambda) - chromatic and the reciprocal (nu) -aspects by reciprocal geometric translations of the lightlike Pythagoras theorem, and by the direction cosine for double cones. The most elementary resonance condition in the lightlike Pythagoras theorem is given by the transformation of the grating constants gx, gy, gz of the hexagonal 3D grating to (lambda) h1h2h3 equals (lambda) 111 with cos (alpha) equals 0.5. Through normalization of the chromaticity in the von Laue-interferences to (lambda) 111, the (nu) (lambda) equals (lambda) h1h2h3/(lambda) 111-factor of phase velocity becomes the crucial resonance factor, the 'regulating device' of the spatiotemporal interaction between 3D grating and light, space and time. In the reciprocal space equal/unequal weights and times in spectral metrics result at positions of interference maxima defined by hyperbolas and circles. A database becomes built up by optical interference for trichromatic image preprocessing, motion detection in vector space, multiple range data analysis, patchwide multiple correlations in the spatial frequency spectrum, etc.

  4. A multi-domain 3D Euler solver for flows in solid propellant rocket motor with AFT fin

    NASA Astrophysics Data System (ADS)

    Chaouat, Bruno; Vuillot, Francois

    1992-07-01

    The steady state three-dimensional flow field is computed by means of finite volume explicit NI centered scheme that solves the Euler equations. The treatment of boundary conditions is based on the use of characteristic relations. Application to a geometry including an aft end fin is detailed. The built in multi-domain capability of the code was used to divide the computational domain into three simpler sub-domains. The results are analyzed in terms of erosive burning and nozzle material ablation risks.

  5. 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

  6. Imaging the eye fundus with real-time en-face spectral domain optical coherence tomography.

    PubMed

    Bradu, Adrian; Podoleanu, Adrian Gh

    2014-04-01

    Real-time display of processed en-face spectral domain optical coherence tomography (SD-OCT) images is important for diagnosis. However, due to many steps of data processing requirements, such as Fast Fourier transformation (FFT), data re-sampling, spectral shaping, apodization, zero padding, followed by software cut of the 3D volume acquired to produce an en-face slice, conventional high-speed SD-OCT cannot render an en-face OCT image in real time. Recently we demonstrated a Master/Slave (MS)-OCT method that is highly parallelizable, as it provides reflectivity values of points at depth within an A-scan in parallel. This allows direct production of en-face images. In addition, the MS-OCT method does not require data linearization, which further simplifies the processing. The computation in our previous paper was however time consuming. In this paper we present an optimized algorithm that can be used to provide en-face MS-OCT images much quicker. Using such an algorithm we demonstrate around 10 times faster production of sets of en-face OCT images than previously obtained as well as simultaneous real-time display of up to 4 en-face OCT images of 200 × 200 pixels(2) from the fovea and the optic nerve of a volunteer. We also demonstrate 3D and B-scan OCT images obtained from sets of MS-OCT C-scans, i.e. with no FFT and no intermediate step of generation of A-scans.

  7. Imaging the eye fundus with real-time en-face spectral domain optical coherence tomography.

    PubMed

    Bradu, Adrian; Podoleanu, Adrian Gh

    2014-04-01

    Real-time display of processed en-face spectral domain optical coherence tomography (SD-OCT) images is important for diagnosis. However, due to many steps of data processing requirements, such as Fast Fourier transformation (FFT), data re-sampling, spectral shaping, apodization, zero padding, followed by software cut of the 3D volume acquired to produce an en-face slice, conventional high-speed SD-OCT cannot render an en-face OCT image in real time. Recently we demonstrated a Master/Slave (MS)-OCT method that is highly parallelizable, as it provides reflectivity values of points at depth within an A-scan in parallel. This allows direct production of en-face images. In addition, the MS-OCT method does not require data linearization, which further simplifies the processing. The computation in our previous paper was however time consuming. In this paper we present an optimized algorithm that can be used to provide en-face MS-OCT images much quicker. Using such an algorithm we demonstrate around 10 times faster production of sets of en-face OCT images than previously obtained as well as simultaneous real-time display of up to 4 en-face OCT images of 200 × 200 pixels(2) from the fovea and the optic nerve of a volunteer. We also demonstrate 3D and B-scan OCT images obtained from sets of MS-OCT C-scans, i.e. with no FFT and no intermediate step of generation of A-scans. PMID:24761303

  8. Imaging the eye fundus with real-time en-face spectral domain optical coherence tomography

    PubMed Central

    Bradu, Adrian; Podoleanu, Adrian Gh.

    2014-01-01

    Real-time display of processed en-face spectral domain optical coherence tomography (SD-OCT) images is important for diagnosis. However, due to many steps of data processing requirements, such as Fast Fourier transformation (FFT), data re-sampling, spectral shaping, apodization, zero padding, followed by software cut of the 3D volume acquired to produce an en-face slice, conventional high-speed SD-OCT cannot render an en-face OCT image in real time. Recently we demonstrated a Master/Slave (MS)-OCT method that is highly parallelizable, as it provides reflectivity values of points at depth within an A-scan in parallel. This allows direct production of en-face images. In addition, the MS-OCT method does not require data linearization, which further simplifies the processing. The computation in our previous paper was however time consuming. In this paper we present an optimized algorithm that can be used to provide en-face MS-OCT images much quicker. Using such an algorithm we demonstrate around 10 times faster production of sets of en-face OCT images than previously obtained as well as simultaneous real-time display of up to 4 en-face OCT images of 200 × 200 pixels2 from the fovea and the optic nerve of a volunteer. We also demonstrate 3D and B-scan OCT images obtained from sets of MS-OCT C-scans, i.e. with no FFT and no intermediate step of generation of A-scans. PMID:24761303

  9. Limited Proteolysis Reveals That Amyloids from the 3D Domain-Swapping Cystatin B Have a Non-Native β-Sheet Topology.

    PubMed

    Davis, Peter J; Holmes, David; Waltho, Jonathan P; Staniforth, Rosemary A

    2015-07-31

    3D domain-swapping proteins form multimers by unfolding and then sharing of secondary structure elements, often with native-like interactions. Runaway domain swapping is proposed as a mechanism for folded proteins to form amyloid fibres, with examples including serpins and cystatins. Cystatin C amyloids cause a hereditary form of cerebral amyloid angiopathy whilst cystatin B aggregates are found in cases of Unverricht-Lundborg Syndrome, a progressive form of myoclonic epilepsy. Under conditions that favour fibrillisation, cystatins populate stable 3D domain-swapped dimers both in vitro and in vivo that represent intermediates on route to the formation of fibrils. Previous work on cystatin B amyloid fibrils revealed that the α-helical region of the protein becomes disordered and identified the conservation of a continuous 20-residue elongated β-strand (residues 39-58), the latter being a salient feature of the dimeric 3D domain-swapped structure. Here we apply limited proteolysis to cystatin B amyloid fibrils and show that not only the α-helical N-terminal of the protein (residues 1-35) but also the C-terminal of the protein (residues 80-98) can be removed without disturbing the underlying fibril structure. This observation is incompatible with previous models of cystatin amyloid fibrils where the β-sheet is assumed to retain its native antiparallel arrangement. We conclude that our data favour a more generic, at least partially parallel, arrangement for cystatin β-sheet structure in mature amyloids and propose a model that remains consistent with available data for amyloids from either cystatin B or cystatin C.

  10. 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

  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. 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

  13. Examining cardiomyocyte development with spectral domain phase microscopy

    NASA Astrophysics Data System (ADS)

    Ellerbee, Audrey K.; Creazzo, Tony L.; Izatt, Joseph A.

    2007-02-01

    Phase-sensitive detection has long been recognized as a mechanism for increasing imaging contrast. The proliferation of quantitative phase contrast techniques and the breadth of emerging applications reflects the potential for achieving subdiffraction- limited resolution of cellular structure and dynamic phenomena with phase. Our laboratory developed spectral domain phase microscopy (SDPM) as a simple, phase-stable tool for studying cell dynamics and structure. As a functional extension of optical coherence tomography (OCT), SDPM inherited the high-resolution depth-sectioning capabilities for which OCT is well known, but adds to this an ability to discriminate sub-coherence length changes in optical pathlength within target samples at discrete axial positions. Early demonstrations of SDPM showed it to be extremely sensitive to thickness changes in biological and non-biological samples; the results of our previous studies investigating cell surface motion in cardiomyocyte contractility, cytoplasmic streaming rates in single-celled organisms, and rheological properties of the cytoskeleton suggest that SDPM can contribute insights of biological relevance. The principal aim of this work is to refine SDPM to enable imaging, interrogation, and quantification of parameters of interest in developing cardiomyocytes. In this manuscript, we report on the technology advances that enable multidimensional SDPM, and the results of new inotropic imaging studies of chick embryo cardiomyocytes.

  14. 3D scene reconstruction based on multi-view distributed video coding in the Zernike domain for mobile applications

    NASA Astrophysics Data System (ADS)

    Palma, V.; Carli, M.; Neri, A.

    2011-02-01

    In this paper a Multi-view Distributed Video Coding scheme for mobile applications is presented. Specifically a new fusion technique between temporal and spatial side information in Zernike Moments domain is proposed. Distributed video coding introduces a flexible architecture that enables the design of very low complex video encoders compared to its traditional counterparts. The main goal of our work is to generate at the decoder the side information that optimally blends temporal and interview data. Multi-view distributed coding performance strongly depends on the side information quality built at the decoder. At this aim for improving its quality a spatial view compensation/prediction in Zernike moments domain is applied. Spatial and temporal motion activity have been fused together to obtain the overall side-information. The proposed method has been evaluated by rate-distortion performances for different inter-view and temporal estimation quality conditions.

  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. Spectral-Domain Optical Coherence Tomography and Fundus Autofluorescence Evaluation of Torpedo Maculopathy.

    PubMed

    Thomas, Akshay S; Flaxel, Christina J; Pennesi, Mark E

    2015-01-01

    The authors describe the spectral-domain optical coherence tomography and fundus autofluorescence findings in a case of torpedo maculopathy. Spectral-domain optical coherence tomography revealed loss or disruption of the retinal pigment epithelium and overlying disruption of the outer neurosensory retina. Fundus autofluorescence revealed reduced fundus autofluorescence of the lesion surrounded by a rim of increased fundus autofluorescence. PMID:26484432

  17. Spectral-domain optical coherence tomography and fundus autofluorescence evaluation of torpedo maculopathy.

    PubMed

    Thomas, Akshay S; Flaxel, Christina J; Pennesi, Mark E

    2015-01-01

    The authors describe the spectral-domain optical coherence tomography and fundus autofluorescence findings in a case of torpedo maculopathy. Spectral-domain optical coherence tomography revealed loss or disruption of the retinal pigment epithelium and overlying disruption of the outer neurosensory retina. Fundus autofluorescence revealed reduced fundus autofluorescence of the lesion surrounded by a rim of increased fundus autofluorescence. PMID:25751084

  18. Expressions for the Global Gravimetric Moho Modeling in Spectral Domain

    NASA Astrophysics Data System (ADS)

    Tenzer, Robert; Chen, Wenjin

    2014-08-01

    We apply a newly developed numerical method to improve the Moho geometry by the implementation of gravity data. This method utilizes expressions for the gravimetric forward and inverse modeling derived in a frequency domain. Methods for a spectral analysis and synthesis of the gravity field and crust density structures are applied in the gravimetric forward modeling of the consolidated crust-stripped gravity disturbances, which have a maximum correlation with the (a priori) Moho model. These gravity disturbances are obtained from the Earth's gravity disturbances after applying the topographic and stripping gravity corrections of major known anomalous crust density structures; in the absence of a global mantle model, mantle density heterogeneities are disregarded. The isostatic scheme applied is based on a complete compensation of the crust relative to the upper mantle density. The functional relation is established between the (unknown) Moho depths and the complete crust-stripped isostatic gravity disturbances, which according to the adopted isostatic scheme have (theoretically) a minimum correlation with the Moho geometry. The system of observation equations, which describes the relation between spherical functions of the isostatic gravity field and the Moho geometry, is defined by means of a linearized Fredholm integral equation of the first kind. The Moho depths are determined based on solving the gravimetric inverse problem. The regularization is applied to stabilize the ill-posed solution. This numerical procedure is utilized to determine the Moho depths globally. The gravimetric result is presented and compared with the seismic Moho model. Our gravimetric result has a relatively good agreement with the CRUST2.0 Moho model by means of the RMS of differences (of 3.5 km). However, the gravimetric solution has a systematic bias. We explain this bias between the gravimetric and seismic Moho models by the unmodelled mantle heterogeneities and uncertainties in the

  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. A parameter-free dynamic alternative to hyper-viscosity for coupled transport equations: Application to the simulation of 3D squall lines using spectral elements

    NASA Astrophysics Data System (ADS)

    Marras, Simone; Giraldo, Francis X.

    2015-02-01

    The stabilization of high order spectral elements to solve the transport equations for tracers in the atmosphere remains an active topic of research among atmospheric modelers. This paper builds on our previous work on variational multiscale stabilization (VMS) and discontinuity capturing (DC) (Marras et al. (2012) [7]) and shows the applicability of VMS+DC to realistic atmospheric problems 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 damp the high order modes characterizing the spectral element solution of complex coupled transport problems. The method has important properties that techniques of more common use often lack: 1) it is free of a user-defined parameter, 2) it is anisotropic in that it only acts along the flow direction, 3) it is numerically consistent, and 4) it can improve the monotonicity of high-order spectral elements. The proposed method is assessed by comparing the results against those obtained with a fourth-order hyper-viscosity programmed in the same code. The main conclusion that arises is that tuning can be fully avoided without loss of accuracy if the dissipative scheme is properly designed. Finally, the cost of parallel communication is that of a second order operator which means that fewer communications are required by VMS+DC than by a hyper-viscosity method; fewer communications translate into a faster and more scalable code, which is of vital importance as we approach the exascale range of computing.

  1. 3D Lithospheric Imaging by Time-Domain Full-Waveform Inversion of Teleseismic Body-Waves

    NASA Astrophysics Data System (ADS)

    Beller, S.; Monteiller, V.; Operto, S.; Nolet, G.; Combe, L.; Metivier, L.; Virieux, J.; Nissen-Meyer, T.; Paul, A.

    2014-12-01

    With the deployment of dense seismic arrays and the continuous growth of computing facilities, full-waveform inversion (FWI) of teleseismic data has become a method of choice for high-resolution lithospheric imaging. FWI can be recast as a local optimization problem that seeks to estimate Earth's elastic properties by iteratively minimizing the misfit function between observed and modeled seismograms.In passive teleseismic configurations, the seismic source no longer corresponds to a point source embedded in the targeted medium but rather corresponds to a wavefront incoming from the outside of the model. We develop a 3-dimensional time-domain full-waveform inversion program that is more designed for this configuration. The gradient of the misfit function is efficiently computed with the adjoint-state method. A velocity-stress finite-difference time-domain modeling engine, which is interfaced with the so-called total-field/scattered-field method, is used to propagate in the targeted medium the incident wavefield inferred from a global Earth simulation (AxiSEM). Such interfacing is required to account for the multiple arrivals in the incoming wavefield and the sphericity of the Earth. Despite the limited number of nearly plane-wave sources, the interaction of the incident wavefield with the topography (P-Sv conversions and P-P reflections acting as secondary sources) provides a suitable framework to record both transmitted wavefields and reflected wavefields from lithospheric reflectors. These recordings of both transmitted and reflected waves makes FWI amenable to a broadband-wavenumber (i.e., high resolution) reconstruction of the lithosphere.Feasibility of the method is assessed with a realistic synthetic model representative of the Western Alps. One key issue is the estimation of the temporal source excitation, as there might be some trade-off between the source estimation and the subsurface update. To avoid being trapped in a local minimum, we follow a

  2. 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.

  3. 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.

  4. Design, implementation, and characterization of spectrometer-based spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Palawong, Kunakorn; Pongchalee, Pornthep; Chuamchaitrakool, Porntip; Tachatraiphop, Sukanya; Widjaja, Joewono; Meemon, Panomsak

    2014-06-01

    We report the implementation of a high speed and high resolution spectrometer-based spectral domain optical coherence tomography (SD-OCT) system. A high speed near-infrared spectrometer was designed and built, utilizing a high speed line-array CMOS detector and all off-the-shelf optical components. The acquisition speed of more than 100,000 spectra per second was achieved, enabling a high speed 3D imaging of the implemented SD-OCT system. Here, we report the performance characterization, i.e. resolution, imaging depth, and sensitivity of the implemented system. The penetration depth and depth resolution of the system are currently 2 mm and 14.1 μm, respectively. The lateral resolution of the system was quantified by the Modulation transfer function (MTF) measurement to be about 15.5 μm. over the lateral field-of-view (x-y axes) of 30 mm × 30 mm. The acquisition speed of the system was 20 frames per second.

  5. 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.

  6. Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.

    PubMed

    Chu, Chia-Han; Lo, Wei-Cheng; Wang, Hsin-Wei; Hsu, Yen-Chu; Hwang, Jenn-Kang; Lyu, Ping-Chiang; Pai, Tun-Wen; Tang, Chuan Yi

    2010-10-14

    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 loop

  7. 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.

  8. Extension of a spectral time-stepping domain decomposition method for dispersive and dissipative wave propagation.

    PubMed

    Botts, Jonathan; Savioja, Lauri

    2015-04-01

    For time-domain modeling based on the acoustic wave equation, spectral methods have recently demonstrated promise. This letter presents an extension of a spectral domain decomposition approach, previously used to solve the lossless linear wave equation, which accommodates frequency-dependent atmospheric attenuation and assignment of arbitrary dispersion relations. Frequency-dependence is straightforward to assign when time-stepping is done in the spectral domain, so combined losses from molecular relaxation, thermal conductivity, and viscosity can be approximated with little extra computation or storage. A mode update free from numerical dispersion is derived, and the model is confirmed with a numerical experiment.

  9. 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.

  10. 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.

  11. Spectral multi-domain for large-scale fluid dynamic simulations

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    A number of successful applications of a spectral collocation method extended by a multi-domain patching technique are shown. The multi-domain technique can be used to improve resolution for problems with widely disparate scales, and to reduce the ill-conditioning of the spectral operators for problems in which a large number of points are required for distributed resolution. A new nonreflecting outflow boundary treatment for unsteady transition-to-turbulence simulations is also presented, which relies on the multi-domain technique. The role of multi-domain in improving the efficiency of such calculations is discussed.

  12. 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.

  13. Retinal Structure of Birds of Prey Revealed by Ultra-High Resolution Spectral-Domain Optical Coherence Tomography

    PubMed Central

    Ruggeri, Marco; Major, James C.; McKeown, Craig; Knighton, Robert W.; Puliafito, Carmen A.

    2010-01-01

    Purpose. To reveal three-dimensional (3-D) information about the retinal structures of birds of prey in vivo. Methods. An ultra-high resolution spectral-domain optical coherence tomography (SD-OCT) system was built for in vivo imaging of retinas of birds of prey. The calibrated imaging depth and axial resolution of the system were 3.1 mm and 2.8 μm (in tissue), respectively. 3-D segmentation was performed for calculation of the retinal nerve fiber layer (RNFL) map. Results. High-resolution OCT images were obtained of the retinas of four species of birds of prey: two diurnal hawks (Buteo platypterus and Buteo brachyurus) and two nocturnal owls (Bubo virginianus and Strix varia). These images showed the detailed retinal anatomy, including the retinal layers and the structure of the deep and shallow foveae. The calculated thickness map showed the RNFL distribution. Traumatic injury to one bird's retina was also successfully imaged. Conclusions. Ultra-high resolution SD-OCT provides unprecedented high-quality 2-D and 3-D in vivo visualization of the retinal structures of birds of prey. SD-OCT is a powerful imaging tool for vision research in birds of prey. PMID:20554605

  14. Measurement of multiple psi torsion angles in uniformly 13C,15N-labeled alpha-spectrin SH3 domain using 3D 15N-13C-13C-15N MAS dipolar-chemical shift correlation spectroscopy.

    PubMed

    Ladizhansky, Vladimir; Jaroniec, Christopher P; Diehl, Annette; Oschkinat, Hartmut; Griffin, Robert G

    2003-06-01

    We demonstrate the simultaneous measurement of several backbone torsion angles psi in the uniformly (13)C,(15)N-labeled alpha-Spectrin SH3 domain using two different 3D 15N-13C-13C-15N dipolar-chemical shift magic-angle spinning (MAS) NMR experiments. The first NCCN experiment utilizes double quantum (DQ) spectroscopy combined with the INADEQUATE type 13C-13C chemical shift correlation. The decay of the DQ coherences formed between 13C'(i) and 13C(alphai) spin pairs is determined by the "correlated" dipolar field due to 15N(i)-13C(alphai) and 13C'(i)-15N(i+1) dipolar couplings and is particularly sensitive to variations of the torsion angle in the regime |psi| > 140 degrees. However, the ability of this experiment to constrain multiple psi-torsion angles is limited by the resolution of the 13C(alpha)-(13)CO correlation spectrum. This problem is partially addressed in the second approach described here, which is an NCOCA NCCN experiment. In this case the resolution is enhanced by the superior spectral dispersion of the 15N resonances present in the 15N(i+1)-13C(alphai) part of the NCOCA chemical shift correlation spectrum. For the case of the 62-residue alpha-spectrin SH3 domain, we determined 13 psi angle constraints with the INADEQUATE NCCN experiment and 22 psi constraints were measured in the NCOCA NCCN experiment.

  15. Spectroscopy by joint spectral and time domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Szkulmowski, Maciej; Tamborski, Szymon; Wojtkowski, Maciej

    2015-03-01

    We present the methodology for spectroscopic examination of absorbing media being the combination of Spectral Optical Coherence Tomography and Fourier Transform Spectroscopy. The method bases on the joint Spectral and Time OCT computational scheme and simplifies data analysis procedure as compared to the mostly used windowing-based Spectroscopic OCT methods. The proposed experimental setup is self-calibrating in terms of wavelength-pixel assignment. The performance of the method in measuring absorption spectrum was checked with the use of the reflecting phantom filled with the absorbing agent (indocyanine green). The results show quantitative accordance with the controlled exact results provided by the reference method.

  16. 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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Zhou, Jian; Qi, Jinyi

    2014-02-01

    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.

  19. 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.

  20. 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

  1. Terahertz Detection Based on Spectral-Domain Interferometry Using Mach-Zehnder Interferometer

    NASA Astrophysics Data System (ADS)

    Ibrahim, Akram; Sharma, Gargi; Singh, Kanwarpal; Ozaki, Tsuneyuki

    2016-09-01

    We demonstrate the use of a Mach-Zehnder interferometer (MZI) to improve the performance of terahertz electric field measurements based on spectral-domain interferometry. The interferometer is introduced into the probe beam line to improve the temporal overlap between the two probe pulses. The probe pulse in the sample arm of the interferometer passes through the detection crystal and overlaps with the terahertz pulse, while the probe pulse in the reference arm does not. We measure the phase change between spectral components of these two pulses using spectral-domain interferometry. Using this new technique, we enable an unlimited temporal scanning window without the loss in the signal-to-noise ratio, thus overcoming the major limitation of conventional spectral-domain interferometry techniques for terahertz electric field detection.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Qian, Cheng; Ding, Dazhi; Fan, Zhenhong; Chen, Rushan

    2015-03-01

    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.

  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. Volumetric imaging of inner retina with adaptive optics spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zhang, Yan, II; Cense, Barry; Jonnal, Ravi S.; Gao, Weihua; Jones, Steve; Olivier, Scot; Miller, Donald T.

    2007-02-01

    Adaptive optics (AO) coupled with ultra-fast spectral-domain optical coherence tomography (SD-OCT) has achieved the necessary 3D resolution, sensitivity, and speed for imaging the microscopic retina at the cellular level. While this technology has been rigorously applied to evaluating the 3D morphology of cone photoreceptors, similar detailed studies of cell-sized structures in the inner retina have yet to be undertaken. In this paper, we improve the technical performance of our AO ultrafast SD-OCT and investigate its use for imaging the microscopic inner retina, in particular the nerve fiber layer (NFL) and retinal capillary network. To maximize lateral resolution within the inner retina, focus was controlled with a high stroke, 37-actuator bimorph mirror (AOptix) that also served as the wavefront corrector of the AO. The AO system operated at a closed-loop rate of 25 Hz. The SD-OCT sub-system consisted of a superluminescent diode (λ= 842 nm, Δλ= 50 nm) and a 512 pixel line scan charge-coupled device (CCD) that acquired 72,000 A-scans/sec. Three different B-scan lengths (36, 60, and 120 A-scans/B-scan), which correspond to B-scan exposure durations of 0.5, 0.83, and 1.67 ms, were evaluated to determine the maximum B-scan length that could be tolerated without noticeable loss in image quality due to eye motion in the well fixated eye. Additional technical improvements included sub-pixel registration to remove instrument error and axial registration of the volume images. Small volume images were acquired at 2 and 7 degrees retinal eccentricity with focus systematically shifted through the retina. Small capillaries, some approaching the smallest in the human eye, were readily detected with AO SD-OCT. Appearance of the nerve fiber layer varied noticeably with depth. The most inner portion (presumably the inner limiting membrane) appeared as a thin irregular surface with little characteristic speckle noise. Within the NFL, complex striation patterns (presumably NFL

  6. Profile and Determinants of Retinal Optical Intensity in Normal Eyes with Spectral Domain Optical Coherence Tomography

    PubMed Central

    Chen, Haoyu; Yang, Jianling; Shi, Fei; Zheng, Ce; Zhu, Weifang; Xiang, Dehui; Chen, Xinjian; Zhang, Mingzhi

    2016-01-01

    Purpose To investigate the profile and determinants of retinal optical intensity in normal subjects using 3D spectral domain optical coherence tomography (SD OCT). Methods A total of 231 eyes from 231 healthy subjects ranging in age from 18 to 80 years were included and underwent a 3D OCT scan. Forty-four eyes were randomly chosen to be scanned by two operators for reproducibility analysis. Distribution of optical intensity of each layer and regions specified by the Early Treatment of Diabetic Retinopathy Study (ETDRS) were investigated by analyzing the OCT raw data with our automatic graph-based algorithm. Univariate and multivariate analyses were performed between retinal optical intensity and sex, age, height, weight, spherical equivalent (SE), axial length, image quality, disc area and rim/disc area ratio (R/D area ratio). Results For optical intensity measurements, the intraclass correlation coefficient of each layer ranged from 0.815 to 0.941, indicating good reproducibility. Optical intensity was lowest in the central area of retinal nerve fiber layer, ganglion cell layer, inner plexiform layer, inner nuclear layer, outer plexiform layer and photoreceptor layer, except for the retinal pigment epithelium (RPE). Optical intensity was positively correlated with image quality in all retinal layers (0.553<β<0.851, p<0.01), and negatively correlated with age in most retinal layers (-0.362<β<-0.179, p<0.01), except for the RPE (β = 0.456, p<0.01), outer nuclear layer and photoreceptor layer (p>0.05). There was no relationship between retinal optical intensity and sex, height, weight, SE, axial length, disc area and R/D area ratio. Conclusions There was a specific pattern of distribution of retinal optical intensity in different regions. The optical intensity was affected by image quality and age. Image quality can be used as a reference for normalization. The effect of age needs to be taken into consideration when using OCT for diagnosis. PMID:26863010

  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. 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.

  10. 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

  11. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

    PubMed

    Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

    2011-07-01

    The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

  12. Spatially-dense, multi-spectral, frequency-domain diffuse optical tomography of breast cancer

    NASA Astrophysics Data System (ADS)

    Ban, Han Yong

    Diffuse optical tomography (DOT) employs near-infrared light to image the concentration of chromophores and cell organelles in tissue and thereby providing access to functional parameters that can differentiate cancerous from normal tissues. This thesis describes research at the bench and in the clinic that explores and identifies the potential of DOT breast cancer imaging. The bench and clinic instrumentation differ but share important features: they utilize a very large, spatially dense, set of source-detector pairs (10 7) for imaging in the parallel-plate geometry. The bench experiments explored three-dimensional (3D) image resolution and fidelity as a function of numerous parameters and also ascertained the effects of a chest wall phantom. The chest wall is always present but is typically ignored in breast DOT. My experiments clarified chest wall influences and developed schemes to mitigate these effects. Mostly, these schemes involved selective data exclusion, but their efficacy also depended on reconstruction approach. Reconstruction algorithms based on analytic (fast) Fourier inversion and linear algebraic techniques were explored. The clinical experiments centered around a DOT instrument that I designed, constructed, and have begun to test (in-vitro and in-vivo). This instrumentation offers many features new to the field. Specifically, the imager employs spatially-dense, multi-spectral, frequency-domain data; it possesses the world's largest optical source-detector density yet reported, facilitated by highly-parallel CCD-based frequency-domain imaging based on gain-modulation heterodyne detection. The instrument thus measures both phase and amplitude of the diffusive light waves. Other features include both frontal and sagittal breast imaging capabilities, ancillary cameras for measurement of breast boundary profiles, real-time data normalization, and mechanical improvements for patient comfort. The instrument design and construction is my most significant

  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. Spectral domain optical coherence tomography imaging in optic disk pit associated with outer retinal dehiscence

    PubMed Central

    Wong, Chee Wai; Wong, Doric; Mathur, Ranjana

    2014-01-01

    A 37-year-old Bangladeshi male presented with an inferotemporal optic disk pit and serous macular detachment in the left eye. Imaging with spectral domain optical coherence tomography (OCT) revealed a multilayer macular schisis pattern with a small subfoveal outer retinal dehiscence. This case illustrates a rare phenotype of optic disk maculopathy with macular schisis and a small outer retinal layer dehiscence. Spectral domain OCT was a useful adjunct in delineating the retinal layers in optic disk pit maculopathy, and revealed a small area of outer retinal layer dehiscence that could only have been detected on high-resolution OCT. PMID:25349471

  15. Doppler flow imaging of cytoplasmic streaming using spectral domain phase microscopy

    NASA Astrophysics Data System (ADS)

    Choma, Michael A.; Ellerbee, Audrey K.; Yazdanfar, Siavash; Izatt, Joseph A.

    2006-03-01

    Spectral domain phase microscopy (SDPM) is a function extension of spectral domain optical coherence tomography. SDPM achieves exquisite levels of phase stability by employing common-path interferometry. We discuss the theory and limitations of Doppler flow imaging using SDPM, demonstrate monitoring the thermal contraction of a glass sample with nanometer per second velocity sensitivity, and apply this technique to measurement of cytoplasmic streaming in an Amoeba proteus pseudopod. We observe reversal of cytoplasmic flow induced by extracellular CaCl2, and report results that suggest parabolic flow of cytoplasm in the A. proteus pseudopod.

  16. Sparse OCT: optimizing compressed sensing in spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Liu, Xuan; Kang, Jin U.

    2011-03-01

    We applied compressed sensing (CS) to spectral domain optical coherence tomography (SD-OCT). Namely, CS was applied to the spectral data in reconstructing A-mode images. This would eliminate the need for a large amount of spectral data for image reconstruction and processing. We tested the CS method by randomly undersampling k-space SD-OCT signal. OCT images are reconstructed by solving an optimization problem that minimizes the l1 norm to enforce sparsity, subject to data consistency constraints. Variable density random sampling and uniform density random sampling were studied and compared, which shows the former undersampling scheme can achieve accurate signal recovery using less data.

  17. Real-time dispersion-compensated image reconstruction for compressive sensing spectral domain optical coherence tomography.

    PubMed

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

    2014-09-01

    In this work, we propose a novel dispersion compensation method that enables real-time compressive sensing (CS) spectral domain optical coherence tomography (SD OCT) image reconstruction. We show that dispersion compensation can be incorporated into CS SD OCT by multiplying the dispersion-correcting terms by the undersampled spectral data before CS reconstruction. High-quality SD OCT imaging with dispersion compensation was demonstrated at a speed in excess of 70 frames per s using 40% of the spectral measurements required by the well-known Shannon/Nyquist theory. The data processing and image display were performed on a conventional workstation having three graphics processing units.

  18. 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

  19. Selective inner retinal layer involvement in early syphilitic retinitis as evidenced by spectral domain OCT

    PubMed Central

    Klemencic, Stephanie A.; Newman, Tricia L.; Messner, Leonard V.

    2011-01-01

    Retinitis as a feature of syphilitic uveitis in immunocompromised individuals is a common finding. We present spectral domain OCT images of early syphilitic retinitis pre and post treatment with penicillin. This case suggests that the inner retinal layers may be selectively involved with early syphilitic retinitis. Early treatment is important to avoid outer layer retinal involvement and to decrease ocular morbidity.

  20. Bone Remodeling in Choroidal Osteoma Monitored by Fundus Photography and Spectral-Domain Optical Coherence Tomography

    PubMed Central

    Kamalden, Tengku Ain; Lingam, Gopal; Sundar, Gangadhara

    2014-01-01

    Choroidal osteoma is a benign ossifying tumor of the choroid, consisting of mature bone tissue. It has been described to enlarge and evolve at varying rates over time. Here, we report and quantify the progression of a unilateral choroidal osteoma in a 7-year-old boy by fundus photography, and document tumor remodeling by spectral domain optical coherence tomography images. PMID:27175357

  1. In-vivo full depth of eye imaging spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Dai, Cuixia; Zhou, Chuanqing; Jiao, Shuliang; Xi, Peng; Ren, Qiushi

    2011-09-01

    It is necessary to apply the spectral-domain optical coherence tomography (SD-OCT) to image the whole eye segment for practically iatrical application, but the imaging depth of SD-OCT is limited by the spectral resolution of the spectrometer. By now, no result about this research has been reported. In our study, a new dual channel dual focus OCT system is adopted to image the whole eye segment. The cornea and the crystalline lens are simultaneously imaged by using full range complex spectral-domain OCT in one channel, the retina is detected by the other. The new system was successfully tested in imaging of the volunteer' eye in vivo. The preliminary results presented in this paper demonstrated the feasibility of this approach.

  2. 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)

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    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.

  6. Broadband CARS spectral phase retrieval using a time-domain Kramers-Kronig transform.

    PubMed

    Liu, Yuexin; Lee, Young Jong; Cicerone, Marcus T

    2009-05-01

    We describe a closed-form approach for performing a Kramers-Kronig (KK) transform that can be used to rapidly and reliably retrieve the phase, and thus the resonant imaginary component, from a broadband coherent anti-Stokes Raman scattering (CARS) spectrum with a nonflat background. In this approach we transform the frequency-domain data to the time domain, perform an operation that ensures a causality criterion is met, then transform back to the frequency domain. The fact that this method handles causality in the time domain allows us to conveniently account for spectrally varying nonresonant background from CARS as a response function with a finite rise time. A phase error accompanies KK transform of data with finite frequency range. In examples shown here, that phase error leads to small (<1%) errors in the retrieved resonant spectra.

  7. Spatially resolved 3D noise

    NASA Astrophysics Data System (ADS)

    Haefner, David P.; Preece, Bradley L.; Doe, Joshua M.; Burks, Stephen D.

    2016-05-01

    When evaluated with a spatially uniform irradiance, an imaging sensor exhibits both spatial and temporal variations, which can be described as a three-dimensional (3D) random process considered as noise. In the 1990s, NVESD engineers developed an approximation to the 3D power spectral density (PSD) for noise in imaging systems known as 3D noise. In this correspondence, we describe how the confidence intervals for the 3D noise measurement allows for determination of the sampling necessary to reach a desired precision. We then apply that knowledge to create a smaller cube that can be evaluated spatially across the 2D image giving the noise as a function of position. The method presented here allows for both defective pixel identification and implements the finite sampling correction matrix. In support of the reproducible research effort, the Matlab functions associated with this work can be found on the Mathworks file exchange [1].

  8. Privacy protection in surveillance systems based on JPEG DCT baseline compression and spectral domain watermarking

    NASA Astrophysics Data System (ADS)

    Sablik, Thomas; Velten, Jörg; Kummert, Anton

    2015-03-01

    An novel system for automatic privacy protection in digital media based on spectral domain watermarking and JPEG compression is described in the present paper. In a first step private areas are detected. Therefore a detection method is presented. The implemented method uses Haar cascades to detects faces. Integral images are used to speed up calculations and the detection. Multiple detections of one face are combined. Succeeding steps comprise embedding the data into the image as part of JPEG compression using spectral domain methods and protecting the area of privacy. The embedding process is integrated into and adapted to JPEG compression. A Spread Spectrum Watermarking method is used to embed the size and position of the private areas into the cover image. Different methods for embedding regarding their robustness are compared. Moreover the performance of the method concerning tampered images is presented.

  9. Source-domain spectral EEG analysis of sports-related concussion via Measure Projection Analysis.

    PubMed

    Balkan, Ozgur; Virji-Babul, Naznin; Miyakoshi, Makoto; Makeig, Scott; Garudadri, Harinath

    2015-01-01

    Here, we investigated EEG-based source-level spectral differences between adolescents with sports-related concussions and healthy age matched controls. We transformed resting state EEG collected in both groups to the source domain using Independent Component Analysis (ICA) and computed the component process power spectra. For group-level analysis in the source domain, we used a probabilistic framework, Measure Projection Analysis (MPA), that has advantages over parametric k-means clustering of brain sources. MPA revealed that some frontal brain sources in the concussed group had significantly more power in the beta band (p<;0.005) and significantly less delta (p<;0.01) and theta band power (p<;0.05) than the healthy control group. These results suggest that a shift in spectral profile toward higher frequencies in some frontal brain regions might distinguish individuals with concussion from healthy controls. PMID:26737184

  10. 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

  11. EN FACE SPECTRAL-DOMAIN OPTICAL COHERENCE TOMOGRAPHY OUTER RETINAL ANALYSIS AND RELATION TO VISUAL ACUITY

    PubMed Central

    Kiernan, Daniel F.; Zelkha, Ruth; Hariprasad, Seenu M.; Lim, Jennifer I.; Blair, Michael P.; Mieler, William F.

    2013-01-01

    Purpose To describe a method of en face visualization and quantification of the photoreceptor inner segment/outer segment junction area, using spectral-domain optical coherence tomography, and association with visual acuity. Methods Case series of 74 eyes in 53 patients. Central 1-mm and 400-mm en face areas were analyzed with a computer algorithm. Results The presence or absence of inner segment/outer segment junction was visible on both spectral-domain optical coherence tomography en face and retinal cross sections. Thirty eyes (40.6%) had no retinal pathology and an average logMAR visual acuity of 0.116. Twenty-five eyes (33.8%) had intraretinal edema, with visual acuity of 0.494. Nineteen eyes had nonneovascular age-related macular degeneration (dry age-related macular degeneration, 25.6%), with visual acuity of 0.392. In all eyes, central 1-mm and 400-µm en face areas were 58.3 ± 25.0% and 56.4 ± 26.0%, which showed significant correlation with visual acuity (Pearson correlation, r = −0.66 and −0.56, both P < 0.001). This correlation was greater than correlation of visual acuity with central subfield thickness (r = 0.39, P < 0.001), macular volume (r = 0.36, P = 0.002), and average macular thickness (r = 0.37, P = 0.001). However, no variables were significantly correlated with dry age-related macular degeneration eyes. Conclusion Central en face inner segment/outer segment junction areas are significantly correlated with visual acuity in most eyes. This may correlate better with visual acuity than other spectral-domain optical coherence tomography values, as a reflection of photoreceptor integrity. Dry age-related macular degeneration may disrupt the plane used to formulate the en face display. Advancements in spectral-domain optical coherence tomography may provide routine en face visualization analysis. PMID:22466459

  12. 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.

  13. 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

  14. Spectral domain phase microscopy: a new tool for measuring cellular dynamics and cytoplasmic flow

    NASA Astrophysics Data System (ADS)

    McDowell, Emily J.; Choma, Michael A.; Ellerbee, Audrey K.; Izatt, Joseph A.

    2005-03-01

    Broadband interferometry is an attractive technique for the detection of cellular motions because it provides depth-resolved interferometric phase information via coherence gating. Here a phase sensitive technique called spectral domain phase microscopy (SDPM) is presented. SDPM is a functional extension of spectral domain optical coherence tomography that allows for the detection of cellular motions and dynamics with nanometer-scale sensitivity. This sensitivity is made possible by the inherent phase stability of spectral domain OCT combined with common-path interferometry. The theory that underlies this technique is presented, the sensitivity of the technique is demonstrated by the measurement of the thermal expansion coefficient of borosilicate glass, and the response of an Amoeba proteus to puncture of its cell membrane is measured. We also exploit the phase stability of SDPM to perform Doppler flow imaging of cytoplasmic streaming in A. proteus. We show reversal of cytoplasmic flow in response to stimuli, and we show that the cytoplasmic flow is laminar (i.e. parabolic) in nature. We are currently investigating the use of SDPM in a variety of different cell types.

  15. 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

  16. 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.

  17. Wavelength-Filter Based Spectral Calibrated Wave number - Linearization in 1.3 mm Spectral Domain Optical Coherence

    PubMed Central

    Wijeisnghe, Ruchire Eranga Henry; Cho, Nam Hyun; Park, Kibeom; Shin, Yongseung; Kim, Jeehyun

    2014-01-01

    In this study, we demonstrate the enhanced spectral calibration method for 1.3 μm spectral-domain optical coherence tomography (SD-OCT). The calibration method using wavelength-filter simplifies the SD-OCT system, and also the axial resolution and the entire speed of the OCT system can be dramatically improved as well. An externally connected wavelength-filter is utilized to obtain the information of the wavenumber and the pixel position. During the calibration process the wavelength-filter is placed after a broadband source by connecting through an optical circulator. The filtered spectrum with a narrow line width of 0.5 nm is detected by using a line-scan camera. The method does not require a filter or a software recalibration algorithm for imaging as it simply resamples the OCT signal from the detector array without employing rescaling or interpolation methods. One of the main drawbacks of SD-OCT is the broadened point spread functions (PSFs) with increasing imaging depth can be compensated by increasing the wavenumber-linearization order. The sensitivity of our system was measured at 99.8 dB at an imaging depth of 2.1 mm compared with the uncompensated case. PMID:25688338

  18. A structural basis for Staphylococcal complement subversion: X-ray structure of the complement-binding domain of Staphylococcus aureus protein Sbi in complex with ligand C3d.

    PubMed

    Clark, Elizabeth A; Crennell, Susan; Upadhyay, Abhishek; Zozulya, Alexey V; Mackay, Julia D; Svergun, Dmitri I; Bagby, Stefan; van den Elsen, Jean M H

    2011-01-01

    The structure of the complement-binding domain of Staphylococcus aureus protein Sbi (Sbi-IV) in complex with ligand C3d is presented. The 1.7Å resolution structure reveals the molecular details of the recognition of thioester-containing fragment C3d of the central complement component C3, involving interactions between residues of Sbi-IV helix α2 and the acidic concave surface of C3d. The complex provides a structural basis for the binding preference of Sbi for native C3 over C3b and explains how Sbi-IV inhibits the interaction between C3d and complement receptor 2. A second C3d binding site on Sbi-IV is identified in the crystal structure that is not observed in related S. aureus C3 inhibitors Efb-C and Ehp. This binding mode perhaps hints as to how Sbi-IV, as part of Sbi, forms a C3b-Sbi adduct and causes futile consumption of C3, an extraordinary aspect of Sbi function that is not shared by any other known Staphylococcal complement inhibitor.

  19. Numerical and Experimental Aspects of Data Acquisition and Processing in Application to Temperature Resolved 3-D Sub-Millimeter Spectroscopy for Astrophysics and Spectral Assignment.

    NASA Astrophysics Data System (ADS)

    Medvedev, Ivan R.; Fortman, Sarah M.; Neese, Christopher F.; De Lucia, Frank C.

    2009-06-01

    Experimental determination of the lower state energy for every transition in molecular spectra, made possible by temperature resolved 3-D spectroscopy, opens new frontiers in our ability to predict molecular spectra over a wide range of temperatures and to assign rotational spectra in many vibrational states. Our improved collisional cooling cell design extends temperature coverage of this technique to 77 K. This enhances our ability to simulate molecular spectra at temperatures of astronomical relevance. We are reporting on experimental and numerical aspects of dealing with exceptionally high information content of these spectra. New data reduction algorithms allow us to process this data in timely fashion in an attempt to make them available to astronomical community.

  20. 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.

  1. 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.

  2. Spectral domain-optical coherence tomography to detect localized retinal nerve fiber layer defects in glaucomatous eyes.

    PubMed

    Vizzeri, Gianmarco; Balasubramanian, Madhusudhanan; Bowd, Christopher; Weinreb, Robert N; Medeiros, Felipe A; Zangwill, Linda M

    2009-03-01

    This study examines the ability of RTVue, Cirrus and Spectralis OCT Spectral domain-optical coherence tomographs (SD-OCT) to detect localized retinal nerve fiber layer defects in glaucomatous eyes. In this observational case series, four glaucoma patients (8 eyes) were selected from the University of California, San Diego Shiley Eye Center and the Diagnostic Innovations in Glaucoma Study (DIGS) based on the presence of documented localized RNFL defects in at least one eye confirmed by masked stereophotograph assessment. One RTVue 3D Disc scan, one RTVue NHM4 scan, one Cirrus Optic Disk Cube 200x200 scan and one Spectralis scan centered on the optic disc (15x15 scan angle, 768 A-scans x 73 B-scans) were obtained on all undilated eyes within a single session. Results were compared with those obtained from stereophotographs. In 6 eyes the presence of localized RNFL defects was detected by stereophotography. In general, by qualitatively evaluating the retinal thickness maps generated, all SD-OCT instruments examined were able to confirm the presence of localized glaucomatous structural damage seen on stereophotographs. This study confirms SD-OCT is a promising technology for glaucoma detection as it may assist clinicians identify the presence of localized glaucomatous structural damage. PMID:19259242

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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)

  8. 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

  9. 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. PMID:27563573

  10. Broad spectral domain fluorescence wavelength modulation of visible and near-infrared emissive polymersomes.

    PubMed

    Ghoroghchian, P Peter; Frail, Paul R; Susumu, Kimihiro; Park, Tae-Hong; Wu, Sophia P; Uyeda, H Tetsuo; Hammer, Daniel A; Therien, Michael J

    2005-11-01

    Incorporation of an extended family of multi[(porphinato)zinc(II)] (PZn)-based supermolecular fluorophores into the lamellar membranes of polymersomes (50 nm to 50 mum diameter polymer vesicles) gives rise to electrooptically diverse nano-to-micron (meso) scale soft materials. Studies that examine homogeneous suspensions of 100 nm diameter emissive polymersomes demonstrate fluorescence energy modulation over a broad spectral domain of the visible and near-infrared (600-900 nm). These polymersomal structures highlight that the nature of intermembranous polymer-to-fluorophore contacts depends on the position and identity of the porphyrins' phenyl ring substituents. Emissive polymersomes are shown to possess reduced spectral heterogeneity with respect to the established optical signatures of these PZn-based supermolecular fluorophores in solution; additionally, selection of fluorophore ancillary substituents predictably controls the nature of polymer-emitter noncovalent interactions to provide an important additional mechanism to further modulate the fluorescence band maxima of these meso-scale emissive vesicles.

  11. 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.

  12. Design and optimization of a spectrometer for spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Hosseiny, Hamid; Carmelo Rosa, Carla

    2014-08-01

    There are several factors such as the chosen optical source, central wavelength, spectral bandwidth, spectrometer optical components and the detector specifications that affect the overall performance of a spectral domain optical coherence tomography (SD-OCT) imaging system. Among these factors a good design and implementation of the spectrometer is of paramount importance as it directly affects the system resolution, sensitivity fall-off, maximum imaging depth, SNR and in general the system performance. This study demonstrates the design steps and some considerations during the design of a spectrometer. The imaging performance of this design is assessed. The obtained experimental results prove an improvement of the overall performance of the common path SD-OCT imaging system and agree with the expected outcome from the design stage.

  13. Spectral domain analysis of electromagnetic wave scattering by an infinite plane metallic grating

    NASA Astrophysics Data System (ADS)

    Uchida, Kazunori; Noda, Takeaki; Matsunaga, Toshiaki

    1987-01-01

    A new method, based on the spectral domain analysis, is presented for solving the electromagnetic wave scattering by an infinite plane metallic grating. The key point of the present method is discretization of spectral formulation in terms of the sampling theorem. Two different polarizations, transverse magnetic and transverse electric excitations, are considered here. The accuracy of the present method is examined numerically by comparison with the rigorous Wiener-Hopf solutions which are applicable only to a special case. Since the end effect of a conducting strip is taken into account analytically, final results show enough convergence to evaluate the near fields as well as the far fields with small matrix calculations. Some numerical examples are shown mainly for surface current distributions to clarify the differences between the two different polarizations.

  14. Investigations of soft and hard tissues in oral cavity by spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Madjarova, Violeta Dimitrova; Yasuno, Yoshiaki; Makita, Shuichi; Hori, Yasuaki; Voeffray, Jean-Baptiste; Itoh, Masahide; Yatagai, Toyohiko; Tamura, Masami; Nanbu, Toshiyuki

    2006-02-01

    Fourier Domain Optical Coherence Tomography (SD-OCT) systems for dental measurements are demonstrated. Two systems have been developed. The first system is fiber based Michelson interferometer with super luminescent diodes at 1310 nm and 100 nm FWHM as a light source. The sensitivity of the system was 106 dB with depth measurement range in air of 2.5 mm. The second systems is a fiber based Mach-Zehnder interferometer with wavelength scanning laser as light source at center wavelength of 1310 nm, wavelength range of 110 nm and scanning rate of 20 KHz. The sensitivity of the system is 112 dB and depth measurement range in air is 6 mm. Both systems can acquire real-time three dimensional (3-D) images in the range of several second. The systems were applied for early caries detection in tooth, for diagnostics of tooth condition after operational tooth treatment, and for diagnostics of the alveolar bone structure. In-vivo measurements were performed on two volunteers. The systems were able to detect discontinuities in tooth and resin filling after tooth treatment. In addition early carries lesion was detected in one of the volunteers. The 3-D profile of the alveolar bone was acquired for first time with non-contact method.

  15. Analysis of the pre-retinal opacities in Gaucher Disease using spectral domain optical coherent tomography.

    PubMed

    Sheck, Leo H N; Wilson, Callum J; Vincent, Andrea L

    2012-12-01

    Fundal opacities have been reported in patients with Gaucher disease, a rare autosomal recessive lysosomal storage disease, prior to the advent of optical coherent tomography. This report provides a detailed analysis of the fundal opacities in a 14-year-old girl with genetically proven Gaucher disease using spectral domain optical coherent tomography. It illustrates clearly that these opacities were pre-retinal opacities located at the vitreo-retinal interface associated with localized posterior vitreous detachments, rather than vitreous opacities as previously suggested in the literature. PMID:22950450

  16. 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

  17. Fast calculation method for computer-generated cylindrical hologram based on wave propagation in spectral domain.

    PubMed

    Jackin, Boaz Jessie; Yatagai, Toyohiko

    2010-12-01

    A fast calculation method for computer generation of cylindrical holograms is proposed. The calculation method is based on wave propagation in spectral domain and in cylindrical co-ordinates, which is otherwise similar to the angular spectrum of plane waves in cartesian co-ordinates. The calculation requires only two FFT operations and hence is much faster. The theoretical background of the calculation method, sampling conditions and simulation results are presented. The generated cylindrical hologram has been tested for reconstruction in different view angles and also in plane surfaces.

  18. 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.

  19. Feasibility of spectral-domain phase-sensitive optical coherence tomography for middle ear vibrometry.

    PubMed

    Subhash, Hrebesh M; Nguyen-Huynh, Anh; Wang, Ruikang K; Jacques, Steven L; Choudhury, Niloy; Nuttall, Alfred L

    2012-06-01

    We describe a novel application of spectral-domain phase-sensitive optical coherence tomography (SD PS-OCT) to detect the tiny motions of the middle ear structures, such as the tympanic membrane and ossicular chain, and their morphological features for differential diagnosis of CHL. This technique has the potential to provide meaningful vibration of ossicles with a vibration sensitivity of ≈ 0.5 nm at 1 kHz of acoustic stimulation. To the best of our knowledge, this is the first demonstration of depth-resolved vibration imaging of ossicles with a PS-OCT system at a nanometer scale.

  20. 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.

  1. Modifications of intensity-interferometric spectral-domain optical coherence tomography with dispersion cancellation

    NASA Astrophysics Data System (ADS)

    Shirai, Tomohiro

    2015-04-01

    Intensity-interferometric spectral-domain (SD) optical coherence tomography (OCT) developed recently enables axial-scan-free cross-sectional imaging with group-velocity dispersion cancellation and a factor-of-\\sqrt{2} resolution improvement. This paper is concerned with a simple and practical method of realizing OCT of this kind. Specifically, we demonstrate theoretically and experimentally that intensity-interferometric SD-OCT can be realized in a simple way by means of a slightly modified conventional SD-OCT setup.

  2. Spectral-Domain Optical Coherence Tomography Documentation of Transsynaptic Retinal Degeneration.

    PubMed

    Schwartz, Stephen G; Pasol, Joshua; Lam, Byron L; Flynn, Harry W

    2016-08-01

    Patients with post-geniculate neurologic disease and corresponding visual field loss may have ophthalmologic abnormalities detectable by spectral-domain optical coherence tomography (SD-OCT), presumably by transsynaptic retrograde retinal degeneration. Here, three such patients (ages 13 years through 75 years) illustrate thinning of the macula and ganglion cell complex corresponding to zones of visual field loss. Thinning of the retinal nerve fiber layer is not notable in these patients. SD-OCT may be a useful technique in diagnosing and following patients with post-geniculate neurologic disease. [Ophthalmic Surg Lasers Imaging Retina. 2016;47:768-772.]. PMID:27548455

  3. 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. PMID:25230400

  4. 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.

  5. 3d-3d correspondence revisited

    NASA Astrophysics Data System (ADS)

    Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr

    2016-04-01

    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. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  6. 3d-3d correspondence revisited

    DOE PAGES

    Chung, Hee -Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr

    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. Image reconstruction from nonuniformly spaced samples in spectral-domain optical coherence tomography

    PubMed Central

    Ke, Jun; Lam, Edmund Y.

    2012-01-01

    In spectral-domain optical coherence tomography (SD-OCT), data samples are collected nonuniformly in the wavenumber domain, requiring a measurement re-sampling process before a conventional fast Fourier transform can be applied to reconstruct an image. This re-sampling necessitates extra computation and often introduces errors in the data. Instead, we develop an inverse imaging approach to reconstruct an SD-OCT image. We make use of total variation (TV) as a constraint to preserve the image edges, and estimate the two-dimensional cross-section of a sample directly from the SD-OCT measurements rather than processing for each A-line. Experimental results indicate that compared with the conventional method, our technique gives a smaller noise residual. The potential of using the TV constraint to suppress sensitivity falloff in SD-OCT is also demonstrated with experiment data. PMID:22574262

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Depth-Encoded Spectral Domain Phase Microscopy for Simultaneous Multi-Site Nanoscale Optical Measurements

    PubMed Central

    Hendargo, Hansford C.; Bower, Bradley A.; Reinstein, Alex S.; Shepherd, Neal; Tao, Yuankai K.; Izatt, Joseph A.

    2011-01-01

    Spectral domain phase microscopy (SDPM) is an extension of spectral domain optical coherence tomography (SDOCT) that exploits the extraordinary phase stability of spectrometer-based systems with common-path geometry to resolve sub-wavelength displacements within a sample volume. This technique has been implemented for high resolution axial displacement and velocity measurements in biological samples, but since axial displacement information is acquired serially along the lateral dimension, it has been unable to measure fast temporal dynamics in extended samples. Depth-Encoded SDPM (DESDPM) uses multiple sample arms with unevenly spaced common path reference reflectors to multiplex independent SDPM signals from separate lateral positions on a sample simultaneously using a single interferometer, thereby reducing the time required to detect unique optical events to the integration period of the detector. Here, we introduce DESDPM and demonstrate the ability to acquire useful phase data concurrently at two laterally separated locations in a phantom sample as well as a biological preparation of spontaneously beating chick cardiomyocytes. DESDPM may be a useful tool for imaging fast cellular phenomena such as nervous conduction velocity or contractile motion. PMID:21886940

  13. Depth-Encoded Spectral Domain Phase Microscopy for Simultaneous Multi-Site Nanoscale Optical Measurements.

    PubMed

    Hendargo, Hansford C; Bower, Bradley A; Reinstein, Alex S; Shepherd, Neal; Tao, Yuankai K; Izatt, Joseph A

    2011-09-01

    Spectral domain phase microscopy (SDPM) is an extension of spectral domain optical coherence tomography (SDOCT) that exploits the extraordinary phase stability of spectrometer-based systems with common-path geometry to resolve sub-wavelength displacements within a sample volume. This technique has been implemented for high resolution axial displacement and velocity measurements in biological samples, but since axial displacement information is acquired serially along the lateral dimension, it has been unable to measure fast temporal dynamics in extended samples. Depth-Encoded SDPM (DESDPM) uses multiple sample arms with unevenly spaced common path reference reflectors to multiplex independent SDPM signals from separate lateral positions on a sample simultaneously using a single interferometer, thereby reducing the time required to detect unique optical events to the integration period of the detector. Here, we introduce DESDPM and demonstrate the ability to acquire useful phase data concurrently at two laterally separated locations in a phantom sample as well as a biological preparation of spontaneously beating chick cardiomyocytes. DESDPM may be a useful tool for imaging fast cellular phenomena such as nervous conduction velocity or contractile motion.

  14. Hybrid Finite Element-Fast Spectral Domain Multilayer Boundary Integral Modeling of Doubly Periodic Structures

    SciTech Connect

    T.F. Eibert; J.L. Volakis; Y.E. Erdemli

    2002-03-03

    Hybrid finite element (FE)--boundary integral (BI) analysis of infinite periodic arrays is extended to include planar multilayered Green's functions. In this manner, a portion of the volumetric dielectric region can be modeled via the finite element method whereas uniform multilayered regions can be modeled using a multilayered Green's function. As such, thick uniform substrates can be modeled without loss of efficiency and accuracy. The multilayered Green's function is analytically computed in the spectral domain and the resulting BI matrix-vector products are evaluated via the fast spectral domain algorithm (FSDA). As a result, the computational cost of the matrix-vector products is kept at O(N). Furthermore, the number of Floquet modes in the expansion are kept very few by placing the BI surfaces within the computational unit cell. Examples of frequency selective surface (FSS) arrays are analyzed with this method to demonstrate the accuracy and capability of the approach. One example involves complicated multilayered substrates above and below an inhomogeneous filter element and the other is an optical ring-slot array on a substrate several hundred wavelengths in thickness. Comparisons with measurements are included.

  15. 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?

  16. 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.

  17. Ultra-fast one micron spectral domain ultra-high sensitive optical micro-angiography for in vivo visualization of ocular circulation of human retina and choroid

    NASA Astrophysics Data System (ADS)

    An, Lin; Wang, Ruikang K.

    2011-03-01

    In this paper, an ultra high speed (92 kHz A-line rate) one micron spectral domain ultra high sensitive optical microangiography system was demonstrated and successfully applied on posterior part of human eye for in vivo visualizing blood perfusions of both retina and choroid. A 1 μm ASE module was utilized as the light source, which could provide much more penetration depth than conventional 800 nm system. Running at 200 frames per second, it would cost ~5 seconds for the system to finish acquiring one 3D data set, which covers ~3×3 mm2 on the retina. Applying the OMAG algorithm onto the slow axis (C-scan direction), our system can extract detailed capillary level ocular perfusion maps for different layers of both retina and choroid. The excellent agreement with the standard text book shows great potential in clinical application.

  18. Resolving the 3D spatial orientation of helix I in the closed state of the colicin E1 channel domain by FRET. Insights into the integration mechanism.

    PubMed

    Lugo, Miguel R; Ho, Derek; Merrill, A Rod

    2016-10-15

    Current evidence suggests that the closed-state membrane model for the channel-forming domain of colicin E1 involves eight amphipathic α-helices (helices I-VII and X) that adopt a two-dimensional arrangement on the membrane surface. Two central hydrophobic α-helices in colicin E1 (VIII and IX) adopt a transmembrane location-the umbrella model. Helices I and II have been shown to participate in the channel by forming a transmembrane segment (TM1) in the voltage-induced open channel state. Consequently, it is paramount to determine the relative location and orientation of helix I in the two-dimensional arrangement of the membrane. A new, low-resolution, three-dimensional model of the closed state of the colicin E1 channel was constructed based on FRET measurements between three naturally occurring Trp residues and three sites in helix I, in addition to previously reported FRET distances for the channel domain. Furthermore, a new mechanism for the channel integration process involving the transition of the soluble to membrane-bound form is presented based on a plethora of kinetic data for this process.

  19. Determination of the spatial TDR-sensor characteristics in strong dispersive subsoil using 3D-FEM frequency domain simulations in combination with microwave dielectric spectroscopy

    NASA Astrophysics Data System (ADS)

    Wagner, Norman; Trinks, Eberhard; Kupfer, Klaus

    2007-04-01

    The spatial sensor characteristics of a 6 cm TDR flat band cable sensor section was simulated with finite element modelling (high frequency structure simulator—HFSS) under certain conditions: (i) in direct contact with the surrounding material (air, water of different salinities, different synthetic and natural soils (sand-silt-clay mixtures)), (ii) with consideration of a defined gap of different size filled with air or water and (iii) the cable sensor pressed at a borehole-wall. The complex dielectric permittivity ɛsstarf(ω, τi) or complex electrical conductivity σsstarf(ω, τi) = iωɛsstarf(ω, τi) of the investigated saturated and unsaturated soils was examined in the frequency range 50 MHz-20 GHz at room temperature and atmospheric pressure with a HP8720D-network analyser. Three soil-specific relaxation processes are assumed to act in the investigated frequency-temperature-pressure range: one primary α-process (main water relaxation) and two secondary (α', β)-processes due to clay-water-ion interactions (bound water relaxation and the Maxwell-Wagner effect). The dielectric relaxation behaviour of every process is described with the use of a simple fractional relaxation model. 3D finite element simulation is performed with a λ/3 based adaptive mesh refinement at a solution frequency of 1 MHz, 10 MHz, 0.1 GHz, 1 GHz and 12.5 GHz. The electromagnetic field distribution, S-parameter and step responses were examined. The simulation adequately reproduces the spatial and temporal electrical and magnetic field distribution. High-lossy soils cause, as a function of increasing gravimetric water content and bulk density, an increase in TDR signal rise time as well as a strong absorption of multiple reflections. An air or water gap works as a quasi-waveguide, i.e. the influence of the surrounding medium is strongly reduced. Appropriate TDR-travel-time distortions can be quantified.

  20. Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome.

    PubMed

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

    2016-08-01

    The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using 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 rRNA 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.

  1. 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)

  2. 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

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

    PubMed

    Lee, Tae Hee; Heo, Hwan; Park, Sang Woo

    2016-09-01

    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

  4. 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.

  5. 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.

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

    PubMed

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

    2015-01-01

    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. PMID:26385655

  7. Numerical simulation validation of nonuniform, nonharmonic analysis of spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Uchida, Tetsuya; Inuzuka, Yuya; Hasegawa, Masaya; Hirobayashi, Shigeki; Misawa, Tadanobu

    2015-03-01

    In spectral-domain optical coherence tomography (SD-OCT), the limited resolution of the spectrometer causes nonuniformity of the interference signal. The latter, in turn, causes the sensitivity of SD-OCT to decrease, thereby limiting the imaging range and decreasing the axial resolution. We addressed this problem by applying nonuniform, nonharmonic analysis (NUNHA) with software that features high-frequency resolution without interpolation. We demonstrate the application of NUNHA in SD-OCT and compare it with conventional frequency analysis methods by simulating nonuniform interference signals. The results suggest that application of NUNHA in SD-OCT can provide acquisition of a clearer tomographic image, accurate analysis of fine and complex structures, and preservation of resolution and sensitivity at regions deep within a sample. This is because it reduces the influence of nonuniformity caused by the spectrometer and is unaffected by distortion due to interpolation.

  8. Analysis of the signal fall-off in spectral domain optical coherence tomography systems

    NASA Astrophysics Data System (ADS)

    Hagen-Eggert, M.; Koch, P.; Hüttmann, G.

    2012-01-01

    The influence of the individual spectrometer components on the depth dependent sensitivity fall-off (roll-off) in spectral-domain optical coherence tomography (SD-OCT) is investigated. We present a method for the characterization of the roll-off in SD-OCT systems via modulation transfer function (MTF) analysis. The MTF of different image sensors was measured in a newly developed setup, which uses the interference of two coherent light beams. Different contributions, i.e. diffraction, aberrations and sampling effects, to the MTF of a spectrometer of commercially available SD-OCT systems is calculated and is compared with roll-off measurements. The difference was below -2 dB at 90 % of the maximum measurement depth.

  9. Frequency-domain nonlinear regression algorithm for spectral analysis of broadband SFG spectroscopy.

    PubMed

    He, Yuhan; Wang, Ying; Wang, Jingjing; Guo, Wei; Wang, Zhaohui

    2016-03-01

    The resonant spectral bands of the broadband sum frequency generation (BB-SFG) spectra are often distorted by the nonresonant portion and the lineshapes of the laser pulses. Frequency domain nonlinear regression (FDNLR) algorithm was proposed to retrieve the first-order polarization induced by the infrared pulse and to improve the analysis of SFG spectra through simultaneous fitting of a series of time-resolved BB-SFG spectra. The principle of FDNLR was presented, and the validity and reliability were tested by the analysis of the virtual and measured SFG spectra. The relative phase, dephasing time, and lineshapes of the resonant vibrational SFG bands can be retrieved without any preset assumptions about the SFG bands and the incident laser pulses. PMID:26974068

  10. Efficient rational Chebyshev pseudo-spectral method with domain decomposition for optical waveguides modal analysis.

    PubMed

    Abdrabou, Amgad; Heikal, A M; Obayya, S S A

    2016-05-16

    We propose an accurate and computationally efficient rational Chebyshev multi-domain pseudo-spectral method (RC-MDPSM) for modal analysis of optical waveguides. For the first time, we introduce rational Chebyshev basis functions to efficiently handle semi-infinite computational subdomains. In addition, the efficiency of these basis functions is enhanced by employing an optimized algebraic map; thus, eliminating the use of PML-like absorbing boundary conditions. For leaky modes, we derived a leaky modes boundary condition at the guide-substrate interface providing an efficient technique to accurately model leaky modes with very small refractive index imaginary part. The efficiency and numerical precision of our technique are demonstrated through the analysis of high-index contrast dielectric and plasmonic waveguides, and the highly-leaky ARROW structure; where finding ARROW leaky modes using our technique clearly reflects its robustness.

  11. Three-dimensional spectral domain optical coherence tomography in chronic exposure to welding arc.

    PubMed

    Saxena, Sandeep; Mishra, Nibha; Meyer, Carsten H

    2014-01-01

    Three-dimensional spectral domain optical coherence tomography was performed in a 26-year-old man with chronic exposure to welding arc. Advanced macular visualisation provided significant findings of inner segment-ellipsoid zone disruption with the presence of cystoid changes and hyper-reflective material in the area of disruption. The external limiting membrane was intact in both the eyes. C-scan retinal pigment epithelium fit map of the left eye revealed a well-delineated defect whereas the right eye showed a poorly delineated smaller defect. The hyper-reflective material can be hypothesised to originate from the disrupted photoreceptor layer. The hyper-reflective material was more evident in the left eye which could be correlated with more marked diminution of vision and a prominent yellow lesion at the fovea. PMID:24832707

  12. Spectral Domain Optical Coherence Tomography Features and Classification Systems for Diabetic Macular Edema: A Review.

    PubMed

    Ruia, Surabhi; Saxena, Sandeep; Gemmy Cheung, Chui Ming; Gilhotra, Jagjit S; Lai, Timothy Y Y

    2016-01-01

    Spectral domain optical coherence tomography (SD-OCT) is fast becoming the current standard of care for the detection and assessment of diabetic macular edema. With the application of SD-OCT for imaging of retinal microstructure and measurement of retinal thickness, new information regarding disease characteristics has been gathered, which was unrecognized previously. Retinal thickness measurements on SD-OCT have also been used for deciding the management and monitoring of the disease. Since its development, OCT has enhanced the understanding of retinal anatomical changes in diabetic retinopathy. Several authors have used SD-OCT to classify diabetic macular edema with the purpose of correlating the pathophysiology with disease severity. The classification systems have helped monitor the treatment efficacy and provide prognostic information on the treatment outcome. The following review article summarizes these classifications. PMID:27632028

  13. Plane-wave diffraction by a wedge: A spectral domain approach

    NASA Astrophysics Data System (ADS)

    Ciarkowski, A.; Mittra, R.

    1981-11-01

    In this paper we investigate the canonical problem of plane wave diffraction by a wedge in the context of the spectral domain approach which exploits the relationship between the induced current on a scatterer and its far field. We show how the Sommerfeld solution to the wedge diffraction problem can be manipulated in a form which enables one to interpret the far scattered field as the Fourier transform of the physical optics current on the two faces of the wedge, augmented by the fringe current near the tip of the wedge. We also show that the uniform asymptotic expansion derived by Lee and Deschamps on the basis of the Lewis, Ahluwalia and Boersma ansatz can be rigorously obtained using the approach presented in this paper.

  14. Plane-wave diffraction by a wedge - A spectral domain approach

    NASA Astrophysics Data System (ADS)

    Ciarkowski, A.; Boersma, J.; Mittra, R.

    1984-01-01

    The canonical problem of plane wave diffraction by a wedge in the context of the spectral domain approach which exploits the relationship between the induced current on a scatterer and its far field is investigated. It is shown how the exact solution to the wedge diffraction problem can be manipulated in a form which enables one to interpret the far scattered field as the Fourier transform of the physical optics (PO) current on the two faces of the wedge augmented by the fringe current near the tip of the wedge. A uniform asymptotic expansion for the total field which slightly modifies the Ansatz in the uniform asymptotic theory of electromagnetic edge diffraction is constructed.

  15. 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.

  16. 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.

  17. Spectral domain optical coherence tomography imaging of punctate outer retinal toxoplasmosis

    PubMed Central

    Lujan, Brandon J.

    2014-01-01

    Punctate outer retinal toxoplasmosis is a recognized phenotype of this common ocular parasite. We present a case presenting with poor visual acuity, but with prompt treatment regaining excellent vision by the final time point. Imaging demonstrates progression of an active lesion adjacent to an inactive retinal scar with color photography, fluorescein angiography, and Spectral Domain Optical Coherence Tomography (SD-OCT). SD-OCT imaging of the chorioretinal scar demonstrated alternating hypertrophy and atrophy of the retinal pigment epithelium along with a discrete break in Bruch’s membrane. At baseline, the active lesion demonstrated a large collection of inflammatory subretinal fluid adjacent to an area of active retinitis. Over time, the subretinal material was found to resolve, there was restoration of the foveal anatomy, and the area of retinitis progressed into a chorioretinal scar. PMID:24843310

  18. Depth enhancement in spectral domain optical coherence tomography using bidirectional imaging modality with a single spectrometer

    NASA Astrophysics Data System (ADS)

    Ravichandran, Naresh Kumar; Wijesinghe, Ruchire Eranga; Shirazi, Muhammad Faizan; Park, Kibeom; Jeon, Mansik; Jung, Woonggyu; Kim, Jeehyun

    2016-07-01

    A method for depth enhancement is presented using a bidirectional imaging modality for spectral domain optical coherence tomography (SD-OCT). Two precisely aligned sample arms along with two reference arms were utilized in the optical configuration to scan the samples. Using exemplary images of the optical resolution target, Scotch tape, a silicon sheet with two needles, and a leaf, we demonstrated how the developed bidirectional SD-OCT imaging method increases the ability to characterize depth-enhanced images. The results of the developed system were validated by comparing the images with the standard OCT configuration (single-sample arm setup). Given the advantages of higher resolution and the ability to visualize deep morphological structures, this method can be utilized to increase the depth dependent fall-off in samples with limited thickness. Thus, the proposed bidirectional imaging modality is apt for cross-sectional imaging of entire samples, which has the potential capability to improve the diagnostic ability.

  19. 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.

  20. Enhanced joint spectral and time domain optical coherence tomography for quantitative flow velocity measurement

    NASA Astrophysics Data System (ADS)

    Walther, Julia; Koch, Edmund

    2011-06-01

    Recently, a new method called joint spectral and time domain optical coherence tomography (STdOCT) for flow velocity measurement in spectral domain OCT (SD OCT) was presented. This method analyzes the detected timeresolved interference fringe spectra by using a two-dimensional fast Fourier transformation (2D FFT) to determine directly the Doppler frequency shift instead of calculating the phase difference at each depth position of adjacent A-scans. There, it was found that STdOCT is more robust for measurements with low signal to noise ratio than the classic phase-resolved Doppler OCT (DOCT) making it attractive first for imaging fast flow velocities at which a strong Doppler angle dependent signal damping occurs due to interference fringe washout and second for investigating large blood vessels with a big diameter and a highly damped signal of blood with increasing depth due to strong scattering and absorption in the near-infrared wavelength range. In the present study, we would like to introduce an enhanced algorithm for STdOCT permitting a more precise flow velocity measurement in comparison to the conventional STdOCT. The new method determines the amplitude of the broadened Doppler frequency shift by calculating the center of gravity via the complex analytical signal as a result of the second FFT instead of detecting the maximum intensity signal. Furthermore, the comparison with phase-resolved DOCT was done experimentally by using a flow phantom consisting of a 1% Intralipid emulsion and a 320 μm glass capillary. As a result, the enhanced STdOCT and DOCT processed data are completely equivalent.

  1. 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.

  2. 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.

  3. Tumor-penetrating peptide fused EGFR single-domain antibody enhances cancer drug penetration into 3D multicellular spheroids and facilitates effective gastric cancer therapy

    PubMed Central

    Sha, Huizi; Zou, Zhengyun; Xin, Kai; Bian, Xinyu; Cai, Xueting; Lu, Wuguang; Chen, Jiao; Chen, Gang; Huang, Leaf; Blair, Andrew M.; Cao, Peng; Liu, Baorui

    2016-01-01

    Human tumors, including gastric cancer, frequently express high levels of epidermal growth factor receptors (EGFRs), which are associated with a poor prognosis. Targeted delivery of anticancer drugs to cancerous tissues shows potential in sparing unaffected tissues. However, it has been a major challenge for drug penetration in solid tumor tissues due to the complicated tumor microenvironment. We have constructed a recombinant protein named anti-EGFR-iRGD consisting of an anti-EGFR VHH (the variable domain from the heavy chain of the antibody) fused to iRGD, a tumor-specific binding peptide with high permeability. Anti-EGFR-iRGD, which targets EGFR and αvβ3, spreads extensively throughout both the multicellular spheroids and the tumor mass. The recombinant protein anti-EGFR-iRGD also exhibited antitumor activity in tumor cell lines, multicellular spheroids, and mice. Moreover, anti-EGFR-iRGD could improve anticancer drugs, such as doxorubicin (DOX), bevacizumab, nanoparticle permeability and efficacy in multicellular spheroids. This study draws attention to the importance of iRGD peptide in the therapeutic approach of anti-EGFR-iRGD. As a consequence, anti-EGFR-iRGD could be a drug candidate for cancer treatment and a useful adjunct of other anticancer drugs. PMID:25553823

  4. Full range complex spectral domain optical coherence tomography without additional phase shifters.

    PubMed

    Baumann, Bernhard; Pircher, Michael; Götzinger, Erich; Hitzenberger, Christoph K

    2007-10-01

    We demonstrate a new full range complex spectral domain optical coherence tomography (FRC SD-OCT) method. Other than FRC SD-OCT systems reported in literature, which employed devices such as electro-/acousto optic modulators or piezo-driven mirrors providing the phase modulations necessary for retrieval of the complex-valued signal, the system presented works without any additional phase shifting device. The required phase shift is introduced by the galvanometer scanner used for transversally scanning the sample beam. By means of a slight displacement of the probe beam with respect to the scanning mirror's pivot axis, the sample arm length and thus the phase is continuously modulated as the beam is scanned in lateral direction. From such modulated spectral data, the complex-valued data yielding a twofold increase of accessible depth range can be calculated using an algorithm based on the Hilbert transform. To demonstrate the performance of our method quantitative measurements of the suppression of mirror images as a function of induced phase shift were performed. In order to validate the FRC SD-OCT technique for high-speed imaging of biological tissue, we present full-range images of the human anterior chamber in vivo. PMID:19550607

  5. Numerical modeling of wave propagation in functionally graded materials using time-domain spectral Chebyshev elements

    NASA Astrophysics Data System (ADS)

    Hedayatrasa, Saeid; Bui, Tinh Quoc; Zhang, Chuanzeng; Lim, Chee Wah

    2014-02-01

    Numerical modeling of the Lamb wave propagation in functionally graded materials (FGMs) by a two-dimensional time-domain spectral finite element method (SpFEM) is presented. The high-order Chebyshev polynomials as approximation functions are used in the present formulation, which provides the capability to take into account the through thickness variation of the material properties. The efficiency and accuracy of the present model with one and two layers of 5th order spectral elements in modeling wave propagation in FGM plates are analyzed. Different excitation frequencies in a wide range of 28-350 kHz are investigated, and the dispersion properties obtained by the present model are verified by reference results. The through thickness wave structure of two principal Lamb modes are extracted and analyzed by the symmetry and relative amplitude of the vertical and horizontal oscillations. The differences with respect to Lamb modes generated in homogeneous plates are explained. Zero-crossing and wavelet signal processing-spectrum decomposition procedures are implemented to obtain phase and group velocities and their dispersion properties. So it is attested how this approach can be practically employed for simulation, calibration and optimization of Lamb wave based nondestructive evaluation techniques for the FGMs. The capability of modeling stress wave propagation through the thickness of an FGM specimen subjected to impact load is also investigated, which shows that the present method is highly accurate as compared with other existing reference data.

  6. 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

    2015-12-01

    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. PMID:26393783

  7. Probing the 3-D Structure, Dynamics, and Stability of Bacterial Collagenase Collagen Binding Domain (apo- versus holo-) by Limited Proteolysis MALDI-TOF MS

    NASA Astrophysics Data System (ADS)

    Sides, Cynthia R.; Liyanage, Rohana; Lay, Jackson O.; Philominathan, Sagaya Theresa Leena; Matsushita, Osamu; Sakon, Joshua

    2012-03-01

    Pairing limited proteolysis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to probe clostridial collagenase collagen binding domain (CBD) reveals the solution dynamics and stability of the protein, as these factors are crucial to CBD effectiveness as a drug-delivery vehicle. MS analysis of proteolytic digests indicates initial cleavage sites, thereby specifying the less stable and highly accessible regions of CBD. Modulation of protein structure and stability upon metal binding is shown through MS analysis of calcium-bound and cobalt-bound CBD proteolytic digests. Previously determined X-ray crystal structures illustrate that calcium binding induces secondary structure transformation in the highly mobile N-terminal arm and increases protein stability. MS-based detection of exposed residues confirms protein flexibility, accentuates N-terminal dynamics, and demonstrates increased global protein stability exported by calcium binding. Additionally, apo- and calcium-bound CBD proteolysis sites correlate well with crystallographic B-factors, accessibility, and enzyme specificity. MS-observed cleavage sites with no clear correlations are explained either by crystal contacts of the X-ray crystal structures or by observed differences between Molecules A and B in the X-ray crystal structures. The study newly reveals the absence of the βA strand and thus the very dynamic N-terminal linker, as corroborated by the solution X-ray scattering results. Cobalt binding has a regional effect on the solution phase stability of CBD, as limited proteolysis data implies the capture of an intermediate-CBD solution structure when cobalt is bound.

  8. A Numerical Method for Solving the 3D Unsteady Incompressible Navier-Stokes Equations in Curvilinear Domains with Complex Immersed Boundaries

    PubMed Central

    Ge, Liang; Sotiropoulos, Fotis

    2008-01-01

    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 [1]. 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 through a mechanical, bileaflet heart valve mounted in a model straight aorta with an anatomical-like triple sinus. PMID:19194533

  9. Higher-order in time "quasi-unconditionally stable" ADI solvers for the compressible Navier-Stokes equations in 2D and 3D curvilinear domains

    NASA Astrophysics Data System (ADS)

    Bruno, Oscar P.; Cubillos, Max

    2016-02-01

    This paper introduces alternating-direction implicit (ADI) solvers of higher order of time-accuracy (orders two to six) for the compressible Navier-Stokes equations in two- and three-dimensional curvilinear domains. The higher-order accuracy in time results from 1) An application of the backward differentiation formulae time-stepping algorithm (BDF) in conjunction with 2) A BDF-like extrapolation technique for certain components of the nonlinear terms (which makes use of nonlinear solves unnecessary), as well as 3) A novel application of the Douglas-Gunn splitting (which greatly facilitates handling of boundary conditions while preserving higher-order accuracy in time). As suggested by our theoretical analysis of the algorithms for a variety of special cases, an extensive set of numerical experiments clearly indicate that all of the BDF-based ADI algorithms proposed in this paper are "quasi-unconditionally stable" in the following sense: each algorithm is stable for all couples (h , Δt)of spatial and temporal mesh sizes in a problem-dependent rectangular neighborhood of the form (0 ,Mh) × (0 ,Mt). In other words, for each fixed value of Δt below a certain threshold, the Navier-Stokes solvers presented in this paper are stable for arbitrarily small spatial mesh-sizes. The second-order formulation has further been rigorously shown to be unconditionally stable for linear hyperbolic and parabolic equations in two-dimensional space. Although implicit ADI solvers for the Navier-Stokes equations with nominal second-order of temporal accuracy have been proposed in the past, the algorithms presented in this paper are the first ADI-based Navier-Stokes solvers for which second-order or better accuracy has been verified in practice under non-trivial (non-periodic) boundary conditions.

  10. Clay composition and swelling potential estimation of soils using depth of absorption bands in the SWIR (1100-2500 nm) spectral domain

    NASA Astrophysics Data System (ADS)

    Dufréchou, Grégory; Granjean, Gilles; Bourguignon, Anne

    2014-05-01

    Swelling soils contain clay minerals that change volume with water content and cause extensive and expensive damage on infrastructures. Presence of clay minerals is traditionally a good estimator of soils swelling and shrinking behavior. Montmorillonite (i.e. smectite group), illite, kaolinite are the most common minerals in soils and are usually associated to high, moderate, and low swelling potential when they are present in significant amount. Characterization of swelling potential and identification of clay minerals of soils using conventional analysis are slow, expensive, and does not permit integrated measurements. SWIR (1100-2500 nm) spectral domain are characterized by significant spectral absorption bands related to clay content that can be used to recognize main clay minerals. Hyperspectral laboratory using an ASD Fieldspec Pro spectrometer provides thus a rapid and less expensive field surface sensing that permits to measure soil spectral properties. This study presents a new laboratory reflectance spectroscopy method that used depth of clay diagnostic absorption bands (1400 nm, 1900 nm, and 2200 nm) to compare natural soils to synthetic montmorillonite-illite-kaolinite mixtures. We observe in mixtures that illite, montmorillonite, and kaolinite content respectively strongly influence the depth of absorption bands at 1400 nm (D1400), 1900 nm (D1900), and 2200 nm (D2200). To attenuate or removed effects of abundance and grain size, depth of absorption bands ratios were thus used to performed (i) 3D (using D1900/D2200, D1400/D1900, and D2200/D1400 as axis), and (ii) 2D (using D1400/D1900 and D1900/D2200 as axis) diagrams of synthetic mixtures. In this case we supposed that the overall reduction or growth of depth absorption bands should be similarly affected by the abundance and grain size of materials in soil. In 3D and 2D diagrams, the mixtures define a triangular shape formed by two clay minerals as external envelop and the three clay minerals mixtures

  11. Macular spectral domain optical coherence tomography findings in Tanzanian endemic optic neuropathy.

    PubMed

    Kisimbi, John; Shalchi, Zaid; Mahroo, Omar A; Mhina, Celina; Sanyiwa, Anna J; Mabey, Denise; Mohamed, Moin; Plant, Gordon T

    2013-11-01

    Bilateral optic neuropathy in Dar es Salaam is now considered endemic and is estimated to affect 0.3-2.4% of young adults. The condition is characterized by a subacute bilateral loss of central vision of unknown aetiology. Findings of spectral domain optical coherence tomography have not previously been reported for these patients. All patients diagnosed with endemic optic neuropathy over a 2-year period at the Muhimbili National Hospital underwent spectral domain optical coherence tomography macular imaging. Scans were graded qualitatively for severity of retinal nerve fibre layer loss as well as the presence of microcystic macular changes, which have not previously been described in this condition. Of the 128 patients included (54.7% male; median age 20 years), severe retinal nerve fibre layer loss was found in 185 eyes (74.0%). There was full concordance in retinal nerve fibre layer thickness between the two eyes in 113 (91.1%) patients. Microcystic macular spaces were found in 16 (12.5%) patients and were bilateral in nine (7.0%) individuals. These changes were typically more prominent in the nasal than the temporal macula, predominantly involving the inner nuclear layer, and often occurred in an annular configuration that was evident on en face infra-red imaging, though not discernible on colour fundus photography or clinically. All patients with microcystic macular changes had severe thinning of the retinal nerve fibre layer (P = 0.02). Four patients in whom cystic spaces were demonstrated had sequential scans, and there was no detectable alteration in the configuration of these changes over a period of up to 16 months. This is the first study to document optical coherence tomography findings in endemic optic neuropathy. We have observed symmetrical severe loss of the caeco-central projection (papillomacular bundle) with otherwise well-preserved macular architecture. Also, we have observed microcystic retinal changes in a significant proportion of patients

  12. Spectral characterization and 3D molecular modeling studies of metal complexes involving the O, N-donor environment of quinazoline-4(3H)-one Schiff base and their biological studies.

    PubMed

    Siddappa, Kuruba; Mane, Sunilkumar B; Manikprabhu, Deene

    2014-01-01

    A simple condensation of 3-amino-2-methylquinazoline-4-one with 2-hydroxy-1-naphthaldehyde produced new tridentate ONO donor Schiff base ligand with efficient yield. The structural characterization of ligand and its Cu(II), Ni(II), Co(II), Mn(II), Zn(II), and Cd(II) complexes were achieved by the aid of elemental analysis, spectral characterization such as (UV-visible, IR, NMR, mass, and ESR), and magnetic data. The analytical and spectroscopic studies suggest the octahedral geometries of Cu(II), Co(II), Ni(II) and Mn(II) complexes and tetrahedral geometry of Zn(II) and Cd(II) complexes with the tridentate ONO Schiff base ligand. Furthermore, the conclusions drawn from these studies afford further support to the mode of bonding discussed on the basis of their 3D molecular modeling studies by considering different bond lengths, bond angles, and bond distance. The ligand and its metal complexes evaluated for their antimicrobial activity against Staphylococcus aureus (MTCC number 7443), Bacillus subtilis (MTCC number 9878), Escherichia coli (MTCC number 1698), Aspergillus niger (MTCC number 281), and Aspergillus flavus (MTCC number 277). The MIC of these compounds was found to be most active at 10 μ g/mL concentration in inhibiting the growth of the tested organisms. The DNA cleavage activity of all the complexes was studied by gel electrophoresis method. PMID:24678278

  13. Spectral Characterization and 3D Molecular Modeling Studies of Metal Complexes Involving the O, N-Donor Environment of Quinazoline-4(3H)-one Schiff Base and Their Biological Studies

    PubMed Central

    Siddappa, Kuruba; Mane, Sunilkumar B.

    2014-01-01

    A simple condensation of 3-amino-2-methylquinazoline-4-one with 2-hydroxy-1-naphthaldehyde produced new tridentate ONO donor Schiff base ligand with efficient yield. The structural characterization of ligand and its Cu(II), Ni(II), Co(II), Mn(II), Zn(II), and Cd(II) complexes were achieved by the aid of elemental analysis, spectral characterization such as (UV-visible, IR, NMR, mass, and ESR), and magnetic data. The analytical and spectroscopic studies suggest the octahedral geometries of Cu(II), Co(II), Ni(II) and Mn(II) complexes and tetrahedral geometry of Zn(II) and Cd(II) complexes with the tridentate ONO Schiff base ligand. Furthermore, the conclusions drawn from these studies afford further support to the mode of bonding discussed on the basis of their 3D molecular modeling studies by considering different bond lengths, bond angles, and bond distance. The ligand and its metal complexes evaluated for their antimicrobial activity against Staphylococcus aureus (MTCC number 7443), Bacillus subtilis (MTCC number 9878), Escherichia coli (MTCC number 1698), Aspergillus niger (MTCC number 281), and Aspergillus flavus (MTCC number 277). The MIC of these compounds was found to be most active at 10 μg/mL concentration in inhibiting the growth of the tested organisms. The DNA cleavage activity of all the complexes was studied by gel electrophoresis method. PMID:24678278

  14. 3-D Terahertz Synthetic-Aperture Imaging and Spectroscopy

    NASA Astrophysics Data System (ADS)

    Henry, Samuel C.

    Terahertz (THz) wavelengths have attracted recent interest in multiple disciplines within engineering and science. Situated between the infrared and the microwave region of the electromagnetic spectrum, THz energy can propagate through non-polar materials such as clothing or packaging layers. Moreover, many chemical compounds, including explosives and many drugs, reveal strong absorption signatures in the THz range. For these reasons, THz wavelengths have great potential for non-destructive evaluation and explosive detection. Three-dimensional (3-D) reflection imaging with considerable depth resolution is also possible using pulsed THz systems. While THz imaging (especially 3-D) systems typically operate in transmission mode, reflection offers the most practical configuration for standoff detection, especially for objects with high water content (like human tissue) which are opaque at THz frequencies. In this research, reflection-based THz synthetic-aperture (SA) imaging is investigated as a potential imaging solution. THz SA imaging results presented in this dissertation are unique in that a 2-D planar synthetic array was used to generate a 3-D image without relying on a narrow time-window for depth isolation cite [Shen 2005]. Novel THz chemical detection techniques are developed and combined with broadband THz SA capabilities to provide concurrent 3-D spectral imaging. All algorithms are tested with various objects and pressed pellets using a pulsed THz time-domain system in the Northwest Electromagnetics and Acoustics Research Laboratory (NEAR-Lab).

  15. 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.

  16. 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.

  17. Bootstrapping 3D fermions

    DOE PAGES

    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.

  18. All-fiber spectral-domain optical coherence tomography with high resolution by using a PCF-based broadband coupler and a k-domain linearization method

    NASA Astrophysics Data System (ADS)

    Kwon, Oh-Jang; Kim, Sunduck; Yoon, Min-Seok; Han, Young-Geun

    2012-11-01

    We demonstrate spectral-domain optical coherence tomography (SD-OCT) with high axial resolution and high image acquisition speed, which is realized by using a broadband coupler based on a photonic crystal fiber (PCF). The PCF-based coupler with broad bandwidth was fabricated by using a fused biconical tapered (FBT) method, and the axial resolution of the SD-OCT was improved to be 2 µm. The image acquisition speed of the SD-OCT was estimated to be 500 Hz. A k-domain linearization method was exploited to compensate for the mismatched spectral information between the wave-number and the pixel position at the CCD, which was induced by the nonlinearity of the diffraction grating plate.

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

    PubMed

    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

  20. 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.

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

    PubMed

    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.

  2. 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.

  3. Prediction of spontaneous closure of traumatic macular hole with spectral domain optical coherence tomography

    PubMed Central

    Chen, Haoyu; Chen, Weiqi; Zheng, Kangken; Peng, Kun; Xia, Honghe; Zhu, Lei

    2015-01-01

    It has been known that some traumatic macular holes can close spontaneously. However, knowledge about the types of macular hole that can close spontaneously is limited. In this retrospective study, we investigated patients with traumatic macular hole who were followed-up for at least 6 months without any surgical intervention. Clinical data and spectral domain optical coherence tomography (SD-OCT) images were compared between groups with and without macular hole closure. Overall, 27 eyes were included. Spontaneous closure of macular hole was observed in 10 (37.0%) eyes. The holes with spontaneous closure had smaller minimum diameter (244.9 ± 114.4 vs. 523.9 ± 320.0 μm, p = 0.007) and less intraretinal cysts (10% vs. 76.5%, p = 0.001) compared to the holes that did not close spontaneously. The area under the curve of receiver operative characteristic was 0.812 and 0.832 for minimum diameter of macular hole and presence of intraretinal cysts respectively. Multivariate logistic regression showed that the presence of intraretinal cysts was an independent predictive factor for closure of macular holes. The group with spontaneous macular hole closure had a high chance of visual improvement. Our study suggests that the absence of intraretinal cysts on SD-OCT can predict spontaneous closure of traumatic macular hole. PMID:26196460

  4. Ultra-fast displaying Spectral Domain Optical Doppler Tomography system using a Graphics Processing Unit.

    PubMed

    Jeong, Hyosang; Cho, Nam Hyun; Jung, Unsang; Lee, Changho; Kim, Jeong-Yeon; Kim, Jeehyun

    2012-01-01

    We demonstrate an ultrafast displaying Spectral Domain Optical Doppler Tomography system using Graphics Processing Unit (GPU) computing. The calculation of FFT and the Doppler frequency shift is accelerated by the GPU. Our system can display processed OCT and ODT images simultaneously in real time at 120 fps for 1,024 pixels × 512 lateral A-scans. The computing time for the Doppler information was dependent on the size of the moving average window, but with a window size of 32 pixels the ODT computation time is only 8.3 ms, which is comparable to the data acquisition time. Also the phase noise decreases significantly with the window size. Since the performance of a real-time display for OCT/ODT is very important for clinical applications that need immediate diagnosis for screening or biopsy. Intraoperative surgery can take much benefit from the real-time display flow rate information from the technology. Moreover, the GPU is an attractive tool for clinical and commercial systems for functional OCT features as well. PMID:22969328

  5. Improvement of axial resolution of spectral domain optical coherence tomography with wide band PLC splitter

    NASA Astrophysics Data System (ADS)

    Eom, Joo Beom; Min, Eun Jung; Lee, Byeong Ha

    2012-06-01

    We report the development and performance of high resolution spectral domain optical coherence tomography (SD-OCT) system based on 2×2 planar lightwave circuit (PLC) splitter that was designed as a single mode splitter at near infrared and used as the beam splitter for a SD-OCT system. The splitter has been made by coupling SMFs to a planar lightwave circuit (PLC) splitter chip. The PLC splitter chip was fabricated to have a single mode property with 740 nm cutoff wavelength and the SMFs, which have 730 nm cutoff wavelength, were securely connected to the PLC chip through fiber block arrays having lithographically fabricated V grooves. With the implemented PLC splitter, we have obtained a low excess loss of 0.4 dB at 840 nm with wide band coupling property. With the proposed 2×2 PLC splitter and fabricated WDM coupler, SD-OCT images of samples successfully obtained by using combined source with 840 nm and 880 nm SLDs.

  6. Myopic Macular Retinoschisis in Teenagers: Clinical Characteristics and Spectral Domain Optical Coherence Tomography Findings

    PubMed Central

    Sun, Chuan-bin; You, Yong-sheng; Liu, Zhe; Zheng, Lin-yan; Chen, Pei-qing; Yao, Ke; Xue, An-quan

    2016-01-01

    To investigate the morphological characteristics of myopic macular retinoschisis (MRS) in teenagers with high myopia, six male (9 eyes) and 3 female (4 eyes) teenagers with typical MRS identified from chart review were evaluated. All cases underwent complete ophthalmic examinations including best corrected visual acuity (BCVA), indirect ophthalmoscopy, colour fundus photography, B-type ultrasonography, axial length measurement, and spectral-domain optical coherence tomography (SD-OCT). The average age was 17.8 ± 1.5 years, average refractive error was −17.04 ± 3.04D, average BCVA was 0.43 ± 0.61, and average axial length was 30.42 ± 1.71 mm. Myopic macular degenerative changes (MDC) by colour fundus photographs revealed Ohno-Matsui Category 1 in 4 eyes, and Category 2 in 9 eyes. Posterior staphyloma was found in 9 eyes. SD-OCT showed outer MRS in all 13 eyes, internal limiting membrane detachment in 7 eyes, vascular microfolds in 2 eyes, and inner MRS in 1 eye. No premacular structures such as macular epiretinal membrane or partially detached posterior hyaloids were found. Our results showed that MRS rarely occurred in highly myopic teenagers, and was not accompanied by premacular structures, severe MDC, or even obvious posterior staphyloma. This finding indicates that posterior scleral expansion is probably the main cause of MRS. PMID:27294332

  7. Visible and near infrared wavelength photonic crystal fiber splitter for multiwavelength spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Eom, Joo Beom; Min, Eun Jung; Lee, Byeong Ha

    2012-01-01

    We report the fabrication and performance of the 2×2 photonic crystal fiber (PCF) splitter that was designed as a single mode splitter at the visible and near infrared and used as the beam splitter for a spectral domain optical coherence tomography (SD-OCT) system. The PCF splitter has been made by coupling PCFs to a planar lightwave circuit (PLC) splitter chip. The PLC splitter chip was fabricated to have a single mode property with 630 nm cutoff wavelength and the PCFs were securely connected to the PLC chip through PCF block arrays having lithographically fabricated V grooves. The core width of the splitter chip was about 4 μm×4 μm and the core-cladding index difference was about 0.15%. With the implemented PCF PLC splitter, we have obtained a low excess loss of 1.2 dB and a low polarization-dependent loss of 0.19 dB at 680 nm with wide band coupling property. With the proposed 2×2 PCF splitter, SD-OCT images of human finger, nail, and tooth successfully obtained by using 680 nm, 840 nm, and 930 nm SLD source. This PCF PLC splitter is expected to have high resolution OCT.

  8. Automated detection of the retinal from OCT spectral domain images of healthy eyes

    NASA Astrophysics Data System (ADS)

    Giovinco, Gaspare; Savastano, Maria Cristina; Ventre, Salvatore; Tamburrino, Antonello

    2015-06-01

    Optical coherence tomography (OCT) has become one of the most relevant diagnostic tools for retinal diseases. Besides being a non-invasive technique, one distinguished feature is its unique capability of providing (in vivo) cross-sectional view of the retinal. Specifically, OCT images show the retinal layers. From the clinical point of view, the identification of the retinal layers opens new perspectives to study the correlation between morphological and functional aspects of the retinal tissue. The main contribution of this paper is a new method/algorithm for the automated segmentation of cross-sectional images of the retina of healthy eyes, obtained by means of spectral domain optical coherence tomography (SD-OCT). Specifically, the proposed segmentation algorithm provides the automated detection of different retinal layers. Tests on experimental SD-OCT scans performed by three different instruments/manufacturers have been successfully carried out and compared to a manual segmentation made by an independent ophthalmologist, showing the generality and the effectiveness of the proposed method.

  9. Automated detection of retinal layers from OCT spectral-domain images of healthy eyes

    NASA Astrophysics Data System (ADS)

    Giovinco, Gaspare; Savastano, Maria Cristina; Ventre, Salvatore; Tamburrino, Antonello

    2015-12-01

    Optical coherence tomography (OCT) has become one of the most relevant diagnostic tools for retinal diseases. Besides being a non-invasive technique, one distinguished feature is its unique capability of providing (in vivo) cross-sectional view of the retina. Specifically, OCT images show the retinal layers. From the clinical point of view, the identification of the retinal layers opens new perspectives to study the correlation between morphological and functional aspects of the retinal tissue. The main contribution of this paper is a new method/algorithm for the automated segmentation of cross-sectional images of the retina of healthy eyes, obtained by means of spectral-domain optical coherence tomography (SD-OCT). Specifically, the proposed segmentation algorithm provides the automated detection of different retinal layers. Tests on experimental SD-OCT scans performed by three different instruments/manufacturers have been successfully carried out and compared to a manual segmentation made by an independent ophthalmologist, showing the generality and the effectiveness of the proposed method.

  10. 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.

  11. 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.

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

    PubMed

    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. PMID:27001162

  13. Automated Fovea Detection in Spectral Domain Optical Coherence Tomography Scans of Exudative Macular Disease.

    PubMed

    Wu, Jing; Waldstein, Sebastian M; Montuoro, Alessio; Gerendas, Bianca S; Langs, Georg; Schmidt-Erfurth, Ursula

    2016-01-01

    In macular spectral domain optical coherence tomography (SD-OCT) volumes, detection of the foveal center is required for accurate and reproducible follow-up studies, structure function correlation, and measurement grid positioning. However, disease can cause severe obscuring or deformation of the fovea, thus presenting a major challenge in automated detection. We propose a fully automated fovea detection algorithm to extract the fovea position in SD-OCT volumes of eyes with exudative maculopathy. The fovea is classified into 3 main appearances to both specify the detection algorithm used and reduce computational complexity. Based on foveal type classification, the fovea position is computed based on retinal nerve fiber layer thickness. Mean absolute distance between system and clinical expert annotated fovea positions from a dataset comprised of 240 SD-OCT volumes was 162.3 µm in cystoid macular edema and 262 µm in nAMD. The presented method has cross-vendor functionality, while demonstrating accurate and reliable performance close to typical expert interobserver agreement. The automatically detected fovea positions may be used as landmarks for intra- and cross-patient registration and to create a joint reference frame for extraction of spatiotemporal features in "big data." Furthermore, reliable analyses of retinal thickness, as well as retinal structure function correlation, may be facilitated. PMID:27660636

  14. Intraoperative Pachymetry Using Spectral-Domain Optical Coherence Tomography during Accelerated Corneal Collagen Crosslinking

    PubMed Central

    Chow, Vanissa W. S.; Biswas, Sayantan; Yu, Marco; Wong, Victoria W. Y.; Jhanji, Vishal

    2013-01-01

    Purpose. To evaluate the role of spectral-domain optical coherence tomography (SDOCT) to measure corneal thickness during accelerated corneal crosslinking (CXL). Methods. Intraoperative pachymetry was performed using SDOCT and ultrasound pachymetry (USP) in 6 eyes of 6 patients with keratoconus. Pachymetry readings were obtained at baseline, after epithelium removal and after 30 minutes of riboflavin instillation. SDOCT measurements of eyes with and without lid speculum during riboflavin instillation were compared. Results. There was no statistically significant difference in central corneal thickness (CCT) measurements between SDOCT and USP (P > 0.05 for all). A significant decrease in both CCT (P = 0.031) and the thinnest corneal thickness (TCT) (P = 0.031) was observed during CXL. There was a greater reduction in CCT (38 ± 6%) with the use of lid speculum as compared to the no-speculum eyes (18 ± 9%) (P = 0.100). TCT was also reduced by a greater extent with the use of lid speculum (40 ± 5% versus 26 ± 7%; P = 0.100). Conclusion. SDOCT can be successfully used to measure intraoperative corneal pachymetry during corneal CXL. SDOCT measurements demonstrated corneal thinning intraoperatively during CXL, which was further accentuated by the use of a lid speculum during the procedure. PMID:23984411

  15. 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

  16. 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.

  17. 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.

  18. Automated Fovea Detection in Spectral Domain Optical Coherence Tomography Scans of Exudative Macular Disease

    PubMed Central

    Wu, Jing; Montuoro, Alessio; Gerendas, Bianca S.; Langs, Georg

    2016-01-01

    In macular spectral domain optical coherence tomography (SD-OCT) volumes, detection of the foveal center is required for accurate and reproducible follow-up studies, structure function correlation, and measurement grid positioning. However, disease can cause severe obscuring or deformation of the fovea, thus presenting a major challenge in automated detection. We propose a fully automated fovea detection algorithm to extract the fovea position in SD-OCT volumes of eyes with exudative maculopathy. The fovea is classified into 3 main appearances to both specify the detection algorithm used and reduce computational complexity. Based on foveal type classification, the fovea position is computed based on retinal nerve fiber layer thickness. Mean absolute distance between system and clinical expert annotated fovea positions from a dataset comprised of 240 SD-OCT volumes was 162.3 µm in cystoid macular edema and 262 µm in nAMD. The presented method has cross-vendor functionality, while demonstrating accurate and reliable performance close to typical expert interobserver agreement. The automatically detected fovea positions may be used as landmarks for intra- and cross-patient registration and to create a joint reference frame for extraction of spatiotemporal features in “big data.” Furthermore, reliable analyses of retinal thickness, as well as retinal structure function correlation, may be facilitated. PMID:27660636

  19. Study on spectral properties of difenoconazole by terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhou, Qian; Liu, Ying; Kou, Kuan; Zhao, Guozhong

    2015-08-01

    The terahertz (THz) and infrared spectra of solid pesticide difenoconazole are studied. The absorption spectra of difenoconazole are obtained at room temperature in the frequency range of 0.2 THz - 2.6 THz by using of terahertz time-domain spectroscopy (THz-TDS) and in the frequency range of 1.8 THz - 10 THz by the Fourier Transform Infrared Spectroscopy (FTIR). The experimental results show five significant absorption peaks in THz frequency range, respectively, 0.66 T, 0.80 T, 1.03 T, 1.31 T and 1.57 T, and those peaks corresponding to the abnormal dispersion. The spectral characteristics between 0.2 THz and 15 THz of difenoconazole are simulated by using of Gaussian03 software based on the single molecular model and the density functional theory (DFT). Both of simulation and experimental results fit well in the terahertz range. Moreover, the quantitative analysis of difenoconazole is studied based on the THz-TDS measurement. The absorption coefficient and refractive index spectra of difenoconazoles at different proportions doped with polyethylene (PE) are obtained. The partial least squares (PLS) model is built. It is possible to predict the concentration of difenoconazole in the mixtures by this method.

  20. 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.

  1. Ultra-fast displaying Spectral Domain Optical Doppler Tomography system using a Graphics Processing Unit.

    PubMed

    Jeong, Hyosang; Cho, Nam Hyun; Jung, Unsang; Lee, Changho; Kim, Jeong-Yeon; Kim, Jeehyun

    2012-01-01

    We demonstrate an ultrafast displaying Spectral Domain Optical Doppler Tomography system using Graphics Processing Unit (GPU) computing. The calculation of FFT and the Doppler frequency shift is accelerated by the GPU. Our system can display processed OCT and ODT images simultaneously in real time at 120 fps for 1,024 pixels × 512 lateral A-scans. The computing time for the Doppler information was dependent on the size of the moving average window, but with a window size of 32 pixels the ODT computation time is only 8.3 ms, which is comparable to the data acquisition time. Also the phase noise decreases significantly with the window size. Since the performance of a real-time display for OCT/ODT is very important for clinical applications that need immediate diagnosis for screening or biopsy. Intraoperative surgery can take much benefit from the real-time display flow rate information from the technology. Moreover, the GPU is an attractive tool for clinical and commercial systems for functional OCT features as well.

  2. Myopic Macular Retinoschisis in Teenagers: Clinical Characteristics and Spectral Domain Optical Coherence Tomography Findings.

    PubMed

    Sun, Chuan-Bin; You, Yong-Sheng; Liu, Zhe; Zheng, Lin-Yan; Chen, Pei-Qing; Yao, Ke; Xue, An-Quan

    2016-01-01

    To investigate the morphological characteristics of myopic macular retinoschisis (MRS) in teenagers with high myopia, six male (9 eyes) and 3 female (4 eyes) teenagers with typical MRS identified from chart review were evaluated. All cases underwent complete ophthalmic examinations including best corrected visual acuity (BCVA), indirect ophthalmoscopy, colour fundus photography, B-type ultrasonography, axial length measurement, and spectral-domain optical coherence tomography (SD-OCT). The average age was 17.8 ± 1.5 years, average refractive error was -17.04 ± 3.04D, average BCVA was 0.43 ± 0.61, and average axial length was 30.42 ± 1.71 mm. Myopic macular degenerative changes (MDC) by colour fundus photographs revealed Ohno-Matsui Category 1 in 4 eyes, and Category 2 in 9 eyes. Posterior staphyloma was found in 9 eyes. SD-OCT showed outer MRS in all 13 eyes, internal limiting membrane detachment in 7 eyes, vascular microfolds in 2 eyes, and inner MRS in 1 eye. No premacular structures such as macular epiretinal membrane or partially detached posterior hyaloids were found. Our results showed that MRS rarely occurred in highly myopic teenagers, and was not accompanied by premacular structures, severe MDC, or even obvious posterior staphyloma. This finding indicates that posterior scleral expansion is probably the main cause of MRS. PMID:27294332

  3. 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.

  4. 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.

  5. 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

  6. Automated Fovea Detection in Spectral Domain Optical Coherence Tomography Scans of Exudative Macular Disease

    PubMed Central

    Wu, Jing; Montuoro, Alessio; Gerendas, Bianca S.; Langs, Georg

    2016-01-01

    In macular spectral domain optical coherence tomography (SD-OCT) volumes, detection of the foveal center is required for accurate and reproducible follow-up studies, structure function correlation, and measurement grid positioning. However, disease can cause severe obscuring or deformation of the fovea, thus presenting a major challenge in automated detection. We propose a fully automated fovea detection algorithm to extract the fovea position in SD-OCT volumes of eyes with exudative maculopathy. The fovea is classified into 3 main appearances to both specify the detection algorithm used and reduce computational complexity. Based on foveal type classification, the fovea position is computed based on retinal nerve fiber layer thickness. Mean absolute distance between system and clinical expert annotated fovea positions from a dataset comprised of 240 SD-OCT volumes was 162.3 µm in cystoid macular edema and 262 µm in nAMD. The presented method has cross-vendor functionality, while demonstrating accurate and reliable performance close to typical expert interobserver agreement. The automatically detected fovea positions may be used as landmarks for intra- and cross-patient registration and to create a joint reference frame for extraction of spatiotemporal features in “big data.” Furthermore, reliable analyses of retinal thickness, as well as retinal structure function correlation, may be facilitated.

  7. Structure-Function relationships using the Cirrus Spectral Domain Optical Coherence Tomograph and Standard Automated Perimetry

    PubMed Central

    Leite, Mauro T.; Zangwill, Linda M.; Weinreb, Robert N.; Rao, Harsha L.; Alencar, Luciana M.; Medeiros, Felipe A.

    2012-01-01

    Purpose To evaluate the relationship between glaucomatous structural damage assessed by the Cirrus Spectral Domain OCT (SDOCT) and functional loss as measured by standard automated perimetry (SAP). Methods Four hundred twenty two eyes (78 healthy, 210 suspects, 134 glaucomatous) of 250 patients were recruited from the longitudinal Diagnostic Innovations in Glaucoma Study (DIGS) and from the African Descent and Glaucoma Evaluation Study (ADAGES). All eyes underwent testing with the Cirrus SDOCT and SAP within a 6-month period. The relationship between parapapillary retinal nerve fiber layer thickness (RNFL) sectors and corresponding topographic SAP locations was evaluated using locally weighted scatterplot smoothing (LOWESS) and regression analysis. SAP sensitivity values were evaluated using both linear as well as logarithmic scales. We also tested the fit of a model (Hood) for structure-function relationship in glaucoma. Results Structure was significantly related to function for all but the nasal thickness sector. The relationship was strongest for superotemporal RNFL thickness and inferonasal sensitivity (R2 = 0.314, P<0.001). The Hood model fitted the data relatively well with 88% of the eyes inside the 95% confidence interval predicted by the model. Conclusion RNFL thinning measured by the Cirrus SDOCT was associated with correspondent visual field loss in glaucoma. PMID:21952500

  8. Visualization and measurement of capillary-driven blood flow using spectral domain optical coherence tomography.

    PubMed

    Cito, Salvatore; Ahn, Yeh-Chan; Pallares, Jordi; Duarte, Rodrigo Martinez; Chen, Zhongping; Madou, Marc; Katakis, Ioanis

    2012-09-01

    Capillary-driven flow (CD-flow) in microchannels plays an important role in many microfluidic devices. These devices, the most popular being those based in lateral flow, are becoming increasingly used in health care and diagnostic applications. CD-flow can passively pump biological fluids as blood, serum or plasma, in microchannels and it can enhance the wall mass transfer by exploiting the convective effects of the flow behind the meniscus. The flow behind the meniscus has not been experimentally identified up to now because of the lack of high-resolution, non-invasive, cross-sectional imaging means. In this study, spectral-domain Doppler optical coherence tomography is used to visualize and measure the flow behind the meniscus in CD-flows of water and blood. Microchannels of polydimethylsiloxane and glass with different cross-sections are considered. The predictions of the flow behind the meniscus of numerical simulations using the power-law model for non-Newtonian fluids are in reasonable agreement with the measurements using blood as working fluid. The extension of the Lucas-Washburn equation to non-Newtonian power-law fluids predicts well the velocity of the meniscus of the experiments using blood. PMID:23795150

  9. Separating Reflective and Fluorescent Components Using High Frequency Illumination in the Spectral Domain.

    PubMed

    Fu, Ying; Lam, Antony; Sato, Imari; Okabe, Takahiro; Sato, Yoichi

    2016-05-01

    Hyperspectral imaging is beneficial to many applications but most traditional methods do not consider fluorescent effects which are present in everyday items ranging from paper to even our food. Furthermore, everyday fluorescent items exhibit a mix of reflection and fluorescence so proper separation of these components is necessary for analyzing them. In recent years, effective imaging methods have been proposed but most require capturing the scene under multiple illuminants. In this paper, we demonstrate efficient separation and recovery of reflectance and fluorescence emission spectra through the use of two high frequency illuminations in the spectral domain. With the obtained fluorescence emission spectra from our high frequency illuminants, we then describe how to estimate the fluorescence absorption spectrum of a material given its emission spectrum. In addition, we provide an in depth analysis of our method and also show that filters can be used in conjunction with standard light sources to generate the required high frequency illuminants. We also test our method under ambient light and demonstrate an application of our method to synthetic relighting of real scenes. PMID:26336113

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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.

  11. Intraretinal Exudates in Coats' Disease as Demonstrated by Spectral-Domain OCT

    PubMed Central

    Kessner, Rivka; Barak, Adiel; Neudorfer, Meira

    2012-01-01

    Purpose To describe the spectral-domain optical coherence tomography (SD-OCT) findings in a case of Coats' disease, with emphasis on the intraretinal exudates. Methods Case report of a 4.5-year-old girl who presented with total exudative retinal detachment and organized exudates in a stellate configuration. SD-OCT was performed before and after treatment, which included surgical drainage of subretinal fluid and indirect laser application during the surgery. Results At presentation, the SD-OCT showed an elevation of the foveal contour, with thickening of the retina, many exudates and a large quantity of subretinal fluid. Two months after the surgical treatment, SD-OCT revealed a significant reduction in the amount of subretinal fluids, but with persistence of the exudates. Conclusion SD-OCT can be used as an important tool in order to describe the changes in each layer of the retina in Coats' disease. Considering the histopathological findings in Coats' disease, it is reasonable to assume that the exudates accumulate in the outer plexiform layer. PMID:22615695

  12. Investigation of retinal vessel autoregulation using real-time spectral domain Doppler optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Bower, Bradley A.; Zhao, Mingtao; Izatt, Joseph A.

    2006-02-01

    Investigation of the autoregulatory mechanism of human retinal perfusion was conducted with a novel real-time spectral domain Doppler optical coherence tomography (SDOCT) system. Volumetric, time-sequential, and Doppler flow imaging was performed in the superior arcade region on normal healthy subjects breathing normal room air and 100% oxygen. The real-time Doppler SDOCT system displays fully processed, high-resolution [512 (axial) x 1000 (lateral) pixels] B-scans at 17 frames/sec in volumetric and time-sequential imaging modes, and also displays fully processed overlaid color Doppler flow images comprising 512 (axial) x 500 (lateral) pixels at 6 frames/sec. OCT fundus images generated from volumetric datasets updated in real time (up to 2 fundus images/sec for 100 x 100 pixel volumes) were used to image and localize retinal vessels for time-sequential and Doppler flow analysis. In preliminary measurements, data acquired following 5 minutes of 100% oxygen inhalation was compared with that acquired 5 minutes post-inhalation. The same arterial segments examined at both time points exhibit constriction in vessel diameter under pure oxygen inhalation of up to 7% and reduction in peak flow velocity as great as 38%, both of which are in good agreement with previous laser Doppler velocimetry studies.

  13. 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.

  14. Venus in 3D

    NASA Astrophysics Data System (ADS)

    Plaut, J. J.

    1993-08-01

    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.

  15. 3D reservoir visualization

    SciTech Connect

    Van, B.T.; Pajon, J.L.; Joseph, P. )

    1991-11-01

    This paper shows how some simple 3D computer graphics tools can be combined to provide efficient software for visualizing and analyzing data obtained from reservoir simulators and geological simulations. The animation and interactive capabilities of the software quickly provide a deep understanding of the fluid-flow behavior and an accurate idea of the internal architecture of a reservoir.

  16. Generation of nearly 3D-unpolarized evanescent optical near fields using total internal reflection.

    PubMed

    Hassinen, Timo; Popov, Sergei; Friberg, Ari T; Setälä, Tero

    2016-07-01

    We analyze the time-domain partial polarization of optical fields composed of two evanescent waves created in total internal reflection by random electromagnetic beams with orthogonal planes of incidence. We show that such a two-beam configuration enables to generate nearly unpolarized, genuine three-component (3D) near fields. This result complements earlier studies on spectral polarization, which state that at least three symmetrically propagating beams are required to produce a 3D-unpolarized near field. The degree of polarization of the near field can be controlled by adjusting the polarization states and mutual correlation of the incident beams.

  17. Generation of nearly 3D-unpolarized evanescent optical near fields using total internal reflection.

    PubMed

    Hassinen, Timo; Popov, Sergei; Friberg, Ari T; Setälä, Tero

    2016-07-01

    We analyze the time-domain partial polarization of optical fields composed of two evanescent waves created in total internal reflection by random electromagnetic beams with orthogonal planes of incidence. We show that such a two-beam configuration enables to generate nearly unpolarized, genuine three-component (3D) near fields. This result complements earlier studies on spectral polarization, which state that at least three symmetrically propagating beams are required to produce a 3D-unpolarized near field. The degree of polarization of the near field can be controlled by adjusting the polarization states and mutual correlation of the incident beams. PMID:27367071

  18. Spectral-domain OCT imaging using a spectrally flexible wavelength-swept fiber laser based on dispersion tuning

    NASA Astrophysics Data System (ADS)

    Takubo, Y.; Yamashita, S.

    2014-05-01

    The broadband source with the arbitrary spectrum based on dispersion tuning technique was demonstrated. While a dispersion-tuned wavelength-swept laser is capable of fast and widely wavelength sweep, it can also be used as a broadband spectrally-flexible source by controlling the sweep waveform. It is the first demonstration of spectrallytunable source to the best of our knowledge. We used the dispersion-tuned laser as a broadband source for SD-OCT system by synchronizing sweep rate of a laser and exposure time of a CCD camera in SD-OCT system. We successfully obtained the images of an adhesive tape and a human finger.

  19. 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

  20. 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

  1. Extension of spectral domain phase microscopy to three-dimensional nanoscale displacement mapping in cardiomyocytes

    NASA Astrophysics Data System (ADS)

    Ellerbee, Audrey K.; Hendargo, Hansford C.; Motomura, Amy R.; Izatt, Joseph A.

    2008-02-01

    Spectral domain phase microscopy (SDPM) is a functional extension of optical coherence tomography (OCT) whose common-path interferometric design enables phase-referenced imaging of dynamic samples. Like OCT, axial resolution in SDPM is determined by the source coherence length, while lateral resolution is limited by diffraction in the microscope optics. Nonetheless, the quantitative phase information SDPM generates is sensitive to sub-Angstrom displacements of scattering structures. Integrative quantitative phase imaging techniques, such as Fourier phase microscopy, Hilbert phase microscopy, and Digital holographic microscopy, have achieved sub-micron motion detection in live cells. In contrast with the techniques, SDPM can achieve full depth discrimination, allowing for resolution of the motion of independent, sub-cellular structures at various cross-sectional planes within the sample. The ability of SDPM to measure Doppler flow in single-celled organisms, time-resolved cellular motions, and rheological information of the cytoskeleton has been previously demonstrated. The objective of this study is to extend the use of SDPM to produce three-dimensional reconstructions of the internal and surface motions of beating cardiomyocytes. Phase information is used to the motion of quantify cellular structures in the axial dimension. Our gated acquisition process involves synchronization of the SDPM detection system with and applied electrical field used to stimulate beating in isolated cardiomyocytes. For a given pacing protocol, we obtain repeat motion measurements in two-dimensions during cellular contraction, building a volume image by repeating the process at multiple discrete slices through the cell. This experiment serves as a proof-of-principle for volumetric imaging of beating cardiomyocytes.

  2. Macular thickness changes evaluated with spectral domain optical coherence tomography after uncomplicated phacoemulsification

    PubMed Central

    Gharbiya, M; Cruciani, F; Cuozzo, G; Parisi, F; Russo, P; Abdolrahimzadeh, S

    2013-01-01

    Purpose To determine macular thickness changes after uncomplicated cataract surgery using spectral domain optical coherence tomography (OCT). Methods This was a prospective non-randomized, clinical study. Data were analysed for 40 healthy patients undergoing uneventful phacoemulsification. OCT measurements were performed before surgery and postoperatively at day 1, week 1 and 2, and month 1, 2, 3, and 6. The retinal map was divided into central point thickness (CPT), central 1-mm subfield (CSF), and two peripheral ring areas with diameters of 3 and 6 mm. Fellow eyes were used as controls. Retinal thickness change between the operated and fellow eyes were compared using unpaired t-test. Correlations were analysed using the Spearman or the Pearson analysis. Results There was a progressive significant increase in retinal thickness of the operated eyes compared with the fellow eyes, with a peak at 1 month (P<0.0001) for the 3- and 6-mm areas and a peak at 2 months for CPT and CSF (P=0.01 and P<0.0001, respectively). At 6 months, retinal thickness was still significantly increased only in the peripheral areas (P<0.0001). There was no significant correlation between macular thickness changes and preoperative factors (age, axial length, anterior chamber depth, posterior vitreous detachment, best-corrected visual acuity), intraoperative factors (length of surgery, effective phaco time, phaco energy) or BCVA change. Conclusions The present study demonstrated a significant increase in macular thickness up to 6 months after uncomplicated cataract surgery. The most important finding was the regional pattern of retinal thickening with an early involvement of the parafoveal area. PMID:23449512

  3. 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

  4. Spectral domain optical coherence tomography for early detection of retinal alterations in patients using hydroxychloroquine

    PubMed Central

    Ulviye, Yigit; Betul, Tugcu; Nur, Tarakcioglu Hatice; Selda, Celik

    2013-01-01

    Objective: To determine whether early toxic effects from hydroxychloroquine (HCQ) could be detected by spectral-domain optical coherence tomography (SD-OCT) before symtomatic visual loss occured. Materials and Methods: Fifteen subjects with a history of the chronic use of hydroxychloroquine monotherapy for less than five years without fundus changes (group 1) and 15 visually normal healthy subjects (group 2) were enrolled in this study. All participants underwent systemic and ocular examination, visual field testing, and macular scan imaging using SD-OCT. Results: There were no significant differences in sex and ages between the groups (P > 0.05). Mean duration of HCQ usage in group 1 was 2.5 ± 1.34 (range:1-5) years. Visual field testing with central 10-2 threshold program was normal in all subjects. Inner retinal thickness in parafoveal and perifoveal area were found to be significantly lower in group 1 compared to group 2 (P < 0.01 for perifoveal, P < 0.05 for parafoveal retinal measurements). However, significant thinning was demonstrated only in full retinal thickness of perifoveal area in group 1 compared to group 2 (P: 0.013). Parafoveal and perifoveal inner retinal thickness measurements of inferior quadrants were significantly reduced in group 1 compared to group 2 (P < 0.01). Conclusion: Significant thinning of inner retinal layer especially in parafoveal and perifoveal areas in the absence of clinical fundus changes was observed in our study. We consider that SD-OCT may determine when inner retinal thinning starts in these patients and may contribute a quantitative approach to the early diagnosis and progression of retinal changes. PMID:23685488

  5. 3D rapid mapping

    NASA Astrophysics Data System (ADS)

    Isaksson, Folke; Borg, Johan; Haglund, Leif

    2008-04-01

    In this paper the performance of passive range measurement imaging using stereo technique in real time applications is described. Stereo vision uses multiple images to get depth resolution in a similar way as Synthetic Aperture Radar (SAR) uses multiple measurements to obtain better spatial resolution. This technique has been used in photogrammetry for a long time but it will be shown that it is now possible to do the calculations, with carefully designed image processing algorithms, in e.g. a PC in real time. In order to get high resolution and quantitative data in the stereo estimation a mathematical camera model is used. The parameters to the camera model are settled in a calibration rig or in the case of a moving camera the scene itself can be used for calibration of most of the parameters. After calibration an ordinary TV camera has an angular resolution like a theodolite, but to a much lower price. The paper will present results from high resolution 3D imagery from air to ground. The 3D-results from stereo calculation of image pairs are stitched together into a large database to form a 3D-model of the area covered.

  6. 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.

  7. ShowMe3D

    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 themore » 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.« less

  8. Spectral-Domain Measurements of Birefringence and Sensing Characteristics of a Side-Hole Microstructured Fiber

    PubMed Central

    Hlubina, Petr; Martynkien, Tadeusz; Olszewski, Jacek; Mergo, Pawel; Makara, Mariusz; Poturaj, Krzysztof; Urbańczyk, Waclaw

    2013-01-01

    We experimentally characterized a birefringent side-hole microstructured fiber in the visible wavelength region. The spectral dependence of the group and phase modal birefringence was measured using the methods of spectral interferometry. The phase modal birefringence of the investigated fiber increases with wavelength, but its positive sign is opposite to the sign of the group modal birefringence. We also measured the sensing characteristics of the fiber using a method of tandem spectral interferometry. Spectral interferograms corresponding to different values of a physical parameter were processed to retrieve the spectral phase functions and to determine the spectral dependence of polarimetric sensitivity to strain, temperature and hydrostatic pressure. A negative sign of the polarimetric sensitivity was deduced from the simulation results utilizing the known modal birefringence dispersion of the fiber. Our experimental results show that the investigated fiber has a very high polarimetric sensitivity to hydrostatic pressure, reaching −200 rad × MPa−1× m−1 at 750 nm. PMID:23989824

  9. 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

  10. Determining the von Mises stress power spectral density for frequency domain fatigue analysis including out-of-phase stress components

    NASA Astrophysics Data System (ADS)

    Bonte, M. H. A.; de Boer, A.; Liebregts, R.

    2007-04-01

    This paper provides a new formula to take into account phase differences in the determination of an equivalent von Mises stress power spectral density (PSD) from multiple random inputs. The obtained von Mises PSD can subsequently be used for fatigue analysis. The formula was derived for use in the commercial vehicle business and was implemented in combination with Finite Element software to predict and analyse fatigue failure in the frequency domain.

  11. 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

  12. 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.

  13. 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

  14. Taming supersymmetric defects in 3d-3d correspondence

    NASA Astrophysics Data System (ADS)

    Gang, Dongmin; Kim, Nakwoo; Romo, Mauricio; Yamazaki, Masahito

    2016-07-01

    We study knots in 3d Chern-Simons theory with complex gauge group {SL}(N,{{C}}), in the context of its relation with 3d { N }=2 theory (the so-called 3d-3d correspondence). The defect has either co-dimension 2 or co-dimension 4 inside the 6d (2,0) theory, which is compactified on a 3-manifold \\hat{M}. We identify such defects in various corners of the 3d-3d correspondence, namely in 3d {SL}(N,{{C}}) CS theory, in 3d { N }=2 theory, in 5d { N }=2 super Yang-Mills theory, and in the M-theory holographic dual. We can make quantitative checks of the 3d-3d correspondence by computing partition functions at each of these theories. This Letter is a companion to a longer paper [1], which contains more details and more results.

  15. 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.

  16. Optimal Spectral Domain Selection for Maximizing Archaeological Signatures: Italy Case Studies

    PubMed Central

    Cavalli, Rosa Maria; Pascucci, Simone; Pignatti, Stefano

    2009-01-01

    Different landscape elements, including archaeological remains, can be automatically classified when their spectral characteristics are different, but major difficulties occur when extracting and classifying archaeological spectral features, as archaeological remains do not have unique shape or spectral characteristics. The spectral anomaly characteristics due to buried remains depend strongly on vegetation cover and/or soil types, which can make feature extraction more complicated. For crop areas, such as the test sites selected for this study, soil and moisture changes within near-surface archaeological deposits can influence surface vegetation patterns creating spectral anomalies of various kinds. In this context, this paper analyzes the usefulness of hyperspectral imagery, in the 0.4 to 12.8 μm spectral region, to identify the optimal spectral range for archaeological prospection as a function of the dominant land cover. MIVIS airborne hyperspectral imagery acquired in five different archaeological areas located in Italy has been used. Within these archaeological areas, 97 test sites with homogenous land cover and characterized by a statistically significant number of pixels related to the buried remains have been selected. The archaeological detection potential for all MIVIS bands has been assessed by applying a Separability Index on each spectral anomaly-background system of the test sites. A scatterplot analysis of the SI values vs. the dominant land cover fractional abundances, as retrieved by spectral mixture analysis, was performed to derive the optimal spectral ranges maximizing the archaeological detection. This work demonstrates that whenever we know the dominant land cover fractional abundances in archaeological sites, we can a priori select the optimal spectral range to improve the efficiency of archaeological observations performed by remote sensing data. PMID:22573985

  17. 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.

  18. Artifacts in spectral-domain optical coherence tomography measurements in glaucoma.

    PubMed

    Asrani, Sanjay; Essaid, Luma; Alder, Brian D; Santiago-Turla, Cecilia

    2014-04-01

    IMPORTANCE Spectral-domain optical coherence tomography (SD-OCT) has an integral role in the diagnosis and treatment of glaucoma. Understanding the types of artifacts commonly seen in the imaging of patients being evaluated for glaucoma will help physicians better implement these data in the care of patients. OBJECTIVES To determine the frequency and distribution of SD-OCT imaging artifacts in patients being evaluated for glaucoma and to provide examples of common artifacts. DESIGN, SETTING, AND PARTICIPANTS A retrospective cross-sectional study design was used to examine SD-OCT images (using Spectralis SD-OCT) of 277 consecutive patients who had a diagnosis of glaucoma of any stage or had suspected glaucoma. Retinal nerve fiber layer (RNFL) and macular thickness scans were included. For each scan, the final printout and the source images that generated the final printout were examined. If present, artifacts were classified as evident on the final printout or not and were categorized as to the primary source of the artifact (eg, ocular pathologic features or technician errors). Examples of common artifacts are provided. MAIN OUTCOMES AND MEASURES The presence of imaging artifacts. RESULTS In 277 consecutive patients, 131 macular thickness scans were obtained, and 277 RNFL scans were obtained. Of the macular thickness scans, 37 (28.2%; 95% CI, 20.8%-36.1%) had imaging artifacts. Six of these artifacts were not obvious on the final printout. Of the RNFL scans, 55 (19.9%; 95% CI, 15.2%-24.6%) contained artifacts. Seven of these artifacts were not evident on the final printout. The most common cause of artifacts for macular thickness and RNFL scans was ocular pathologic features, primarily the presence of an epiretinal membrane. CONCLUSIONS AND RELEVANCE It is likely that SD-OCT-related imaging artifacts occur in 15.2% to 36.1% of scans obtained in patients being evaluated for glaucoma. Some of these artifacts may not be evident on the final printout. Physicians should

  19. 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

  20. Anatomic vs. Acquired Image Frame Discordance in Spectral Domain Optical Coherence Tomography Minimum Rim Measurements

    PubMed Central

    Yang, Hongli; Hardin, Christy; Reyes, Luke; Reynaud, Juan; Gardiner, Stuart K.; Fortune, Brad; Demirel, Shaban; Burgoyne, Claude F.

    2014-01-01

    Purpose To quantify the effects of using the fovea to Bruch's membrane opening (FoBMO) axis as the nasal-temporal midline for 30° sectoral (clock-hour) spectral domain optical coherence tomography (SDOCT) optic nerve head (ONH) minimum rim width (MRW) and area (MRA) calculations. Methods The internal limiting membrane and BMO were delineated within 24 radial ONH B-scans in 222 eyes of 222 participants with ocular hypertension and glaucoma. For each eye the fovea was marked within the infrared reflectance image, the FoBMO angle (θ) relative to the acquired image frame (AIF) horizontal was calculated, the ONH was divided into 30°sectors using a FoBMO or AIF nasal/temporal axis, and SDOCT MRW and MRA were quantified within each FoBMO vs. AIF sector. For each sector, focal rim loss was calculated as the MRW and MRA gradients (i.e. the difference between the value for that sector and the one clockwise to it divided by 30°). Sectoral FoBMO vs. AIF discordance was calculated as the difference between the FoBMO and AIF values for each sector. Generalized estimating equations were used to predict the eyes and sectors of maximum FoBMO vs. AIF discordance. Results The mean FoBMO angle was −6.6±4.2° (range: −17° to +7°). FoBMO vs. AIF discordance in sectoral mean MRW and MRA was significant for 7 of 12 and 6 of 12 sectors, respectively (p<0.05, Wilcoxon test, Bonferroni correction). Eye-specific, FoBMO vs. AIF sectoral discordance was predicted by sectoral rim gradient (p<0.001) and FoBMO angle (p<0.001) and achieved maximum values of 83% for MRW and 101% for MRA. Conclusions Using the FoBMO axis as the nasal-temporal axis to regionalize the ONH rather than a line parallel to the AIF horizontal axis significantly influences clock-hour SDOCT rim values. This effect is greatest in eyes with large FoBMO angles and sectors with focal rim loss. PMID:24643069

  1. Retinal Nerve Fiber Layer Thickness Measurement Comparison Using Spectral Domain and Swept Source Optical Coherence Tomography

    PubMed Central

    Ha, Ahnul; Lee, Seung Hyen; Lee, Eun Ji

    2016-01-01

    Purpose To investigate the retinal nerve fiber layer (RNFL) thickness concordance when measured by spectral domain (SD) and swept source (SS) optical coherence tomography (OCT), and to compare glaucoma-discriminating capability. Methods RNFL thicknesses were measured with the scan circle, centered on the optic nerve head, in 55 healthy, 41 glaucoma suspected, and 87 glaucomatous eyes. The RNFL thickness measured by the SD-OCT (sdRNFL thickness) and SS-OCT (ssRNFL thickness) were compared using the t-test. Bland-Altman analysis was performed to examine their agreement. We compared areas under the receiver operating characteristics curve and examined sdRNFL and ssRNFL thickness for discriminating glaucomatous eyes from healthy eyes, and from glaucoma suspect eyes. Results The average ssRNFL thickness was significantly greater than sdRNFL thickness in healthy (110.0 ± 7.9 vs. 100.1 ± 6.8 µm, p < 0.001), glaucoma suspect (96.8 ± 9.3 vs. 89.6 ± 7.9 µm, p < 0.001), and glaucomatous eyes (74.3 ± 14.2 vs. 69.1 ± 12.4 µm, p = 0.011). Bland-Altman analysis showed that there was a tendency for the difference between ssRNFL and sdRNFL to increase in eyes with thicker RNFL. The area under the curves of the average sdRNFL and ssRNFL thickness for discriminating glaucomatous eyes from healthy eyes (0.984 vs. 0.986, p = 0.491) and glaucoma suspect eyes (0.936 vs. 0.918, p = 0.132) were comparable. Conclusions There was a tendency for ssRNFL thickness to increase, compared with sdRNFL thickness, in eyes with thicker RNFL. The ssRNFL thickness had comparable diagnostic capability compared with sdRNFL thickness for discriminating glaucomatous eyes from healthy eyes and glaucoma suspect eyes. PMID:27051263

  2. 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

  3. 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.

  4. 3D Elastic Wavefield Tomography

    NASA Astrophysics Data System (ADS)

    Guasch, L.; Warner, M.; Stekl, I.; Umpleby, A.; Shah, N.

    2010-12-01

    Wavefield tomography, or waveform inversion, aims to extract the maximum information from seismic data by matching trace by trace the response of the solid earth to seismic waves using numerical modelling tools. Its first formulation dates from the early 80's, when Albert Tarantola developed a solid theoretical basis that is still used today with little change. Due to computational limitations, the application of the method to 3D problems has been unaffordable until a few years ago, and then only under the acoustic approximation. Although acoustic wavefield tomography is widely used, a complete solution of the seismic inversion problem requires that we account properly for the physics of wave propagation, and so must include elastic effects. We have developed a 3D tomographic wavefield inversion code that incorporates the full elastic wave equation. The bottle neck of the different implementations is the forward modelling algorithm that generates the synthetic data to be compared with the field seismograms as well as the backpropagation of the residuals needed to form the direction update of the model parameters. Furthermore, one or two extra modelling runs are needed in order to calculate the step-length. Our approach uses a FD scheme explicit time-stepping by finite differences that are 4th order in space and 2nd order in time, which is a 3D version of the one developed by Jean Virieux in 1986. We chose the time domain because an explicit time scheme is much less demanding in terms of memory than its frequency domain analogue, although the discussion of wich domain is more efficient still remains open. We calculate the parameter gradients for Vp and Vs by correlating the normal and shear stress wavefields respectively. A straightforward application would lead to the storage of the wavefield at all grid points at each time-step. We tackled this problem using two different approaches. The first one makes better use of resources for small models of dimension equal

  5. 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.

  6. 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.

  7. 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

  8. 3D multiplexed immunoplasmonics microscopy.

    PubMed

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

    2016-07-21

    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

  9. 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

  10. '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.

  11. Martian terrain - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    This area of terrain near the Sagan Memorial Station was taken on Sol 3 by the Imager for Mars Pathfinder (IMP). 3D glasses are necessary to identify surface detail.

    The IMP is a stereo imaging system with color capability provided by 24 selectable filters -- twelve filters per 'eye.' It stands 1.8 meters above the Martian surface, and has a resolution of two millimeters at a range of two meters.

    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

  12. 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

  13. 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.

  14. Design of 3d Topological Data Structure for 3d Cadastre Objects

    NASA Astrophysics Data System (ADS)

    Zulkifli, N. A.; Rahman, A. Abdul; Hassan, M. I.

    2016-09-01

    This paper describes the design of 3D modelling and topological data structure for cadastre objects based on Land Administration Domain Model (LADM) specifications. Tetrahedral Network (TEN) is selected as a 3D topological data structure for this project. Data modelling is based on the LADM standard and it is used five classes (i.e. point, boundary face string, boundary face, tetrahedron and spatial unit). This research aims to enhance the current cadastral system by incorporating 3D topology model based on LADM standard.

  15. Exploring interaction with 3D volumetric displays

    NASA Astrophysics Data System (ADS)

    Grossman, Tovi; Wigdor, Daniel; Balakrishnan, Ravin

    2005-03-01

    Volumetric displays generate true volumetric 3D images by actually illuminating points in 3D space. As a result, viewing their contents is similar to viewing physical objects in the real world. These displays provide a 360 degree field of view, and do not require the user to wear hardware such as shutter glasses or head-trackers. These properties make them a promising alternative to traditional display systems for viewing imagery in 3D. Because these displays have only recently been made available commercially (e.g., www.actuality-systems.com), their current use tends to be limited to non-interactive output-only display devices. To take full advantage of the unique features of these displays, however, it would be desirable if the 3D data being displayed could be directly interacted with and manipulated. We investigate interaction techniques for volumetric display interfaces, through the development of an interactive 3D geometric model building application. While this application area itself presents many interesting challenges, our focus is on the interaction techniques that are likely generalizable to interactive applications for other domains. We explore a very direct style of interaction where the user interacts with the virtual data using direct finger manipulations on and around the enclosure surrounding the displayed 3D volumetric image.

  16. In vivo functional imaging of embryonic chick heart using ultrafast 1310nm-band spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Li, Peng; Yin, Xin; Wang, Ruikang K.

    2013-02-01

    During the cardiac development, the cardiac wall and the blood flow actively interact with each other, and determine the biomechanical environment to which the embryonic heart exposes. Employing an ultrafast 1310nm-band dual-camera spectral domain optical coherence tomography (SDOCT), the radial strain rate of the myocardial wall can be extracted with high signal-to-noise ratio, at the same time the Doppler velocity of the blood flow can also be displayed. The ability to simultaneously characterize these two cardiac tissues provides a powerful approach to better understand the interaction between the cardiac wall and the blood flow, which is important to the investigation of cardiac development.

  17. ATTENUATION OF THE GANGLION CELL LAYER IN A PREMATURE INFANT REVEALED WITH HANDHELD SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY

    PubMed Central

    Goldberg, Mara R.; Zakka, Fouad R.; Carroll, Joseph J.

    2016-01-01

    Purpose: To report on subclinical retinal abnormalities shown through handheld spectral domain optical coherence tomography on a premature infant. Methods: Case report. Results: The initial and follow-up exams on a premature infant revealed severely attenuated ganglion cell and nerve fiber layers. There was cystoid macular edema in both eyes at the initial visits, which resolved by the 1-year follow-up. Discussion: Optical coherence tomography can reveal significant retinal abnormalities in premature infants which are not detectable through funduscopic exam. Documenting such findings may be useful for the comprehensive management of vision problems in children with a history of premature birth. PMID:26529438

  18. Temporal coherence shaping based on spectral-domain destructive interference of pulses with different self-phase modulations

    NASA Astrophysics Data System (ADS)

    Wei, D.; Takamasu, K.; Matsumoto, H.

    2013-03-01

    We show via a numerical simulation that the temporal coherence function (TCF) can be shaped by the destructive interference of pulses characterized by different amounts of self-phase modulation (SPM) in the spectral domain. We find that pulse spectra destructively interfering with one another can yield a TCF with distinct peaks. Numerical investigation demonstrates that the shape of the TCF is changeable not only by broadening the spectrum but also by overlapping spectra of the pulses that have experienced different amounts of SPM.

  19. Experimental Electrically Reconfigurable Time-Domain Spectral Amplitude Encoding/Decoding in an Optical Code Division Multiple Access System

    NASA Astrophysics Data System (ADS)

    Tainta, Santiago; Erro, María J.; Garde, María J.; Muriel, Miguel A.

    2013-11-01

    An electrically reconfigurable time-domain spectral amplitude encoding/decoding scheme is proposed herein. The setup is based on the concept of temporally pulse shaping dual to spatial arrangements. The transmitter is based on a short pulse source and uses two conjugate dispersive fiber gratings and an electro-optic intensity modulator placed in between. Proof of concept results are shown for an optical pulse train operating at 1.25 Gbps using codes from the Hadamard family with a length of eight chips. The system is electrically reconfigurable, compatible with fiber systems, and permits scalability in the size of the codes by modifying only the modulator velocity.

  20. 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.

  1. Design and experimental investigation of highly efficient resonance-domain diffraction gratings in the visible spectral region.

    PubMed

    Barlev, Omri; Golub, Michael A; Friesem, Asher A; Nathan, Menachem

    2012-12-01

    Surface-relief resonance-domain diffraction gratings with deep and dense grooves provide considerable changes in light propagation direction, wavefront curvature, and nearly 100% Bragg diffraction efficiency usually attributed only to volume optical holograms. In this paper, we present design, computer simulation, fabrication, and experimental results of binary resonance-domain diffraction gratings in the visible spectral region. Performance of imperfectly fabricated diffraction groove profiles was optimized by controlling the DC and the depth of the grooves. Indeed, more than 97% absolute Bragg diffraction efficiency was measured at the 635 nm wavelength with binary gratings having periods of 520 nm and groove depths of about 1000 nm, fabricated by direct electron-beam lithography and reactive ion etching.

  2. 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

  3. Implementation of spectral basis functions in BEM/FEM/GSM Domain Decomposition Methods devoted to scattering and radiation applications

    NASA Astrophysics Data System (ADS)

    Barka, André; Picard, Clément

    2008-03-01

    In this paper, we discuss several improvements of a substructuring Domain Decomposition Method (DDM) devoted to Electromagnetic computations, based on the Boundary Element Method (BEM) and the Finite Element Method (FEM). This computation procedure is applied to the analysis of antenna performance on board vehicles as well as Radar Cross Section (RCS). The benefits of the subdomain Computational Electromagnetic Method are mainly the ability to deal with collaborative studies involving several companies, and the reduction of the computation costs by one or more orders of magnitude, especially in the context of parametric studies. Furthermore, this paper proposes a Spectral Basis Function (SBF) defined on fictitious surfaces surrounding equipment, to deal with both the computation of antenna far field patterns and RCS in a multi-domain mode. By masking the complexity of the equipment (wires, thin surfaces, materials, supply network, weapons) the external domain of the vehicle can be closed so that the Combined Field Integral Equation (CFIE) can be used, which is better conditioned than the Electric Field Integral Equation (EFIE). This calculation procedure leads to a faster convergence when using iterative Multi Level Fast Multiple Algorithms (MLFMA). The accuracy and efficiency of this technique is assessed by performing the computation of the diffraction and radiation of several test-objects in a multi-domain way cross compared with reference integral equation results.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Fourier domain optical coherence tomography artifact and speckle reduction by autoregressive spectral estimation without a loss of resolution

    NASA Astrophysics Data System (ADS)

    Bousi, Evgenia; Pitris, Costas

    2015-03-01

    Fourier Domain (FD) Optical Coherence Tomography (OCT) interferograms require a Fourier transformation in order to be converted to A-Scans representing the backscattering intensity from the different depths of the tissue microstructure. Most often, this transformation is performed using a discrete Fourier transform, i.e. the well-known Fast Fourier Transform (FFT). However, there are many alternatives for performing the necessary spectral conversion. Autoregressive (AR) spectral estimation techniques are one such example. The parametric nature of AR techniques offers several advantages, compared to the commonly-used FFT, including better convergence and less susceptibility to noise. They can also be adjusted to represent more or less of the signal detail depending on the order of the autoregression. These features make them uniquely suited for processing the FD OCT data. The advantages of the proposed methodology are illustrated on in vivo skin imaging data and the resolution is verified on single back-reflections from a glass surface. AR spectral estimation can be used to convert the interferograms to A-Scans while at the same time reducing the artifacts caused by high intensity back-reflections (by -20 dB) and diminishing the speckle (by -12 dB) all without the degradation in the resolution associated with other techniques.

  9. Power spectral density estimation by spline smoothing in the frequency domain

    NASA Technical Reports Server (NTRS)

    Defigueiredo, R. J. P.; Thompson, J. R.

    1972-01-01

    An approach, based on a global averaging procedure, is presented for estimating the power spectrum of a second order stationary zero-mean ergodic stochastic process from a finite length record. This estimate is derived by smoothing, with a cubic smoothing spline, the naive estimate of the spectrum obtained by applying FFT techniques to the raw data. By means of digital computer simulated results, a comparison is made between the features of the present approach and those of more classical techniques of spectral estimation.

  10. Power spectral density estimation by spline smoothing in the frequency domain.

    NASA Technical Reports Server (NTRS)

    De Figueiredo, R. J. P.; Thompson, J. R.

    1972-01-01

    An approach, based on a global averaging procedure, is presented for estimating the power spectrum of a second order stationary zero-mean ergodic stochastic process from a finite length record. This estimate is derived by smoothing, with a cubic smoothing spline, the naive estimate of the spectrum obtained by applying Fast Fourier Transform techniques to the raw data. By means of digital computer simulated results, a comparison is made between the features of the present approach and those of more classical techniques of spectral estimation.-

  11. 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.

  12. 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.

  13. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-01-01

    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.  

  14. 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.  

  15. Ultrawide-field parallel spectral domain optical coherence tomography for nondestructive inspection of glass

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    Aiming at the requirements of real-time inspection in material industry, an ultrawide-field parallel SD-OCT system capable of visualizing cross-sectional image of internal structures by a single shot of a 2-D CMOS camera is developed. To achieve ultrawide-field parallel detection, one meniscus lens with negative dioptric is introduced as an additional relay lens and imaging optics including sample arm, relay lenses and spectrometer are optimized as a whole for desirable imaging quality. The developed system has an ultrawide-field of 35 mm and an axial range of 8 mm in air. The maximum on-axis sensitivity and the axial resolution are experimentally determined to be 65 dB and 17.7 μm, respectively. The on-axis lateral resolution is measured to be 44 μm in parallel direction and 22 μm in scanning direction. The system is applied to obtain 3-D volume images of a set of glass-samples covering an area of about 28 mm by 15 mm with thicknesses ranging between 2.1 mm and 4 mm, from which defects such as solid inclusion, micro-deformation and bubble are identified either on the surfaces or inside the samples.

  16. Characterization of ink-jet printed RGB color filters with spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Czajkowski, J.; Vilmi, P.; Lauri, J.; Sliz, R.; Fabritius, T.; Myllylä, R.

    2012-09-01

    We present the use of sub-micron resolution optical coherence tomography (SMR SD-OCT) in volumetric characterization of ink- jet printed color filters, aimed for electronic paper display (EPD). The device used in the study is based on supercontinuum light source, Michelson interferometer centered at 600 nm and employs 400-800 nm spectral region. Spectra are acquired at a continuous rate of 140,000 per second. Color filter array of 143 μm x 141 μm sized and 6 rtm deep ink pools was studied. The volumetric OCT reconstruction was done using the experimental SMR SD-OCT device and a commercial SD-OCT imaging system. The ink layer in the pools was estimated to be 2μm thin. The optical profilometer was used for reference measurements.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. [3-D ultrasound in gastroenterology].

    PubMed

    Zoller, W G; Liess, H

    1994-06-01

    Three-dimensional (3D) sonography represents a development of noninvasive diagnostic imaging by real-time two-dimensional (2D) sonography. The use of transparent rotating scans, comparable to a block of glass, generates a 3D effect. The objective of the present study was to optimate 3D presentation of abdominal findings. Additional investigations were made with a new volumetric program to determine the volume of selected findings of the liver. The results were compared with the estimated volumes of 2D sonography and 2D computer tomography (CT). For the processing of 3D images, typical parameter constellations were found for the different findings, which facilitated processing of 3D images. In more than 75% of the cases examined we found an optimal 3D presentation of sonographic findings with respect to the evaluation criteria developed by us for the 3D imaging of processed data. Great differences were found for the estimated volumes of the findings of the liver concerning the three different techniques applied. 3D ultrasound represents a valuable method to judge morphological appearance in abdominal findings. The possibility of volumetric measurements enlarges its potential diagnostic significance. Further clinical investigations are necessary to find out if definite differentiation between benign and malign findings is possible.

  2. Spectral-Domain Optical Coherence Tomography, Wide-Field Photography, and Fundus Autofluorescence Correlation of Posterior Ophthalmomyiasis Interna.

    PubMed

    Paulus, Yannis M; Butler, Nicholas J

    2016-07-01

    Posterior ophthalmomyiasis interna is a rare, potentially devastating infestation of the posterior segment by fly larvae. The authors report the first demonstration of spectral-domain optical coherence tomography (SD-OCT) (Spectralis; Heidelberg Engineering, Heidelberg, Germany), wide-field angiography (Optos, Dunfermline, Scotland) and photography, and fundus autofluorescence with temporal progression during a period of 6 months. A 12-year-old white female presented with acute, painless vision loss with hand motions visual acuity. No larva was visible, so she was treated with oral ivermectin. Visual acuity improved to 20/80. OCT demonstrated hyporeflective spaces of the outer retina and retinal pigment epithelium, which resolved during 1-month period with improved ellipsoid layer by 6 months. Fundus autofluorescence demonstrated linear hypoautofluorescent tracks. [Ophthalmic Surg Lasers Imaging Retina. 2016;47:682-685.]. PMID:27434903

  3. 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

  4. In vivo early retinal structural alterations following laser photocoagulation using three-dimensional spectral domain optical coherence tomography.

    PubMed

    Saxena, Sandeep; Mishra, Nibha; Ruia, Surabhi; Akduman, Levent

    2016-01-01

    To study the retinal structural alterations and surface topography of retinal pigment epithelium (RPE) immediately following laser photocoagulation up to day 7. Cross-sectional retinal imaging and RPE segmentation maps on spectral domain optical coherence tomography were obtained immediately at hour 1, day 1, day 4 and day 7 following 532 nm neodymium:YAG laser photocoagulation in a 56-year-old male patient for branch retinal vein occlusion. Immediately postlaser, loss of reflectivity of all the retinal layers was observed. At hour 1, hyper-reflectivity of outer retinal layers was observed with increase in hyporeflective spaces by day 1. Immediately postlaser, pitting of the RPE was observed on surface topography which regressed at day 1. On day 4, smooth RPE surface topography was observed with the occurrence of small elevated areas on day 7. The present report provides an insight into the in vivo changes in the retinal structure and RPE surface topography after laser photocoagulation. PMID:27402655

  5. Isolated cotton-wool spots of unknown etiology: management and sequential spectral domain optical coherence tomography documentation.

    PubMed

    Ioannides, Antonis; Georgakarakos, Nikolaos D; Elaroud, Ibrahim; Andreou, Petros

    2011-01-01

    Cotton-wool spots (CWSs) are common retinal manifestations of many diseases including diabetes mellitus, systemic hypertension, and acquired immunodeficiency syndrome. Clinically they appear as whitish, fluffy patches on the retina and eventually fade with time. In this study, spectral domain optical coherence tomography (SD-OCT) with mapping was used to demonstrate in vivo the characteristics of an isolated CWS in a 59-year-old patient as well as its appearance immediately after ophthalmoscopic resolution. Presented here is the work-up and management of this clinical problem for the ophthalmologist. The authors propose that SD-OCT could be a valuable research tool in characterizing and following the dynamic CWS changes at individual retinal layer level, with potential clinical applications as a screening or diagnostic tool in CWS-related diseases. PMID:22034565

  6. Isolated cotton-wool spots of unknown etiology: management and sequential spectral domain optical coherence tomography documentation

    PubMed Central

    Ioannides, Antonis; Georgakarakos, Nikolaos D; Elaroud, Ibrahim; Andreou, Petros

    2011-01-01

    Cotton-wool spots (CWSs) are common retinal manifestations of many diseases including diabetes mellitus, systemic hypertension, and acquired immunodeficiency syndrome. Clinically they appear as whitish, fluffy patches on the retina and eventually fade with time. In this study, spectral domain optical coherence tomography (SD-OCT) with mapping was used to demonstrate in vivo the characteristics of an isolated CWS in a 59-year-old patient as well as its appearance immediately after ophthalmoscopic resolution. Presented here is the work-up and management of this clinical problem for the ophthalmologist. The authors propose that SD-OCT could be a valuable research tool in characterizing and following the dynamic CWS changes at individual retinal layer level, with potential clinical applications as a screening or diagnostic tool in CWS-related diseases. PMID:22034565

  7. 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.

  8. Spectral-domain low coherence interferometry/optical coherence tomography system for fine needle breast biopsy guidance

    NASA Astrophysics Data System (ADS)

    Iftimia, N. V.; Mujat, M.; Ustun, T.; Ferguson, R. D.; Danthu, V.; Hammer, D. X.

    2009-02-01

    A novel technology and instrumentation for fine needle aspiration (FNA) breast biopsy guidance is presented. This technology is based on spectral-domain low coherence interferometry (SD-LCI). The method, apparatus, and preliminary in vitro/in vivo results proving the viability of the method and apparatus are presented in detail. An advanced tissue classification algorithm, preliminarily tested on breast tissue specimens and a mouse model of breast cancer is presented as well. Over 80% sensitivity and specificity in differentiating all tissue types and 93% accuracy in differentiating fatty tissue from fibrous or tumor tissue was obtained with this technology and apparatus. These results suggest that SD-LCI could help for more precise needle placement during the FNA biopsy and therefore could substantially reduce the number of the nondiagnostic aspirates and improve the sensitivity and specificity of the FNA procedures.

  9. 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

  10. In vivo tear film thickness measurement and tear film dynamics visualization using spectral domain optical coherence tomography.

    PubMed

    Aranha Dos Santos, Valentin; Schmetterer, Leopold; Gröschl, Martin; Garhofer, Gerhard; Schmidl, Doreen; Kucera, Martin; Unterhuber, Angelika; Hermand, Jean-Pierre; Werkmeister, René M

    2015-08-10

    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 non-invasive fully automated approach to measure tear film thickness based on spectral domain optical coherence tomography and on an efficient delay estimator. Silicon wafer phantom were used to validate the thickness measurement. The technique was applied in vivo in healthy subjects. Series of tear film thickness maps were generated, allowing for the visualization of tear film dynamics. Our results show that the in vivo central tear film thickness measurements are precise and repeatable with a coefficient of variation of about 0.65% and that repeatable tear film dynamics can be observed. The presented approach could be used in clinical setting to study patients with dry eye disease and monitor their treatments.

  11. 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. PMID:26657435

  12. 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.

  13. 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.

  14. 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.

  15. Resonance domain surface relief diffractive lens for the visible spectral region.

    PubMed

    Barlev, Omri; Golub, Michael A

    2013-03-01

    Early expectations for a role of diffractive lenses were dramatically lessened by their high order overlapping foci, low optical powers, and competing advances in refractive micro-optics. By bringing the Bragg properties of volume holograms to diffractive lenses we got rid of ghost diffractive orders and the critical trade-off between diffraction efficiency, number of phase levels, and spatial feature-size. Binary off-axis resonance domain diffractive lens with high numerical aperture of 0.16 was designed with analytical effective grating theory, fabricated by direct e-beam writing, etched in fused silica and experimentally investigated. More than 81% measured diffraction efficiency exceeds twice the limits of thin binary optics.

  16. Full range complex spectral domain optical coherence tomography for volumetric imaging at 47 000 A-scans per second

    NASA Astrophysics Data System (ADS)

    An, Lin; Subhash, Hrebesh M.; Wang, Ruikang K.

    2010-08-01

    In this paper we demonstrate a high speed spectral domain optical coherence tomography (SDOCT) system capable of achieving full range complex imaging at a line scan rate of 47 kHz. By applying a beam-offset method, a constant modulation frequency is introduced into each B-scan that enables reconstruction of the full range complex SDOCT images of in vivo tissue samples. To make use of the full capacity of the detection camera used in the system, system control software is developed that streams the raw spectral fringe data directly into the computer memory. In order to assess performance of the high speed full range SDOCT system for imaging biological specimen, we present results imaged from the cuticle of the fingernail of a human volunteer in vivo and from chick embryos ex vivo. We also show the high sensitivity advantages of full range complex imaging as compared to conventional SDOCT. To the best of our knowledge, an imaging rate of 47 000 A-scans per second is the highest imaging rate that has ever been reported for full range complex imaging. Notwithstanding, the method reported here has no limitations on the imaging speed and thus offers a useful tool to achieve volumetric imaging of living samples where the high sensitivity region around zero delay line in the system can be utilized for imaging.

  17. High-resolution coherence domain reflectometry using 1.55 μm supercontinuum source and quadrature spectral detection

    NASA Astrophysics Data System (ADS)

    Smith, Elwyn; Wada, Naoya; Chujo, Wataru; Sampson, David D.

    2002-06-01

    High-power ultra-broadband sources such as a supercontinuum are very attractive in optical coherence tomography (OCT) and optical coherence-domain reflectometry (OCDR) due to their very high resolution potential. However, the large and extensive coherence-function sidelobes typical of such sources preclude their use in conventional OCDR and OCT systems. In addition, device or sample dispersion over such broad bandwidths may also significantly limit the achievable performance. Here we describe a novel experiment using a supercontinuum source with a static Michelson interferometer to perform OCDR at 1.55micrometers . Quadrature spectral detection is used to maximize the scanning range and to allow direct compensation for both the undesirable spectral shape of the source and for the dispersion in the system. Such a non-scanning-interferometer approach is an interesting possible alternative for very broadband, ultra-high resolution OCT systems. We demonstrate that an otherwise obscured small reflection next to a large reflection can be revealed by appropriately weighting the data to reshape the supercontinuum spectrum and compensate for dispersion. Significant reduction of the supercontinuum coherence function sidelobes is achieved, and a resolution in air of 7micrometers (FWHM) is obtained, or less than 5micrometers in media of refractive index 1.45.

  18. High-resolution, dual-depth spectral-domain optical coherence tomography with interlaced detection for whole-eye imaging.

    PubMed

    Kim, Hyung-Jin; Kim, Pil Un; Hyeon, Min Gyu; Choi, Youngwoon; Kim, Jeehyun; Kim, Beop-Min

    2016-09-10

    Dual-depth spectral-domain optical coherence tomography (SD-OCT) enables high-resolution in vivo whole-eye imaging. Two orthogonally polarized beams from a source are focused simultaneously on two axial positions of the anterior segment and the retina. For the detector arm, a 1×2 ultrafast optical switch sequentially delivers two spectral interference signals to a single spectrometer, which extends the in-air axial depth range up to 9.44 mm. An off-pivot complex conjugate removal technique doubles the depth range for all anterior segment imaging. The graphics-processing-unit-based parallel signal processing algorithm supports fast two- and three-dimensional image displays. The obtained high-resolution anterior and retinal images are measured biometrically. The dual-depth SD-OCT system has an axial resolution of ∼6.4  μm in air, and the sensitivity is 91.79 dB at 150 μm from the zero-delay line. PMID:27661354

  19. 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. PMID:24217734

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. Multibaseline IFSAR for 3D target reconstruction

    NASA Astrophysics Data System (ADS)

    Ertin, Emre; Moses, Randolph L.; Potter, Lee C.

    2008-04-01

    We consider three dimensional target construction from SAR data collected on multiple complete circular apertures at different elevation angle. The 3-D resolution of circular SAR systems is constrained by two factors: the sparse sampling in elevation and the limited azimuthal persistence of the reflectors in the scene. Three dimensional target reconstruction with multipass circular SAR data is further complicated by nonuniform elevation spacing in real flight paths and non-constant elevation angle throughout the circular pass. In this paper we first develop parametric spectral estimation methods that extend standard IFSAR method of height estimation to apertures at more than two elevation angles. Next, we show that linear interpolation of the phase history data leads to unsatisfactory performance in 3-D reconstruction from nonuniformly sampled elevation passes. We then present a new sparsity regularized interpolation algorithm to preprocess nonuniform elevation samples to create a virtual uniform linear array geometry. We illustrate the performance of the proposed method using simulated backscatter data.

  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. 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.

  8. Metrological characterization of 3D imaging devices

    NASA Astrophysics Data System (ADS)

    Guidi, G.

    2013-04-01

    Manufacturers often express the performance of a 3D imaging device in various non-uniform ways for the lack of internationally recognized standard requirements for metrological parameters able to identify the capability of capturing a real scene. For this reason several national and international organizations in the last ten years have been developing protocols for verifying such performance. Ranging from VDI/VDE 2634, published by the Association of German Engineers and oriented to the world of mechanical 3D measurements (triangulation-based devices), to the ASTM technical committee E57, working also on laser systems based on direct range detection (TOF, Phase Shift, FM-CW, flash LADAR), this paper shows the state of the art about the characterization of active range devices, with special emphasis on measurement uncertainty, accuracy and resolution. Most of these protocols are based on special objects whose shape and size are certified with a known level of accuracy. By capturing the 3D shape of such objects with a range device, a comparison between the measured points and the theoretical shape they should represent is possible. The actual deviations can be directly analyzed or some derived parameters can be obtained (e.g. angles between planes, distances between barycenters of spheres rigidly connected, frequency domain parameters, etc.). This paper shows theoretical aspects and experimental results of some novel characterization methods applied to different categories of active 3D imaging devices based on both principles of triangulation and direct range detection.

  9. 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.

  10. 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.

  11. Accepting the T3D

    SciTech Connect

    Rich, D.O.; Pope, S.C.; DeLapp, J.G.

    1994-10-01

    In April, a 128 PE Cray T3D was installed at Los Alamos National Laboratory`s Advanced Computing Laboratory as part of the DOE`s High-Performance Parallel Processor Program (H4P). In conjunction with CRI, the authors implemented a 30 day acceptance test. The test was constructed in part to help them understand the strengths and weaknesses of the T3D. In this paper, they briefly describe the H4P and its goals. They discuss the design and implementation of the T3D acceptance test and detail issues that arose during the test. They conclude with a set of system requirements that must be addressed as the T3D system evolves.

  12. 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.

  13. 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

  14. 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

  15. LASTRAC.3d: Transition Prediction in 3D Boundary Layers

    NASA Technical Reports Server (NTRS)

    Chang, Chau-Lyan

    2004-01-01

    Langley Stability and Transition Analysis Code (LASTRAC) is a general-purpose, physics-based transition prediction code released by NASA for laminar flow control studies and transition research. This paper describes the LASTRAC extension to general three-dimensional (3D) boundary layers such as finite swept wings, cones, or bodies at an angle of attack. The stability problem is formulated by using a body-fitted nonorthogonal curvilinear coordinate system constructed on the body surface. The nonorthogonal coordinate system offers a variety of marching paths and spanwise waveforms. In the extreme case of an infinite swept wing boundary layer, marching with a nonorthogonal coordinate produces identical solutions to those obtained with an orthogonal coordinate system using the earlier release of LASTRAC. Several methods to formulate the 3D parabolized stability equations (PSE) are discussed. A surface-marching procedure akin to that for 3D boundary layer equations may be used to solve the 3D parabolized disturbance equations. On the other hand, the local line-marching PSE method, formulated as an easy extension from its 2D counterpart and capable of handling the spanwise mean flow and disturbance variation, offers an alternative. A linear stability theory or parabolized stability equations based N-factor analysis carried out along the streamline direction with a fixed wavelength and downstream-varying spanwise direction constitutes an efficient engineering approach to study instability wave evolution in a 3D boundary layer. The surface-marching PSE method enables a consistent treatment of the disturbance evolution along both streamwise and spanwise directions but requires more stringent initial conditions. Both PSE methods and the traditional LST approach are implemented in the LASTRAC.3d code. Several test cases for tapered or finite swept wings and cones at an angle of attack are discussed.

  16. Finite difference time domain modeling of finite-sized electromagnetic source over periodic structure via a plane wave spectral expansion approach

    NASA Astrophysics Data System (ADS)

    Qiang, Rui; Chen, Ji; Yang, Fan

    2010-10-01

    A novel three-dimensional time domain method is developed to study interactions between finite-sized electromagnetic sources and infinite periodic structures. The method is based on a periodic finite difference time domain method combined with the spectral expansion of electromagnetic sources. Using this method, only a single periodic cell needs to be modeled in finite difference time domain simulations. The convergence, guidelines on using the algorithm, and the acceleration scheme for the algorithm are discussed. Several periodic structures are simulated by this proposed method. It is shown that this method can significantly reduce the required computer memory and computational time.

  17. 3D Face modeling using the multi-deformable method.

    PubMed

    Hwang, Jinkyu; Yu, Sunjin; Kim, Joongrock; Lee, Sangyoun

    2012-01-01

    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. PMID:23201976

  18. 3D Face Modeling Using the Multi-Deformable Method

    PubMed Central

    Hwang, Jinkyu; Yu, Sunjin; Kim, Joongrock; Lee, Sangyoun

    2012-01-01

    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. PMID:23201976

  19. Spectral domain optical coherence tomography in patients after successful management of postoperative endophthalmitis following cataract surgery by pars plana vitrectomy

    PubMed Central

    2014-01-01

    Background Acute severe postoperative endophthalmitis may lead to severe vision loss. The aim of this study was the analysis of macular microstructure imaged by spectral domain optical coherence tomography in patients after pars plana vitrectomy due to postcataract endophthalmitis. Methods A cross sectional study was carried out in 17 patients who had cataract surgery in both eyes and underwent unilateral pars plana vitrectomy due to postcataract endophthalmitis. Postoperative best corrected visual acuity was determined in both eyes. Evaluation of macular thickness, macular volume, peripapillary retinal nerve fiber layer thickness and choroidal thickness using enhanced depth imaging technique was performed by spectral domain optical coherence tomography. The measurements obtained in the operated eye were compared to the fellow eye by Wilcoxon matched pair test. Correlation test was performed by Spearman rank order. Results A mean postoperative best corrected visual acuity of 63 ± 30 ETDRS letters versus 75 ± 21 letters was achieved in the study and fellow eyes, respectively, after a mean of 5.3 ± 4.5 months (p = 0.1). The mean macular thickness was 320.6 ± 28.8 μm SD in the study eyes compared to 318.4 ± 18.8 μm in the fellow eyes (p = 0.767). No differences were noted in macular volume (p = 0.97) and in peripapillary retinal nerve fiber layer thickness (p = 0.31). Choroidal thickness was significantly lower in the study eyes compared to the fellow eyes (p = 0.018). Epiretinal membrane was found in 7 eyes after endophthalmitis, while in the fellow eyes only in 3 cases (p = 0.13, Fisher’s exact test). Conclusion Choroidal thickness decreased significantly after endophthalmitis, but there was no functional correlation with the changes in choroidal microstructure. The development of epiretinal membranes may be associated with either vitrectomy or endophthalmitis in the history. Absence of other significant

  20. 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

  1. 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.

  2. 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.

  3. Remote 3D Medical Consultation

    NASA Astrophysics Data System (ADS)

    Welch, Greg; Sonnenwald, Diane H.; Fuchs, Henry; Cairns, Bruce; Mayer-Patel, Ketan; Yang, Ruigang; State, Andrei; Towles, Herman; Ilie, Adrian; Krishnan, Srinivas; Söderholm, Hanna M.

    Two-dimensional (2D) video-based telemedical consultation has been explored widely in the past 15-20 years. Two issues that seem to arise in most relevant case studies are the difficulty associated with obtaining the desired 2D camera views, and poor depth perception. To address these problems we are exploring the use of a small array of cameras to synthesize a spatially continuous range of dynamic three-dimensional (3D) views of a remote environment and events. The 3D views can be sent across wired or wireless networks to remote viewers with fixed displays or mobile devices such as a personal digital assistant (PDA). The viewpoints could be specified manually or automatically via user head or PDA tracking, giving the remote viewer virtual head- or hand-slaved (PDA-based) remote cameras for mono or stereo viewing. We call this idea remote 3D medical consultation (3DMC). In this article we motivate and explain the vision for 3D medical consultation; we describe the relevant computer vision/graphics, display, and networking research; we present a proof-of-concept prototype system; and we present some early experimental results supporting the general hypothesis that 3D remote medical consultation could offer benefits over conventional 2D televideo.

  4. 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.

  5. 3D-Printed Microfluidics.

    PubMed

    Au, Anthony K; Huynh, Wilson; Horowitz, Lisa F; Folch, Albert

    2016-03-14

    The advent of soft lithography allowed for an unprecedented expansion in the field of microfluidics. However, the vast majority of PDMS microfluidic devices are still made with extensive manual labor, are tethered to bulky control systems, and have cumbersome user interfaces, which all render commercialization difficult. On the other hand, 3D printing has begun to embrace the range of sizes and materials that appeal to the developers of microfluidic devices. Prior to fabrication, a design is digitally built as a detailed 3D CAD file. The design can be assembled in modules by remotely collaborating teams, and its mechanical and fluidic behavior can be simulated using finite-element modeling. As structures are created by adding materials without the need for etching or dissolution, processing is environmentally friendly and economically efficient. We predict that in the next few years, 3D printing will replace most PDMS and plastic molding techniques in academia.

  6. GPU accelerated real-time multi-functional spectral-domain optical coherence tomography system at 1300 nm.

    PubMed

    Wang, Yan; Oh, Christian M; Oliveira, Michael C; Islam, M Shahidul; Ortega, Arthur; Park, B Hyle

    2012-07-01

    We present a GPU accelerated multi-functional spectral domain optical coherence tomography system at 1300 nm. The system is capable of real-time processing and display of every intensity image, comprised of 512 pixels by 2048 A-lines acquired at 20 frames per second. The update rate for all four images with size of 512 pixels by 2048 A-lines simultaneously (intensity, phase retardation, flow and en face view) is approximately 10 frames per second. Additionally, we report for the first time the characterization of phase retardation and diattenuation by a sample comprised of a stacked set of polarizing film and wave plate. The calculated optic axis orientation, phase retardation and diattenuation match well with expected values. The speed of each facet of the multi-functional OCT CPU-GPU hybrid acquisition system, intensity, phase retardation, and flow, were separately demonstrated by imaging a horseshoe crab lateral compound eye, a non-uniformly heated chicken muscle, and a microfluidic device. A mouse brain with thin skull preparation was imaged in vivo and demonstrated the capability of the system for live multi-functional OCT visualization. PMID:22772175

  7. Grading of Age-Related Macular Degeneration: Comparison between Color Fundus Photography, Fluorescein Angiography, and Spectral Domain Optical Coherence Tomography

    PubMed Central

    Mokwa, Nils F.; Keane, Pearse A.; Kirchhof, Bernd; Sadda, Srinivas R.

    2013-01-01

    Purpose. To compare color fundus photography (FP), fluorescein angiography (FA), and spectral domain optical coherence tomography (SDOCT) for the detection of age-related macular degeneration (AMD), choroidal neovascularisation (CNV), and CNV activity. Methods. FPs, FAs, and SDOCT volume scans from 120 eyes of 66 AMD and control patients were randomly collected. Control eyes were required to show no AMD, but other retinal pathology was allowed. The presence of drusen, pigmentary changes, CNV, and signs for CNV activity was independently analyzed for all imaging modalities. Results. AMD was diagnosed based on FP in 75 eyes. SDOCT and FA showed sensitivity (specificity) of 89% (76%) and 92% (82%), respectively. CNV was present on FA in 68 eyes. Sensitivity (specificity) was 78% (100%) for FP and 94% (98%) for SDOCT. CNV activity was detected by SDOCT or FA in 60 eyes with an agreement in 46 eyes. Sensitivity was 88% for SDOCT and 88% for FA. FP showed sensitivity of 38% and specificity of 98%. Conclusions. CNV lesions and activity may be missed by FP alone, but FP may help identifying drusen and pigmentary changes. SDOCT is highly sensitive for the detection of AMD, CNV, and CNV activity; however, it cannot fully replace FA. PMID:23762528

  8. 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

  9. 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

  10. Retinal pigment epithelial changes in chronic Vogt-Koyanagi-Harada disease: fundus autofluorescence and spectral domain optical coherence tomography findings

    PubMed Central

    Vasconcelos-Santos, Daniel V.; Sohn, Elliott H.; Sadda, Srinivas; Rao, Narsing A.

    2009-01-01

    Purpose To determine whether fundus autofluorescence (FAF) and spectral-domain optical coherence tomography (SD-OCT) imaging allows better assessment of RPE and outer retina (OR) in subjects with chronic VKH compared to examination and angiography alone. Methods Cross-sectional analysis of a series of seven consecutive patients with chronic VKH undergoing FAF and SD-OCT. Chronic VKH was defined as during >3 months. Color fundus photographs were correlated to FAF and SD-OCT images. The images were later correlated to fluorescein angiography (FA) and indocyanine green angiography (ICG-A). Results All patients had sunset glow fundus, which resulted in no apparent corresponding abnormality on FAF or SD-OCT. Lesions with decreased autofluorescence signal were observed in 11 eyes (85%), being associated with loss of the RPE and involvement of OR on SD-OCT. In 5 eyes (38%) some of these lesions were very subtle on clinical examination but easily detected by FAF. Lesions with increased autofluorescence signal were seen in 8 eyes (61.5%), showing variable involvement of the OR on SD-OCT and corresponding clinically to areas of RPE proliferation and cystoid macular edema. Conclusion Combined use of FAF and SD-OCT imaging allowed noninvasive delineation of RPE/OR changes in patients with chronic VKH, which were consistent with previous histopathological reports. Some of these changes were not apparent on clinical examination. PMID:20010321

  11. Clinical use and research applications of Heidelberg retinal angiography and spectral-domain optical coherence tomography - a review.

    PubMed

    Hassenstein, Andrea; Meyer, Carsten H

    2009-01-01

    Fluorescein angiography (FA) was discovered by Nowotny and Alvis in the 1960s of the 20th century and has evolved to become the 'Gold standard' for macular diagnostics. Scanning laser imaging technology achieved enhancement of contrast and resolution. The combined Heidelberg retina angiograph (HRA2) adds novel innovative features to established fundus cameras. The principle of confocal scanning laser imaging provides a high resolution of retinal and choroidal vasculature with low light exposure providing comfort and safety for the patient. Enhanced contrast, details and image sharpness image are generated using confocality. For the visualization of the choroid an indocyanine green angiography (ICGA) is the most suitable application. The main indications for ICGA are age-related macular degeneration, choroidal polypoidal vasculopathy and choroidal haemangiomas. Simultaneous digital FA and ICGA images with three-dimensional resolution offer improved diagnosis of retinal and choroidal pathologies. High-speed ICGA dynamic imaging can identify feeder vessels and retinal choroidal anastomoses, ensuring safer treatment of choroidal neovascularization. Autofluorescence imaging and fundus reflectance imaging with blue and infrared light offer new follow-up parameters for retinal diseases. Finally, the real-time optical coherence tomography provides a new level of accuracy for assessment of the angiographic and morphological correlation. The combination of various macular diagnostic tools, such as infrared, blue reflectance, fundus autofluorescence, FA, ICGA and also spectral domain optical coherence tomography, lead to a better understanding and improved knowledge of macular diseases. PMID:19338610

  12. Investigating the spectral characteristics of backscattering from heterogeneous spherical nuclei using broadband finite-difference time-domain simulations

    NASA Astrophysics Data System (ADS)

    Chao, Guo-Shan; Sung, Kung-Bin

    2010-01-01

    Reflectance spectra measured from epithelial tissue have been used to extract size distribution and refractive index of cell nuclei for noninvasive detection of precancerous changes. Despite many in vitro and in vivo experimental results, the underlying mechanism of sizing nuclei based on modeling nuclei as homogeneous spheres and fitting the measured data with Mie theory has not been fully explored. We describe the implementation of a three-dimensional finite-difference time-domain (FDTD) simulation tool using a Gaussian pulse as the light source to investigate the wavelength-dependent characteristics of backscattered light from a nuclear model consisting of a nucleolus and clumps of chromatin embedded in homogeneous nucleoplasm. The results show that small-sized heterogeneities within the nuclei generate about five times higher backscattering than homogeneous spheres. More interestingly, backscattering spectra from heterogeneous spherical nuclei show periodic oscillations similar to those from homogeneous spheres, leading to high accuracy of estimating the nuclear diameter by comparison with Mie theory. In addition to the application in light scattering spectroscopy, the reported FDTD method could be adapted to study the relations between measured spectral data and nuclear structures in other optical imaging and spectroscopic techniques for in vivo diagnosis.

  13. Investigating the spectral characteristics of backscattering from heterogeneous spheroidal nuclei using broadband finite-difference time-domain simulations

    NASA Astrophysics Data System (ADS)

    Chao, Guo-Shan; Sung, Kung-Bin

    2010-02-01

    Backscattered light spectra have been used to extract size distribution of cell nuclei in epithelial tissues for noninvasive detection of precancerous lesions. In existing experimental studies, size estimation is achieved by assuming nuclei as homogeneous spheres or spheroids and fitting the measured data with models based on Mie theory. However, the validity of simplifying nuclei as homogeneous spheres has not been thoroughly examined. In this study, we investigate the spectral characteristics of backscattering from models of spheroidal nuclei under plane wave illumination using three-dimensional finite-difference time-domain (FDTD) simulation. A modulated Gaussian pulse is used to obtain wavelength dependent scattering intensity with a single FDTD run. The simulated model of nuclei consists of a nucleolus and randomly distributed chromatin condensation in homogeneous cytoplasm and nucleoplasm. The results show that backscattering spectra from spheroidal nuclei have similar oscillating patterns to those from homogeneous spheres with the diameter equal to the projective length of the spheroidal nucleus along the propagation direction. The strength of backscattering is enhanced in heterogeneous spheroids as compared to homogeneous spheroids. The degree of which backscattering spectra of heterogeneous nuclei deviate from Mie theory is highly dependent on the distribution of chromatin/nucleolus but not sensitive to nucleolar size, refractive index fluctuation or chromatin density.

  14. 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.

  15. Axial resolution improvement in spectral domain optical coherence tomography using a depth-adaptive maximum-a-posterior framework

    NASA Astrophysics Data System (ADS)

    Boroomand, Ameneh; Tan, Bingyao; Wong, Alexander; Bizheva, Kostadinka

    2015-03-01

    The axial resolution of Spectral Domain Optical Coherence Tomography (SD-OCT) images degrades with scanning depth due to the limited number of pixels and the pixel size of the camera, any aberrations in the spectrometer optics and wavelength dependent scattering and absorption in the imaged object [1]. Here we propose a novel algorithm which compensates for the blurring effect of these factors of the depth-dependent axial Point Spread Function (PSF) in SDOCT images. The proposed method is based on a Maximum A Posteriori (MAP) reconstruction framework which takes advantage of a Stochastic Fully Connected Conditional Random Field (SFCRF) model. The aim is to compensate for the depth-dependent axial blur in SD-OCT images and simultaneously suppress the speckle noise which is inherent to all OCT images. Applying the proposed depth-dependent axial resolution enhancement technique to an OCT image of cucumber considerably improved the axial resolution of the image especially at higher imaging depths and allowed for better visualization of cellular membrane and nuclei. Comparing the result of our proposed method with the conventional Lucy-Richardson deconvolution algorithm clearly demonstrates the efficiency of our proposed technique in better visualization and preservation of fine details and structures in the imaged sample, as well as better speckle noise suppression. This illustrates the potential usefulness of our proposed technique as a suitable replacement for the hardware approaches which are often very costly and complicated.

  16. 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

  17. 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.

  18. 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). PMID:24977582

  19. GPU-accelerated non-uniform fast Fourier transform-based compressive sensing spectral domain optical coherence tomography

    PubMed Central

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

    2014-01-01

    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)×1000(lateral). PMID:24977582

  20. 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.

  1. Full-range spectral domain optical coherence tomography using fiber-based sample scanner as self-phase shifter

    NASA Astrophysics Data System (ADS)

    Min, Eun Jung; Shin, Jun Geun; Lee, Jae Hwi; Lee, Byeong Ha

    2012-06-01

    We propose full-range spectral domain optical coherence tomography equipped with a fiber-based sample scanner, which is used for sample scanning and phase shifting for full-range image at the same time. For a fiber-based sample scanner, since the fiber tip oscillates as a free standing cantilever in general, unintentional phase shift occurs inevitably. The unintentional phase shift was used for eliminating the bothersome complex conjugate ghost image of OCT. In addition, fiber was tilted a few degree to give proper phase shift. In this scheme, moreover, image can be obtained without any physical modification of the scanner. To realize this technique, we constructed the SD-OCT system and fabricated a magnetically actuated single-body lensed fiber scanner due to advantages of simple design, low operating voltage, cost-effectiveness and low insertion loss. The scanner was made of lensed fiber loaded with an iron-based bead and a solenoid which is placed perpendicular to the lensed fiber. When a sinusoidal current is applied into the solenoid, the lensed fiber oscillated due to magnetic force between the iron-based bead and the solenoid. With the suggested full range method, we obtained contrast enhanced full-range SD OCT images of pearl and tooth. This simple and effective method can be applied to any fiber-based scanner and it has great potential as a handheld probe/endoscopic probe in biomedical imaging field.

  2. Effect of Hydroxychloroquine on the Retinal Layers: A Quantitative Evaluation with Spectral-Domain Optical Coherence Tomography.

    PubMed

    Uslu, Hasim; Gurler, Bulent; Yildirim, Aydin; Tatar, Mehmet Gurkan; Aylin Kantarcı, Feride; Goker, Hasan; Pehlevan, Hatice Seval; Colak, Hatice Nur

    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

  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. Lateral resolution enhancement via imbricated spectral domain optical coherence tomography in a maximum-a-posterior reconstruction framework

    NASA Astrophysics Data System (ADS)

    Boroomand, A.; Shafiee, M. J.; Wong, A.; Bizheva, K.

    2015-03-01

    The lateral resolution of a Spectral Domain Optical Coherence Tomography (SD-OCT) image is limited by the focusing properties of the OCT imaging probe optics, the wavelength range which SD-OCT system operates at, spherical and chromatic aberrations induced by the imaging optics, the optical properties of the imaged object, and in the special case of in-vivo retinal imaging by the optics of the eye. This limitation often results in challenges with resolving fine details and structures of the imaged sample outside of the Depth-Of-Focus (DOF) range. We propose a novel technique for generating Laterally Resolved OCT (LR-OCT) images using OCT measurements acquired with intentional imbrications. The proposed, novel method is based on a Maximum A Posteriori (MAP) reconstruction framework which takes advantage of a Stochastic Fully Connected Conditional Random Field (SFCRF) model to compensate for the artifacts and noise when reconstructing a LR-OCT image from imbricated OCT measurement. The proposed lateral resolution enhancement method was tested on synthetic OCT measurement as well as on a human cornea SDOCT image to evaluate the usefulness of the proposed approach in lateral resolution enhancement. Experimental results show that applying this method to OCT images, noticeably improves the sharpness of morphological features in the OCT image and in lateral direction, thus demonstrating better delineation of fine dot shape details in the synthetic OCT test, as well as better delineation of the keratocyte cells in the human corneal OCT test image.

  5. GPU accelerated real-time multi-functional spectral-domain optical coherence tomography system at 1300 nm.

    PubMed

    Wang, Yan; Oh, Christian M; Oliveira, Michael C; Islam, M Shahidul; Ortega, Arthur; Park, B Hyle

    2012-07-01

    We present a GPU accelerated multi-functional spectral domain optical coherence tomography system at 1300 nm. The system is capable of real-time processing and display of every intensity image, comprised of 512 pixels by 2048 A-lines acquired at 20 frames per second. The update rate for all four images with size of 512 pixels by 2048 A-lines simultaneously (intensity, phase retardation, flow and en face view) is approximately 10 frames per second. Additionally, we report for the first time the characterization of phase retardation and diattenuation by a sample comprised of a stacked set of polarizing film and wave plate. The calculated optic axis orientation, phase retardation and diattenuation match well with expected values. The speed of each facet of the multi-functional OCT CPU-GPU hybrid acquisition system, intensity, phase retardation, and flow, were separately demonstrated by imaging a horseshoe crab lateral compound eye, a non-uniformly heated chicken muscle, and a microfluidic device. A mouse brain with thin skull preparation was imaged in vivo and demonstrated the capability of the system for live multi-functional OCT visualization.

  6. 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.

  7. 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.

  8. GRIN lens rod based probe for endoscopic spectral domain optical coherence tomography with fast dynamic focus tracking

    NASA Astrophysics Data System (ADS)

    Xie, Tuqiang; Guo, Shuguang; Chen, Zhongping; Mukai, David; Brenner, Matthew

    2006-04-01

    In this manuscript, a GRIN (gradient index) lens rod based probe for endoscopic spectral domain optical coherence tomography (OCT) with dynamic focus tracking is presented. Current endoscopic OCT systems have a fixed focal plane or working distance. In contrast, the focus of this endoscopic OCT probe can dynamically be adjusted at a high speed (500 mm/s) without changing reference arm length to obtain high quality OCT images for contact or non-contact tissue applications, or for areas of difficult access for probes. The dynamic focusing range of the probe can be from 0 to 7.5 mm without moving the probe itself. The imaging depth is 2.8 mm and the lateral scanning range is up to 2.7 mm or 4.5 mm (determined by the diameter of different GRIN lens rods). Three dimensional imaging can be performed using this system over an area of tissue corresponding to the GRIN lens surface. The experimental results demonstrate that this GRIN lens rod based OCT system can perform a high quality non-contact in vivo imaging. This rigid OCT probe is solid and can be adapted to safely access internal organs, to perform front or side view imaging with an imaging speed of 8 frames per second, with all moving parts proximal to the GRIN lens, and has great potential for use in extremely compact OCT endoscopes for in vivo imaging in both biological research and clinical applications.

  9. Infrared autofluorescence, short-wave autofluorescence and spectral-domain optical coherence tomography of optic disk melanocytomas

    PubMed Central

    Zhang, Peng; Hui, Yan-Nian; Xu, Wen-Qin; Zhang, Zi-Feng; Wang, Hai-Yan; Sun, Dong-Jie; Wang, Yu-Sheng

    2016-01-01

    AIM To investigate the findings of infrared fundus autofluorescence (IR-AF) and spectral-domain optical coherence tomography (SD-OCT) in eyes with optic disc melanocytoma (ODM). METHODS IR-AF findings and those of other ophthalmologic imaging examinations, including short-wave autofluorescence (SW-AF), fluorescein angiography (FA), fundus color photography, and SD-OCT of 8 eyes of 8 consecutive cases with ODM were assessed. RESULTS The ODMs in all cases (100%) presented similar IR-AF, SW-AF, and FA findings. On IR-AF images, ODMs showed outstanding hyper-AF with well-defined outline. On SW-AF images, the area of ODMs presented as hypo-AF. FA images revealed the leaking retinal telangiectasia on the surface of the ODMs. On SD-OCT images in 8 cases (100%), the ODMs were sloped with highly reflective surface, which were disorganized retina and optic nerve layers. In 7 cases (87.5%), peripapillary choroids were involved. The melanocytomas of 8 cases (100%) presented as optically empty spaces. Vitreous seeds were found in one case (12.5%). CONCLUSION IR-AF imaging may provide a new modality to evaluate the pathologic features of ODMs, and together with SW-AF imaging, offers a new tool to study biological characteristics associated with ODMs. SD-OCT is a valuable tool in delimitating the tumor extension and providing morphological information about the adjacent retinal tissue. PMID:27275427

  10. 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).

  11. Analysis of the Outer Retina Reconstructed by High-Resolution, Three-Dimensional Spectral Domain Optical Coherence Tomography

    PubMed Central

    Kaluzny, Jakub J.; Wojtkowski, Maciej; Sikorski, Bartosz L.; Szkulmowski, Maciej; Szkulmowska, Anna; Bajraszewski, Tomasz; Fujimoto, James G.; Duker, Jay S.; Schuman, Joel S.; Kowalczyk, Andrzej

    2009-01-01

    Background and Objective A retrospective cross-sectional study was conducted to demonstrate an analysis of an outer retinal layer reconstructed by the three-dimensional and high-speed spectral domain optical coherence tomography (SD-OCT) instrument. Patients and Methods New measurement protocols for SD-OCT and methods of analysis and visualization of the individual segmented retinal layer reconstructed by SD-OCT were proposed. Three contour maps representing mutual distances between the basal part of the retinal pigment epithelium, the junction between the inner and outer segments of photoreceptors, and a reference contour representing the shape of a healthy retina were introduced. Results The analysis of the outer retina was performed on pathological eyes. Three cases of central serous chorioretinopathy, age-related macular degeneration, and acute zonal occult outer retinopathy are demonstrated. Conclusion Three contour maps reconstructed for clinical cases demonstrate high variability of observed patterns depending on analyzed pathology. The authors believe this can help to present OCT data simultaneously in a more comprehensive and convenient way to assist in everyday clinical diagnosis. PMID:19320297

  12. 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.

  13. 3D stochastic inversion of magnetic data

    NASA Astrophysics Data System (ADS)

    Shamsipour, Pejman; Chouteau, Michel; Marcotte, Denis

    2011-04-01

    A stochastic inversion method based on a geostatistical approach is presented to recover 3D susceptibility models from magnetic data. The aim of applying geostatistics is to provide quantitative descriptions of natural variables distributed in space or in time and space. Cokriging, the method which is used in this paper, is a method of estimation that minimizes the theoretical estimation error variance by using auto- and cross-correlations of several variables. The covariances for total field, susceptibility and total field-susceptibility are estimated using the observed data. Then, the susceptibility is cokriged or simulated as the primary variable. In order to avoid the natural tendency of the estimated structure to lay near the surface, depth weighting is included in the cokriging system. The algorithm assumes there is no remanent magnetization and the observation data represent only induced magnetization effects. The method is applied on different synthetic models to demonstrate its suitability for 3D inversion of magnetic data. A case study using ground measurements of total field at the Perseverance mine (Quebec, Canada) is presented. The recovered 3D susceptibility model provides beneficial information that can be used to analyze the geology of massive sulfide for the domain under study.

  14. 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…

  15. SNL3dFace

    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 featuresmore » 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.« less

  16. 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.

  17. 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…

  18. 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

  19. 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

    2015-01-01

    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 analyse

  20. 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

  1. DSI3D-RCS: Theory manual

    SciTech Connect

    Madsen, N.; Steich, D.; Cook, G.; Eme, B.

    1995-03-16

    The DSI3D-RCS code is designed to numerically evaluate radar cross sections on complex objects by solving Maxwell`s curl equations in the time-domain and in three space dimensions. The code has been designed to run on the new parallel processing computers as well as on conventional serial computers. The DSI3D-RCS code is unique for the following reasons: Allows the use of unstructured non-orthogonal grids, allows a variety of cell or element types, reduces to be the Finite Difference Time Domain (FDTD) method when orthogonal grids are used, preserves charge or divergence locally (and globally), is conditionally stable, is non-dissipative, is accurate for non-orthogonal grids. This method is derived using a Discrete Surface Integration (DSI) technique. As formulated, the DSI technique can be used with essentially arbitrary unstructured grids composed of convex polyhedral cells. This implementation of the DSI algorithm allows the use of unstructured grids that are composed of combinations of non-orthogonal hexahedrons, tetrahedrons, triangular prisms and pyramids. This algorithm reduces to the conventional FDTD method when applied on a structured orthogonal hexahedral grid.

  2. TACO3D. 3-D Finite Element Heat Transfer Code

    SciTech Connect

    Mason, W.E.

    1992-03-04

    TACO3D is a three-dimensional, finite-element program for heat transfer analysis. An extension of the two-dimensional TACO program, it can perform linear and nonlinear analyses and can be used to solve either transient or steady-state problems. The program accepts time-dependent or temperature-dependent material properties, and materials may be isotropic or orthotropic. A variety of time-dependent and temperature-dependent boundary conditions and loadings are available including temperature, flux, convection, and radiation boundary conditions and internal heat generation. Additional specialized features treat enclosure radiation, bulk nodes, and master/slave internal surface conditions (e.g., contact resistance). Data input via a free-field format is provided. A user subprogram feature allows for any type of functional representation of any independent variable. A profile (bandwidth) minimization option is available. The code is limited to implicit time integration for transient solutions. TACO3D has no general mesh generation capability. Rows of evenly-spaced nodes and rows of sequential elements may be generated, but the program relies on separate mesh generators for complex zoning. TACO3D does not have the ability to calculate view factors internally. Graphical representation of data in the form of time history and spatial plots is provided through links to the POSTACO and GRAPE postprocessor codes.

  3. Functional imaging of hemodynamic stimulus response in the rat retina with ultrahigh-speed spectral / Fourier domain OCT

    NASA Astrophysics Data System (ADS)

    Choi, WooJhon; Baumann, Bernhard; Clermont, Allen C.; Feener, Edward P.; Boas, David A.; Fujimoto, James G.

    2013-03-01

    Measuring retinal hemodynamics in response to flicker stimulus is important for investigating pathophysiology in small animal models of diabetic retinopathy, because a reduction in the hyperemic response is thought to be one of the earliest changes in diabetic retinopathy. In this study, we investigated functional imaging of retinal hemodynamics in response to flicker stimulus in the rat retina using an ultrahigh speed spectral / Fourier domain OCT system at 840nm with an axial scan rate of 244kHz. At 244kHz the nominal axial velocity range that could be measured without phase wrapping was +/-37.7mm/s. Pulsatile total retinal arterial blood flow as a function of time was measured using an en face Doppler approach where a 200μm × 200μm area centered at the central retinal artery was repeatedly raster scanned at a volume acquisition rate of 55Hz. Three-dimensional capillary imaging was performed using speckle decorrelation which has minimal angle dependency compared to other angiography techniques based on OCT phase information. During OCT imaging, a flicker stimulus could be applied to the retina synchronously by inserting a dichroic mirror in the imaging interface. An acute transient increase in total retinal blood flow could be detected. At the capillary level, an increase in the degree of speckle decorrelation in capillary OCT angiography images could also be observed, which indicates an increase in the velocity of blood at the capillary level. This method promises to be useful for the investigation of small animal models of ocular diseases.

  4. Peripapillary Retinal Nerve Fiber Layer Assessment of Spectral Domain Optical Coherence Tomography and Scanning Laser Polarimetry to Diagnose Preperimetric Glaucoma

    PubMed Central

    Rao, Harsha L.; Yadav, Ravi K.; Addepalli, Uday K.; Chaudhary, Shashikant; Senthil, Sirisha; Choudhari, Nikhil S.; Garudadri, Chandra S.

    2014-01-01

    Purpose To compare the abilities of peripapillary retinal nerve fiber layer (RNFL) parameters of spectral domain optical coherence tomograph (SDOCT) and scanning laser polarimeter (GDx enhanced corneal compensation; ECC) in detecting preperimetric glaucoma. Methods In a cross-sectional study, 35 preperimetric glaucoma eyes (32 subjects) and 94 control eyes (74 subjects) underwent digital optic disc photography and RNFL imaging with SDOCT and GDx ECC. Ability of RNFL parameters of SDOCT and GDx ECC to discriminate preperimetric glaucoma eyes from control eyes was compared using area under receiver operating characteristic curves (AUC), sensitivities at fixed specificities and likelihood ratios (LR). Results AUC of the global average RNFL thickness of SDOCT (0.786) was significantly greater (p<0.001) than that of GDx ECC (0.627). Sensitivities at 95% specificity of the corresponding parameters were 20% and 8.6% respectively. AUCs of the inferior, superior and temporal quadrant RNFL thickness parameters of SDOCT were also significantly (p<0.05) greater than the respective RNFL parameters of GDx ECC. LRs of outside normal limits category of SDOCT parameters ranged between 3.3 and 4.0 while the same of GDx ECC parameters ranged between 1.2 and 2.1. LRs of within normal limits category of SDOCT parameters ranged between 0.4 and 0.7 while the same of GDx ECC parameters ranged between 0.7 and 1.0. Conclusions Abilities of the RNFL parameters of SDOCT and GDx ECC to diagnose preperimetric glaucoma were only moderate. Diagnostic abilities of the RNFL parameters of SDOCT were significantly better than that of GDx ECC in preperimetric glaucoma. PMID:25279801

  5. Factors Affecting the Ability of the Spectral Domain Optical Coherence Tomograph to Detect Photographic Retinal Nerve Fiber Layer Defects

    PubMed Central

    Rao, Harsha L.; Addepalli, Uday K.; Yadav, Ravi K.; Choudhari, Nikhil S.; Senthil, Sirisha; Garudadri, Chandra S.

    2014-01-01

    Purpose To evaluate the ability of normative database classification (color-coded maps) of spectral domain optical coherence tomograph (SDOCT) in detecting wedge shaped retinal nerve fiber layer (RNFL) defects identified on photographs and the factors affecting the ability of SDOCT in detecting these RNFL defects. Methods In a cross-sectional study, 238 eyes (476 RNFL quadrants) of 172 normal subjects and 85 eyes (103 RNFL quadrants with wedge shaped RNFL defects) of 66 glaucoma patients underwent RNFL imaging with SDOCT. Logistic regression models were used to evaluate the factors associated with false positive and false negative RNFL classifications of the color-coded maps of SDOCT. Results False positive classification at a p value of <5% was seen in 108 of 476 quadrants (22.8%). False negative classification at a p value of <5% was seen in 16 of 103 quadrants (15.5%). Of the 103 quadrants with RNFL defects, 64 showed a corresponding VF defect in the opposite hemisphere and 39 were preperimetric. Higher signal strength index (SSI) of the scan was less likely to have a false positive classification (odds ratio: 0.97, p = 0.01). Presence of an associated visual field defect (odds ratio: 0.17, p = 0.01) and inferior quadrant RNFL defects as compared to superior (odds ratio: 0.24, p = 0.04) were less likely to show false negative classifications. Conclusions Scans with lower signal strengths were more likely to show false positive RNFL classifications, and preperimetric and superior quadrant RNFL defects were more likely to show false negative classifications on color-coded maps of SDOCT. PMID:25536188

  6. Agreement of angle closure assessments between gonioscopy, anterior segment optical coherence tomography and spectral domain optical coherence tomography

    PubMed Central

    Tay, Elton Lik Tong; Yong, Vernon Khet Yau; Lim, Boon Ang; Sia, Stelson; Wong, Elizabeth Poh Ying; Yip, Leonard Wei Leon

    2015-01-01

    AIM To determine angle closure agreements between gonioscopy and anterior segment optical coherence tomography (AS-OCT), as well as gonioscopy and spectral domain OCT (SD-OCT). A secondary objective was to quantify inter-observer agreements of AS-OCT and SD-OCT assessments. METHODS Seventeen consecutive subjects (33 eyes) were recruited from the study hospital's Glaucoma clinic. Gonioscopy was performed by a glaucomatologist masked to OCT results. OCT images were read independently by 2 other glaucomatologists masked to gonioscopy findings as well as each other's analyses of OCT images. RESULTS Totally 84.8% and 45.5% of scleral spurs were visualized in AS-OCT and SD-OCT images respectively (P<0.01). The agreement for angle closure between AS-OCT and gonioscopy was fair at k=0.31 (95% confidence interval, CI: 0.03-0.59) and k=0.35 (95% CI: 0.07-0.63) for reader 1 and 2 respectively. The agreement for angle closure between SD-OCT and gonioscopy was fair at k=0.21 (95% CI: 0.07-0.49) and slight at k=0.17 (95% CI: 0.08-0.42) for reader 1 and 2 respectively. The inter-reader agreement for angle closure in AS-OCT images was moderate at 0.51 (95% CI: 0.13-0.88). The inter-reader agreement for angle closure in SD-OCT images was slight at 0.18 (95% CI: 0.08-0.45). CONCLUSION Significant proportion of scleral spurs were not visualised with SD-OCT imaging resulting in weaker inter-reader agreements. Identifying other angle landmarks in SD-OCT images will allow more consistent angle closure assessments. Gonioscopy and OCT imaging do not always agree in angle closure assessments but have their own advantages, and should be used together and not exclusively. PMID:25938053

  7. Safety and efficacy of oral fluorescein angiography in detecting macular edema in comparison with spectral domain optical coherence tomography

    PubMed Central

    Barteselli, Giulio; Chhablani, Jay; Lee, Su Na; Wang, Haiyan; Emam, Sharif El; Kozak, Igor; Cheng, Lingyun; Bartsch, Dirk-Uwe; Azen, Stanley; Freeman, William R.

    2013-01-01

    Purpose To evaluate the safety of oral fluorescein angiography (FA) and to compare its efficacy in detection of macular edema (ME) with spectral-domain optical coherence tomography (SD-OCT). Methods Results of imaging studies for 1,928 eyes of 1,019 patients who had simultaneously undergone both oral FA and SD-OCT by a confocal laser ophthalmoscope (cSLO) were reviewed. Sensitivity in detecting ME, discrepancy rate, and “kappa” agreement were determined for both the techniques, and with eyes stratified by disease diagnosis. Results No allergic reactions occurred after oral FA. Mild gastric discomfort was noted in <1% of the patients. 1,840 eyes (95.4%) showed concordance between the two techniques and “kappa” agreement was 90.3%. For ME, oral FA showed an overall sensitivity of 0.97 and SD-OCT of 0.91. Equivalent sensitivity was found in cases of wet age-related macular degeneration (0.99). Oral FA was more sensitive than SD-OCT in cases of retinovascular diseases. SD-OCT showed higher sensitivity in cases of macular holes. Detection of ME by SD-OCT was significantly higher in cases of intense leakage on oral FA (p<0.001). Conclusions Oral FA proved to be a safe and adequate technique to evaluate ME. It is more sensitive than SD-OCT in detection of ME in cases of retinovascular diseases, but can fail to detect ME in cases of macular holes. A non-invasive examination with simultaneous oral FA and SD-OCT may be considered to obtain a comprehensive evaluation of the presence of ME from different pathologies. PMID:23584697

  8. Semi-automated 2D Bruch's membrane shape analysis in papilledema using spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Wang, Jui-Kai; Sibony, Patrick A.; Kardon, Randy H.; Kupersmith, Mark J.; Garvin, Mona K.

    2015-03-01

    Recent studies have shown that the Bruch's membrane (BM) and retinal pigment epithelium (RPE), visualized on spectral-domain optical coherence tomography (SD-OCT), is deformed anteriorly towards the vitreous in patients with intracranial hypertension and papilledema. The BM/RPE shape has been quantified using a statistical-shape-model approach; however, to date, the approach has involved the tedious and time-consuming manual placement of landmarks and correspondingly, only the shape (and shape changes) of a limited number of patients has been studied. In this work, we first present a semi-automated approach for the extraction of 20 landmarks along the BM from an optic-nerve-head (ONH) centered OCT slice from each patient. In the approach, after the manual placement of the two Bruch's membrane opening (BMO) points, the remaining 18 landmarks are automatically determined using a graph-based segmentation approach. We apply the approach to the OCT scans of 116 patients (at baseline) enrolled in the Idiopathic Intracranial Hypertension Treatment Trial and generate a statistical shape model using principal components analysis. Using the resulting shape model, the coefficient (shape measure) corresponding to the second principal component (eigenvector) for each set of landmarks indicates the degree of the BM/RPE is oriented away from the vitreous. Using a subset of 20 patients, we compare the shape measure computed using this semi-automated approach with the resulting shape measure when (1) all landmarks are specified manually (Experiment I); and (2) a different expert specifies the two BMO points (Experiment II). In each case, a correlation coefficient >= 0.99 is obtained.

  9. A Pilot Study on Feasibility and Effectiveness of Intraoperative Spectral-Domain Optical Coherence Tomography in Glaucoma Procedures

    PubMed Central

    Kumar, Rajesh S.; Jariwala, Manan U.; V, Sathidevi A.; Venugopal, Jayasree P.; Puttaiah, Narendra K.; Balu, Ramgopal; Rao A. S, Dhanaraj; Shetty, Rohit

    2015-01-01

    Purpose To demonstrate the use of a spectral-domain optical coherence tomography (SDOCT) integrated surgical microscope in glaucoma surgery. Methods An SDOCT system was used to interface directly with an ophthalmic surgical microscope, to allow real-time intraoperative SDOCT (iOCT) imaging during glaucoma procedures like phaco-trabeculectomy, Ahmed glaucoma valve (AGV) implantation, gonio-synechiolysis, and bleb needling. The various surgical steps during glaucoma surgeries where iOCT can be of potential help in guiding the surgeon were recorded. Results High-resolution, cross-sectional images of the relevant structures were achieved with the iOCT system in all procedures. The surgeon could determine the depth of the scleral dissection, the intrastomal bed, the path of the AGV tube in the eye, the release of peripheral anterior synechiae and the efficacy of needling with respect to breakage of loculations; most of these are technically ‘blind' procedures, where the outcomes are determined postoperatively. Metallic instruments cast a shadow on tissues below, thereby restricting the use of the device in its current state. Conclusions The iOCT system provided high quality, intraoperative, real-time imaging, which could possibly improve the safety and efficacy of the surgical procedures in glaucoma. Further studies and modifications to the iOCT are required to better understand and increase the uptake of this technology in daily practice. Translational Relevance The iOCT, with further advancements in its technology, could potentially provide the surgeon both quantitative and qualitative, real-time depth and tissue proximity details, thus improving the safety and accuracy of glaucoma surgery. PMID:25767745

  10. Subfoveal fluid in healthy full term newborns observed by hand-held Spectral Domain Optical Coherence Tomography

    PubMed Central

    Cabrera, Michelle T; Maldonado, Ramiro S; Toth, Cynthia A; O’Connell, Rachelle V; Chen, Bei Bei; Chiu, Stephanie J; Farsiu, Sina; Wallace, David K; Stinnett, Sandra S; Panayotti, Gabriela M Maradiaga; Swamy, Geeta K; Freedman, Sharon F

    2011-01-01

    Purpose To report retinal findings for healthy newborn infants imaged with hand held Spectral Domain Optical Coherence Tomography (SD-OCT). Design Prospective observational case series. Methods Thirty-nine full term newborn infants had dilated retinal examinations by indirect ophthalmoscopy and retinal imaging by handheld SD-OCT, without sedation, at the Duke Birthing Center. Results Of the 39 infants imaged, 44% (17/39) were male. Race/ethnicity composition was 56% white, 38% black, 3% Asian, and 3% Hispanic. Median gestational age was 39 weeks (range 36 to 41). Six of the 39 infants (15%) had bilateral subfoveal fluid on SD-OCT not seen by indirect ophthalmoscopy. Eight infants (21%) had retinal hemorrhages noted on dilated retinal examination, 1 of which had subretinal fluid on SD-OCT. Subretinal fluid was noted on follow up examination to have resolved on SD-OCT 1 to 4 months later. Infants with bilateral subretinal fluid had an older gestational age compared to infants without subretinal fluid (median 40.4 vs. 39.1 weeks, respectively, P=0.03) and were more likely to have had mothers with diabetes (2/6 vs. 0/33, respectively, P=0.02). Vaginal versus C-section delivery was not significantly different between the two groups. Conclusions Some healthy full term infants have bilateral subfoveal fluid not obvious on dilated retinal examination. This fluid resolves within several months. The visual significance of this finding is unknown, but clinicians should be aware it is common when evaluating newborn infants for retinal pathology using SD-OCT. PMID:21925640

  11. Assessment of estimated retinal atrophy progression in Stargardt macular dystrophy using spectral-domain optical coherence tomography

    PubMed Central

    Strauss, Rupert W; Muñoz, Beatriz; Wolfson, Yulia; Sophie, Raafay; Fletcher, Emily; Bittencourt, Millena G; Scholl, Hendrik P N

    2016-01-01

    Aims To estimate disease progression based on analysis of macular volume measured by spectral-domain optical coherence tomography (SD-OCT) in patients affected by Stargardt macular dystrophy (STGD1) and to evaluate the influence of software errors on these measurements. Methods 58 eyes of 29 STGD1 patients were included. Numbers and types of algorithm errors were recorded and manually corrected. In a subgroup of 36 eyes of 18 patients with at least two examinations over time, total macular volume (TMV) and volumes of all nine Early Treatment of Diabetic Retinopathy Study (ETDRS) subfields were obtained. Random effects models were used to estimate the rate of change per year for the population, and empirical Bayes slopes were used to estimate yearly decline in TMV for individual eyes. Results 6958 single B-scans from 190 macular cube scans were analysed. 2360 (33.9%) showed algorithm errors. Mean observation period for follow-up data was 15 months (range 3–40). The median (IQR) change in TMV using the empirical Bayes estimates for the individual eyes was −0.103 (−0.145, −0.059) mm3 per year. The mean (±SD) TMV was 6.321±1.000 mm3 at baseline, and rate of decline was −0.118 mm3 per year (p=0.003). Yearly mean volume change was −0.004 mm3 in the central subfield (mean baseline=0.128 mm3), −0.032 mm3 in the inner (mean baseline=1.484 mm3) and −0.079 mm3 in the outer ETDRS subfields (mean baseline=5.206 mm3). Conclusions SD-OCT measurements allow monitoring the decline in retinal volume in STGD1; however, they require significant manual correction of software errors. PMID:26568636

  12. Diurnal Choroidal Thickness Changes in Normal Eyes of Turkish People Measured by Spectral Domain Optical Coherence Tomography

    PubMed Central

    Osmanbasoglu, Ozen Ayrancı; Ozkaya, Abdullah; Ozpınar, Yavuz; Yazici, Ahmet Taylan; Demirok, Ahmet

    2013-01-01

    Purpose. To analyse the diurnal variation of central choroidal thickness (CCT) in healthy emetropic patients during working hours. Methods. Fifty healthy young emmetrpic volunteers were included in this study. CCT was measured at 9 AM and 4 PM with spectral domain optical coherence tomography (Spectralis, Heidelberg Engineering) with enhanced depth imaging. Diurnal variation of CCT, the correlation between rigth and left eyes and the demographic factors affecting this variation were assessed. Findings. The mean CCT at 9 AM and 4 PM was 308.7 ± 64.5 μm and 308.7 ± 62 μm, respectively, with a mean diurnal amplitude of −0.03 ± 14.7 μm, ranging between −55 μm and 47 μm, the difference was statistically insignificant (P: 0.9). There were positive correlations between right and left eyes among CCT measurements at 9 AM, 4 PM and the mean amplitude of diurnal change (r: 0.65, P < 0.01; r: 0.60, P < 0.01; r: 0.45, P: 0.00, resp.). There was a statistically significant negative correlation between the magnitude of diurnal change and age (r: −0.27, P: 0.01). Conclusion. Although the mean CCT in the all group does not show significant variation during working hours, the pattern of diurnal variation may vary from person to person according to age, and there is a great harmony between the two eyes. PMID:23589769

  13. SOLSPEC investigation on board the International Space Station: The Absolute Solar Spectral Irradiance in the Infrared Domain

    NASA Astrophysics Data System (ADS)

    Thuillier, Gérard; Harder, Jerry; Shapiro, Alexander; Woods, Thomas; Perrin, Jean-Marie; Snow, Marty; Sukhodolov, Timofei; Schmutz, Werner

    2015-04-01

    Onboard the SOLAR payload of the International Space Station (ISS), the SOLSPEC spectrometer measures the solar spectral irradiance (SSI) from 16 to 2900 nm. This instrument uses lamps to monitor its behavior in orbit. In particular, it employs two tungsten ribbon lamps in the IR domain (1000-2900 nm). Initially, the infrared absolute irradiance scale was determined from the preflight laboratory calibration coefficients and the in-flight measurements gathered at first light in April 2008. Subsequent publications suggest a systematic discrepancy between SOLAR-ISS measurements and the ATLAS 3 spectrum obtained from SOLSPEC observations onboard the shuttle-ATLAS missions with the discrepancy reaching 10 % at 1800 nm. We show that such a discrepancy has strong implications for the Total Solar Irradiance (TSI) and the brightness temperature of the lower solar photosphere. Furthermore, comparisons with independent spectra either obtained on ground and in space will be also shown and commented. The origin of the ATLAS 3 to SOLSPEC differences have been extensively analyzed; the onboard lamp and solar data time series indicates that the IR spectrometer did not reach a permanent regime until after several months of operation. The solar measurements at first light and in permanent regime show a difference, which provides an effective wavelength dependent correction factor for the first light spectrum. The SOLSPEC-ISS spectrum obtained in this permanent regime is consistent with the ATLAS 3 spectrum within their combined uncertainties and will be identified in the literature as SOLAR 2rev. We present analysis of this SOLAR 2rev spectrum in terms of its contribution to TSI, the lower photospheric temperature, and comparisons with independently measured IR spectra from ground-based and on-orbit platforms.

  14. 3D electron microscopy of biological nanomachines: principles and applications.

    PubMed

    Sorzano, C O S; Jonic, S; Cottevieille, M; Larquet, E; Boisset, N; Marco, S

    2007-11-01

    Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.

  15. S3D: An interactive surface grid generation tool

    NASA Technical Reports Server (NTRS)

    Luh, Raymond Ching-Chung; Pierce, Lawrence E.; Yip, David

    1992-01-01

    S3D, an interactive software tool for surface grid generation, is described. S3D provides the means with which a geometry definition based either on a discretized curve set or a rectangular set can be quickly processed towards the generation of a surface grid for computational fluid dynamics (CFD) applications. This is made possible as a result of implementing commonly encountered surface gridding tasks in an environment with a highly efficient and user friendly graphical interface. Some of the more advanced features of S3D include surface-surface intersections, optimized surface domain decomposition and recomposition, and automated propagation of edge distributions to surrounding grids.

  16. Forensic 3D scene reconstruction

    NASA Astrophysics Data System (ADS)

    Little, Charles Q.; Small, Daniel E.; Peters, Ralph R.; Rigdon, J. B.

    2000-05-01

    Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in