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Sample records for quantitative tomography simulations

  1. Concluding Report: Quantitative Tomography Simulations and Reconstruction Algorithms

    SciTech Connect

    Aufderheide, M B; Martz, H E; Slone, D M; Jackson, J A; Schach von Wittenau, A E; Goodman, D M; Logan, C M; Hall, J M

    2002-02-01

    In this report we describe the original goals and final achievements of this Laboratory Directed Research and Development project. The Quantitative was Tomography Simulations and Reconstruction Algorithms project (99-ERD-015) funded as a multi-directorate, three-year effort to advance the state of the art in radiographic simulation and tomographic reconstruction by improving simulation and including this simulation in the tomographic reconstruction process. Goals were to improve the accuracy of radiographic simulation, and to couple advanced radiographic simulation tools with a robust, many-variable optimization algorithm. In this project, we were able to demonstrate accuracy in X-Ray simulation at the 2% level, which is an improvement of roughly a factor of 5 in accuracy, and we have successfully coupled our simulation tools with the CCG (Constrained Conjugate Gradient) optimization algorithm, allowing reconstructions that include spectral effects and blurring in the reconstructions. Another result of the project was the assembly of a low-scatter X-Ray imaging facility for use in nondestructive evaluation applications. We conclude with a discussion of future work.

  2. Simulation-based evaluation of the resolution and quantitative accuracy of temperature-modulated fluorescence tomography

    PubMed Central

    Lin, Yuting; Nouizi, Farouk; Kwong, Tiffany C.; Gulsen, Gultekin

    2016-01-01

    Conventional fluorescence tomography (FT) can recover the distribution of fluorescent agents within a highly scattering medium. However, poor spatial resolution remains its foremost limitation. Previously, we introduced a new fluorescence imaging technique termed “temperature-modulated fluorescence tomography” (TM-FT), which provides high-resolution images of fluorophore distribution. TM-FT is a multimodality technique that combines fluorescence imaging with focused ultrasound to locate thermo-sensitive fluorescence probes using a priori spatial information to drastically improve the resolution of conventional FT. In this paper, we present an extensive simulation study to evaluate the performance of the TM-FT technique on complex phantoms with multiple fluorescent targets of various sizes located at different depths. In addition, the performance of the TM-FT is tested in the presence of background fluorescence. The results obtained using our new method are systematically compared with those obtained with the conventional FT. Overall, TM-FT provides higher resolution and superior quantitative accuracy, making it an ideal candidate for in vivo preclinical and clinical imaging. For example, a 4 mm diameter inclusion positioned in the middle of a synthetic slab geometry phantom (D:40 mm × W :100 mm) is recovered as an elongated object in the conventional FT (x = 4.5 mm; y = 10.4 mm), while TM-FT recovers it successfully in both directions (x = 3.8 mm; y = 4.6 mm). As a result, the quantitative accuracy of the TM-FT is superior because it recovers the concentration of the agent with a 22% error, which is in contrast with the 83% error of the conventional FT. PMID:26368884

  3. Quantitative photoacoustic tomography

    PubMed Central

    Yuan, Zhen; Jiang, Huabei

    2009-01-01

    In this paper, several algorithms that allow for quantitative photoacoustic reconstruction of tissue optical, acoustic and physiological properties are described in a finite-element method based framework. These quantitative reconstruction algorithms are compared, and the merits and limitations associated with these methods are discussed. In addition, a multispectral approach is presented for concurrent reconstructions of multiple parameters including deoxyhaemoglobin, oxyhaemoglobin and water concentrations as well as acoustic speed. Simulation and in vivo experiments are used to demonstrate the effectiveness of the reconstruction algorithms presented. PMID:19581254

  4. Quantitative assessment of photoacoustic tomography systems integrating clinical ultrasound transducers using novel tissue-simulating phantoms

    NASA Astrophysics Data System (ADS)

    Vogt, William C.; Jia, Congxian; Wear, Keith A.; Garra, Brian S.; Pfefer, Joshua

    2015-03-01

    Photoacoustic Tomography (PAT) systems based on commercial ultrasound instruments have the benefit of dualmodality imaging, which increases their appeal from a clinical standpoint. However, factors that influence PAT system performance have not been thoroughly investigated and standardized test methods have not been established for image quality evaluation. To address these issues we have adapted phantom-based approaches from ultrasound imaging standards and implemented them to assess a PAT system developed for vascular imaging. Our system comprises a tunable near-infrared pulsed laser and a commercial ultrasound imaging system, including four interchangeable linear array clinical ultrasound transducers with varying center frequencies, acoustic bandwidths and geometries. Phantoms consisted of a customized polyvinyl chloride (PVC) plastisol gel that simulates both optical and acoustic properties of breast tissue. One phantom incorporates a sub-resolution filament array suitable for bimodal ultrasound-photoacoustic imaging, while another contains an array of hemoglobin-filled cylindrical inclusions at various depths. Key performance characteristics were evaluated, including spatial resolution, signal uniformity, contrast, and penetration depth. These characteristics were evaluated at 750 nm at radiant exposures below ANSI safety limits. Effects of transducer properties on imaging performance were evaluated. Axial and lateral resolution ranged from 0.27-0.83 mm and 0.28-1.8 mm, respectively, and penetration depths from 1.9-4.2 cm were achieved. These results demonstrate variation in PAT system performance based on clinical transducer selection, as well as the utility of realistic phantom-based test methods in performing benchtop evaluations of system performance.

  5. Quantitative computed tomography of bone.

    PubMed

    Rüegsegger, P; Stebler, B; Dambacher, M

    1982-07-01

    Computed tomography (CT) is well accepted as an imaging procedure, but comparatively little effort has been made to utilize the potential capability of CT to quantify tissue densities and composition. There are two reasons for this. First, precision and accuracy of quantification are limited by nonlinear effects. These effects are nonlocal and are object and scanner dependent. Second, intraindividual and interindividual variations of tissue compositions are considerable. Single energy measurements require restrictive assumptions on tissue compositions. The diagnosis and treatment monitoring of osteopenic bone diseases with low-dose CT is given as an example of a successful application of quantitative CT. With a special-purpose CT system and an analytic procedure for the quantification of bone at peripheral measuring sites, longitudinal examinations were performed. Low-dose quantitative CT permitted quantification, on an individual basis, of the bone loss of immobilization osteoporosis on a week-by-week basis. Changes due to postmenopausal osteoporosis are less drastic, and so measurement at intervals of months is adequate. In women after menopause, 3-month intervals were used in evaluating the natural course of osteoporosis and in quantifying the effects of sodium fluoride treatment on trabecular bone. Low-dose quantitative CT has proved to be a sensitive and highly reproducible procedure for the noninvasive evaluation of bone loss or bone accretion. During a disease or therapy, each patient can be evaluated individually. PMID:7121079

  6. Multigrid-based reconstruction algorithm for quantitative photoacoustic tomography

    PubMed Central

    Li, Shengfu; Montcel, Bruno; Yuan, Zhen; Liu, Wanyu; Vray, Didier

    2015-01-01

    This paper proposes a multigrid inversion framework for quantitative photoacoustic tomography reconstruction. The forward model of optical fluence distribution and the inverse problem are solved at multiple resolutions. A fixed-point iteration scheme is formulated for each resolution and used as a cost function. The simulated and experimental results for quantitative photoacoustic tomography reconstruction show that the proposed multigrid inversion can dramatically reduce the required number of iterations for the optimization process without loss of reliability in the results. PMID:26203371

  7. Multigrid-based reconstruction algorithm for quantitative photoacoustic tomography.

    PubMed

    Li, Shengfu; Montcel, Bruno; Yuan, Zhen; Liu, Wanyu; Vray, Didier

    2015-07-01

    This paper proposes a multigrid inversion framework for quantitative photoacoustic tomography reconstruction. The forward model of optical fluence distribution and the inverse problem are solved at multiple resolutions. A fixed-point iteration scheme is formulated for each resolution and used as a cost function. The simulated and experimental results for quantitative photoacoustic tomography reconstruction show that the proposed multigrid inversion can dramatically reduce the required number of iterations for the optimization process without loss of reliability in the results. PMID:26203371

  8. Spectral computed tomography for quantitative decomposition of vulnerable plaques using a dual-energy technique: a Monte Carlo simulation study

    NASA Astrophysics Data System (ADS)

    Jo, B. D.; Park, S.-J.; Kim, H. M.; Kim, D. H.; Kim, H.-J.

    2016-02-01

    A spectral computed tomography (CT) system based on an energy-resolved photon-counting Cadmium Zinc Telluride (CZT) detector with a dual energy technique can provide spectral information and can possibly distinguish between two or more materials with a single X-ray exposure using energy thresholds. This work provides the potential for three-material decomposition of vulnerable plaques using two inverse fitting functions. Additionally, there exists the possibility of using gold nanoparticles as a contrast agent for the spectral CT system in conjunction with a CZT photon-counting detector. In this simulation study, we used fan beam CT geometry that consisted of a 90 kVp X-ray spectrum and performed calculations by using the SpekCal program (REAL Software, Inc.) with Monte Carlo simulations. A basic test phantom was imaged with the spectral CT system for the calibration and decomposition process. This phantom contained three different materials, including lipid, iodine and gold nanoparticles, with six holes 3 mm in diameter. In addition to reducing pile-up and charge sharing effect, the photon counting detector was considered an ideal detector. Then, the accuracy of material decomposition techniques with two inverse fitting functions were evaluated between decomposed images and reference images in terms of root mean square error (RMSE). The results showed that decomposed images had a good volumetric fraction for each material, and the RMSE between the measured and true volumes of lipid, iodine and gold nanoparticle fractions varied from 12.51% to 1.29% for inverse fitting functions. The study indicated that spectral CT in conjunction with a CZT photon-counting detector in conjunction with a dual energy technique can be used to identifying materials and may be a promising modality for quantifying material properties of vulnerable plaques.

  9. Quantitative Simulation Games

    NASA Astrophysics Data System (ADS)

    Černý, Pavol; Henzinger, Thomas A.; Radhakrishna, Arjun

    While a boolean notion of correctness is given by a preorder on systems and properties, a quantitative notion of correctness is defined by a distance function on systems and properties, where the distance between a system and a property provides a measure of "fit" or "desirability." In this article, we explore several ways how the simulation preorder can be generalized to a distance function. This is done by equipping the classical simulation game between a system and a property with quantitative objectives. In particular, for systems that satisfy a property, a quantitative simulation game can measure the "robustness" of the satisfaction, that is, how much the system can deviate from its nominal behavior while still satisfying the property. For systems that violate a property, a quantitative simulation game can measure the "seriousness" of the violation, that is, how much the property has to be modified so that it is satisfied by the system. These distances can be computed in polynomial time, since the computation reduces to the value problem in limit average games with constant weights. Finally, we demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.

  10. Bayesian Image Reconstruction in Quantitative Photoacoustic Tomography.

    PubMed

    Tarvainen, Tanja; Pulkkinen, Aki; Cox, Ben; Kaipio, Jari; Arridge, Simon

    2013-08-30

    Quantitative photoacoustic tomography is an emerging imaging technique aimed at estimating chromophore concentrations inside tissues from photoacoustic images, which are formed by combining optical information and ultrasonic propagation. This is a hybrid imaging problem in which the solution of one inverse problem acts as the data for another ill-posed inverse problem. In the optical reconstruction of quantitative photoacoustic tomography, the data is obtained as a solution of an acoustic inverse initial value problem. Thus, both the data and the noise are affected by the method applied to solve the acoustic inverse problem. In this paper, the noise of optical data is modelled as Gaussian distributed with mean and covariance approximated by solving several acoustic inverse initial value problems using acoustic noise samples as data. Furthermore, Bayesian approximation error modelling is applied to compensate for the modelling errors in the optical data caused by the acoustic solver. The results show that modelling of the noise statistics and the approximation errors can improve the optical reconstructions. PMID:24001987

  11. Beam Hardening Corrections in Quantitative Computed Tomography

    SciTech Connect

    Vedula, Venumadhav; Venugopal, Manoharan; Raghu, C.; Pandey, Pramod

    2007-03-21

    Volumetric computed tomography (VCT) is the emerging 3D NDE inspection technique that gives highest throughput and better image quality. Industrial components in general demands higher x-ray energy for inspection for which polychromatic x-ray sources are used in common. Polychromatic nature of the x-rays gives rise to non-linear effects in the VCT projection data measurements called to be the beam hardening (BH) effects. BH produces prominent artifacts in the reconstructed images thereby deteriorating the image quality. Quantitative analysis such as density quantification, dimensional analysis etc., becomes difficult with the presence of these artifacts. This paper describes the BH correction using preprocessing technique for the homogeneous materials. Selection of effective energy at which the monoenergetic linear attenuation coefficient of a particular material equals to that of the polyenergetic beam is critical for BH correction. Various methods to determine the effective energy and their consequence in the quantitative measurements have been investigated in the present study. In this paper, BH corrections for heterogeneous materials have also been explored.

  12. Quantitative investigations of megavoltage computed tomography

    NASA Astrophysics Data System (ADS)

    Rogers, Myron; Kerr, Andrew; Salomons, Greg; Schreiner, L. John

    2005-04-01

    Megavoltage computed tomography (MVCT) has been an active area of research and development in image guided radiation therapy. We have been investigating a particular implementation of MVCT in conjunction with studies of the potential for tomotherapy with a Cobalt-60 radiation source. In this paper, we present results comparing MVCT using a Co-60 source and a 4 MV linear accelerator to conventional kVCT imaging. The Co-60 and linac MVCT measurements were obtained with a first generation benchtop CT imager; the KVCT measurements were obtained using a Philips AcQSim CT Simulator). Phantoms containing various inserts ranging in density from air, through lung, soft tissue and bone equivalent materials and extending to high atomic number metals were imaged with the three modalities. The results enable characterization of image artifacts, CT number linearity and beam hardening. The MVCT images have sufficient contrast that soft tissue regions with 2.8% difference in electron density can be visualized. In MVCT, a linear relationship between CT numbers and electron densities extends to materials with Z ~ 60. In the 4MV CT imaging there is a position dependence of the CT numbers within a uniform water phantom, which is absent in Co-60 CT images, indicating the presence of beam hardening artifacts in the linac MVCT images. The differences between kVCT and MVCT will be discussed considering the variation of the photon interactions dominating the images. Our investigations indicate that MVCT has properties that may potentially extend its utility beyond radiation therapy.

  13. Quantitative photoacoustic tomography using illuminations from a single direction.

    PubMed

    Pulkkinen, Aki; Cox, Ben T; Arridge, Simon R; Kaipio, Jari P; Tarvainen, Tanja

    2015-03-01

    Quantitative photoacoustic tomography is an emerging imaging technique aimed at estimating optical parameters inside tissues from photoacoustic images, which are formed by combining optical information and ultrasonic propagation. This optical parameter estimation problem is ill-posed and needs to be approached within the framework of inverse problems. It has been shown that, in general, estimating the spatial distribution of more than one optical parameter is a nonunique problem unless more than one illumination pattern is used. Generally, this is overcome by illuminating the target from various directions. However, in some cases, for example when thick samples are investigated, illuminating the target from different directions may not be possible. In this work, the use of spatially modulated illumination patterns at one side of the target is investigated with simulations. The results show that the spatially modulated illumination patterns from a single direction could be used to provide multiple illuminations for quantitative photoacoustic tomography. Furthermore, the results show that the approach can be used to distinguish absorption and scattering inclusions located near the surface of the target. However, when compared to a full multidirection illumination setup, the approach cannot be used to image as deep inside tissues. PMID:25803187

  14. Investigation of a diffuse optical tomography-assisted quantitative photoacoustic tomography in reflection geometry

    NASA Astrophysics Data System (ADS)

    Xu, Chen; Kumavor, Patrick D.; Aguirre, Andres; Zhu, Quing

    2011-03-01

    In this paper, we report the experimental investigation of a novel fitting procedure which can detect and quantitatively characterize the optical contrasts of targets using diffuse optical tomography (DOT)-assisted photoacoustic tomography. The hybrid system combines a 64-channel photoacoustic system with a 9-source, 14-detector frequency-domain DOT system. A white probe was used to house the ultrasound transducer, the optical sources and detectors. The experiment was performed in the reflection mode which is more realistic to clinical applications. The fitting procedure included a complete photoacoustic forward model, which incorporated an analytical model of light transport and a model of acoustic propagation. Using the structural information from the PAT images and the background information from DOT measurements, the photoacoustic forward model was used to recover the target absorption coefficient quantitatively. Phantom absorbers, 1 cm in diameter, with absorption coefficients ranging from 0.08 to 0.28 cm-1 were imaged at depths of up to 3.0 cm. The fitting results were at least 85% of their true values for both high and low contrast targets. Blood sample in a thin tube of radius 0.6 mm, that was simulating a blood vessel, was also imaged, and the reconstructed images and fitted absorption coefficients are presented. These results illustrate the promising application of this fitting procedure for tissue absorption coefficient characterization and consequently breast cancer diagnosis.

  15. Weighted filtered backprojection for quantitative fluorescence optical projection tomography.

    PubMed

    Darrell, A; Meyer, H; Marias, K; Brady, M; Ripoll, J

    2008-07-21

    Reconstructing images from a set of fluorescence optical projection tomography (OPT) projections is a relatively new problem. Several physical aspects of fluorescence OPT necessitate a different treatment of the inverse problem to that required for non-fluorescence tomography. Given a fluorophore within the depth of field of the imaging system, the power received by the optical system, and therefore the CCD detector, is related to the distance of the fluorophore from the objective entrance pupil. Additionally, due to the slight blurring of images of sources positioned off the focal plane, the CCD image of a fluorophore off the focal plane is lower in intensity than the CCD image of an identical fluorophore positioned on the focal plane. The filtered backprojection (FBP) algorithm does not take these effects into account and so cannot be expected to yield truly quantitative results. A full model of image formation is introduced which takes into account the effects of isotropic emission and defocus. The model is used to obtain a weighting function which is used in a variation of the FBP algorithm called weighted filtered backprojection (WFBP). This new algorithm is tested with simulated data and with experimental data from a phantom consisting of fluorescent microspheres embedded in an agarose gel. PMID:18583727

  16. Toward quantitative core-loss EFTEM tomography.

    PubMed

    Jin-Phillipp, N Y; Koch, C T; van Aken, P A

    2011-07-01

    Core-loss EFTEM tomography provides three-dimensional structural and chemical information. Multiple inelastic scattering occurring in thick specimens as well as orientation-dependent diffraction contrast due to multiple elastic scattering, however, often limit its applications. After demonstrating the capability of core-loss EFTEM tomography to reconstruct just a few monolayers thin carbon layer covering a Fe catalyst particle we discuss its application to thicker samples. We propose an approximate multiple-scattering correction method based on the use of zero-loss images and apply it successfully to copper whiskers, providing a significant improvement of the reconstructed 3D elemental distribution. We conclude this paper by a general discussion on experimental parameters affecting the accuracy of EFTEM 3D elemental mapping. PMID:21864765

  17. Quantitative Electron Tomography of Rubber Composites

    NASA Astrophysics Data System (ADS)

    Staniewicz, Lech; Vaudey, Thomas; Degrandcourt, Christophe; Couty, Marc; Gaboriaud, Fabien; Midgley, Paul

    2014-06-01

    Rubber composite materials have many applications, one example being tyre manufacture. The presence of a filler material in the composite (such as carbon black or silica) causes its mechanical properties to differ in several ways when compared to pure rubber such as viscoelastic behaviour (the Payne effect), increased tensile strength and improved wear resistance. To fully understand these properties, it is necessary to characterise how the filler material is organised on the nanoscale. Using composite materials representative of those found in tyres, this work illustrates the use of electron tomography and machine learning methods as tools to describe the percolation behaviour of the filler; in this case, we focus on the largest proportion of particles absorbed into one single object as a function of particle spacing.

  18. Quantitative comparison of analysis methods for spectroscopic optical coherence tomography: reply to comment

    PubMed Central

    Bosschaart, Nienke; van Leeuwen, Ton G.; Aalders, Maurice C.G.; Faber, Dirk J.

    2014-01-01

    We reply to the comment by Kraszewski et al on “Quantitative comparison of analysis methods for spectroscopic optical coherence tomography.” We present additional simulations evaluating the proposed window function. We conclude that our simulations show good qualitative agreement with the results of Kraszewski, in support of their conclusion that SOCT optimization should include window shape, next to choice of window size and analysis algorithm. PMID:25401016

  19. Gold Nanoparticle Quantitation by Whole Cell Tomography.

    PubMed

    Sanders, Aric W; Jeerage, Kavita M; Schwartz, Cindi L; Curtin, Alexandra E; Chiaramonti, Ann N

    2015-12-22

    Many proposed biomedical applications for engineered gold nanoparticles require their incorporation by mammalian cells in specific numbers and locations. Here, the number of gold nanoparticles inside of individual mammalian stem cells was characterized using fast focused ion beam-scanning electron microscopy based tomography. Enhanced optical microscopy was used to provide a multiscale map of the in vitro sample, which allows cells of interest to be identified within their local environment. Cells were then serially sectioned using a gallium ion beam and imaged using a scanning electron beam. To confirm the accuracy of single cross sections, nanoparticles in similar cross sections were imaged using transmission electron microscopy and scanning helium ion microscopy. Complete tomographic series were then used to count the nanoparticles inside of each cell and measure their spatial distribution. We investigated the influence of slice thickness on counting single particles and clusters as well as nanoparticle packing within clusters. For 60 nm citrate stabilized particles, the nanoparticle cluster packing volume is 2.15 ± 0.20 times the volume of the bare gold nanoparticles. PMID:26563983

  20. Quantitative contrast-enhanced optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Winetraub, Yonatan; SoRelle, Elliott D.; Liba, Orly; de la Zerda, Adam

    2016-01-01

    We have developed a model to accurately quantify the signals produced by exogenous scattering agents used for contrast-enhanced Optical Coherence Tomography (OCT). This model predicts distinct concentration-dependent signal trends that arise from the underlying physics of OCT detection. Accordingly, we show that real scattering particles can be described as simplified ideal scatterers with modified scattering intensity and concentration. The relation between OCT signal and particle concentration is approximately linear at concentrations lower than 0.8 particle per imaging voxel. However, at higher concentrations, interference effects cause signal to increase with a square root dependence on the number of particles within a voxel. Finally, high particle concentrations cause enough light attenuation to saturate the detected signal. Predictions were validated by comparison with measured OCT signals from gold nanorods (GNRs) prepared in water at concentrations ranging over five orders of magnitude (50 fM to 5 nM). In addition, we validated that our model accurately predicts the signal responses of GNRs in highly heterogeneous scattering environments including whole blood and living animals. By enabling particle quantification, this work provides a valuable tool for current and future contrast-enhanced in vivo OCT studies. More generally, the model described herein may inform the interpretation of detected signals in modalities that rely on coherence-based detection or are susceptible to interference effects.

  1. Quantitative Tomography of Organic Photovoltaic Blends at the Nanoscale.

    PubMed

    Pfannmöller, M; Heidari, H; Nanson, L; Lozman, O R; Chrapa, M; Offermans, T; Nisato, G; Bals, S

    2015-10-14

    The success of semiconducting organic materials has enabled green technologies for electronics, lighting, and photovoltaics. However, when blended together, these materials have also raised novel fundamental questions with respect to electronic, optical, and thermodynamic properties. This is particularly important for organic photovoltaic cells based on the bulk heterojunction. Here, the distribution of nanoscale domains plays a crucial role depending on the specific device structure. Hence, correlation of the aforementioned properties requires 3D nanoscale imaging of materials domains, which are embedded in a multilayer device. Such visualization has so far been elusive due to lack of contrast, insufficient signal, or resolution limits. In this Letter, we introduce spectral scanning transmission electron tomography for reconstruction of entire volume plasmon spectra from rod-shaped specimens. We provide 3D structural correlations and compositional mapping at a resolution of approximately 7 nm within advanced organic photovoltaic tandem cells. Novel insights that are obtained from quantitative 3D analyses reveal that efficiency loss upon thermal annealing can be attributed to subtle, fundamental blend properties. These results are invaluable in guiding the design and optimization of future devices in plastic electronics applications and provide an empirical basis for modeling and simulation of organic solar cells. PMID:26390367

  2. Quantitative cone beam X-ray luminescence tomography/X-ray computed tomography imaging

    SciTech Connect

    Chen, Dongmei; Zhu, Shouping Chen, Xueli; Chao, Tiantian; Cao, Xu; Zhao, Fengjun; Huang, Liyu; Liang, Jimin

    2014-11-10

    X-ray luminescence tomography (XLT) is an imaging technology based on X-ray-excitable materials. The main purpose of this paper is to obtain quantitative luminescence concentration using the structural information of the X-ray computed tomography (XCT) in the hybrid cone beam XLT/XCT system. A multi-wavelength luminescence cone beam XLT method with the structural a priori information is presented to relieve the severe ill-posedness problem in the cone beam XLT. The nanophosphors and phantom experiments were undertaken to access the linear relationship of the system response. Then, an in vivo mouse experiment was conducted. The in vivo experimental results show that the recovered concentration error as low as 6.67% with the location error of 0.85 mm can be achieved. The results demonstrate that the proposed method can accurately recover the nanophosphor inclusion and realize the quantitative imaging.

  3. The APOSTEL recommendations for reporting quantitative optical coherence tomography studies

    PubMed Central

    Cruz-Herranz, Andrés; Balk, Lisanne J.; Oberwahrenbrock, Timm; Saidha, Shiv; Martinez-Lapiscina, Elena H.; Lagreze, Wolf A.; Schuman, Joel S.; Villoslada, Pablo; Calabresi, Peter; Balcer, Laura; Petzold, Axel; Green, Ari J.; Paul, Friedemann; Brandt, Alexander U.

    2016-01-01

    Objective: To develop consensus recommendations for reporting of quantitative optical coherence tomography (OCT) study results. Methods: A panel of experienced OCT researchers (including 11 neurologists, 2 ophthalmologists, and 2 neuroscientists) discussed requirements for performing and reporting quantitative analyses of retinal morphology and developed a list of initial recommendations based on experience and previous studies. The list of recommendations was subsequently revised during several meetings of the coordinating group. Results: We provide a 9-point checklist encompassing aspects deemed relevant when reporting quantitative OCT studies. The areas covered are study protocol, acquisition device, acquisition settings, scanning protocol, funduscopic imaging, postacquisition data selection, postacquisition data analysis, recommended nomenclature, and statistical analysis. Conclusions: The Advised Protocol for OCT Study Terminology and Elements recommendations include core items to standardize and improve quality of reporting in quantitative OCT studies. The recommendations will make reporting of quantitative OCT studies more consistent and in line with existing standards for reporting research in other biomedical areas. The recommendations originated from expert consensus and thus represent Class IV evidence. They will need to be regularly adjusted according to new insights and practices. PMID:27225223

  4. Assessment of metabolic bone diseases by quantitative computed tomography

    SciTech Connect

    Richardson, M.L.; Genant, H.K.; Cann, C.E.; Ettinger, B.; Gordan, G.S.; Kolb, F.O.; Reiser, U.J.

    1985-05-01

    Advances in the radiologic sciences have permitted the development of numerous noninvasive techniques for measuring the mineral content of bone, with varying degrees of precision, accuracy, and sensitivity. The techniques of standard radiography, radiogrammetry, photodensitometry, Compton scattering, neutron activation analysis, single and dual photon absorptiometry, and quantitative computed tomography (QCT) are described and reviewed in depth. Results from previous cross-sectional and longitudinal QCT investigations are given. They then describe a current investigation in which they studied 269 subjects, including 173 normal women, 34 patients with hyperparathyroidism, 24 patients with steroid- induced osteoporosis, and 38 men with idiopathic osteoporosis. Spinal quantitative computed tomography, radiogrammetry, and single photon absorptiometry were performed, and a spinal fracture index was calculated on all patients. The authors found a disproportionate loss of spinal trabecular mineral compared to appendicular mineral in the men with idiopathic osteoporosis and the patients with steroid-induced osteoporosis. They observed roughly equivalent mineral loss in both the appendicular and axial regions in the hyperparathyroid patients. The appendicular cortical measurements correlated moderately well with each other but less well with spinal trabecular QCT. The spinal fracture index correlated well with QCT and less well with the appendicular measurements.

  5. Quantitative phase microscopy and synthetic aperture tomography of live cells

    NASA Astrophysics Data System (ADS)

    Lue, Niyom

    For more than a decade MIT's George R. Harrison Spectroscopy Laboratory has been developing quantitative phase microscopy (QPM) for biological study. Measurements of a point field were made in the mid 90s, then extended to the full 2D field, and recently, to 3D by using tomography. In the first part of this thesis improvements in the techniques of Fourier Phase Microscopy (FPM) and Hilbert Phase Microscopy (HPM) and their applications to characterize cells and tissues are reported. Tomographic phase microscopy (TPM) provides quantitative information and highly detailed structural information about a live cell, but in its current form it can only examine one cell at a time. Many biological applications including statistical analysis of a large collection of cells such as flow cytometry need a tomography technique that can measure many cells at a time. For the second part of this thesis we have developed a new tomography technique that can measure many cells continuously. In this study we demonstrate the new technique by translating a live cell across a focused beam. This beam is composed of many angular plane waves, and by applying a so-called synthetic aperture algorithm we retrieve individual wave components of the focused beam. We demonstrate for the first time that we can retrieve the field of the focused beam and synthesize any arbitrary angular plane wave. We then construct a 3D map of the variations of the refractive index in a live cell from a series of these synthesized angular plane waves. This new technique is the first step needed to analyze cells flowing through a beam to provide a high-throughput 3D refractive index tomograms that can be used as a new kind of statistical optical assay of living cells.

  6. Quantitative computed tomography imaging of airway remodeling in severe asthma.

    PubMed

    Grenier, Philippe A; Fetita, Catalin I; Brillet, Pierre-Yves

    2016-02-01

    Asthma is a heterogeneous condition and approximately 5-10% of asthmatic subjects have severe disease associated with structure changes of the airways (airway remodeling) that may develop over time or shortly after onset of disease. Quantitative computed tomography (QCT) imaging of the tracheobronchial tree and lung parenchyma has improved during the last 10 years, and has enabled investigators to study the large airway architecture in detail and assess indirectly the small airway structure. In severe asthmatics, morphologic changes in large airways, quantitatively assessed using 2D-3D airway registration and recent algorithms, are characterized by airway wall thickening, luminal narrowing and bronchial stenoses. Extent of expiratory gas trapping, quantitatively assessed using lung densitometry, may be used to assess indirectly small airway remodeling. Investigators have used these quantitative imaging techniques in order to attempt severity grading of asthma, and to identify clusters of asthmatic patients that differ in morphologic and functional characteristics. Although standardization of image analysis procedures needs to be improved, the identification of remodeling pattern in various phenotypes of severe asthma and the ability to relate airway structures to important clinical outcomes should help target treatment more effectively. PMID:26981458

  7. Assessment of metabolic bone diseases by quantitative computed tomography

    NASA Technical Reports Server (NTRS)

    Richardson, M. L.; Genant, H. K.; Cann, C. E.; Ettinger, B.; Gordan, G. S.; Kolb, F. O.; Reiser, U. J.

    1985-01-01

    Advances in the radiologic sciences have permitted the development of numerous noninvasive techniques for measuring the mineral content of bone, with varying degrees of precision, accuracy, and sensitivity. The techniques of standard radiography, radiogrammetry, photodensitometry, Compton scattering, neutron activation analysis, single and dual photon absorptiometry, and quantitative computed tomography (QCT) are described and reviewed in depth. Results from previous cross-sectional and longitudinal QCT investigations are given. They then describe a current investigation in which they studied 269 subjects, including 173 normal women, 34 patients with hyperparathyroidism, 24 patients with steroid-induced osteoporosis, and 38 men with idiopathic osteoporosis. Spinal quantitative computed tomography, radiogrammetry, and single photon absorptiometry were performed, and a spinal fracture index was calculated on all patients. The authors found a disproportionate loss of spinal trabecular mineral compared to appendicular mineral in the men with idiopathic osteoporosis and the patients with steroid-induced osteoporosis. They observed roughly equivalent mineral loss in both the appendicular and axial regions in the hyperparathyroid patients. The appendicular cortical measurements correlated moderately well with each other but less well with spinal trabecular QCT. The spinal fracture index correlated well with QCT and less well with the appendicular measurements. Knowledge of appendicular cortical mineral status is important in its own right but is not a valid predictor of axial trabecular mineral status, which may be disproportionately decreased in certain diseases. Quantitative CT provides a reliable means of assessing the latter region of the skeleton, correlates well with the spinal fracture index (a semiquantitative measurement of end-organ failure), and offers the clinician a sensitive means of following the effects of therapy.

  8. Bayesian parameter estimation in spectral quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Pulkkinen, Aki; Cox, Ben T.; Arridge, Simon R.; Kaipio, Jari P.; Tarvainen, Tanja

    2016-03-01

    Photoacoustic tomography (PAT) is an imaging technique combining strong contrast of optical imaging to high spatial resolution of ultrasound imaging. These strengths are achieved via photoacoustic effect, where a spatial absorption of light pulse is converted into a measurable propagating ultrasound wave. The method is seen as a potential tool for small animal imaging, pre-clinical investigations, study of blood vessels and vasculature, as well as for cancer imaging. The goal in PAT is to form an image of the absorbed optical energy density field via acoustic inverse problem approaches from the measured ultrasound data. Quantitative PAT (QPAT) proceeds from these images and forms quantitative estimates of the optical properties of the target. This optical inverse problem of QPAT is illposed. To alleviate the issue, spectral QPAT (SQPAT) utilizes PAT data formed at multiple optical wavelengths simultaneously with optical parameter models of tissue to form quantitative estimates of the parameters of interest. In this work, the inverse problem of SQPAT is investigated. Light propagation is modelled using the diffusion equation. Optical absorption is described with chromophore concentration weighted sum of known chromophore absorption spectra. Scattering is described by Mie scattering theory with an exponential power law. In the inverse problem, the spatially varying unknown parameters of interest are the chromophore concentrations, the Mie scattering parameters (power law factor and the exponent), and Gruneisen parameter. The inverse problem is approached with a Bayesian method. It is numerically demonstrated, that estimation of all parameters of interest is possible with the approach.

  9. Quantitative cerebral blood flow with Optical Coherence Tomography

    PubMed Central

    Srinivasan, Vivek J.; Sakadžić, Sava; Gorczynska, Iwona; Ruvinskaya, Svetlana; Wu, Weicheng; Fujimoto, James G.; Boas, David A.

    2010-01-01

    Absolute measurements of cerebral blood flow (CBF) are an important endpoint in studies of cerebral pathophysiology. Currently no accepted method exists for in vivo longitudinal monitoring of CBF with high resolution in rats and mice. Using three-dimensional Doppler Optical Coherence Tomography and cranial window preparations, we present methods and algorithms for regional CBF measurements in the rat cortex. Towards this end, we develop and validate a quantitative statistical model to describe the effect of static tissue on velocity sensitivity. This model is used to design scanning protocols and algorithms for sensitive 3D flow measurements and angiography of the cortex. We also introduce a method of absolute flow calculation that does not require explicit knowledge of vessel angles. We show that OCT estimates of absolute CBF values in rats agree with prior measures by autoradiography, suggesting that Doppler OCT can perform absolute flow measurements in animal models. PMID:20174075

  10. Optical coherence Doppler tomography for quantitative cerebral blood flow imaging

    PubMed Central

    You, Jiang; Du, Congwu; Volkow, Nora D.; Pan, Yingtian

    2014-01-01

    Optical coherence Doppler tomography (ODT) is a promising neurotechnique that permits 3D imaging of the cerebral blood flow (CBF) network; however, quantitative CBF velocity (CBFv) imaging remains challenging. Here we present a simple phase summation method to enhance slow capillary flow detection sensitivity without sacrificing dynamic range for fast flow and vessel tracking to improve angle correction for absolute CBFv quantification. Flow phantom validation indicated that the CBFv quantification accuracy increased from 15% to 91% and the coefficient of variation (CV) decreased 9.3-fold; in vivo mouse brain validation showed that CV decreased 4.4-/10.8- fold for venular/arteriolar flows. ODT was able to identify cocaine-elicited microischemia and quantify CBFv disruption in branch vessels and capillaries that otherwise would have not been possible. PMID:25401033

  11. Quantitative features in the computed tomography of healthy lungs.

    PubMed Central

    Fromson, B H; Denison, D M

    1988-01-01

    This study set out to determine whether quantitative features of lung computed tomography scans could be identified that would lead to a tightly defined normal range for use in assessing patients. Fourteen normal subjects with apparently healthy lungs were studied. A technique was developed for rapid and automatic extraction of lung field data from the computed tomography scans. The Hounsfield unit histograms were constructed and, when normalised for predicted lung volumes, shown to be consistent in shape for all the subjects. A three dimensional presentation of the data in the form of a "net plot" was devised, and from this a logarithmic relationship between the area of each lung slice and its mean density was derived (r = 0.9, n = 545, p less than 0.0001). The residual density, calculated as the difference between measured density and density predicted from the relationship with area, was shown to be normally distributed with a mean of 0 and a standard deviation of 25 Hounsfield units (chi 2 test: p less than 0.05). A presentation combining this residual density with the net plot is described. PMID:3353883

  12. Quantitative computed tomography detects peripheral airway disease in asthmatic children.

    PubMed

    Jain, Neal; Covar, Ronina A; Gleason, Melanie C; Newell, John D; Gelfand, Erwin W; Spahn, Joseph D

    2005-09-01

    The aim of this study was to compare air-trapping as quantified by high-resolution computed tomography (HRCT) of the chest with measures of lung function and airway inflammation in children with mild to moderate asthma. Plethysmography indices, respiratory resistance, and reactance before and after bronchodilator with impulse oscillation (IOS), exhaled nitric oxide (eNO), total eosinophil count (TEC), and serum eosinophil cationic protein (ECP) levels were measured in 21 subjects. A single-cut HRCT image at end-expiration was obtained. Air-trapping was quantified and expressed in terms of the pixel index (PI) by determining the percentage of pixels in lung fields below -856 and -910 Hounsfeld units (HU). Pairwise linear correlations between PI and other parameters were evaluated. Subjects had only mild airflow limitation based on prebronchodilator forced expiratory volume in 1 sec (FEV(1)), but were hyperinflated and had air-trapping based on elevated total lung capacity (TLC) and residual volume (RV)/TLC ratio, respectively. The PI at -856 HU was positively correlated with % predicted TLC, total gas volume (TGV), and ECP level, and was inversely correlated with FEV(1)/forced vital capacity (FVC) and % predicted forced expiratory flow between 25-75% FVC (FEF(25-75)). The PI at -910 HU correlated similarly with these variables, and also correlated positively with IOS bronchodilator reversibility. This data suggest that quantitative HRCT may be a useful tool in the evaluation of peripheral airflow obstruction in children with asthma. PMID:16015663

  13. Semiautomatic Software For Quantitative Analysis Of Cardiac Positron Tomography Studies

    NASA Astrophysics Data System (ADS)

    Ratib, Osman; Bidaut, Luc; Nienaber, Christoph; Krivokapich, Janine; Schelbert, Heinrich R.; Phelps, Michael E.

    1988-06-01

    In order to derive accurate values for true tissue radiotracers concentrations from gated positron emission tomography (PET) images of the heart, which are critical for quantifying noninvasively regional myocardial blood flow and metabolism, appropriate corrections for partial volume effect (PVE) and contamination from adjacent anatomical structures are required. We therefore developed an integrated software package for quantitative analysis of tomographic images which provides for such corrections. A semiautomatic edge detection technique outlines and partitions the myocardium into sectors. Myocardial wall thickness is measured on the images perpendicularly to the detected edges and used to correct for PVE. The programs automatically correct for radioactive decay, activity calibration and cross contaminations for both static and dynamic studies. Parameters derived with these programs include tracer concentrations and their changes over time. They are used for calculating regional metabolic rates and can be further displayed as color coded parametric images. The approach was validated for PET imaging in 11 dog experiments. 2D echocardiograms (Echo) were recorded simultaneously to validate the edge detection and wall thickness measurement techniques. After correction for PVE using automatic WT measurement, regional tissue tracer concentrations derived from PET images correlated well with true tissue concentrations as determined by well counting (r=0.98). These preliminary studies indicate that the developed automatic image analysis technique allows accurate and convenient evaluation of cardiac PET images for the measurement of both, regional tracer tissue concentrations as well as regional myocardial function.

  14. Quantitative Computed Tomography Protocols Affect Material Mapping and Quantitative Computed Tomography-Based Finite-Element Analysis Predicted Stiffness.

    PubMed

    Giambini, Hugo; Dragomir-Daescu, Dan; Nassr, Ahmad; Yaszemski, Michael J; Zhao, Chunfeng

    2016-09-01

    Quantitative computed tomography-based finite-element analysis (QCT/FEA) has become increasingly popular in an attempt to understand and possibly reduce vertebral fracture risk. It is known that scanning acquisition settings affect Hounsfield units (HU) of the CT voxels. Material properties assignments in QCT/FEA, relating HU to Young's modulus, are performed by applying empirical equations. The purpose of this study was to evaluate the effect of QCT scanning protocols on predicted stiffness values from finite-element models. One fresh frozen cadaveric torso and a QCT calibration phantom were scanned six times varying voltage and current and reconstructed to obtain a total of 12 sets of images. Five vertebrae from the torso were experimentally tested to obtain stiffness values. QCT/FEA models of the five vertebrae were developed for the 12 image data resulting in a total of 60 models. Predicted stiffness was compared to the experimental values. The highest percent difference in stiffness was approximately 480% (80 kVp, 110 mAs, U70), while the lowest outcome was ∼1% (80 kVp, 110 mAs, U30). There was a clear distinction between reconstruction kernels in predicted outcomes, whereas voltage did not present a clear influence on results. The potential of QCT/FEA as an improvement to conventional fracture risk prediction tools is well established. However, it is important to establish research protocols that can lead to results that can be translated to the clinical setting. PMID:27428281

  15. Bone morphometry and mineral density measurement using quantitative computed tomography

    SciTech Connect

    Jacobson, D.R.

    1991-01-01

    Application of computed tomography (CT) to the study of bone structure and density was explored and developed. A review of bone mineral densitometry (BMD) methodology and general principles of quantitative CT (QCT) are presented. A method for QCT of the spine was developed using a flexible tissue equivalent reference placed adjacent to the patient. A methodology for the development and production of tissue equivalent materials is also presented. Patient equivalent phantoms were used to characterize the method, and phantom studies were performed at five clinical sites. A protocol is defined for measuring the inside diameter of the lumbar pedicular canal. Data generated from this study has proven invaluable in the planning for lumbar fusion surgery when screws are to be used for immobilization. Pedicular canal data from 33 patients is presented. QCT was also used to quantify several parameters of the femoral shaft for use in hip replacement surgical planning. Parameters studied include inside diameter, BMD, endosteal BMD and proximal shaft morphology. The structure and trabecular BMD of the proximal femur was extensively studied using QCT. A large variation was found in the fat content of marrow within the proximal femur, and phantom studies were performed to quantify the effect of fat on trabecular QCT BMD. Cadaveric trabecular bone samples with marrow were analyzed physically to determine water, fat, non-fat soft tissue, and ash content. Multiple thin-slice CT studies were performed on cadaveric femurs. A structural model of the proximal femur was developed in which the structural support is provided primarily by trabecular bone. This model may have profound implications in the study of femoral fractures and prosthetic hardware design.

  16. Quantitative ultrasonic computed tomography using phase-insensitive pyroelectric detectors

    NASA Astrophysics Data System (ADS)

    Zeqiri, Bajram; Baker, Christian; Alosa, Giuseppe; Wells, Peter N. T.; Liang, Hai-Dong

    2013-08-01

    The principle of using ultrasonic computed tomography (UCT) clinically for mapping tissue acoustic properties was suggested almost 40 years ago. Despite strong research activity, UCT been unable to rival its x-ray counterpart in terms of the ability to distinguish tissue pathologies. Conventional piezoelectric detectors deployed in UCT are termed phase-sensitive (PS) and it is well established that this property can lead to artefacts related to refraction and phase-cancellation that mask true tissue structure, particularly for reconstructions involving attenuation. Equally, it has long been known that phase-insensitive (PI) detectors are more immune to this effect, although sufficiently sensitive devices for clinical use have not been available. This paper explores the application of novel PI detectors to UCT. Their operating principle is based on exploiting the pyroelectric properties of the piezoelectric polymer polyvinylidene difluoride. An important detector performance characteristic which makes it particularly suited to UCT, is the lack of directionality of the PI response, relative to the PS detector mode of operation. The performance of the detectors is compared to conventional PS detection methods, for quantitatively assessing the attenuation distribution within various test objects, including a two-phase polyurethane phantom. UCT images are presented for a range of single detector apertures; tomographic reconstruction images being compared with the known structure of phantoms containing inserts as small as 3 mm, which were readily imaged. For larger diameter inserts (>10 mm), the transmitter-detector combination was able to establish the attenuation coefficient of the insert to within ±10% of values determined separately from plane-wave measurements on representative material plaques. The research has demonstrated that the new PI detectors are significantly less susceptible to refraction and phase-cancellation artefacts, generating realistic images in

  17. Quantitative electron tomography and its application to polymer nanostructures

    NASA Astrophysics Data System (ADS)

    Jinnai, Hiroshi

    2009-03-01

    The transmission electron microtomography (TEMT) is a powerful tool to visualize three-dimensional (3D) structures in many fields of materials science. Recently, researchers are trying not only to visualize 3D nano-structures but also to quantify them in order to seek a possible correlation between the 3D structures and materials' properties. However, one of the serious problems that prohibit TEMT from truly quantitative 3D images is the ``missing wedge'' in the Fourier space that is caused by the limitation of angular range available in transmission electron microscopes (TEM). Please note that the computerized tomography (CT), on which TEMT is based, requires projections from entire tilt angles, i.e. ±90^o. Thus, the most faithful tactics for the CT is to tilt specimen over ±90^o. In order to realize such requirement, a rod-shaped ZrO2/polymer nano-composite whose diameter is ca. 150 nm was attached at the tip of a specially modified specimen holder without any supporting film. A complete set of tomograms has been generated for the first time from the 181 projections that were taken over the angular range of ±90^o. One of the structural parameters characterizing the nano-composite, a volume fraction of ZrO2, , was measured as a function of the maximum tilt angle, α. It was found that was in excellent agreement with the known volume fraction of ZrO2 when α=90^o, i.e., ±90^o tilt, while increased with decreasing α. When α=60^o that is a typical maximum tilt angle, the measured was larger by 20˜30% than the true value. In addition to the above TEMT experimental technique, some applications of TEMT to polymer nano-structures will be presented at the conference time.

  18. Quantitative ultrasonic computed tomography using phase-insensitive pyroelectric detectors.

    PubMed

    Zeqiri, Bajram; Baker, Christian; Alosa, Giuseppe; Wells, Peter N T; Liang, Hai-Dong

    2013-08-01

    The principle of using ultrasonic computed tomography (UCT) clinically for mapping tissue acoustic properties was suggested almost 40 years ago. Despite strong research activity, UCT been unable to rival its x-ray counterpart in terms of the ability to distinguish tissue pathologies. Conventional piezoelectric detectors deployed in UCT are termed phase-sensitive (PS) and it is well established that this property can lead to artefacts related to refraction and phase-cancellation that mask true tissue structure, particularly for reconstructions involving attenuation. Equally, it has long been known that phase-insensitive (PI) detectors are more immune to this effect, although sufficiently sensitive devices for clinical use have not been available. This paper explores the application of novel PI detectors to UCT. Their operating principle is based on exploiting the pyroelectric properties of the piezoelectric polymer polyvinylidene difluoride. An important detector performance characteristic which makes it particularly suited to UCT, is the lack of directionality of the PI response, relative to the PS detector mode of operation. The performance of the detectors is compared to conventional PS detection methods, for quantitatively assessing the attenuation distribution within various test objects, including a two-phase polyurethane phantom. UCT images are presented for a range of single detector apertures; tomographic reconstruction images being compared with the known structure of phantoms containing inserts as small as 3 mm, which were readily imaged. For larger diameter inserts (>10 mm), the transmitter-detector combination was able to establish the attenuation coefficient of the insert to within ±10% of values determined separately from plane-wave measurements on representative material plaques. The research has demonstrated that the new PI detectors are significantly less susceptible to refraction and phase-cancellation artefacts, generating realistic images in

  19. Monte Carlo Simulation of Emission Tomography and other Medical Imaging Techniques

    NASA Astrophysics Data System (ADS)

    Harrison, Robert L.

    2010-01-01

    As an introduction to Monte Carlo simulation of emission tomography, this paper reviews the history and principles of Monte Carlo simulation, then applies these principles to emission tomography using the public domain simulation package SimSET (a Simulation System for Emission Tomography) as an example. Finally, the paper discusses how the methods are modified for X-ray computed tomography and radiotherapy simulations.

  20. Simulation Study of Single Photon Emission Computed Tomography for Industrial Applications

    NASA Astrophysics Data System (ADS)

    Roy, Tushar; Sarkar, P. S.; Sinha, Amar

    2008-09-01

    SPECT (Single Photon Emission Computed Tomography) provides for an invaluable non-invasive technique for the characterization and activity distribution of the gamma-emitting source. For many applications of radioisotopes for medical and industrial application, not only the positional information of the distribution of radioisotopes is needed but also its strength. The well-established X-ray radiography or transmission tomography techniques do not yield sufficient quantitative information about these objects. Emission tomography is one of the important methods for such characterization. Application of parallel beam, fan beam and 3D cone beam emission tomography methods have been discussed in this paper. Simulation studies to test these algorithms have been carried out to validate the technique.

  1. Deterministic simulation of thermal neutron radiography and tomography

    NASA Astrophysics Data System (ADS)

    Pal Chowdhury, Rajarshi; Liu, Xin

    2016-05-01

    In recent years, thermal neutron radiography and tomography have gained much attention as one of the nondestructive testing methods. However, the application of thermal neutron radiography and tomography is hindered by their technical complexity, radiation shielding, and time-consuming data collection processes. Monte Carlo simulations have been developed in the past to improve the neutron imaging facility's ability. In this paper, a new deterministic simulation approach has been proposed and demonstrated to simulate neutron radiographs numerically using a ray tracing algorithm. This approach has made the simulation of neutron radiographs much faster than by previously used stochastic methods (i.e., Monte Carlo methods). The major problem with neutron radiography and tomography simulation is finding a suitable scatter model. In this paper, an analytic scatter model has been proposed that is validated by a Monte Carlo simulation.

  2. Accounting for filter bandwidth improves the quantitative accuracy of bioluminescence tomography

    NASA Astrophysics Data System (ADS)

    Taylor, Shelley L.; Mason, Suzannah K. G.; Glinton, Sophie L.; Cobbold, Mark; Dehghani, Hamid

    2015-09-01

    Bioluminescence imaging is a noninvasive technique whereby surface weighted images of luminescent probes within animals are used to characterize cell count and function. Traditionally, data are collected over the entire emission spectrum of the source using no filters and are used to evaluate cell count/function over the entire spectrum. Alternatively, multispectral data over several wavelengths can be incorporated to perform tomographic reconstruction of source location and intensity. However, bandpass filters used for multispectral data acquisition have a specific bandwidth, which is ignored in the reconstruction. In this work, ignoring the bandwidth is shown to introduce a dependence of the recovered source intensity on the bandwidth of the filters. A method of accounting for the bandwidth of filters used during multispectral data acquisition is presented and its efficacy in increasing the quantitative accuracy of bioluminescence tomography is demonstrated through simulation and experiment. It is demonstrated that while using filters with a large bandwidth can dramatically decrease the data acquisition time, if not accounted for, errors of up to 200% in quantitative accuracy are introduced in two-dimensional planar imaging, even after normalization. For tomographic imaging, the use of this method to account for filter bandwidth dramatically improves the quantitative accuracy.

  3. Quantitative evaluation of optical coherence tomography signal enhancement with gold nanoshells.

    PubMed

    Agrawal, Anant; Huang, Stanley; Wei Haw Lin, Alex; Lee, Min-Ho; Barton, Jennifer K; Drezek, Rebekah A; Pfefer, T Joshua

    2006-01-01

    Nanoshell-enhanced optical coherence tomography (OCT) is a novel technique with the potential for molecular imaging and improved disease detection. However, optimization of this approach will require a quantitative understanding of the influence of nanoshell parameters on detected OCT signals. In this study, OCT was performed at 1310 nm in water and turbid tissue-simulating phantoms to which nanoshells were added. The effect of nanoshell concentration, core diameter, and shell thickness on signal enhancement was characterized. Experimental results indicated trends that were consistent with predicted optical properties-a monotonic increase in signal intensity and attenuation with increasing shell and core size. Threshold concentrations for a 2-dB OCT signal intensity gain were determined for several nanoshell geometries. For the most highly backscattering nanoshells tested-291-nm core diameter, 25-nm shell thickness-a concentration of 10(9) nanoshells/mL was needed to produce this signal increase. Based on these results, we discuss various practical considerations for optimizing nanoshell-enhanced OCT. Quantitative experimental data presented here will facilitate optimization of OCT-based diagnostics and may also be relevant to other reflectance-based approaches as well. PMID:16965149

  4. Considering sources and detectors distributions for quantitative photoacoustic tomography

    PubMed Central

    Song, Ningning; Deumié, Carole; Da Silva, Anabela

    2014-01-01

    Photoacoustic tomography (PAT) is a hybrid imaging modality that takes advantage of high optical contrast brought by optical imaging and high spatial resolution brought by ultrasound imaging. However, the quantification in photoacoustic imaging is challenging. Multiple optical illumination approach has proven to achieve uncoupling of diffusion and absorption effects. In this paper, this protocol is adopted and synthetic photoacoustic data, blurred with some noise, were generated. The influence of the distribution of optical sources and transducers on the reconstruction of the absorption and diffusion coefficients maps is studied. Specific situations with limited view angles were examined. The results show multiple illuminations with a wide field improve the reconstructions. PMID:25426322

  5. Quantitative simultaneous positron emission tomography and magnetic resonance imaging

    PubMed Central

    Ouyang, Jinsong; Petibon, Yoann; Huang, Chuan; Reese, Timothy G.; Kolnick, Aleksandra L.; El Fakhri, Georges

    2014-01-01

    Abstract. Simultaneous positron emission tomography and magnetic resonance imaging (PET-MR) is an innovative and promising imaging modality that is generating substantial interest in the medical imaging community, while offering many challenges and opportunities. In this study, we investigated whether MR surface coils need to be accounted for in PET attenuation correction. Furthermore, we integrated motion correction, attenuation correction, and point spread function modeling into a single PET reconstruction framework. We applied our reconstruction framework to in vivo animal and patient PET-MR studies. We have demonstrated that our approach greatly improved PET image quality. PMID:26158055

  6. Quantitative simultaneous positron emission tomography and magnetic resonance imaging.

    PubMed

    Ouyang, Jinsong; Petibon, Yoann; Huang, Chuan; Reese, Timothy G; Kolnick, Aleksandra L; El Fakhri, Georges

    2014-10-01

    Simultaneous positron emission tomography and magnetic resonance imaging (PET-MR) is an innovative and promising imaging modality that is generating substantial interest in the medical imaging community, while offering many challenges and opportunities. In this study, we investigated whether MR surface coils need to be accounted for in PET attenuation correction. Furthermore, we integrated motion correction, attenuation correction, and point spread function modeling into a single PET reconstruction framework. We applied our reconstruction framework to in vivo animal and patient PET-MR studies. We have demonstrated that our approach greatly improved PET image quality. PMID:26158055

  7. Quantitative computed tomography for spinal mineral assessment: current status

    NASA Technical Reports Server (NTRS)

    Genant, H. K.; Cann, C. E.; Ettinger, B.; Gordan, G. S.; Kolb, F. O.; Reiser, U.; Arnaud, C. D.

    1985-01-01

    Quantitative CT (QCT) is an established method for the noninvasive assessment of bone mineral content in the vertebral spongiosum and other anatomic locations. The potential strengths of QCT relative to dual photon absorptiometry (DPA) are its capability for precise three-dimensional anatomic localization providing a direct density measurement and its capability for spatial separation of highly responsive cancellous bone from less responsive cortical bone. The extraction of this quantitative information from the CT image, however, requires sophisticated calibration and positioning techniques and careful technical monitoring.

  8. Cell death monitoring using quantitative optical coherence tomography methods

    NASA Astrophysics Data System (ADS)

    Farhat, Golnaz; Yang, Victor X. D.; Kolios, Michael C.; Czarnota, Gregory J.

    2011-03-01

    Cell death is characterized by a series of predictable morphological changes, which modify the light scattering properties of cells. We present a multi-parametric approach to detecting changes in subcellular morphology related to cell death using optical coherence tomography (OCT). Optical coherence tomography data were acquired from acute myeloid leukemia (AML) cells undergoing apoptosis over a period of 48 hours. Integrated backscatter (IB) and spectral slope (SS) were computed from OCT backscatter spectra and statistical parameters were extracted from a generalized gamma (GG) distribution fit to OCT signal intensity histograms. The IB increased by 2-fold over 48 hours with significant increases observed as early as 4 hours. The SS increased in steepness by 2.5-fold with significant changes at 12 hours, while the GG parameters were sensitive to apoptotic changes at 24 to 48 hours. Histology slides indicated nuclear condensation and fragmentation at 24 hours, suggesting the late scattering changes could be related to nuclear structure. A second series of measurements from AML cells treated with cisplatin, colchicine or ionizing radiation suggested that the GG parameters could potentially differentiate between modes of cell death. Distinct cellular morphology was observed in histology slides obtained from cells treated under each condition.

  9. Monte Carlo Simulation Of Emission Tomography And Other Medical Imaging Techniques

    PubMed Central

    Harrison, Robert L.

    2010-01-01

    An introduction to Monte Carlo simulation of emission tomography. This paper reviews the history and principles of Monte Carlo simulation, then applies these principles to emission tomography using the public domain simulation package SimSET (a Simulation System for Emission Tomography) as an example. Finally, the paper discusses how the methods are modified for X-ray computed tomography and radiotherapy simulations. PMID:20733931

  10. Quantitative phase tomography by using x-ray microscope with Foucault knife-edge scanning filter

    NASA Astrophysics Data System (ADS)

    Watanabe, Norio; Tsuburaya, Yuji; Shimada, Akihiro; Aoki, Sadao

    2016-01-01

    Quantitative phase tomography was evaluated by using a differential phase microscope with a Foucault knife-edge scanning filter. A 3D x-ray phase image of polystyrene beads was obtained at 5.4 keV. The reconstructed refractive index was fairly good agreement with the Henke's tabulated data.

  11. Quantitative X-ray dark-field and phase tomography using single directional speckle scanning technique

    NASA Astrophysics Data System (ADS)

    Wang, Hongchang; Kashyap, Yogesh; Sawhney, Kawal

    2016-03-01

    X-ray dark-field contrast tomography can provide important supplementary information inside a sample to the conventional absorption tomography. Recently, the X-ray speckle based technique has been proposed to provide qualitative two-dimensional dark-field imaging with a simple experimental arrangement. In this letter, we deduce a relationship between the second moment of scattering angle distribution and cross-correlation degradation of speckle and establish a quantitative basis of X-ray dark-field tomography using single directional speckle scanning technique. In addition, the phase contrast images can be simultaneously retrieved permitting tomographic reconstruction, which yields enhanced contrast in weakly absorbing materials. Such complementary tomography technique can allow systematic investigation of complex samples containing both soft and hard materials.

  12. Quantitative and Qualitative Simulation in Computer Based Training.

    ERIC Educational Resources Information Center

    Stevens, Albert; Roberts, Burce

    1983-01-01

    Computer-based systems combining quantitative simulation with qualitative tutorial techniques provide learners with sophisticated individualized training. The teaching capabilities and operating procedures of Steamer, a simulated steam plant, are described. (Author/MBR)

  13. Quantitative Computed Tomography and Image Analysis for Advanced Muscle Assessment

    PubMed Central

    Edmunds, Kyle Joseph; Gíslason, Magnus K.; Arnadottir, Iris D.; Marcante, Andrea; Piccione, Francesco; Gargiulo, Paolo

    2016-01-01

    Medical imaging is of particular interest in the field of translational myology, as extant literature describes the utilization of a wide variety of techniques to non-invasively recapitulate and quantity various internal and external tissue morphologies. In the clinical context, medical imaging remains a vital tool for diagnostics and investigative assessment. This review outlines the results from several investigations on the use of computed tomography (CT) and image analysis techniques to assess muscle conditions and degenerative process due to aging or pathological conditions. Herein, we detail the acquisition of spiral CT images and the use of advanced image analysis tools to characterize muscles in 2D and 3D. Results from these studies recapitulate changes in tissue composition within muscles, as visualized by the association of tissue types to specified Hounsfield Unit (HU) values for fat, loose connective tissue or atrophic muscle, and normal muscle, including fascia and tendon. We show how results from these analyses can be presented as both average HU values and compositions with respect to total muscle volumes, demonstrating the reliability of these tools to monitor, assess and characterize muscle degeneration. PMID:27478562

  14. Noninvasive Risk Stratification of Lung Adenocarcinoma using Quantitative Computed Tomography

    PubMed Central

    Raghunath, Sushravya; Maldonado, Fabien; Rajagopalan, Srinivasan; Karwoski, Ronald A.; DePew, Zackary S.; Bartholmai, Brian J.; Peikert, Tobias; Robb, Richard A.

    2014-01-01

    Introduction Lung cancer remains the leading cause of cancer-related deaths in the US and worldwide. Adenocarcinoma is the most common type of lung cancer and encompasses lesions with widely variable clinical outcomes. In the absence of noninvasive risk stratification, individualized patient management remains challenging. Consequently a subgroup of pulmonary nodules of the lung adenocarcinoma spectrum is likely treated more aggressively than necessary. Methods Consecutive patients with surgically resected pulmonary nodules of the lung adenocarcinoma spectrum (lesion size ≤ 3 cm, 2006–2009) and available pre-surgical high-resolution computed tomography (HRCT) imaging were identified at Mayo Clinic Rochester. All cases were classified using an unbiased Computer-Aided Nodule Assessment and Risk Yield (CANARY) approach based on the quantification of pre-surgical HRCT characteristics. CANARY-based classification was independently correlated to postsurgical progression-free survival. Results CANARY analysis of 264 consecutive patients identified three distinct subgroups. Independent comparisons of 5-year disease-free survival (DFS) between these subgroups demonstrated statistically significant differences in 5-year DFS, 100%, 72.7% and 51.4%, respectively (p = 0.0005). Conclusions Non-invasive CANARY based risk stratification identifies subgroups of patients with pulmonary nodules of the adenocarcinoma spectrum characterized by distinct clinical outcomes. This technique may ultimately improve the current expert opinion-based approach to the management of these lesions by facilitating individualized patient management. PMID:25170645

  15. Simulation of Medical Imaging Systems: Emission and Transmission Tomography

    NASA Astrophysics Data System (ADS)

    Harrison, Robert L.

    Simulation is an important tool in medical imaging research. In patient scans the true underlying anatomy and physiology is unknown. We have no way of knowing in a given scan how various factors are confounding the data: statistical noise; biological variability; patient motion; scattered radiation, dead time, and other data contaminants. Simulation allows us to isolate a single factor of interest, for instance when researchers perform multiple simulations of the same imaging situation to determine the effect of statistical noise or biological variability. Simulations are also increasingly used as a design optimization tool for tomographic scanners. This article gives an overview of the mechanics of emission and transmission tomography simulation, reviews some of the publicly available simulation tools, and discusses trade-offs between the accuracy and efficiency of simulations.

  16. SU-D-210-03: Limited-View Multi-Source Quantitative Photoacoustic Tomography

    SciTech Connect

    Feng, J; Gao, H

    2015-06-15

    Purpose: This work is to investigate a novel limited-view multi-source acquisition scheme for the direct and simultaneous reconstruction of optical coefficients in quantitative photoacoustic tomography (QPAT), which has potentially improved signal-to-noise ratio and reduced data acquisition time. Methods: Conventional QPAT is often considered in two steps: first to reconstruct the initial acoustic pressure from the full-view ultrasonic data after each optical illumination, and then to quantitatively reconstruct optical coefficients (e.g., absorption and scattering coefficients) from the initial acoustic pressure, using multi-source or multi-wavelength scheme.Based on a novel limited-view multi-source scheme here, We have to consider the direct reconstruction of optical coefficients from the ultrasonic data, since the initial acoustic pressure can no longer be reconstructed as an intermediate variable due to the incomplete acoustic data in the proposed limited-view scheme. In this work, based on a coupled photo-acoustic forward model combining diffusion approximation and wave equation, we develop a limited-memory Quasi-Newton method (LBFGS) for image reconstruction that utilizes the adjoint forward problem for fast computation of gradients. Furthermore, the tensor framelet sparsity is utilized to improve the image reconstruction which is solved by Alternative Direction Method of Multipliers (ADMM). Results: The simulation was performed on a modified Shepp-Logan phantom to validate the feasibility of the proposed limited-view scheme and its corresponding image reconstruction algorithms. Conclusion: A limited-view multi-source QPAT scheme is proposed, i.e., the partial-view acoustic data acquisition accompanying each optical illumination, and then the simultaneous rotations of both optical sources and ultrasonic detectors for next optical illumination. Moreover, LBFGS and ADMM algorithms are developed for the direct reconstruction of optical coefficients from the

  17. The potential optical coherence tomography in tooth bleaching quantitative assessment

    NASA Astrophysics Data System (ADS)

    Ni, Y. R.; Guo, Z. Y.; Shu, S. Y.; Zeng, C. C.; Zhong, H. Q.; Chen, B. L.; Liu, Z. M.; Bao, Y.

    2011-12-01

    In this paper, we report the outcomes from a pilot study on using OCT functional imaging method to evaluate and quantify color alteration in the human teeth in vitro. The image formations of the dental tissues without and with treatment 35% hydrogen peroxide were obtained by an OCT system at a 1310 nm central wavelength. One parameter for the quantification of optical properties from OCT measurements is introduced in our study: attenuate coefficient (μ). And the attenuate coefficient have significant decrease ( p < 0.001) in dentine as well as a significant increase ( p < 0.001) in enamel was observed during tooth bleaching process. From the experimental results, it is found that attenuate coefficient could be useful to assess color alteration of the human tooth samples. OCT has a potential to become an effective tool for the assessment tooth bleaching. And our experiment offer a now method to evaluate color change in visible region by quantitative analysis of the infrared region information from OCT.

  18. Quantitation of the human basal ganglia with Positron Emission Tomography

    SciTech Connect

    Bendriem, B.; Dewey, S.L.; Schlyer, D.J.; Wolf, A.P.; Volkow, N.D.

    1990-01-01

    The accurate measurement of the concentration of a radioisotope in small structures with PET requires a correction for quantitation loss due to the partial volume effect and the effect of scattered radiation. To evaluate errors associated with measures in the human basal ganglia (BG) we have built a unilateral model of the BG that we have inserted in a 20 cm cylinder. The recovery coefficient (RC = measured activity/true activity) for our BG phantom has been measured on a CTI tomograph (model 931-08/12) with different background concentrations (contrast) and at different axial locations in the gantry. The BG was visualized on 4 or 5 slices depending on its position in the gantry and on the contrast used. The RC was 0.75 with no background (contrast equal to 1.0). Increasing the relative radioactivity concentration in the background increased the RC from 0.75 to 2.00 when the contrast was {minus}0.7 (BG < Background). The RC was also affected by the size and the shape of the region of interest (ROI) used (RC from 0.75 to 0.67 with ROI size from 0.12 to 1.41 cm{sup 2}). These results show that accurate RC correction depends not only on the volume of the structure but also on its contrast with its surroundings as well as on the selection of the ROI. They also demonstrate that the higher the contrast the more sensitive to axial positioning PET measurements in the BG are. These data provide us with some information about the variability of PET measurements in small structure like the BG and we have proposed some strategies to improve the reproducibility. 18 refs., 3 figs., 5 tabs.

  19. Qualitative, semi-quantitative, and quantitative simulation of the osmoregulation system in yeast

    PubMed Central

    Pang, Wei; Coghill, George M.

    2015-01-01

    In this paper we demonstrate how Morven, a computational framework which can perform qualitative, semi-quantitative, and quantitative simulation of dynamical systems using the same model formalism, is applied to study the osmotic stress response pathway in yeast. First the Morven framework itself is briefly introduced in terms of the model formalism employed and output format. We then built a qualitative model for the biophysical process of the osmoregulation in yeast, and a global qualitative-level picture was obtained through qualitative simulation of this model. Furthermore, we constructed a Morven model based on existing quantitative model of the osmoregulation system. This model was then simulated qualitatively, semi-quantitatively, and quantitatively. The obtained simulation results are presented with an analysis. Finally the future development of the Morven framework for modelling the dynamic biological systems is discussed. PMID:25864377

  20. Reservoir characterization with sequential Gaussian simulation constrained by diffraction tomography

    SciTech Connect

    Lo, T.W.; Bermawi, A.

    1994-12-31

    A geostatistical approach for reservoir characterization that honors both surface seismic data and wireline data is described. It first computes a velocity profiles with seismic diffraction tomography, then, performs kriging with an external drift and sequential Gaussian simulation using the velocity profiles as soft data and the sonic logs as hard data. The product is a velocity profile with a resolution as high as that of the smoothed sonic logs, showing lateral velocity variations constrained by surface seismic data.

  1. Quantitative assessment of the retinal microvasculature using optical coherence tomography angiography

    NASA Astrophysics Data System (ADS)

    Chu, Zhongdi; Lin, Jason; Gao, Chen; Xin, Chen; Zhang, Qinqin; Chen, Chieh-Li; Roisman, Luis; Gregori, Giovanni; Rosenfeld, Philip J.; Wang, Ruikang K.

    2016-06-01

    Optical coherence tomography angiography (OCTA) is clinically useful for the qualitative assessment of the macular microvasculature. However, there is a need for comprehensive quantitative tools to help objectively analyze the OCT angiograms. Few studies have reported the use of a single quantitative index to describe vessel density in OCT angiograms. In this study, we introduce a five-index quantitative analysis of OCT angiograms in an attempt to detect and assess vascular abnormalities from multiple perspectives. The indices include vessel area density, vessel skeleton density, vessel diameter index, vessel perimeter index, and vessel complexity index. We show the usefulness of the proposed indices with five illustrative cases. Repeatability is tested on both a healthy case and a stable diseased case, giving interclass coefficients smaller than 0.031. The results demonstrate that our proposed quantitative analysis may be useful as a complement to conventional OCTA for the diagnosis of disease and monitoring of treatment.

  2. Quantitative computer simulations of extraterrestrial processing operations

    NASA Technical Reports Server (NTRS)

    Vincent, T. L.; Nikravesh, P. E.

    1989-01-01

    The automation of a small, solid propellant mixer was studied. Temperature control is under investigation. A numerical simulation of the system is under development and will be tested using different control options. Control system hardware is currently being put into place. The construction of mathematical models and simulation techniques for understanding various engineering processes is also studied. Computer graphics packages were utilized for better visualization of the simulation results. The mechanical mixing of propellants is examined. Simulation of the mixing process is being done to study how one can control for chaotic behavior to meet specified mixing requirements. An experimental mixing chamber is also being built. It will allow visual tracking of particles under mixing. The experimental unit will be used to test ideas from chaos theory, as well as to verify simulation results. This project has applications to extraterrestrial propellant quality and reliability.

  3. Quantitative comparison of direct phase retrieval algorithms in in-line phase tomography

    SciTech Connect

    Langer, Max; Cloetens, Peter; Guigay, Jean-Pierre; Peyrin, Francoise

    2008-10-15

    A well-known problem in x-ray microcomputed tomography is low sensitivity. Phase contrast imaging offers an increase of sensitivity of up to a factor of 10{sup 3} in the hard x-ray region, which makes it possible to image soft tissue and small density variations. If a sufficiently coherent x-ray beam, such as that obtained from a third generation synchrotron, is used, phase contrast can be obtained by simply moving the detector downstream of the imaged object. This setup is known as in-line or propagation based phase contrast imaging. A quantitative relationship exists between the phase shift induced by the object and the recorded intensity and inversion of this relationship is called phase retrieval. Since the phase shift is proportional to projections through the three-dimensional refractive index distribution in the object, once the phase is retrieved, the refractive index can be reconstructed by using the phase as input to a tomographic reconstruction algorithm. A comparison between four phase retrieval algorithms is presented. The algorithms are based on the transport of intensity equation (TIE), transport of intensity equation for weak absorption, the contrast transfer function (CTF), and a mixed approach between the CTF and TIE, respectively. The compared methods all rely on linearization of the relationship between phase shift and recorded intensity to yield fast phase retrieval algorithms. The phase retrieval algorithms are compared using both simulated and experimental data, acquired at the European Synchrotron Radiation Facility third generation synchrotron light source. The algorithms are evaluated in terms of two different reconstruction error metrics. While being slightly less computationally effective, the mixed approach shows the best performance in terms of the chosen criteria.

  4. Macropore Flow in Soil Columns: Investigations with Computer Tomography and Lattice Boltzmann Simulations

    NASA Astrophysics Data System (ADS)

    Schaap, M. G.; Tuller, M.; Guber, A.; Martin, M. A.; Martinez, F. S.; Pachepsky, Y.

    2007-12-01

    Soil structure greatly affects the ability of soil to transmit and to retain water, chemicals, and colloidal particles that can carry contaminants or be contaminants themselves, e.g. pathogenic microorganisms. No theory or empirical relationships have been developed to date to quantitatively relate parameters of soil structure and parameters of the contaminant transport in soils. The absence of theoretical advances in this area seriously hampers the ability to address issues of public concern, e.g. spread of contaminants introduced in the environment by agricultural activities. Recently, computer tomography of soils has become available to generate detailed images of soil pore space with high resolution and density. Successful applications of computer tomography in medical and material sciences show the great potential of this technique to create an exhaustive characterization of soil structure heterogeneity. In this presentation we investigate saturated flow through twelve undisturbed macroporous soil columns (7.62- cm sample diameter and 18-cm length) with lattice Boltzmann simulations. Saturated flow was measured for the complete columns, as well as on 2 cm sections for selected columns. Computed X-Ray tomography was performed on each of the columns, using the 420 kV X-ray source of a HYTEC FlashCT high-speed industrial CT scanner. The resolution was 116 microns per voxel, yielding a final tomography image of 656x656x1482 (~ 6.3 10E8) voxels. X-Ray CT observations typically provide "gray-scale" representations of the imaged object that must be segmented to yield discrete pore and particle geometry. Many segmentation algorithms are available, each yielding different final pore geometries thus potentially creating uncertainties in subsequent flow analyses. Lattice Boltzmann (LB) simulations will be presented only for some of the columns as the simulations are extremely computationally intensive (each simulation requires ~ 60 GB of computer RAM at the observed

  5. Efficient photon transport in positron emission tomography simulations using VMC++

    NASA Astrophysics Data System (ADS)

    Kawrakow, I.; Mitev, K.; Gerganov, G.; Madzhunkov, J.; Kirov, A.

    2008-02-01

    vmcPET, a VMC++ based fast code for simulating photon transport through the patient geometry for use in positron emission tomography related calculations, is presented. vmcPET is shown to be between 250 and 425 times faster than GATE in completely analog mode and up to 50000 times faster when using advanced variance reduction techniques. Excellent agreement between vmcPET and EGSnrc and GATE benchmarks is found. vmcPET is coupled to GATE via phase-space files of particles emerging from the patient geometry.

  6. Simulation study of respiratory-induced errors in cardiac positron emission tomography/computed tomography

    SciTech Connect

    Fitzpatrick, Gianna M.; Wells, R. Glenn

    2006-08-15

    Heart disease is a leading killer in Canada and positron emission tomography (PET) provides clinicians with in vivo metabolic information for diagnosing heart disease. Transmission data are usually acquired with {sup 68}Ge, although the advent of PET/CT scanners has made computed tomography (CT) an alternative option. The fast data acquisition of CT compared to PET may cause potential misregistration problems, leading to inaccurate attenuation correction (AC). Using Monte Carlo simulations and an anthropomorphic dynamic computer phantom, this study determines the magnitude and location of respiratory-induced errors in radioactivity uptake measured in cardiac PET/CT. A homogeneous tracer distribution in the heart was considered. The AC was based on (1) a time-averaged attenuation map (2) CT maps from a single phase of the respiratory cycle, and (3) CT maps phase matched to the emission data. Circumferential profiles of the heart uptake were compared and differences of up to 24% were found between the single-phase CT-AC method and the true phantom values. Simulation results were supported by a PET/CT canine study which showed differences of up to 10% in the heart uptake in the lung-heart boundary region when comparing {sup 68}Ge- to CT-based AC with the CT map acquired at end inhalation.

  7. Quantitative polarization and flow evaluation of choroid and sclera by multifunctional Jones matrix optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Sugiyama, S.; Hong, Y.-J.; Kasaragod, D.; Makita, S.; Miura, M.; Ikuno, Y.; Yasuno, Y.

    2016-03-01

    Quantitative evaluation of optical properties of choroid and sclera are performed by multifunctional optical coherence tomography. Five normal eyes, five glaucoma eyes and one choroidal atrophy eye are examined. The refractive error was found to be correlated with choroidal birefringence, polarization uniformity, and flow in addition to scleral birefringence among normal eyes. The significant differences were observed between the normal and the glaucoma eyes, as for choroidal polarization uniformity, flow and scleral birefringence. An automatic segmentation algorithm of retinal pigment epithelium and chorioscleral interface based on multifunctional signals is also presented.

  8. Numerical simulations of the thermoacoustic computed tomography breast imaging system

    NASA Astrophysics Data System (ADS)

    Kiser, William Lester, Jr.

    A thermoacoustic wave is produced when an object absorbs energy and experiences a subsequent thermal expansion. We have developed a Thermoacoustic Computed Tomography (TACT) breast imaging system to exploit the thermoacoustic phenomena as a method of soft tissue imaging. By exposing the breast to short pulses of 434 MHz microwaves, ultrasonic pulses are generated and detected with a hemispherical transducer array submersed in a water bath. Filtering and back projecting the transducer signals generates a 3-D image that maps the localized microwave absorption properties of the breast. In an effort to understand the factors limiting image quality, the TACT system was numerically simulated. The simulations were used to generate the transducer signals that would be collected by the TACT system during a scan of an object. These simulated data streams were then fed into the system image reconstruction software to provide images of simulated phantoms. The effects of transducer diameter, transducer response, transducer array geometry and stimulating pulse width on the spatial and contrast resolution of the system were quantified using the simulations. The spatial resolution was highly dependent upon location in the imaging volume. This was due to the off axis response of transducers of finite aperture. Simulated data were compared with experimental data, obtained by imaging a parallel-piped resolution phantom, to verify the accuracy of the simulation code. A contrast-detail phantom was numerically simulated to determine the ability of the system to image spheres of diameters <1 cm with absorption values on the order of physiologic saline, when located in a background of noise. The results of the contrast-detail analysis were dependent on the location of the spheres in the imaging volume and the diameter of the simulated transducers. This work sets the foundation for the initial image quality studies of the TACT system. Improvements to the current imaging system, based on

  9. Simulated quantum process tomography of quantum gates with Rydberg superatoms

    NASA Astrophysics Data System (ADS)

    Beterov, I. I.; Saffman, M.; Yakshina, E. A.; Tretyakov, D. B.; Entin, V. M.; Hamzina, G. N.; Ryabtsev, I. I.

    2016-06-01

    We have numerically simulated quantum tomography of single-qubit and two-qubit quantum gates with qubits represented by mesoscopic ensembles containing random numbers of atoms. Such ensembles of strongly interacting atoms in the regime of Rydberg blockade are known as Rydberg superatoms. The stimulated Raman adiabatic passage (STIRAP) in the regime of Rydberg blockade is used for determining Rydberg excitation in the ensemble, required for the storage of quantum information in the collective state of the atomic ensemble and implementation of two-qubit gates. The optimized shapes of the STIRAP pulses are used to achieve high fidelity of the population transfer. Our simulations confirm the validity and high fidelity of single-qubit and two-qubit gates with Rydberg superatoms.

  10. Diffraction tomography applied to simulated ultrasound through breast tissue

    NASA Astrophysics Data System (ADS)

    Chambers, David H.

    2002-11-01

    Diffraction tomography is used to obtain images of sound speed and attenuation of a slice of breast tissue obtained from the Visible Woman data set. Simulated ultrasound data was generated using an acoustic propagation code run on the ASCI Blue Pacific computer at Lawrence Livermore National Laboratory. Data was generated for a slice of healthy tissue, and a slice with simulated lesions to determine the ability of the imaging method to detect various abnormalities in the breast. In addition, the time reversal operator for the slice was constructed from the data and the eigenfunctions backpropagated into the slice as first suggested by Mast [Mast, Nachman, and Waag, J. Acoust. Soc. Am. 102(2)] to identify structures associated with each time reversal mode for both the healthy tissue and tissue with lesions.

  11. Quantitative three-dimensional photoacoustic tomography of the finger joints: an in vivo study

    NASA Astrophysics Data System (ADS)

    Sun, Yao; Sobel, Eric; Jiang, Huabei

    2009-11-01

    We present for the first time in vivo full three-dimensional (3-D) photoacoustic tomography (PAT) of the distal interphalangeal joint in a human subject. Both absorbed energy density and absorption coefficient images of the joint are quantitatively obtained using our finite-element-based photoacoustic image reconstruction algorithm coupled with the photon diffusion equation. The results show that major anatomical features in the joint along with the side arteries can be imaged with a 1-MHz transducer in a spherical scanning geometry. In addition, the cartilages associated with the joint can be quantitatively differentiated from the phalanx. This in vivo study suggests that the 3-D PAT method described has the potential to be used for early diagnosis of joint diseases such as osteoarthritis and rheumatoid arthritis.

  12. Experimental assessment of bone mineral density using quantitative computed tomography in holstein dairy cows.

    PubMed

    Maetani, Ayami; Itoh, Megumi; Nishihara, Kahori; Aoki, Takahiro; Ohtani, Masayuki; Shibano, Kenichi; Kayano, Mitsunori; Yamada, Kazutaka

    2016-08-01

    The aim of this study was to assess the measurement of bone mineral density (BMD) by quantitative computed tomography (QCT), comparing the relationships of BMD between QCT and dual-energy X-ray absorptiometry (DXA) and between QCT and radiographic absorptiometry (RA) in the metacarpal bone of Holstein dairy cows (n=27). A significant positive correlation was found between QCT and DXA measurements (r=0.70, P<0.01), and a significant correlation was found between QCT and RA measurements (r=0.50, P<0.01). We conclude that QCT provides quantitative evaluation of BMD in dairy cows, because BMD measured by QCT showed positive correlations with BMD measured by the two conventional methods: DXA and RA. PMID:27075115

  13. Quantitative microvascular hemoglobin mapping using visible light spectroscopic Optical Coherence Tomography

    PubMed Central

    Chong, Shau Poh; Merkle, Conrad W.; Leahy, Conor; Radhakrishnan, Harsha; Srinivasan, Vivek J.

    2015-01-01

    Quantification of chromophore concentrations in reflectance mode remains a major challenge for biomedical optics. Spectroscopic Optical Coherence Tomography (SOCT) provides depth-resolved spectroscopic information necessary for quantitative analysis of chromophores, like hemoglobin, but conventional SOCT analysis methods are applicable only to well-defined specular reflections, which may be absent in highly scattering biological tissue. Here, by fitting of the dynamic scattering signal spectrum in the OCT angiogram using a forward model of light propagation, we quantitatively determine hemoglobin concentrations directly. Importantly, this methodology enables mapping of both oxygen saturation and total hemoglobin concentration, or alternatively, oxyhemoglobin and deoxyhemoglobin concentration, simultaneously. Quantification was verified by ex vivo blood measurements at various pO2 and hematocrit levels. Imaging results from the rodent brain and retina are presented. Confounds including noise and scattering, as well as potential clinical applications, are discussed. PMID:25909026

  14. Experimental assessment of bone mineral density using quantitative computed tomography in holstein dairy cows

    PubMed Central

    MAETANI, Ayami; ITOH, Megumi; NISHIHARA, Kahori; AOKI, Takahiro; OHTANI, Masayuki; SHIBANO, Kenichi; KAYANO, Mitsunori; YAMADA, Kazutaka

    2016-01-01

    The aim of this study was to assess the measurement of bone mineral density (BMD) by quantitative computed tomography (QCT), comparing the relationships of BMD between QCT and dual-energy X-ray absorptiometry (DXA) and between QCT and radiographic absorptiometry (RA) in the metacarpal bone of Holstein dairy cows (n=27). A significant positive correlation was found between QCT and DXA measurements (r=0.70, P<0.01), and a significant correlation was found between QCT and RA measurements (r=0.50, P<0.01). We conclude that QCT provides quantitative evaluation of BMD in dairy cows, because BMD measured by QCT showed positive correlations with BMD measured by the two conventional methods: DXA and RA. PMID:27075115

  15. A computer simulation study of imaging flexural inhomogeneities using plate-wave diffraction tomography.

    PubMed

    Rohde, A H; Veidt, M; Rose, L R F; Homer, J

    2008-03-01

    This paper investigates the feasibility of plate-wave diffraction tomography for the reconstruction of flexural inhomogeneities in plates using the results of computer simulation studies. The numerical implementation of the fundamental reconstruction algorithm, which has recently been developed by Wang and Rose [C.H. Wang, L.R.F. Rose, Plate-wave diffraction tomography for structural health monitoring, Rev. Quant. Nondestr. Eval. 22 (2003) 1615-1622] is investigated addressing the essential effects of applying the discrete form of the Fourier diffraction theorem for solving the inverse problem as discussed by Kak and Slaney [A.C. Kak, M. Slaney, Principles of Computerized Tomographic Imaging, IEEE Press, New York, 1988] for the acoustic case, viz. diffraction limited sensitivity, influence of weak scatterer assumption, damage location and scatter field data processing in time and Fourier space as well as experimental limitations such as finite receiver length and limited views. The feasibility of the imaging technique is investigated for cylindrical inhomogeneities of various severities and relative position within the interrogation space and a normal incident interrogation configuration. The results show that plate-wave diffraction tomography enables the quantitative reconstruction of location, size and severity of plate damage with excellent sensitivity and offers the potential for detecting corrosion thinning, disbonds and delamination damage in structural integrity management applications. PMID:18022207

  16. Quantitative material decomposition using spectral computed tomography with an energy-resolved photon-counting detector

    NASA Astrophysics Data System (ADS)

    Lee, Seungwan; Choi, Yu-Na; Kim, Hee-Joung

    2014-09-01

    Dual-energy computed tomography (CT) techniques have been used to decompose materials and characterize tissues according to their physical and chemical compositions. However, these techniques are hampered by the limitations of conventional x-ray detectors operated in charge integrating mode. Energy-resolved photon-counting detectors provide spectral information from polychromatic x-rays using multiple energy thresholds. These detectors allow simultaneous acquisition of data in different energy ranges without spectral overlap, resulting in more efficient material decomposition and quantification for dual-energy CT. In this study, a pre-reconstruction dual-energy CT technique based on volume conservation was proposed for three-material decomposition. The technique was combined with iterative reconstruction algorithms by using a ray-driven projector in order to improve the quality of decomposition images and reduce radiation dose. A spectral CT system equipped with a CZT-based photon-counting detector was used to implement the proposed dual-energy CT technique. We obtained dual-energy images of calibration and three-material phantoms consisting of low atomic number materials from the optimal energy bins determined by Monte Carlo simulations. The material decomposition process was accomplished by both the proposed and post-reconstruction dual-energy CT techniques. Linear regression and normalized root-mean-square error (NRMSE) analyses were performed to evaluate the quantitative accuracy of decomposition images. The calibration accuracy of the proposed dual-energy CT technique was higher than that of the post-reconstruction dual-energy CT technique, with fitted slopes of 0.97-1.01 and NRMSEs of 0.20-4.50% for all basis materials. In the three-material phantom study, the proposed dual-energy CT technique decreased the NRMSEs of measured volume fractions by factors of 0.17-0.28 compared to the post-reconstruction dual-energy CT technique. It was concluded that the

  17. Quantitative material decomposition using spectral computed tomography with an energy-resolved photon-counting detector.

    PubMed

    Lee, Seungwan; Choi, Yu-Na; Kim, Hee-Joung

    2014-09-21

    Dual-energy computed tomography (CT) techniques have been used to decompose materials and characterize tissues according to their physical and chemical compositions. However, these techniques are hampered by the limitations of conventional x-ray detectors operated in charge integrating mode. Energy-resolved photon-counting detectors provide spectral information from polychromatic x-rays using multiple energy thresholds. These detectors allow simultaneous acquisition of data in different energy ranges without spectral overlap, resulting in more efficient material decomposition and quantification for dual-energy CT. In this study, a pre-reconstruction dual-energy CT technique based on volume conservation was proposed for three-material decomposition. The technique was combined with iterative reconstruction algorithms by using a ray-driven projector in order to improve the quality of decomposition images and reduce radiation dose. A spectral CT system equipped with a CZT-based photon-counting detector was used to implement the proposed dual-energy CT technique. We obtained dual-energy images of calibration and three-material phantoms consisting of low atomic number materials from the optimal energy bins determined by Monte Carlo simulations. The material decomposition process was accomplished by both the proposed and post-reconstruction dual-energy CT techniques. Linear regression and normalized root-mean-square error (NRMSE) analyses were performed to evaluate the quantitative accuracy of decomposition images. The calibration accuracy of the proposed dual-energy CT technique was higher than that of the post-reconstruction dual-energy CT technique, with fitted slopes of 0.97-1.01 and NRMSEs of 0.20-4.50% for all basis materials. In the three-material phantom study, the proposed dual-energy CT technique decreased the NRMSEs of measured volume fractions by factors of 0.17-0.28 compared to the post-reconstruction dual-energy CT technique. It was concluded that the

  18. Objective interpretation of induced polarization tomography using a quantitative approach for the investigation of periglacial environments

    NASA Astrophysics Data System (ADS)

    Banville, David Roy; Fortier, Richard; Dupuis, Christian

    2016-07-01

    The objective interpretation of induced polarization tomography for applications in periglacial environments is sometimes challenging using smoothness-regularized least square inversion because strong resistivity contrasts are often present. Ambiguities arise from the regularization process which smooths the contrast between layers and from artifacts created by the inversion. In periglacial environments, where frozen and thawed ground can coexist with large resistivity contrasts, such artefacts are often found in the models of electrical resistivity. To assess reliable cryohydrogeological models from the inversion of induced polarization tomography, quantitative interpretation criteria are needed. The present work describes a methodology based on forward-inverse modeling to build a cryohydrogeological model from induced polarization data and prior information using the resistivity and chargeability gradients to map transitions between adjacent layers. This methodology is tested on field-data acquired over a coarse grained aquifer within a glaciomarine deposit and ice-rich permafrost mounds within marine sediments. Delineation of the permafrost base is achieved despite the presence of an inversion artefact. The results of the interpretation are used to further constrain the inversion in order to map the ice-content based on the resistivity model and an empirical relationship. The proposed methodology provides a way to extract quantitative information even in difficult environmental settings.

  19. Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography

    PubMed Central

    Rah, Jong-Cheol; Bas, Erhan; Colonell, Jennifer; Mishchenko, Yuriy; Karsh, Bill; Fetter, Richard D.; Myers, Eugene W.; Chklovskii, Dmitri B.; Svoboda, Karel; Harris, Timothy D.; Isaac, John T. R.

    2013-01-01

    The subcellular locations of synapses on pyramidal neurons strongly influences dendritic integration and synaptic plasticity. Despite this, there is little quantitative data on spatial distributions of specific types of synaptic input. Here we use array tomography (AT), a high-resolution optical microscopy method, to examine thalamocortical (TC) input onto layer 5 pyramidal neurons. We first verified the ability of AT to identify synapses using parallel electron microscopic analysis of TC synapses in layer 4. We then use large-scale array tomography (LSAT) to measure TC synapse distribution on L5 pyramidal neurons in a 1.00 × 0.83 × 0.21 mm3 volume of mouse somatosensory cortex. We found that TC synapses primarily target basal dendrites in layer 5, but also make a considerable input to proximal apical dendrites in L4, consistent with previous work. Our analysis further suggests that TC inputs are biased toward certain branches and, within branches, synapses show significant clustering with an excess of TC synapse nearest neighbors within 5–15 μm compared to a random distribution. Thus, we show that AT is a sensitive and quantitative method to map specific types of synaptic input on the dendrites of entire neurons. We anticipate that this technique will be of wide utility for mapping functionally-relevant anatomical connectivity in neural circuits. PMID:24273494

  20. Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography.

    PubMed

    Rah, Jong-Cheol; Bas, Erhan; Colonell, Jennifer; Mishchenko, Yuriy; Karsh, Bill; Fetter, Richard D; Myers, Eugene W; Chklovskii, Dmitri B; Svoboda, Karel; Harris, Timothy D; Isaac, John T R

    2013-01-01

    The subcellular locations of synapses on pyramidal neurons strongly influences dendritic integration and synaptic plasticity. Despite this, there is little quantitative data on spatial distributions of specific types of synaptic input. Here we use array tomography (AT), a high-resolution optical microscopy method, to examine thalamocortical (TC) input onto layer 5 pyramidal neurons. We first verified the ability of AT to identify synapses using parallel electron microscopic analysis of TC synapses in layer 4. We then use large-scale array tomography (LSAT) to measure TC synapse distribution on L5 pyramidal neurons in a 1.00 × 0.83 × 0.21 mm(3) volume of mouse somatosensory cortex. We found that TC synapses primarily target basal dendrites in layer 5, but also make a considerable input to proximal apical dendrites in L4, consistent with previous work. Our analysis further suggests that TC inputs are biased toward certain branches and, within branches, synapses show significant clustering with an excess of TC synapse nearest neighbors within 5-15 μm compared to a random distribution. Thus, we show that AT is a sensitive and quantitative method to map specific types of synaptic input on the dendrites of entire neurons. We anticipate that this technique will be of wide utility for mapping functionally-relevant anatomical connectivity in neural circuits. PMID:24273494

  1. Radiation dose to positron emission tomography technologists during quantitative versus qualitative studies.

    PubMed

    McCormick, V A; Miklos, J A

    1993-05-01

    Positron emission tomography technologists were monitored with thermoluminescent dosimeters (TLDs) during qualitative and quantitative studies. Doses to technologists during specific tasks were also measured. The technologists received at least twice as much radiation during the quantitative as the qualitative studies. The average dose per study for qualitative studies was 0.017 mSv (1.7 mrem) shallow and 0.014 mSv (1.4 mrem) deep. The average dose per study for the quantitative studies was 0.05 mSv (5 mrem) shallow and 0.04 mSv (4 mrem) deep. The average dose per study was based on the TLD dose accumulated over studies conducted over four 2-mo and one 1-mo intervals. The dose incurred by the technologists each time they drew a radioactive dose was 0.002 mSv (0.2 mrem) shallow and 0.001 mSv (0.1 mrem) deep. The doses received during injection were 0.014 mSv (1.4 mrem) shallow and 0.007 mSv (0.7 mrem) deep. Doses received during blood sampling were 0.016 mSv (1.6 mrem) shallow and 0.014 mSv (1.4 mrem) deep. During quantitative studies, the technologist received a much greater dose than during its qualitative counterpart due to the blood sampling process and increased time in the room with the radioactive patient. PMID:8478709

  2. Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST)

    PubMed Central

    Aronova, M. A.; Kim, Y. C.; Harmon, R.; Sousa, A. A.; Zhang, G.; Leapman, R. D.

    2007-01-01

    We describe the development of quantitative electron spectroscopic tomography (QuEST), which provides three-dimensional distributions of elements on a nanometer scale. Specifically, it is shown that QuEST can be applied to map the distribution of phosphorus in unstained sections of embedded cells. A series of 2D elemental maps is derived from images recorded in the energy filtering transmission electron microscope for a range of specimen tilt angles. A quantitative 3-D elemental distribution is then reconstructed from the elemental tilt series. To obtain accurate quantitative elemental distributions it is necessary to correct for plural inelastic scattering at the phosphorus L2,3 edge, which is achieved by acquiring unfiltered and zero-loss images at each tilt angle. The data are acquired automatically using a cross correlation technique to correct for specimen drift and focus change between successive tilt angles. An algorithm based on the simultaneous iterative reconstruction technique (SIRT) is implemented to obtain quantitative information about the number of phosphorus atoms associated with each voxel in the reconstructed volume. We assess the accuracy of QuEST by determining the phosphorus content of ribosomes in a eukaryotic cell, and then apply it to estimate the density of nucleic acid in chromatin of the cell's nucleus. From our experimental data, we estimate that the sensitivity for detecting phosphorus is 20 atoms in a 2.7 nm-sized voxel. PMID:17693097

  3. Diagnosis of simulated condylar bone defects using panoramic radiography, spiral tomography and cone-beam computed tomography: A comparison study

    PubMed Central

    Salemi, Fatemeh; Shokri, Abbas; Baharvand, Maryam

    2015-01-01

    Objectives: Radiographic examination is one of the most important parts of the clinical assessment routine for temporomandibular disorders. The aim of this study was to compare the diagnostic accuracy of cone-beam computed tomography(CBCT) with panoramic radiography and spiral computed tomography for the detection of the simulated mandibular condyle bone lesions. Study Design: The sample consisted of 10 TMJs from 5 dried human skulls. Simulated erosive and osteophytic lesions were created in 3 different sizes using round diamond bur and bone chips, respectively. Panoramic radiography, spiral tomography and cone-beam computed tomography were used in defect detection. Data were statistically analyzed with the Mann-Whitney test. The reliability and degrees of agreement between two observers were also determined by the mean of Cohen’s Kappa analysis. Results: CBCT had a statistically significant superiority than other studied techniques in detection of both erosive and osteophytic lesions with different sizes. There were significant differences between tomography and panoramic in correct detection of both erosive and osteophytic lesions with 1mm and 1.5 mm in size. However, there were no significant differences between Tomography and Panoramic in correct detection of both erosive and osteophytic lesions with 0.5 mm in size. Conclusions: CBCT images provide a greater diagnostic accuracy than spiral tomography and panoramic radiography in the detection of condylar bone erosions and osteophytes. Key words:Bone defect, Condyle, CBCT, Panoramic, radiography. PMID:25810839

  4. Neutron stimulated emission computed tomography: a Monte Carlo simulation approach.

    PubMed

    Sharma, A C; Harrawood, B P; Bender, J E; Tourassi, G D; Kapadia, A J

    2007-10-21

    A Monte Carlo simulation has been developed for neutron stimulated emission computed tomography (NSECT) using the GEANT4 toolkit. NSECT is a new approach to biomedical imaging that allows spectral analysis of the elements present within the sample. In NSECT, a beam of high-energy neutrons interrogates a sample and the nuclei in the sample are stimulated to an excited state by inelastic scattering of the neutrons. The characteristic gammas emitted by the excited nuclei are captured in a spectrometer to form multi-energy spectra. Currently, a tomographic image is formed using a collimated neutron beam to define the line integral paths for the tomographic projections. These projection data are reconstructed to form a representation of the distribution of individual elements in the sample. To facilitate the development of this technique, a Monte Carlo simulation model has been constructed from the GEANT4 toolkit. This simulation includes modeling of the neutron beam source and collimation, the samples, the neutron interactions within the samples, the emission of characteristic gammas, and the detection of these gammas in a Germanium crystal. In addition, the model allows the absorbed radiation dose to be calculated for internal components of the sample. NSECT presents challenges not typically addressed in Monte Carlo modeling of high-energy physics applications. In order to address issues critical to the clinical development of NSECT, this paper will describe the GEANT4 simulation environment and three separate simulations performed to accomplish three specific aims. First, comparison of a simulation to a tomographic experiment will verify the accuracy of both the gamma energy spectra produced and the positioning of the beam relative to the sample. Second, parametric analysis of simulations performed with different user-defined variables will determine the best way to effectively model low energy neutrons in tissue, which is a concern with the high hydrogen content in

  5. Experimental investigation of bone mineral density in Thoroughbreds using quantitative computed tomography.

    PubMed

    Yamada, Kazutaka; Sato, Fumio; Higuchi, Tohru; Nishihara, Kaori; Kayano, Mitsunori; Sasaki, Naoki; Nambo, Yasuo

    2015-01-01

    Bone mineral density (BMD) is one of the indications of the strength and health. BMD measured by quantitative computed tomography (QCT) was compared with that measured by dual energy X-ray absorptiometry (DXA) and radiographic bone aluminum equivalence (RBAE). Limbs were removed from horses that had been euthanized for reasons not associated with this study. Sixteen limbs (left and right metacarpals and metatarsals) from 4 horses were used to compare BMD as measured by QCT with those measured by DXA and RBAE. There was a strong correlation between BMD values measured by QCT and those measured by DXA (R(2)=0.85); correlation was also observed between values obtained by QCT and those obtained by RBAE (R(2)=0.61). To investigate changes in BMD with age, 37 right metacarpal bones, including 7 from horses euthanized because of fracture were examined by QCT. The BMD value of samples from horses dramatically increased until 2 years of age and then plateaued, a pattern similar to the growth curve. The BMD values of bone samples from horses euthanized because of fracture were within the population range, and samples of morbid fracture were not included. The relationship between BMD and age provides a reference for further quantitative studies of bone development and remodeling. Quantitative measurement of BMD using QCT may have great potential for the evaluation of bone biology for breeding and rearing management. PMID:26435681

  6. Experimental investigation of bone mineral density in Thoroughbreds using quantitative computed tomography

    PubMed Central

    YAMADA, Kazutaka; SATO, Fumio; HIGUCHI, Tohru; NISHIHARA, Kaori; KAYANO, Mitsunori; SASAKI, Naoki; NAMBO, Yasuo

    2015-01-01

    ABSTRACT Bone mineral density (BMD) is one of the indications of the strength and health. BMD measured by quantitative computed tomography (QCT) was compared with that measured by dual energy X-ray absorptiometry (DXA) and radiographic bone aluminum equivalence (RBAE). Limbs were removed from horses that had been euthanized for reasons not associated with this study. Sixteen limbs (left and right metacarpals and metatarsals) from 4 horses were used to compare BMD as measured by QCT with those measured by DXA and RBAE. There was a strong correlation between BMD values measured by QCT and those measured by DXA (R2=0.85); correlation was also observed between values obtained by QCT and those obtained by RBAE (R2=0.61). To investigate changes in BMD with age, 37 right metacarpal bones, including 7 from horses euthanized because of fracture were examined by QCT. The BMD value of samples from horses dramatically increased until 2 years of age and then plateaued, a pattern similar to the growth curve. The BMD values of bone samples from horses euthanized because of fracture were within the population range, and samples of morbid fracture were not included. The relationship between BMD and age provides a reference for further quantitative studies of bone development and remodeling. Quantitative measurement of BMD using QCT may have great potential for the evaluation of bone biology for breeding and rearing management. PMID:26435681

  7. Automated quantitative assessment of three-dimensional bioprinted hydrogel scaffolds using optical coherence tomography

    PubMed Central

    Wang, Ling; Xu, Mingen; Zhang, LieLie; Zhou, QingQing; Luo, Li

    2016-01-01

    Reconstructing and quantitatively assessing the internal architecture of opaque three-dimensional (3D) bioprinted hydrogel scaffolds is difficult but vital to the improvement of 3D bioprinting techniques and to the fabrication of functional engineered tissues. In this study, swept-source optical coherence tomography was applied to acquire high-resolution images of hydrogel scaffolds. Novel 3D gelatin/alginate hydrogel scaffolds with six different representative architectures were fabricated using our 3D bioprinting system. Both the scaffold material networks and the interconnected flow channel networks were reconstructed through volume rendering and binarisation processing to provide a 3D volumetric view. An image analysis algorithm was developed based on the automatic selection of the spatially-isolated region-of–interest. Via this algorithm, the spatially-resolved morphological parameters including pore size, pore shape, strut size, surface area, porosity, and interconnectivity were quantified precisely. Fabrication defects and differences between the designed and as-produced scaffolds were clearly identified in both 2D and 3D; the locations and dimensions of each of the fabrication defects were also defined. It concludes that this method will be a key tool for non-destructive and quantitative characterization, design optimisation and fabrication refinement of 3D bioprinted hydrogel scaffolds. Furthermore, this method enables investigation into the quantitative relationship between scaffold structure and biological outcome. PMID:27231597

  8. Automated quantitative assessment of three-dimensional bioprinted hydrogel scaffolds using optical coherence tomography.

    PubMed

    Wang, Ling; Xu, Mingen; Zhang, LieLie; Zhou, QingQing; Luo, Li

    2016-03-01

    Reconstructing and quantitatively assessing the internal architecture of opaque three-dimensional (3D) bioprinted hydrogel scaffolds is difficult but vital to the improvement of 3D bioprinting techniques and to the fabrication of functional engineered tissues. In this study, swept-source optical coherence tomography was applied to acquire high-resolution images of hydrogel scaffolds. Novel 3D gelatin/alginate hydrogel scaffolds with six different representative architectures were fabricated using our 3D bioprinting system. Both the scaffold material networks and the interconnected flow channel networks were reconstructed through volume rendering and binarisation processing to provide a 3D volumetric view. An image analysis algorithm was developed based on the automatic selection of the spatially-isolated region-of-interest. Via this algorithm, the spatially-resolved morphological parameters including pore size, pore shape, strut size, surface area, porosity, and interconnectivity were quantified precisely. Fabrication defects and differences between the designed and as-produced scaffolds were clearly identified in both 2D and 3D; the locations and dimensions of each of the fabrication defects were also defined. It concludes that this method will be a key tool for non-destructive and quantitative characterization, design optimisation and fabrication refinement of 3D bioprinted hydrogel scaffolds. Furthermore, this method enables investigation into the quantitative relationship between scaffold structure and biological outcome. PMID:27231597

  9. Quantitative analysis of Si/SiGeC superlattices using atom probe tomography.

    PubMed

    Estivill, Robert; Grenier, Adeline; Duguay, Sébastien; Vurpillot, François; Terlier, Tanguy; Barnes, Jean-Paul; Hartmann, Jean-Michel; Blavette, Didier

    2015-12-01

    SiGe and its alloys are used as key materials in innovative electronic devices. The analysis of these materials together with the localisation of dopants and impurities on a very fine scale is of crucial importance for better understanding their electronic properties. The quantification of carbon and germanium in an as-grown Si/SiGeC superlattice has been investigated using Atom Probe Tomography as a function of analysis conditions and sample anneal temperature. The mass spectrum is heavily influenced by the analysis conditions and chemical identification is needed. It was found that quantitative results are obtained using a intermediate electric field. The evaporation of carbon ions shows a strong spatial and temporal correlation. A series of annealed samples have been analysed, presenting an inhomogeneous carbon distribution, appearing in the shape of small clusters. These findings confirm previous results and give a better understanding of the processes occurring in these technologically important materials. PMID:25814020

  10. Delineation and quantitation of brain lesions by fuzzy clustering in positron emission tomography.

    PubMed

    Boudraa, A E; Champier, J; Cinotti, L; Bordet, J C; Lavenne, F; Mallet, J J

    1996-01-01

    In this study, we investigate the application of the fuzzy clustering to the anatomical localization and quantitation of brain lesions in Positron Emission Tomography (PET) images. The method is based on the Fuzzy C-Means (FCM) algorithm. The algorithm segments the PET image data points into a given number of clusters. Each cluster is an homogeneous region of the brain (e.g. tumor). A feature vector is assigned to a cluster which has the highest membership degree. Having the label affected by the FCM algorithm to a cluster, one may easily compute the corresponding spatial localization, area and perimeter. Studies concerning the evolution of a tumor after different treatments in two patients are presented. PMID:8891420

  11. Evaluation of dental enamel caries assessment using Quantitative Light Induced Fluorescence and Optical Coherence Tomography.

    PubMed

    Maia, Ana Marly Araújo; de Freitas, Anderson Zanardi; de L Campello, Sergio; Gomes, Anderson Stevens Leônidas; Karlsson, Lena

    2016-06-01

    An in vitro study of morphological alterations between sound dental structure and artificially induced white spot lesions in human teeth, was performed through the loss of fluorescence by Quantitative Light-Induced Fluorescence (QLF) and the alterations of the light attenuation coefficient by Optical Coherence Tomography (OCT). To analyze the OCT images using a commercially available system, a special algorithm was applied, whereas the QLF images were analyzed using the software available in the commercial system employed. When analyzing the sound region against white spot lesions region by QLF, a reduction in the fluorescence intensity was observed, whilst an increase of light attenuation by the OCT system occurred. Comparison of the percentage of alteration between optical properties of sound and artificial enamel caries regions showed that OCT processed images through the attenuation of light enhanced the tooth optical alterations more than fluorescence detected by QLF System. QLF versus OCT imaging of enamel caries: a photonics assessment. PMID:26351155

  12. Sub-cellular quantitative optical diffraction tomography with digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Charrière, Florian; Kühn, Jonas; Colomb, Tristan; Cuche, Etienne; Marquet, Pierre; Depeursinge, Christian

    2007-02-01

    Digital holographic microscopy (DHM) is an interferometric technique, providing quantitative mapping of the phase shift induced by semi-transparent microscopic specimens, such as cells, with sub-wavelength resolution along the optical axis. Thanks to actual PCs and CCDs, DHM provides nowadays cost-effective instruments for real-time measurements at very high acquisition rates, with sub-micron transverse resolution. However, DHM phase images do not reveal the threedimensional (3D) internal distribution of refractive index, but a phase shift resulting from a mean refractive index (RI) integrated over the cellular thickness. Standard optical diffraction tomography (ODT) techniques can be efficiently applied to reveal internal structures and to measure 3D RI spatial distributions, by recording 2D DHM phase data for different sample orientations or illumination beam direction, in order to fill up entirely the Ewald sphere in the Fourier space. The 3D refractive index can then be reconstructed, even in the direct space with backpropagation algorithms or from the Fourier space with inverse Fourier transform. The presented technique opens wide perspectives in 3D cell imaging: the DHM-based micro-tomography furnishes invaluable data on the cell components optical properties, potentially leading to information about organelles intracellular distribution. Results obtained on biological specimens will be presented. Morphometric measurements can be extracted from the tomographic data, by detection based on the refractive index contrast within the 3D reconstructions. Results and perspectives about sub-cellular organelles identification inside the cell will also be exposed.

  13. Swept source optical coherence tomography for quantitative and qualitative assessment of dental composite restorations

    NASA Astrophysics Data System (ADS)

    Sadr, Alireza; Shimada, Yasushi; Mayoral, Juan Ricardo; Hariri, Ilnaz; Bakhsh, Turki A.; Sumi, Yasunori; Tagami, Junji

    2011-03-01

    The aim of this work was to explore the utility of swept-source optical coherence tomography (SS-OCT) for quantitative evaluation of dental composite restorations. The system (Santec, Japan) with a center wavelength of around 1300 nm and axial resolution of 12 μm was used to record data during and after placement of light-cured composites. The Fresnel phenomenon at the interfacial defects resulted in brighter areas indicating gaps as small as a few micrometers. The gap extension at the interface was quantified and compared to the observation by confocal laser scanning microscope after trimming the specimen to the same cross-section. Also, video imaging of the composite during polymerization could provide information about real-time kinetics of contraction stress and resulting gaps, distinguishing them from those gaps resulting from poor adaptation of composite to the cavity prior to polymerization. Some samples were also subjected to a high resolution microfocus X-ray computed tomography (μCT) assessment; it was found that differentiation of smaller gaps from the radiolucent bonding layer was difficult with 3D μCT. Finally, a clinical imaging example using a newly developed dental SS-OCT system with an intra-oral scanning probe (Panasonic Healthcare, Japan) is presented. SS-OCT is a unique tool for clinical assessment and laboratory research on resin-based dental restorations. Supported by GCOE at TMDU and NCGG.

  14. A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples

    NASA Astrophysics Data System (ADS)

    Beasley, D. G.; Alves, L. C.; Barberet, Ph.; Bourret, S.; Devès, G.; Gordillo, N.; Michelet, C.; Le Trequesser, Q.; Marques, A. C.; Seznec, H.; da Silva, R. C.

    2014-07-01

    The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans - a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

  15. In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models

    PubMed Central

    Liu, Junting; Wang, Yabin; Qu, Xiaochao; Li, Xiangsi; Ma, Xiaopeng; Han, Runqiang; Hu, Zhenhua; Chen, Xueli; Sun, Dongdong; Zhang, Rongqing; Chen, Duofang; Chen, Dan; Chen, Xiaoyuan; Liang, Jimin; Cao, Feng; Tian, Jie

    2010-01-01

    Bioluminescence tomography (BLT) is a new optical molecular imaging modality, which can monitor both physiological and pathological processes by using bioluminescent light-emitting probes in small living animal. Especially, this technology possesses great potential in drug development, early detection, and therapy monitoring in preclinical settings. In the present study, we developed a dual modality BLT prototype system with Micro-computed tomography (MicroCT) registration approach, and improved the quantitative reconstruction algorithm based on adaptive hp finite element method (hp-FEM). Detailed comparisons of source reconstruction between the heterogeneous and homogeneous mouse models were performed. The models include mice with implanted luminescence source and tumor-bearing mice with firefly luciferase report gene. Our data suggest that the reconstruction based on heterogeneous mouse model is more accurate in localization and quantification than the homogeneous mouse model with appropriate optical parameters and that BLT allows super-early tumor detection in vivo based on tomographic reconstruction of heterogeneous mouse model signal. PMID:20588440

  16. Simulating realistic predator signatures in quantitative fatty acid signature analysis

    USGS Publications Warehouse

    Bromaghin, Jeffrey F.

    2015-01-01

    Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

  17. Quantitative shear wave imaging optical coherence tomography for noncontact mechanical characterization of myocardium

    NASA Astrophysics Data System (ADS)

    Wang, Shang; Lopez, Andrew L.; Morikawa, Yuka; Tao, Ge; Li, Jiasong; Larina, Irina V.; Martin, James F.; Larin, Kirill V.

    2015-03-01

    Optical coherence elastography (OCE) is an emerging low-coherence imaging technique that provides noninvasive assessment of tissue biomechanics with high spatial resolution. Among various OCE methods, the capability of quantitative measurement of tissue elasticity is of great importance for tissue characterization and pathology detection across different samples. Here we report a quantitative OCE technique, termed quantitative shear wave imaging optical coherence tomography (Q-SWI-OCT), which enables noncontact measurement of tissue Young's modulus based on the ultra-fast imaging of the shear wave propagation inside the sample. A focused air-puff device is used to interrogate the tissue with a low-pressure short-duration air stream that stimulates a localized displacement with the scale at micron level. The propagation of this tissue deformation in the form of shear wave is captured by a phase-sensitive OCT system running with the scan of the M-mode imaging over the path of the wave propagation. The temporal characteristics of the shear wave is quantified based on the cross-correlation of the tissue deformation profiles at all the measurement locations, and linear regression is utilized to fit the data plotted in the domain of time delay versus wave propagation distance. The wave group velocity is thus calculated, which results in the quantitative measurement of the Young's modulus. As the feasibility demonstration, experiments are performed on tissuemimicking phantoms with different agar concentrations and the quantified elasticity values with Q-SWI-OCT agree well with the uniaxial compression tests. For functional characterization of myocardium with this OCE technique, we perform our pilot experiments on ex vivo mouse cardiac muscle tissues with two studies, including 1) elasticity difference of cardiac muscle under relaxation and contract conditions and 2) mechanical heterogeneity of the heart introduced by the muscle fiber orientation. Our results suggest the

  18. Quantitative and dynamic measurements of biological fresh samples with X-ray phase contrast tomography

    PubMed Central

    Hoshino, Masato; Uesugi, Kentaro; Tsukube, Takuro; Yagi, Naoto

    2014-01-01

    X-ray phase contrast tomography using a Talbot grating interferometer was applied to biological fresh samples which were not fixed by any fixatives. To achieve a high-throughput measurement for the fresh samples the X-ray phase contrast tomography measurement procedure was improved. The three-dimensional structure of a fresh mouse fetus was clearly depicted as a mass density map using X-ray phase contrast tomography. The mouse fetus measured in the fresh state was then fixed by formalin and measured in the fixed state. The influence of the formalin fixation on soft tissue was quantitatively evaluated by comparing the fresh and fixed samples. X-ray phase contrast tomography was also applied to the dynamic measurement of a biological fresh sample. Morphological changes of a ring-shaped fresh pig aorta were measured tomographically under different degrees of stretching. PMID:25343804

  19. Quantitative Micro-Computed Tomography Imaging of Vascular Dysfunction in Progressive Kidney Diseases

    PubMed Central

    Ehling, Josef; Bábíčková, Janka; Gremse, Felix; Klinkhammer, Barbara M.; Baetke, Sarah; Knuechel, Ruth; Kiessling, Fabian; Floege, Jürgen; Lammers, Twan; Boor, Peter

    2015-01-01

    Progressive kidney diseases and renal fibrosis are associated with endothelial injury and capillary rarefaction. However, our understanding of these processes has been hampered by the lack of tools enabling the quantitative and noninvasive monitoring of vessel functionality. Here, we used micro-computed tomography (μCT) for anatomical and functional imaging of vascular alterations in three murine models with distinct mechanisms of progressive kidney injury: ischemia-reperfusion (I/R, days 1–56), unilateral ureteral obstruction (UUO, days 1–10), and Alport mice (6–8 weeks old). Contrast-enhanced in vivo μCT enabled robust, noninvasive, and longitudinal monitoring of vessel functionality and revealed a progressive decline of the renal relative blood volume in all models. This reduction ranged from −20% in early disease stages to −61% in late disease stages and preceded fibrosis. Upon Microfil perfusion, high-resolution ex vivo μCT allowed quantitative analyses of three-dimensional vascular networks in all three models. These analyses revealed significant and previously unrecognized alterations of preglomerular arteries: a reduction in vessel diameter, a prominent reduction in vessel branching, and increased vessel tortuosity. In summary, using μCT methodology, we revealed insights into macro-to-microvascular alterations in progressive renal disease and provide a platform that may serve as the basis to evaluate vascular therapeutics in renal disease. PMID:26195818

  20. Quantitative performance characterization of three-dimensional noncontact fluorescence molecular tomography.

    PubMed

    Favicchio, Rosy; Psycharakis, Stylianos; Schönig, Kai; Bartsch, Dusan; Mamalaki, Clio; Papamatheakis, Joseph; Ripoll, Jorge; Zacharakis, Giannis

    2016-02-01

    Fluorescent proteins and dyes are routine tools for biological research to describe the behavior of genes, proteins, and cells, as well as more complex physiological dynamics such as vessel permeability and pharmacokinetics. The use of these probes in whole body in vivo imaging would allow extending the range and scope of current biomedical applications and would be of great interest. In order to comply with a wide variety of application demands, in vivo imaging platform requirements span from wide spectral coverage to precise quantification capabilities. Fluorescence molecular tomography (FMT) detects and reconstructs in three dimensions the distribution of a fluorophore in vivo. Noncontact FMT allows fast scanning of an excitation source and noninvasive measurement of emitted fluorescent light using a virtual array detector operating in free space. Here, a rigorous process is defined that fully characterizes the performance of a custom-built horizontal noncontact FMT setup. Dynamic range, sensitivity, and quantitative accuracy across the visible spectrum were evaluated using fluorophores with emissions between 520 and 660 nm. These results demonstrate that high-performance quantitative three-dimensional visible light FMT allowed the detection of challenging mesenteric lymph nodes in vivo and the comparison of spectrally distinct fluorescent reporters in cell culture. PMID:26891600

  1. Quantitative performance characterization of three-dimensional noncontact fluorescence molecular tomography

    NASA Astrophysics Data System (ADS)

    Favicchio, Rosy; Psycharakis, Stylianos; Schönig, Kai; Bartsch, Dusan; Mamalaki, Clio; Papamatheakis, Joseph; Ripoll, Jorge; Zacharakis, Giannis

    2016-02-01

    Fluorescent proteins and dyes are routine tools for biological research to describe the behavior of genes, proteins, and cells, as well as more complex physiological dynamics such as vessel permeability and pharmacokinetics. The use of these probes in whole body in vivo imaging would allow extending the range and scope of current biomedical applications and would be of great interest. In order to comply with a wide variety of application demands, in vivo imaging platform requirements span from wide spectral coverage to precise quantification capabilities. Fluorescence molecular tomography (FMT) detects and reconstructs in three dimensions the distribution of a fluorophore in vivo. Noncontact FMT allows fast scanning of an excitation source and noninvasive measurement of emitted fluorescent light using a virtual array detector operating in free space. Here, a rigorous process is defined that fully characterizes the performance of a custom-built horizontal noncontact FMT setup. Dynamic range, sensitivity, and quantitative accuracy across the visible spectrum were evaluated using fluorophores with emissions between 520 and 660 nm. These results demonstrate that high-performance quantitative three-dimensional visible light FMT allowed the detection of challenging mesenteric lymph nodes in vivo and the comparison of spectrally distinct fluorescent reporters in cell culture.

  2. Quantitative Three-Dimensional Imaging of Live Avian Embryonic Morphogenesis Via Micro-computed Tomography

    PubMed Central

    Henning, Alyssa L.; Jiang, Michael X.; Yalcin, Huseyin C.; Butcher, Jonathan T.

    2013-01-01

    Many clinically relevant congenital malformations arise during mid to late embryonic stages. This period is challenging to image quantitatively in live embryos, necessitating the use of multiple specimens with increased experimental variability. Here we establish X-ray and blood-pool computed tomography (CT) contrast agent toxicity and teratogenesis thresholds for 3D Micro-CT imaging of live avian embryos. Day 4 chick embryos micro-injected with Visipaque™ (VP) developed for an additional 6 days without defect. X-ray radiation up to 798 mGy was nontoxic. Peak average contrast of 1,060 HU occurred within 1 hr of imaging at 50 μm resolution. VP-enhanced contrast persisted past 24 hr with delayed accumulation in the allantois. Regional volumes of VP-injected embryos were statistically identical to those of fixed embryos perfused with osmium tetroxide. We further quantified longitudinal volumetric morphogenesis of the allantois over 30 hr. These results demonstrate the safety and efficacy of contrast enhanced quantitative micro-CT imaging for live embryos. PMID:21761480

  3. Electrical impedance tomography-based sensing skin for quantitative imaging of damage in concrete

    NASA Astrophysics Data System (ADS)

    Hallaji, Milad; Seppänen, Aku; Pour-Ghaz, Mohammad

    2014-08-01

    This paper outlines the development of a large-area sensing skin for damage detection in concrete structures. The developed sensing skin consists of a thin layer of electrically conductive copper paint that is applied to the surface of the concrete. Cracking of the concrete substrate results in the rupture of the sensing skin, decreasing its electrical conductivity locally. The decrease in conductivity is detected with electrical impedance tomography (EIT) imaging. In previous works, electrically based sensing skins have provided only qualitative information on the damage on the substrate surface. In this paper, we study whether quantitative imaging of the damage is possible. We utilize application-specific models and computational methods in the image reconstruction, including a total variation (TV) prior model for the damage and an approximate correction of the modeling errors caused by the inhomogeneity of the painted sensing skin. The developed damage detection method is tested experimentally by applying the sensing skin to polymeric substrates and a reinforced concrete beam under four-point bending. In all test cases, the EIT-based sensing skin provides quantitative information on cracks and/or other damages on the substrate surface: featuring a very low conductivity in the damage locations, and a reliable indication of the lengths and shapes of the cracks. The results strongly support the applicability of the painted EIT-based sensing skin for damage detection in reinforced concrete elements and other substrates.

  4. 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

  5. Intervertebral disc segmentation and volumetric reconstruction from peripheral quantitative computed tomography imaging.

    PubMed

    Wong, Alexander; Mishra, Akshaya; Yates, Justin; Fieguth, Paul; Clausi, David A; Callaghan, Jack P

    2009-11-01

    An automatic system for segmenting and constructing volumetric representations of excised intervertebral discs from peripheral quantitative computed tomography (PQCT) imagery is presented. The system is designed to allow for automatic quantitative analysis of progressive herniation damage to the intervertebral discs under flexion/extension motions combined with a compressive load. Automatic segmentation and volumetric reconstruction of intervertebral disc from PQCT imagery is a very challenging problem due to factors such as streak artifacts and unclear material density separation between contrasted intervertebral disc and surrounding bone in the PQCT imagery, as well as the formation of multiple contrasted regions under axial scans. To address these factors, a novel multiscale level set approach based on the Mumford-Shah energy functional in iterative bilateral scale space is employed to segment the intervertebral disc regions from the PQCT imagery. A Delaunay triangulation is then performed based on the set of points associated with the intervertebral disc regions to construct the volumetric representation of the intervertebral disc. Experimental results show that the proposed system achieves segmentation and volumetric reconstructions of intervertebral discs with mean absolute distance error below 0.8 mm when compared to ground truth measurements. The proposed system is currently in operational use as a visualization tool for studying progressive intervertebral disc damage. PMID:19635691

  6. Quantitative analysis on PUVA-induced skin photodamages using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zhai, Juan; Guo, Zhouyi; Liu, Zhiming; Xiong, Honglian; Zeng, Changchun; Jin, Ying

    2009-08-01

    Psoralen plus ultraviolet A radiation (PUVA) therapy is a very important clinical treatment of skin diseases such as vitiligo and psoriasis, but associated with an increased risk of skin photodamages especially photoaging. Since skin biopsy alters the original skin morphology and always requires an iatrogenic trauma, optical coherence tomography (OCT) appears to be a promising technique to study skin damage in vivo. In this study, the Balb/c mice had 8-methoxypsralen (8-MOP) treatment prior to UVA radiation was used as PUVA-induced photo-damaged modal. The OCT imaging of photo-damaged group (modal) and normal group (control) in vivo was obtained of mice dorsal skin at 0, 24, 48, 72 hours after irradiation respectively. And then the results were quantitatively analyzed combined with histological information. The experimental results showed that, PUVA-induced photo-damaged skin had an increase in epidermal thickness (ET), a reduction of attenuation coefficient in OCT images signal, and an increase in brightness of the epidermis layer compared with the control group. In conclusion, noninvasive high-resolution imaging techniques such as OCT may be a promising tool for photobiological studies aimed at assessing photo-damage and repair processes in vivo. It can be used to quantitative analysis of changes in photo-damaged skin, such as the ET and collagen in dermis, provides a theoretical basis for treatment and prevention of skin photodamages.

  7. Quantitative reconstruction of PIXE-tomography data for thin samples using GUPIX X-ray emission yields

    NASA Astrophysics Data System (ADS)

    Michelet, C.; Barberet, Ph.; Devès, G.; Bouguelmouna, B.; Bourret, S.; Delville, M.-H.; Le Trequesser, Q.; Gordillo, N.; Beasley, D. G.; Marques, A. C.; Farau, R.; Toko, B. R.; Campbell, J.; Maxwell, J.; Moretto, Ph.; Seznec, H.

    2015-04-01

    We present here a new development of the TomoRebuild software package, to perform quantitative Particle Induced X-ray Emission Tomography (PIXET) reconstruction. X-ray yields are obtained from the GUPIX code. The GUPIX data base is available for protons up to 5 MeV and also in the 20-100 MeV energy range, deuterons up to 6 MeV, 3He and alphas up to 12 MeV. In this version, X-ray yields are calculated for thin samples, i.e. without simulating X-ray attenuation. PIXET data reconstruction is kept as long as possible independent from Scanning Transmission Ion Microscopy Tomography (STIMT). In this way, the local mass distribution (in g/cm3) of each X-ray emitting element is reconstructed in all voxels of the analyzed volume, only from PIXET data, without the need of associated STIMT data. Only the very last step of data analysis requires STIMT data, in order to normalize PIXET data to obtain concentration distributions, in terms of normalized mass fractions (in μg/g). For this, a noise correction procedure has been designed in ImageJ. Moreover sinogram or image misalignment can be corrected, as well as the difference in beam size between the two experiments. The main features of the TomoRebuild code, user friendly design and modular C++ implementation, were kept. The software package is portable and can run on Windows and Linux operating systems. An optional user-friendly graphic interface was designed in Java, as a plugin for the ImageJ graphic software package. Reconstruction examples are presented from biological specimens of Caenorhabditis elegans - a small nematode constituting a reference model for biology studies. The reconstruction results are compared between the different codes TomoRebuild, DISRA and JPIXET, and different reconstruction methods: Filtered BackProjection (FBP) and Maximum Likelihood Expectation Maximization (MLEM).

  8. Quantitative diagnosis of connective tissue disease-associated interstitial pneumonia using thoracic computed tomography images.

    PubMed

    Ozuno, Nobuko Tosaka; Akamatsu, Hokuto; Takahashi, Hiroshi; Fujii, Naoko; Yoshida, Shunji

    2015-12-01

    Patients with polymyositis (PM) or dermatomyositis (DM) frequently show interstitial pneumonia (IP), which is sometimes rapidly progressive or resistant to treatment, thereby significantly affecting the prognosis. The diagnosis and response evaluation of IP are commonly performed qualitatively based on imaging findings, which may cause disagreement among rheumatologists in the evaluation of early lesions and atypical interstitial changes. To determine whether IP could be diagnosed in a quantitative manner during the early stage of PM/DM using a workstation that allows quantitative image processing. Thoracic computed tomography (CT) images of 20 PM/DM patients were reconstructed into a three-dimensional (3D) image using an image processing workstation. The CT values of the constituent voxels were arranged in a histogram of -1000 to +1000 Hounsfield units (HU). The most frequent lung field density was -900 to -801 HU, and relative size was as follows: IP (+) group 0.45 and IP (-) group 0.53. Between -1000 and -701 HU, relative size was not significantly different between the IP (+) group and IP (-) group. Between -700 and -1 HU, the relative size of the lung field was significantly larger in the IP (+) than in the IP (-) group, demonstrating its IP-diagnosing ability. Particularly, within the range from -700 to -301 HU, the macroscopically-assessed ground glass opacity was consistent with the CT value, which, in turn, was closely correlated with KL-6, the pre-existing marker for IP diagnosis. The results of this study may lead to the establishment of quantitative methods of evaluating IP and possible elucidation of the pathogenesis of IP. PMID:26519047

  9. Simulations of an Optical Tactile Sensor Based on Computer Tomography

    NASA Astrophysics Data System (ADS)

    Ohka, Masahiro; Sawamoto, Yasuhiro; Zhu, Ning

    In order to create a robotic tactile sensor of thin shape, a new optical tactile sensor is developed by applying a CT (Computer Tomography) algorithm. The present tactile sensor is comprised of infrared emitting diode arrays, receiving phototransistor arrays and a transparent acrylic plate and a black rubber sheet with projections. Infrared rays emitted from the diode array are directed into one end of the plate and their intensity distribution is measured by the phototransistor array mounted on the other end. If the CT algorithm is directly applied to the tactile sensor, there are two shortcomings: the shape of the sensing area is limited to a circular region and there is a long calculation time. Thus, a new CT algorithm oriented to tactile sensing is proposed for overcoming these problems. In the present algorithm, a square sensing area is divided into an N-by-N array and algebraic equations are derived from the relationship between the input and output light intensities on the assumed light projections. Several reconstruction methods are considered for obtaining pressure values caused in the squares. In the present study, the ART (Algebraic Reconstruction Technique) and LU decomposition methods were employed, and these methods were compared to select the best reconstruction method. In a series of simulations, it was found that the LU decomposition method held an advantage for the present type of tactile sensor because of its robustness against disturbance and short calculation time.

  10. Quantitative evaluation of benzodiazepine receptors in live Papio papio baboons using positron emission tomography

    SciTech Connect

    Brouillet, E.; Chavoix, C.; Khalili-Varasteh, M.; Bottlaender, M.; Hantraye, P.; Yorke, J.C.; Maziere, M. )

    1990-10-01

    The binding of the 11C-labeled benzodiazepine antagonist Ro 15-1788 (flumazenil) was measured in the neocortex of live Papio papio baboons by positron emission tomography. This allowed us to calculate in vivo (i.e., at physiological temperature, neurotransmitters concentrations, and ionic environment) the apparent density of available benzodiazepine receptors (B'max) and the dissociation constant of Ro 15-1788 (Kd). By coadministering increasing doses of unlabeled Ro 15-1788 with (11C)Ro 15-1788 and assuming that nonsaturable radioactivity indicated the free ligand concentration, we were able to obtain saturation isotherms. We showed that a state of quasiequilibrium was reached 50 min after the administration of the radioligand. Linear Scatchard plots allowed us to calculate B'max at 78 and 50 pmol/ml of cerebral tissue in the occipital and frontal cortices, respectively. In both these areas, Kd is on the order of 6 nM, with a Hill number very close to unity. This indicates that Ro 15-1788 binds in vivo with high affinity to an homogeneous population of saturable sites. A similar measurement was carried out on a naturally photosensitive P. papio baboon. Absolute values of B'max, Kd, and Hill number were similar to those of the control baboons. Although results concerning this baboon can only be considered as a case report, this similarity may suggest that its epileptic syndrome is not related to a large change in B'max or Kd, at least in occipital and frontal cortices. Our results showed that quantitative estimation by positron emission tomography of some characteristics of benzodiazepine receptors is possible in live baboons and may represent a supplementary tool for investigating further the molecular mechanisms of benzodiazepine receptor function in physiological and physiopathological conditions.

  11. Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues

    PubMed Central

    Tzoumas, Stratis; Nunes, Antonio; Olefir, Ivan; Stangl, Stefan; Symvoulidis, Panagiotis; Glasl, Sarah; Bayer, Christine; Multhoff, Gabriele; Ntziachristos, Vasilis

    2016-01-01

    Light propagating in tissue attains a spectrum that varies with location due to wavelength-dependent fluence attenuation, an effect that causes spectral corruption. Spectral corruption has limited the quantification accuracy of optical and optoacoustic spectroscopic methods, and impeded the goal of imaging blood oxygen saturation (sO2) deep in tissues; a critical goal for the assessment of oxygenation in physiological processes and disease. Here we describe light fluence in the spectral domain and introduce eigenspectra multispectral optoacoustic tomography (eMSOT) to account for wavelength-dependent light attenuation, and estimate blood sO2 within deep tissue. We validate eMSOT in simulations, phantoms and animal measurements and spatially resolve sO2 in muscle and tumours, validating our measurements with histology data. eMSOT shows substantial sO2 accuracy enhancement over previous optoacoustic methods, potentially serving as a valuable tool for imaging tissue pathophysiology. PMID:27358000

  12. Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues.

    PubMed

    Tzoumas, Stratis; Nunes, Antonio; Olefir, Ivan; Stangl, Stefan; Symvoulidis, Panagiotis; Glasl, Sarah; Bayer, Christine; Multhoff, Gabriele; Ntziachristos, Vasilis

    2016-01-01

    Light propagating in tissue attains a spectrum that varies with location due to wavelength-dependent fluence attenuation, an effect that causes spectral corruption. Spectral corruption has limited the quantification accuracy of optical and optoacoustic spectroscopic methods, and impeded the goal of imaging blood oxygen saturation (sO2) deep in tissues; a critical goal for the assessment of oxygenation in physiological processes and disease. Here we describe light fluence in the spectral domain and introduce eigenspectra multispectral optoacoustic tomography (eMSOT) to account for wavelength-dependent light attenuation, and estimate blood sO2 within deep tissue. We validate eMSOT in simulations, phantoms and animal measurements and spatially resolve sO2 in muscle and tumours, validating our measurements with histology data. eMSOT shows substantial sO2 accuracy enhancement over previous optoacoustic methods, potentially serving as a valuable tool for imaging tissue pathophysiology. PMID:27358000

  13. Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues

    NASA Astrophysics Data System (ADS)

    Tzoumas, Stratis; Nunes, Antonio; Olefir, Ivan; Stangl, Stefan; Symvoulidis, Panagiotis; Glasl, Sarah; Bayer, Christine; Multhoff, Gabriele; Ntziachristos, Vasilis

    2016-06-01

    Light propagating in tissue attains a spectrum that varies with location due to wavelength-dependent fluence attenuation, an effect that causes spectral corruption. Spectral corruption has limited the quantification accuracy of optical and optoacoustic spectroscopic methods, and impeded the goal of imaging blood oxygen saturation (sO2) deep in tissues; a critical goal for the assessment of oxygenation in physiological processes and disease. Here we describe light fluence in the spectral domain and introduce eigenspectra multispectral optoacoustic tomography (eMSOT) to account for wavelength-dependent light attenuation, and estimate blood sO2 within deep tissue. We validate eMSOT in simulations, phantoms and animal measurements and spatially resolve sO2 in muscle and tumours, validating our measurements with histology data. eMSOT shows substantial sO2 accuracy enhancement over previous optoacoustic methods, potentially serving as a valuable tool for imaging tissue pathophysiology.

  14. Direct Numerical Simulation of Liquid Nozzle Spray with Comparison to Shadowgraphy and X-Ray Computed Tomography Experimental Results

    NASA Astrophysics Data System (ADS)

    van Poppel, Bret; Owkes, Mark; Nelson, Thomas; Lee, Zachary; Sowell, Tyler; Benson, Michael; Vasquez Guzman, Pablo; Fahrig, Rebecca; Eaton, John; Kurman, Matthew; Kweon, Chol-Bum; Bravo, Luis

    2014-11-01

    In this work, we present high-fidelity Computational Fluid Dynamics (CFD) results of liquid fuel injection from a pressure-swirl atomizer and compare the simulations to experimental results obtained using both shadowgraphy and phase-averaged X-ray computed tomography (CT) scans. The CFD and experimental results focus on the dense near-nozzle region to identify the dominant mechanisms of breakup during primary atomization. Simulations are performed using the NGA code of Desjardins et al (JCP 227 (2008)) and employ the volume of fluid (VOF) method proposed by Owkes and Desjardins (JCP 270 (2013)), a second order accurate, un-split, conservative, three-dimensional VOF scheme providing second order density fluxes and capable of robust and accurate high density ratio simulations. Qualitative features and quantitative statistics are assessed and compared for the simulation and experimental results, including the onset of atomization, spray cone angle, and drop size and distribution.

  15. Quantitative assessment of the stent/scaffold strut embedment analysis by optical coherence tomography.

    PubMed

    Sotomi, Yohei; Tateishi, Hiroki; Suwannasom, Pannipa; Dijkstra, Jouke; Eggermont, Jeroen; Liu, Shengnan; Tenekecioglu, Erhan; Zheng, Yaping; Abdelghani, Mohammad; Cavalcante, Rafael; de Winter, Robbert J; Wykrzykowska, Joanna J; Onuma, Yoshinobu; Serruys, Patrick W; Kimura, Takeshi

    2016-06-01

    The degree of stent/scaffold embedment could be a surrogate parameter of the vessel wall-stent/scaffold interaction and could have biological implications in the vascular response. We have developed a new specific software for the quantitative evaluation of embedment of struts by optical coherence tomography (OCT). In the present study, we described the algorithm of the embedment analysis and its reproducibility. The degree of embedment was evaluated as the ratio of the embedded part versus the whole strut height and subdivided into quartiles. The agreement and the inter- and intra-observer reproducibility were evaluated using the kappa and the interclass correlation coefficient (ICC). A total of 4 pullbacks of OCT images in 4 randomly selected coronary lesions with 3.0 × 18 mm devices [2 lesions with Absorb BVS and 2 lesions with XIENCE (both from Abbott Vascular, Santa Clara, CA, USA)] from Absorb Japan trial were evaluated by two investigators with QCU-CMS software version 4.69 (Leiden University Medical Center, Leiden, The Netherlands). Finally, 1481 polymeric struts in 174 cross-sections and 1415 metallic struts in 161 cross-sections were analyzed. Inter- and intra-observer reproducibility of quantitative measurements of embedment ratio and categorical assessment of embedment in Absorb BVS and XIENCE had excellent agreement with ICC ranging from 0.958 to 0.999 and kappa ranging from 0.850 to 0.980. The newly developed embedment software showed excellent reproducibility. Computer-assisted embedment analysis could be a feasible tool to assess the strut penetration into the vessel wall that could be a surrogate of acute injury caused by implantation of devices. PMID:26898315

  16. Oxygen extraction fraction measurement using quantitative susceptibility mapping: Comparison with positron emission tomography.

    PubMed

    Kudo, Kohsuke; Liu, Tian; Murakami, Toshiyuki; Goodwin, Jonathan; Uwano, Ikuko; Yamashita, Fumio; Higuchi, Satomi; Wang, Yi; Ogasawara, Kuniaki; Ogawa, Akira; Sasaki, Makoto

    2016-08-01

    The purposes of this study are to establish oxygen extraction fraction (OEF) measurements using quantitative susceptibility mapping (QSM) of magnetic resonance imaging (MRI), and to compare QSM-OEF data with the gold standard (15)O positron emission tomography (PET). Twenty-six patients with chronic unilateral internal carotid artery or middle cerebral artery stenosis or occlusion, and 15 normal subjects were included. MRI scans were conducted using a 3.0 Tesla scanner with a three-dimensional spoiled gradient recalled sequence. QSM images were created using the morphology-enabled dipole inversion method, and OEF maps were generated from QSM images using extraction of venous susceptibility induced by deoxygenated hemoglobin. Significant correlation of relative OEF ratio to contra-lateral hemisphere between QSM-OEF and PET-OEF was observed (r = 0.62, p < 0.001). The local (intra-section) correlation was also significant (r = 0.52, p < 0.001) in patients with increased PET-OEF. The sensitivity and specificity of OEF increase in QSM was 0.63 (5/8) and 0.89 (16/18), respectively, in comparison with PET. In conclusion, good correlation was achieved between QSM-OEF and PET-OEF in the identification of elevated OEF in affected hemispheres of patients with unilateral chronic steno-occlusive disease. PMID:26661168

  17. Quantitative myocardial perfusion imaging by cardiovascular magnetic resonance and positron emission tomography.

    PubMed

    Bratis, K; Mahmoud, I; Chiribiri, A; Nagel, E

    2013-10-01

    Recent studies have demonstrated that a detailed knowledge of the extent of angiographic coronary artery disease (CAD) is not a prerequisite for clinical decision making, and the clinical management of patients with CAD is more and more focused towards the identification of myocardial ischemia and the quantification of ischemic burden. In this view, non-invasive assessment of ischemia and in particular stress imaging techniques are emerging as preferred and non-invasive options. A quantitative assessment of regional myocardial perfusion can provide an objective estimate of the severity of myocardial injury and may help clinicians to discriminate regions of the heart that are at increased risk for myocardial infarction. Positron emission tomography (PET) has established itself as the reference standard for myocardial blood flow (MBF) and myocardial perfusion reserve (MPR) quantification. Cardiac magnetic resonance (CMR) is increasingly used to measure MBF and MPR by means of first-pass signals, with a well-defined diagnostic performance and prognostic value. The aim of this article is to review the currently available evidence on the use of both PET and CMR for quantification of MPR, with particular attention to the studies that directly compared these two diagnostic methods. PMID:23868071

  18. Quantitative upper airway endoscopy with swept-source anatomical optical coherence tomography

    PubMed Central

    Wijesundara, Kushal; Zdanski, Carlton; Kimbell, Julia; Price, Hillel; Iftimia, Nicusor; Oldenburg, Amy L.

    2014-01-01

    Minimally invasive imaging of upper airway obstructions in children and adults is needed to improve clinical decision-making. Toward this goal, we demonstrate an anatomical optical coherence tomography (aOCT) system delivered via a small-bore, flexible endoscope to quantify the upper airway lumen geometry. Helical scans were obtained from a proximally-scanned fiber-optic catheter of 820 μm outer diameter and >2 mm focal length. Coupled with a long coherence length wavelength-swept light source, the system exhibited an SNR roll-off of < 10 dB over a 10 mm range. Operating at 10 rotations/s, the average accuracy of segmented cross-sectional areas was found to be −1.4 ± 1.0%. To demonstrate the capability of this system, aOCT was performed on a pediatric airway phantom and on ex vivo swine trachea. The ability for quantitative endoscopy afforded by this system can aid in diagnosis, medical and surgical decision making, and predictive modeling of upper airway obstructive disorders. PMID:24688814

  19. Emphysema- and airway-dominant COPD phenotypes defined by standardised quantitative computed tomography.

    PubMed

    Subramanian, Deepak R; Gupta, Sumit; Burggraf, Dorothe; Vom Silberberg, Suzan J; Heimbeck, Irene; Heiss-Neumann, Marion S; Haeussinger, Karl; Newby, Chris; Hargadon, Beverley; Raj, Vimal; Singh, Dave; Kolsum, Umme; Hofer, Thomas P; Al-Shair, Khaled; Luetzen, Niklas; Prasse, Antje; Müller-Quernheim, Joachim; Benea, Giorgio; Leprotti, Stefano; Boschetto, Piera; Gorecka, Dorota; Nowinski, Adam; Oniszh, Karina; Castell, Wolfgang Zu; Hagen, Michael; Barta, Imre; Döme, Balázs; Strausz, Janos; Greulich, Timm; Vogelmeier, Claus; Koczulla, Andreas R; Gut, Ivo; Hohlfeld, Jens; Welte, Tobias; Lavae-Mokhtari, Mahyar; Ziegler-Heitbrock, Loems; Brightling, Christopher; Parr, David G

    2016-07-01

    EvA (Emphysema versus Airway disease) is a multicentre project to study mechanisms and identify biomarkers of emphysema and airway disease in chronic obstructive pulmonary disease (COPD). The objective of this study was to delineate objectively imaging-based emphysema-dominant and airway disease-dominant phenotypes using quantitative computed tomography (QCT) indices, standardised with a novel phantom-based approach.441 subjects with COPD (Global Initiative for Chronic Obstructive Lung Disease (GOLD) stages 1-3) were assessed in terms of clinical and physiological measurements, laboratory testing and standardised QCT indices of emphysema and airway wall geometry.QCT indices were influenced by scanner non-conformity, but standardisation significantly reduced variability (p<0.001) and led to more robust phenotypes. Four imaging-derived phenotypes were identified, reflecting "emphysema-dominant", "airway disease-dominant", "mixed" disease and "mild" disease. The emphysema-dominant group had significantly higher lung volumes, lower gas transfer coefficient, lower oxygen (PO2 ) and carbon dioxide (PCO2 ) tensions, higher haemoglobin and higher blood leukocyte numbers than the airway disease-dominant group.The utility of QCT for phenotyping in the setting of an international multicentre study is improved by standardisation. QCT indices of emphysema and airway disease can delineate within a population of patients with COPD, phenotypic groups that have typical clinical features known to be associated with emphysema-dominant and airway-dominant disease. PMID:27230444

  20. Automated quantitation of three-dimensional cardiac positron emission tomography for routine clinical use

    SciTech Connect

    Hicks, K.; Ganti, G.; Mullani, N.; Gould, K.L. )

    1989-11-01

    Visual comparison of rest/stress cardiac positron emission tomography indicates coronary flow reserve for diagnosing and assessing severity of coronary artery disease. An accurate, rapid, automated method for comparison and quantitation of paired cardiac PET studies has been developed to analyze size, intensity, statistical significance of and changes in perfusion or metabolism. The method utilizes polar coordinate maps derived from circumferential profiles of true short axis slices; from the short axis data algorithms determine mean and minimum activity levels in the anterior, septal, lateral, inferior and apical regions of the myocardium, percent of the cardiac image in specific ranges of activity levels or their changes and the percent of myocardium beyond 1.5, 2.0, and 2.5 standard deviations from the normal range with blackout display of the areas beyond these statistical limits for rest, stress, and stress/rest ratio polar maps. Additional applications include comparing stress-stress images to evaluate progression/regression of stenoses, early and late resting rubidium images for determining myocardial viability based on rubidium washout kinetics, and perfusion-metabolic comparisons for quantifying ischemia, viability and necrosis after acute myocardial infarction.

  1. Quantitative analysis of cytoskeletal reorganization during epithelial tissue sealing by large-volume electron tomography.

    PubMed

    Eltsov, Mikhail; Dubé, Nadia; Yu, Zhou; Pasakarnis, Laurynas; Haselmann-Weiss, Uta; Brunner, Damian; Frangakis, Achilleas S

    2015-05-01

    The closure of epidermal openings is an essential biological process that causes major developmental problems such as spina bifida in humans if it goes awry. At present, the mechanism of closure remains elusive. Therefore, we reconstructed a model closure event, dorsal closure in fly embryos, by large-volume correlative electron tomography. We present a comprehensive, quantitative analysis of the cytoskeletal reorganization, enabling separated epidermal cells to seal the epithelium. After establishing contact through actin-driven exploratory filopodia, cells use a single lamella to generate 'roof tile'-like overlaps. These shorten to produce the force, 'zipping' the tissue closed. The shortening overlaps lack detectable actin filament ensembles but are crowded with microtubules. Cortical accumulation of shrinking microtubule ends suggests a force generation mechanism in which cortical motors pull on microtubule ends as for mitotic spindle positioning. In addition, microtubules orient filopodia and lamellae before zipping. Our 4D electron microscopy picture describes an entire developmental process and provides fundamental insight into epidermal closure. PMID:25893916

  2. Light fluence correction for quantitative determination of tissue absorption coefficient using multi-spectral optoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Brochu, Frederic M.; Joseph, James; Tomaszewski, Michal; Bohndiek, Sarah E.

    2015-07-01

    MultiSpectral Optoacoustic Tomography (MSOT) is a fast developing imaging modality, combining the high resolution and penetration depth of ultrasound with the excellent contrast from optical imaging of tissue. Absorption and scattering of the near infrared excitation light modulates the spectral profile of light as it propagates deep into biological tissue, meaning the images obtained provide only qualitative insight into the distribution of tissue chromophores. The goal of this work is to accurately recover the spectral profile of excitation light by modelling light fluence in the data reconstruction, to enable quantitative imaging. We worked with a commercial small animal MSOT scanner and developed our light fluence correction for its' cylindrical geometry. Optoacoustic image reconstruction pinpoints the sources of acoustic waves detected by the transducers and returns the initial pressure amplitude at these points. This pressure is the product of the dimensionless Grüneisen parameter, the absorption coefficient and the light fluence. Under the condition of constant Grüneisen parameter and well modelled light fluence, there is a linear relationship between the initial pressure amplitude measured in the optoacoustic image and the absorption coefficient. We were able to reproduce this linear relationship in different physical regions of an agarose gel phantom containing targets of known optical absorption coefficient, demonstrating that our light fluence model was working. We also demonstrate promising results of light fluence correction effects on in vivo data.

  3. The effect of slice thickness on quantitation of in vivo renal volume with cine computed tomography

    SciTech Connect

    Lerman, L.O.; Bentley, M.D.; Bell, M.R.; Rumberger, J.A.; Romero, J.C. )

    1990-02-26

    The development of fast computed tomography (CT) scanners allows the accurate quantitations of the volume (V) of the in-vivo kidney (K) and its component tissues, using 3 mm thick slices. Utilizing thicker slices may potentially enable the use of shorter scan times with less exposure to contrast media. To determine the relative accuracy of such scans, the right Ks of 14 anesthetized dogs were first scanned, using 3mm thick slices, after a venous bolus injection of iohexol (0.5 cc/kg). The images were then averaged to produce 6 and 10 mm thick slices, and the Vs of the Ks, and their cortical and medullary Vs, determined after boundary identification. Following the scans, the Ks were excised and their Vs determined post-mortem by fluid displacement. The whole K Vs obtained with the 6 and 10 mm thick slices correlated well with those obtained with the 3 mm thick slices. The difference between the in vivo and the post-mortem renal and medullary Vs was consistent with the blood, filtrate and urine contents of the in vivo kidney. In conclusion, the use of 6 and 10 mm thick slices resulted in an overestimation of the in vivo cortical V due to a partial volume effect, which was reflected in a consistent overestimation of KV.

  4. Quantitative analysis of angle-resolved scattering properties of ovarian tissue using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Yang, Yi; Wang, Tianheng; Brewer, Molly; Zhu, Quing

    2012-09-01

    Angle-resolved optical scattering properties of ovarian tissue, on different optical coherence tomography (OCT) imaging planes, were quantitatively measured by fitting the compounded OCT A-lines into a single scattering model. Higher cross correlation value of angle-resolved scattering coefficients between different OCT imaging planes was found in normal ovaries than was present in malignant ovaries. The mean cross correlation coefficient (MCC) was introduced in this pilot study to characterize and differentiate normal, n=6, and malignant, n=4, ovaries. A specificity of 100 percent and a sensitivity of 100 percent were achieved by setting MCC threshold at 0.6. Collagen properties, within the OCT imaging penetration depth, were also qualitatively studied in terms of their content, structure and directivity. The homogeneous three-dimensional collagen fiber network, observed in the normal ovary, effectively explains the stronger cross correlation of angle-resolved scattering properties on different imaging planes while the heterogeneity, observed in the malignant ovary, suggests a weaker correlation.

  5. Noninvasive Quantitative Evaluation of the Dentin Layer during Dental Procedures Using Optical Coherence Tomography

    PubMed Central

    Sinescu, Cosmin; Negrutiu, Meda Lavinia; Bradu, Adrian; Duma, Virgil-Florin; Podoleanu, Adrian Gh.

    2015-01-01

    A routine cavity preparation of a tooth may lead to opening the pulp chamber. The present study evaluates quantitatively, in real time, for the first time to the best of our knowledge, the drilled cavities during dental procedures. An established noninvasive imaging technique, Optical Coherence Tomography (OCT), is used. The main scope is to prevent accidental openings of the dental pulp chamber. Six teeth with dental cavities have been used in this ex vivo study. The real time assessment of the distances between the bottom of the drilled cavities and the top of the pulp chamber was performed using an own assembled OCT system. The evaluation of the remaining dentin thickness (RDT) allowed for the positioning of the drilling tools in the cavities in relation to the pulp horns. Estimations of the safe and of the critical RDT were made; for the latter, the opening of the pulp chamber becomes unavoidable. Also, by following the fractures that can occur when the extent of the decay is too large, the dentist can decide upon the right therapy to follow, endodontic or conventional filling. The study demonstrates the usefulness of OCT imaging in guiding such evaluations during dental procedures. PMID:26078779

  6. Micro/Nano-Computed Tomography Technology for Quantitative Dynamic, Multi-scale Imaging of Morphogenesis

    PubMed Central

    Gregg, Chelsea L.; Recknagel, Andrew K.; Butcher, Jonathan T.

    2015-01-01

    Tissue morphogenesis and embryonic development are dynamic events challenging to quantify, especially considering the intricate events that happen simultaneously in different locations and time. Micro-, and more recently nano-computed tomography (micro/nanoCT), has been used for the past 15 years to characterize large 3D fields of tortuous geometries at high spatial resolution. We and others have advanced micro/nanoCT imaging strategies for quantifying tissue and organ level fate changes throughout morphogenesis. Exogenous soft tissue contrast media enables visualization of vascular lumens and tissues via extravasation. Furthermore, the emergence of antigen specific tissue contrast enables direct quantitative visualization of protein and mRNA expression. Micro-CT X-ray doses appear to be non-embryotoxic, enabling longitudinal imaging studies in live embryos. In this paper we present established soft tissue contrast protocols for obtaining high quality micro/nanoCT images and the image processing techniques useful for quantifying anatomical and physiological information from the datasets. PMID:25245686

  7. Micro/nano-computed tomography technology for quantitative dynamic, multi-scale imaging of morphogenesis.

    PubMed

    Gregg, Chelsea L; Recknagel, Andrew K; Butcher, Jonathan T

    2015-01-01

    Tissue morphogenesis and embryonic development are dynamic events challenging to quantify, especially considering the intricate events that happen simultaneously in different locations and time. Micro- and more recently nano-computed tomography (micro/nanoCT) has been used for the past 15 years to characterize large 3D fields of tortuous geometries at high spatial resolution. We and others have advanced micro/nanoCT imaging strategies for quantifying tissue- and organ-level fate changes throughout morphogenesis. Exogenous soft tissue contrast media enables visualization of vascular lumens and tissues via extravasation. Furthermore, the emergence of antigen-specific tissue contrast enables direct quantitative visualization of protein and mRNA expression. Micro-CT X-ray doses appear to be non-embryotoxic, enabling longitudinal imaging studies in live embryos. In this chapter we present established soft tissue contrast protocols for obtaining high-quality micro/nanoCT images and the image processing techniques useful for quantifying anatomical and physiological information from the data sets. PMID:25245686

  8. Quantitative optical coherence tomography angiography of vascular abnormalities in the living human eye.

    PubMed

    Jia, Yali; Bailey, Steven T; Hwang, Thomas S; McClintic, Scott M; Gao, Simon S; Pennesi, Mark E; Flaxel, Christina J; Lauer, Andreas K; Wilson, David J; Hornegger, Joachim; Fujimoto, James G; Huang, David

    2015-05-01

    Retinal vascular diseases are important causes of vision loss. A detailed evaluation of the vascular abnormalities facilitates diagnosis and treatment in these diseases. Optical coherence tomography (OCT) angiography using the highly efficient split-spectrum amplitude decorrelation angiography algorithm offers an alternative to conventional dye-based retinal angiography. OCT angiography has several advantages, including 3D visualization of retinal and choroidal circulations (including the choriocapillaris) and avoidance of dye injection-related complications. Results from six illustrative cases are reported. In diabetic retinopathy, OCT angiography can detect neovascularization and quantify ischemia. In age-related macular degeneration, choroidal neovascularization can be observed without the obscuration of details caused by dye leakage in conventional angiography. Choriocapillaris dysfunction can be detected in the nonneovascular form of the disease, furthering our understanding of pathogenesis. In choroideremia, OCT's ability to show choroidal and retinal vascular dysfunction separately may be valuable in predicting progression and assessing treatment response. OCT angiography shows promise as a noninvasive alternative to dye-based angiography for highly detailed, in vivo, 3D, quantitative evaluation of retinal vascular abnormalities. PMID:25897021

  9. Global Adjoint Tomography: Combining Big Data with HPC Simulations

    NASA Astrophysics Data System (ADS)

    Bozdag, E.; Lefebvre, M. P.; Lei, W.; Peter, D. B.; Smith, J. A.; Komatitsch, D.; Tromp, J.

    2014-12-01

    The steady increase in data quality and the number of global seismographic stations have substantially grown the amount of data available for construction of Earth models. Meanwhile, developments in the theory of wave propagation, numerical methods and HPC systems have enabled unprecedented simulations of seismic wave propagation in realistic 3D Earth models which lead the extraction of more information from data, ultimately culminating in the use of entire three-component seismograms.Our aim is to take adjoint tomography further to image the entire planet which is one of the extreme cases in seismology due to its intense computational requirements and vast amount of high-quality seismic data that can potentially be assimilated in inversions. We have started low resolution (T > 27 s, soon will be > 17 s) global inversions with 253 earthquakes for a transversely isotropic crust and mantle model on Oak Ridge National Laboratory's Cray XK7 "Titan" system. Recent improvements in our 3D solvers, such as the GPU version of the SPECFEM3D_GLOBE package, will allow us perform higher-resolution (T > 9 s) and longer-duration (~180 m) simulations to take the advantage of high-frequency body waves and major-arc surface waves to improve imbalanced ray coverage as a result of uneven distribution of sources and receivers on the globe. Our initial results after 10 iterations already indicate several prominent features reported in high-resolution continental studies, such as major slabs (Hellenic, Japan, Bismarck, Sandwich, etc.) and enhancement in plume structures (the Pacific superplume, the Hawaii hot spot, etc.). Our ultimate goal is to assimilate seismic data from more than 6,000 earthquakes within the magnitude range 5.5 ≤ Mw ≤ 7.0. To take full advantage of this data set on ORNL's computational resources, we need a solid framework for managing big data sets during pre-processing (e.g., data requests and quality checks), gradient calculations, and post-processing (e

  10. Computer Monte Carlo simulation in quantitative resource estimation

    USGS Publications Warehouse

    Root, D.H.; Menzie, W.D.; Scott, W.A.

    1992-01-01

    The method of making quantitative assessments of mineral resources sufficiently detailed for economic analysis is outlined in three steps. The steps are (1) determination of types of deposits that may be present in an area, (2) estimation of the numbers of deposits of the permissible deposit types, and (3) combination by Monte Carlo simulation of the estimated numbers of deposits with the historical grades and tonnages of these deposits to produce a probability distribution of the quantities of contained metal. Two examples of the estimation of the number of deposits (step 2) are given. The first example is for mercury deposits in southwestern Alaska and the second is for lode tin deposits in the Seward Peninsula. The flow of the Monte Carlo simulation program is presented with particular attention to the dependencies between grades and tonnages of deposits and between grades of different metals in the same deposit. ?? 1992 Oxford University Press.

  11. Quantitative Functional Imaging Using Dynamic Positron Computed Tomography and Rapid Parameter Estimation Techniques

    NASA Astrophysics Data System (ADS)

    Koeppe, Robert Allen

    Positron computed tomography (PCT) is a diagnostic imaging technique that provides both three dimensional imaging capability and quantitative measurements of local tissue radioactivity concentrations in vivo. This allows the development of non-invasive methods that employ the principles of tracer kinetics for determining physiological properties such as mass specific blood flow, tissue pH, and rates of substrate transport or utilization. A physiologically based, two-compartment tracer kinetic model was derived to mathematically describe the exchange of a radioindicator between blood and tissue. The model was adapted for use with dynamic sequences of data acquired with a positron tomograph. Rapid estimation techniques were implemented to produce functional images of the model parameters by analyzing each individual pixel sequence of the image data. A detailed analysis of the performance characteristics of three different parameter estimation schemes was performed. The analysis included examination of errors caused by statistical uncertainties in the measured data, errors in the timing of the data, and errors caused by violation of various assumptions of the tracer kinetic model. Two specific radioindicators were investigated. ('18)F -fluoromethane, an inert freely diffusible gas, was used for local quantitative determinations of both cerebral blood flow and tissue:blood partition coefficient. A method was developed that did not require direct sampling of arterial blood for the absolute scaling of flow values. The arterial input concentration time course was obtained by assuming that the alveolar or end-tidal expired breath radioactivity concentration is proportional to the arterial blood concentration. The scale of the input function was obtained from a series of venous blood concentration measurements. The method of absolute scaling using venous samples was validated in four studies, performed on normal volunteers, in which directly measured arterial concentrations

  12. Quantitative computed tomography measurements of emphysema for diagnosing asthma-chronic obstructive pulmonary disease overlap syndrome

    PubMed Central

    Xie, Mengshuang; Wang, Wei; Dou, Shuang; Cui, Liwei; Xiao, Wei

    2016-01-01

    Background The diagnostic criteria of asthma–COPD overlap syndrome (ACOS) are controversial. Emphysema is characteristic of COPD and usually does not exist in typical asthma patients. Emphysema in patients with asthma suggests the coexistence of COPD. Quantitative computed tomography (CT) allows repeated evaluation of emphysema noninvasively. We investigated the value of quantitative CT measurements of emphysema in the diagnosis of ACOS. Methods This study included 404 participants; 151 asthma patients, 125 COPD patients, and 128 normal control subjects. All the participants underwent pulmonary function tests and a high-resolution CT scan. Emphysema measurements were taken with an Airway Inspector software. The asthma patients were divided into high and low emphysema index (EI) groups based on the percentage of low attenuation areas less than −950 Hounsfield units. The characteristics of asthma patients with high EI were compared with those having low EI or COPD. Results The normal value of percentage of low attenuation areas less than −950 Hounsfield units in Chinese aged >40 years was 2.79%±2.37%. COPD patients indicated more severe emphysema and more upper-zone-predominant distribution of emphysema than asthma patients or controls. Thirty-two (21.2%) of the 151 asthma patients had high EI. Compared with asthma patients with low EI, those with high EI were significantly older, more likely to be male, had more pack-years of smoking, had more upper-zone-predominant distribution of emphysema, and had greater airflow limitation. There were no significant differences in sex ratios, pack-years of smoking, airflow limitation, or emphysema distribution between asthma patients with high EI and COPD patients. A greater number of acute exacerbations were seen in asthma patients with high EI compared with those with low EI or COPD. Conclusion Asthma patients with high EI fulfill the features of ACOS, as described in the Global Initiative for Asthma and Global

  13. Emission Computed Tomography: A New Technique for the Quantitative Physiologic Study of Brain and Heart in Vivo

    DOE R&D Accomplishments Database

    Phelps, M. E.; Hoffman, E. J.; Huang, S. C.; Schelbert, H. R.; Kuhl, D. E.

    1978-01-01

    Emission computed tomography can provide a quantitative in vivo measurement of regional tissue radionuclide tracer concentrations. This facility when combined with physiologic models and radioactively labeled physiologic tracers that behave in a predictable manner allow measurement of a wide variety of physiologic variables. This integrated technique has been referred to as Physiologic Tomography (PT). PT requires labeled compounds which trace physiologic processes in a known and predictable manner, and physiologic models which are appropriately formulated and validated to derive physiologic variables from ECT data. In order to effectively achieve this goal, PT requires an ECT system that is capable of performing truly quantitative or analytical measurements of tissue tracer concentrations and which has been well characterized in terms of spatial resolution, sensitivity and signal to noise ratios in the tomographic image. This paper illustrates the capabilities of emission computed tomography and provides examples of physiologic tomography for the regional measurement of cerebral and myocardial metabolic rate for glucose, regional measurement of cerebral blood volume, gated cardiac blood pools and capillary perfusion in brain and heart. Studies on patients with stroke and myocardial ischemia are also presented.

  14. Integration of Quantitative Positron Emission Tomography Absolute Myocardial Blood Flow Measurements in the Clinical Management of Coronary Artery Disease.

    PubMed

    Gewirtz, Henry; Dilsizian, Vasken

    2016-05-31

    In the >40 years since planar myocardial imaging with(43)K-potassium was introduced into clinical research and management of patients with coronary artery disease (CAD), diagnosis and treatment have undergone profound scientific and technological changes. One such innovation is the current state-of-the-art hardware and software for positron emission tomography myocardial perfusion imaging, which has advanced it from a strictly research-oriented modality to a clinically valuable tool. This review traces the evolving role of quantitative positron emission tomography measurements of myocardial blood flow in the evaluation and management of patients with CAD. It presents methodology, currently or soon to be available, that offers a paradigm shift in CAD management. Heretofore, radionuclide myocardial perfusion imaging has been primarily qualitative or at best semiquantitative in nature, assessing regional perfusion in relative terms. Thus, unlike so many facets of modern cardiovascular practice and CAD management, which depend, for example, on absolute values of key parameters such as arterial and left ventricular pressures, serum lipoprotein, and other biomarker levels, the absolute levels of rest and maximal myocardial blood flow have yet to be incorporated into routine clinical practice even in most positron emission tomography centers where the potential to do so exists. Accordingly, this review focuses on potential value added for improving clinical CAD practice by measuring the absolute level of rest and maximal myocardial blood flow. Physiological principles and imaging fundamentals necessary to understand how positron emission tomography makes robust, quantitative measurements of myocardial blood flow possible are highlighted. PMID:27245647

  15. Bragg peak prediction from quantitative proton computed tomography using different path estimates.

    PubMed

    Wang, Dongxu; Mackie, T Rockwell; Tomé, Wolfgang A

    2011-02-01

    This paper characterizes the performance of the straight-line path (SLP) and cubic spline path (CSP) as path estimates used in reconstruction of proton computed tomography (pCT). The GEANT4 Monte Carlo simulation toolkit is employed to simulate the imaging phantom and proton projections. SLP, CSP and the most-probable path (MPP) are constructed based on the entrance and exit information of each proton. The physical deviations of SLP, CSP and MPP from the real path are calculated. Using a conditional proton path probability map, the relative probability of SLP, CSP and MPP are calculated and compared. The depth dose and Bragg peak are predicted on the pCT images reconstructed using SLP, CSP, and MPP and compared with the simulation result. The root-mean-square physical deviations and the cumulative distribution of the physical deviations show that the performance of CSP is comparable to MPP while SLP is slightly inferior. About 90% of the SLP pixels and 99% of the CSP pixels lie in the 99% relative probability envelope of the MPP. Even at an imaging dose of ∼0.1 mGy the proton Bragg peak for a given incoming energy can be predicted on the pCT image reconstructed using SLP, CSP, or MPP with 1 mm accuracy. This study shows that SLP and CSP, like MPP, are adequate path estimates for pCT reconstruction, and therefore can be chosen as the path estimation method for pCT reconstruction, which can aid the treatment planning and range prediction of proton radiation therapy. PMID:21212472

  16. Quantitative assessment of scatter correction techniques incorporated in next generation dual-source computed tomography

    NASA Astrophysics Data System (ADS)

    Mobberley, Sean David

    Accurate, cross-scanner assessment of in-vivo air density used to quantitatively assess amount and distribution of emphysema in COPD subjects has remained elusive. Hounsfield units (HU) within tracheal air can be considerably more positive than -1000 HU. With the advent of new dual-source scanners which employ dedicated scatter correction techniques, it is of interest to evaluate how the quantitative measures of lung density compare between dual-source and single-source scan modes. This study has sought to characterize in-vivo and phantom-based air metrics using dual-energy computed tomography technology where the nature of the technology has required adjustments to scatter correction. Anesthetized ovine (N=6), swine (N=13: more human-like rib cage shape), lung phantom and a thoracic phantom were studied using a dual-source MDCT scanner (Siemens Definition Flash. Multiple dual-source dual-energy (DSDE) and single-source (SS) scans taken at different energy levels and scan settings were acquired for direct quantitative comparison. Density histograms were evaluated for the lung, tracheal, water and blood segments. Image data were obtained at 80, 100, 120, and 140 kVp in the SS mode (B35f kernel) and at 80, 100, 140, and 140-Sn (tin filtered) kVp in the DSDE mode (B35f and D30f kernels), in addition to variations in dose, rotation time, and pitch. To minimize the effect of cross-scatter, the phantom scans in the DSDE mode was obtained by reducing the tube current of one of the tubes to its minimum (near zero) value. When using image data obtained in the DSDE mode, the median HU values in the tracheal regions of all animals and the phantom were consistently closer to -1000 HU regardless of reconstruction kernel (chapters 3 and 4). Similarly, HU values of water and blood were consistently closer to their nominal values of 0 HU and 55 HU respectively. When using image data obtained in the SS mode the air CT numbers demonstrated a consistent positive shift of up to 35 HU

  17. Generation and 3-Dimensional Quantitation of Arterial Lesions in Mice Using Optical Projection Tomography

    PubMed Central

    Kirkby, Nicholas S.; Low, Lucinda; Wu, Junxi; Miller, Eileen; Seckl, Jonathan R.; Walker, Brian R.; Webb, David J.; Hadoke, Patrick W. F.

    2015-01-01

    The generation and analysis of vascular lesions in appropriate animal models is a cornerstone of research into cardiovascular disease, generating important information on the pathogenesis of lesion formation and the action of novel therapies. Use of atherosclerosis-prone mice, surgical methods of lesion induction, and dietary modification has dramatically improved understanding of the mechanisms that contribute to disease development and the potential of new treatments. Classically, analysis of lesions is performed ex vivo using 2-dimensional histological techniques. This article describes application of optical projection tomography (OPT) to 3-dimensional quantitation of arterial lesions. As this technique is non-destructive, it can be used as an adjunct to standard histological and immunohistochemical analyses. Neointimal lesions were induced by wire-insertion or ligation of the mouse femoral artery whilst atherosclerotic lesions were generated by administration of an atherogenic diet to apoE-deficient mice. Lesions were examined using OPT imaging of autofluorescent emission followed by complementary histological and immunohistochemical analysis. OPT clearly distinguished lesions from the underlying vascular wall. Lesion size was calculated in 2-dimensional sections using planimetry, enabling calculation of lesion volume and maximal cross-sectional area. Data generated using OPT were consistent with measurements obtained using histology, confirming the accuracy of the technique and its potential as a complement (rather than alternative) to traditional methods of analysis. This work demonstrates the potential of OPT for imaging atherosclerotic and neointimal lesions. It provides a rapid, much needed ex vivo technique for the routine 3-dimensional quantification of vascular remodelling. PMID:26067588

  18. Iterative reconstruction for quantitative computed tomography analysis of emphysema: consistent results using different tube currents

    PubMed Central

    Yamashiro, Tsuneo; Miyara, Tetsuhiro; Honda, Osamu; Tomiyama, Noriyuki; Ohno, Yoshiharu; Noma, Satoshi; Murayama, Sadayuki

    2015-01-01

    Purpose To assess the advantages of iterative reconstruction for quantitative computed tomography (CT) analysis of pulmonary emphysema. Materials and methods Twenty-two patients with pulmonary emphysema underwent chest CT imaging using identical scanners with three different tube currents: 240, 120, and 60 mA. Scan data were converted to CT images using Adaptive Iterative Dose Reduction using Three Dimensional Processing (AIDR3D) and a conventional filtered-back projection mode. Thus, six scans with and without AIDR3D were generated per patient. All other scanning and reconstruction settings were fixed. The percent low attenuation area (LAA%; < −950 Hounsfield units) and the lung density 15th percentile were automatically measured using a commercial workstation. Comparisons of LAA% and 15th percentile results between scans with and without using AIDR3D were made by Wilcoxon signed-rank tests. Associations between body weight and measurement errors among these scans were evaluated by Spearman rank correlation analysis. Results Overall, scan series without AIDR3D had higher LAA% and lower 15th percentile values than those with AIDR3D at each tube current (P<0.0001). For scan series without AIDR3D, lower tube currents resulted in higher LAA% values and lower 15th percentiles. The extent of emphysema was significantly different between each pair among scans when not using AIDR3D (LAA%, P<0.0001; 15th percentile, P<0.01), but was not significantly different between each pair among scans when using AIDR3D. On scans without using AIDR3D, measurement errors between different tube current settings were significantly correlated with patients’ body weights (P<0.05), whereas these errors between scans when using AIDR3D were insignificantly or minimally correlated with body weight. Conclusion The extent of emphysema was more consistent across different tube currents when CT scans were converted to CT images using AIDR3D than using a conventional filtered-back projection

  19. Distinct Quantitative Computed Tomography Emphysema Patterns Are Associated with Physiology and Function in Smokers

    PubMed Central

    San José Estépar, Raúl; Mendoza, Carlos S.; Hersh, Craig P.; Laird, Nan; Crapo, James D.; Lynch, David A.; Silverman, Edwin K.; Washko, George R.

    2013-01-01

    Rationale: Emphysema occurs in distinct pathologic patterns, but little is known about the epidemiologic associations of these patterns. Standard quantitative measures of emphysema from computed tomography (CT) do not distinguish between distinct patterns of parenchymal destruction. Objectives: To study the epidemiologic associations of distinct emphysema patterns with measures of lung-related physiology, function, and health care use in smokers. Methods: Using a local histogram-based assessment of lung density, we quantified distinct patterns of low attenuation in 9,313 smokers in the COPDGene Study. To determine if such patterns provide novel insights into chronic obstructive pulmonary disease epidemiology, we tested for their association with measures of physiology, function, and health care use. Measurements and Main Results: Compared with percentage of low-attenuation area less than −950 Hounsfield units (%LAA-950), local histogram-based measures of distinct CT low-attenuation patterns are more predictive of measures of lung function, dyspnea, quality of life, and health care use. These patterns are strongly associated with a wide array of measures of respiratory physiology and function, and most of these associations remain highly significant (P < 0.005) after adjusting for %LAA-950. In smokers without evidence of chronic obstructive pulmonary disease, the mild centrilobular disease pattern is associated with lower FEV1 and worse functional status (P < 0.005). Conclusions: Measures of distinct CT emphysema patterns provide novel information about the relationship between emphysema and key measures of physiology, physical function, and health care use. Measures of mild emphysema in smokers with preserved lung function can be extracted from CT scans and are significantly associated with functional measures. PMID:23980521

  20. Relationship between epicardial fat and quantitative coronary artery plaque progression: insights from computer tomography coronary angiography.

    PubMed

    Psaltis, Peter J; Talman, Andrew H; Munnur, Kiran; Cameron, James D; Ko, Brian S H; Meredith, Ian T; Seneviratne, Sujith K; Wong, Dennis T L

    2016-02-01

    Epicardial fat volume (EFV) has been suggested to promote atherosclerotic plaque development in coronary arteries, and has been correlated with both coronary stenosis and acute coronary events. Although associated with progression of coronary calcification burden, a relationship with progression of coronary atheroma volume has not been previously tested. We studied patients who had clinically indicated serial 320-row multi-detector computer tomography coronary angiography with a median 25-month interval. EFV was measured at baseline and follow-up. In vessels with coronary stenosis, quantitative analysis was performed to measure atherosclerotic plaque burden, volume and aggregate plaque volume at baseline and follow-up. The study comprised 64 patients (58.4 ± 12.2 years, 27 males, 192 vessels, 193 coronary segments). 79 (41 %) coronary segments had stenosis at baseline. Stenotic segments were associated with greater baseline EFV than those without coronary stenosis (117.4 ± 45.1 vs. 102.3 ± 51.6 cm(3), P = 0.046). 46 (24 %) coronary segments displayed either new plaque formation or progression of adjusted plaque burden at follow-up. These were associated with higher baseline EFV than segments without stenosis or those segments that had stenoses that did not progress (128.7 vs. 101.0 vs. 106.7 cm(3) respectively, P = 0.006). On multivariate analysis, baseline EFV was the only independent predictor of coronary atherosclerotic plaque progression or new development (P = 0.014). High baseline EFV is associated with the presence of coronary artery stenosis and plaque volume progression. Accumulation of EFV may be implicated in the evolution and progression of coronary atheroma. PMID:26335371

  1. Characterizing trabecular bone structure for assessing vertebral fracture risk on volumetric quantitative computed tomography

    NASA Astrophysics Data System (ADS)

    Nagarajan, Mahesh B.; Checefsky, Walter A.; Abidin, Anas Z.; Tsai, Halley; Wang, Xixi; Hobbs, Susan K.; Bauer, Jan S.; Baum, Thomas; Wismüller, Axel

    2015-03-01

    While the proximal femur is preferred for measuring bone mineral density (BMD) in fracture risk estimation, the introduction of volumetric quantitative computed tomography has revealed stronger associations between BMD and spinal fracture status. In this study, we propose to capture properties of trabecular bone structure in spinal vertebrae with advanced second-order statistical features for purposes of fracture risk assessment. For this purpose, axial multi-detector CT (MDCT) images were acquired from 28 spinal vertebrae specimens using a whole-body 256-row CT scanner with a dedicated calibration phantom. A semi-automated method was used to annotate the trabecular compartment in the central vertebral slice with a circular region of interest (ROI) to exclude cortical bone; pixels within were converted to values indicative of BMD. Six second-order statistical features derived from gray-level co-occurrence matrices (GLCM) and the mean BMD within the ROI were then extracted and used in conjunction with a generalized radial basis functions (GRBF) neural network to predict the failure load of the specimens; true failure load was measured through biomechanical testing. Prediction performance was evaluated with a root-mean-square error (RMSE) metric. The best prediction performance was observed with GLCM feature `correlation' (RMSE = 1.02 ± 0.18), which significantly outperformed all other GLCM features (p < 0.01). GLCM feature correlation also significantly outperformed MDCTmeasured mean BMD (RMSE = 1.11 ± 0.17) (p< 10-4). These results suggest that biomechanical strength prediction in spinal vertebrae can be significantly improved through characterization of trabecular bone structure with GLCM-derived texture features.

  2. Quantitative Fundus Autofluorescence and Optical Coherence Tomography in Best Vitelliform Macular Dystrophy

    PubMed Central

    Duncker, Tobias; Greenberg, Jonathan P.; Ramachandran, Rithambara; Hood, Donald C.; Smith, R. Theodore; Hirose, Tatsuo; Woods, Russell L.; Tsang, Stephen H.; Delori, François C.; Sparrow, Janet R.

    2014-01-01

    Purpose. Quantitative fundus autofluorescence (qAF), spectral domain optical coherence tomography (SD-OCT) segmentation, and multimodal imaging were performed to elucidate the pathogenesis of Best vitelliform macular dystrophy (BVMD) and to identify abnormalities in lesion versus nonlesion fundus areas. Methods. Sixteen patients with a clinical diagnosis of BVMD were studied. Autofluorescence images (30°, 488-nm excitation) were acquired with a confocal scanning laser ophthalmoscope equipped with an internal fluorescent reference to account for variable laser power and detector sensitivity. The grey levels (GLs) of each image were calibrated to the reference, zero GL, magnification, and normative optical media density, to yield qAF. Horizontal SD-OCT scans were obtained and retinal layers manually segmented. Additionally, color and near-infrared reflectance (NIR-R) images were registered to AF images. All patients were screened for mutations in BEST1. In three additional BVMD patients, in vivo spectrofluorometric measurements were obtained within the vitelliform lesion. Results. Mean nonlesion qAF was within normal limits for age. Maximum qAF within the lesion was markedly increased compared with controls. By SD-OCT segmentation, outer segment equivalent thickness was increased and outer nuclear layer thickness decreased in the lesion. Changes were also present in a transition zone beyond the lesion border. In subclinical patients, no abnormalities in retinal layer thickness were identified. Fluorescence spectra recorded from the vitelliform lesion were consistent with those of retinal pigment epithelial cell lipofuscin. Conclusions. Based on qAF, mutations in BEST1 do not cause increased lipofuscin levels in nonlesion fundus areas. PMID:24526438

  3. Predictors of bone mass by peripheral quantitative computed tomography in early adolescent girls.

    PubMed

    Moyer-Mileur, L; Xie, B; Ball, S; Bainbridge, C; Stadler, D; Jee, W S

    2001-01-01

    This cross-sectional study used peripheral quantitative computed tomography (pQCT) to evaluate the influences of age, body size, puberty, calcium intake, and physical activity on bone acquisition in healthy early adolescent girls. The pQCT technique provides analyses of volumetric bone mineral density (vBMD) (mg/cm(3)) for total as well as cortical and trabecular bone compartments and bone strength expressed as polar strength strain index (mm(2)). Bone mass of the nondominant distal and midshaft tibia by pQCT and lumbar spine and hip by dual X-ray absorptiometry (DXA) were measured in 84 girls ages 11-14 yr. Pubertal stage, menarche status, anthropometrics, and 3-d food intake and physical activity records were collected. Total and cortical bone mineral content and vBMD measurements by pQCT were significantly related to lumbar spine and femoral neck BMD measurements by DXA. We did not note any significant determinants or predictors for trabecular bone mass. Body weight was the most important predictor and determinant of total and cortical bone density and strength in healthy adolescent girls. Menarche, calcium intake, height, body mass index, and weight-bearing physical activity level age were also identified as minor but significant predictors and determinants of bone density and strength. Bone measurements by the pQCT technique provide information on bone acquisition, architecture, and strength during rapid periods of growth and development. Broader cross-sectional studies using the pQCT technique to evaluate the influence of age, gender, ethnicity, puberty, body size, and lifestyle factors on bone acquisition and strength are needed. PMID:11748336

  4. Quantitative monitoring of laser-treated engineered skin using optical coherence tomography

    PubMed Central

    Ahn, Yujin; Lee, Chan-Young; Baek, Songyee; Kim, Taeho; Kim, Pilun; Lee, Sunghoon; Min, Daejin; Lee, Haekwang; Kim, Jeehyun; Jung, Woonggyu

    2016-01-01

    Nowadays, laser therapy is a common method for treating various dermatological troubles such as acne and wrinkles because of its efficient and immediate skin enhancement. Although laser treatment has become a routine procedure in medical and cosmetic fields, the prevention of side-effects, such as hyperpigmentation, redness and burning, still remains a critical issue that needs to be addressed. In order to reduce the side-effects while attaining efficient therapeutic outcomes, it is essential to understand the light-skin interaction through evaluation of physiological changes before and after laser therapy. In this study, we introduce a quantitative tissue monitoring method based on optical coherence tomography (OCT) for the evaluation of tissue regeneration after laser irradiation. To create a skin injury model, we applied a fractional CO2 laser on a customized engineered skin model, which is analogous to human skin in terms of its basic biological function and morphology. The irradiated region in the skin was then imaged by a high-speed OCT system, and its morphologic changes were analyzed by automatic segmentation software. Volumetric OCT images in the laser treated area clearly visualized the wound healing progress at different time points and provided comprehensive information which cannot be acquired through conventional monitoring methods. The results showed that the laser wound in engineered skins was mostly recovered from within 1~2 days with a fast recovery time in the vertical direction. However, the entire recovery period varied widely depending on laser doses and skin type. Our results also indicated that OCT-guided laser therapy would be a very promising protocol for optimizing laser treatment for skin therapy. PMID:27231605

  5. High Resolution Peripheral Quantitative Computed Tomography for Assessment of Bone Quality

    NASA Astrophysics Data System (ADS)

    Kazakia, Galateia

    2014-03-01

    The study of bone quality is motivated by the high morbidity, mortality, and societal cost of skeletal fractures. Over 10 million people are diagnosed with osteoporosis in the US alone, suffering 1.5 million osteoporotic fractures and costing the health care system over 17 billion annually. Accurate assessment of fracture risk is necessary to ensure that pharmacological and other interventions are appropriately administered. Currently, areal bone mineral density (aBMD) based on 2D dual-energy X-ray absorptiometry (DXA) is used to determine osteoporotic status and predict fracture risk. Though aBMD is a significant predictor of fracture risk, it does not completely explain bone strength or fracture incidence. The major limitation of aBMD is the lack of 3D information, which is necessary to distinguish between cortical and trabecular bone and to quantify bone geometry and microarchitecture. High resolution peripheral quantitative computed tomography (HR-pQCT) enables in vivo assessment of volumetric BMD within specific bone compartments as well as quantification of geometric and microarchitectural measures of bone quality. HR-pQCT studies have documented that trabecular bone microstructure alterations are associated with fracture risk independent of aBMD.... Cortical bone microstructure - specifically porosity - is a major determinant of strength, stiffness, and fracture toughness of cortical tissue and may further explain the aBMD-independent effect of age on bone fragility and fracture risk. The application of finite element analysis (FEA) to HR-pQCT data permits estimation of patient-specific bone strength, shown to be associated with fracture incidence independent of aBMD. This talk will describe the HR-pQCT scanner, established metrics of bone quality derived from HR-pQCT data, and novel analyses of bone quality currently in development. Cross-sectional and longitudinal HR-pQCT studies investigating the impact of aging, disease, injury, gender, race, and

  6. Quantitative Fundus Autofluorescence and Optical Coherence Tomography in ABCA4 Carriers

    PubMed Central

    Duncker, Tobias; Stein, Gregory E.; Lee, Winston; Tsang, Stephen H.; Zernant, Jana; Bearelly, Srilaxmi; Hood, Donald C.; Greenstein, Vivienne C.; Delori, François C.; Allikmets, Rando; Sparrow, Janet R.

    2015-01-01

    Purpose To assess whether carriers of ABCA4 mutations have increased RPE lipofuscin levels based on quantitative fundus autofluorescence (qAF) and whether spectral-domain optical coherence tomography (SD-OCT) reveals structural abnormalities in this cohort. Methods Seventy-five individuals who are heterozygous for ABCA4 mutations (mean age, 47.3 years; range, 9–82 years) were recruited as family members of affected patients from 46 unrelated families. For comparison, 57 affected family members with biallelic ABCA4 mutations (mean age, 23.4 years; range, 6–67 years) and two noncarrier siblings were also enrolled. Autofluorescence images (30°, 488-nm excitation) were acquired with a confocal scanning laser ophthalmoscope equipped with an internal fluorescent reference. The gray levels (GLs) of each image were calibrated to the reference, zero GL, magnification, and normative optical media density to yield qAF. Horizontal SD-OCT scans through the fovea were obtained and the thicknesses of the outer retinal layers were measured. Results In 60 of 65 carriers of ABCA4 mutations (age range, 9–60), qAF levels were within normal limits (95% confidence level) observed for healthy noncarrier subjects, while qAF levels of affected family members were significantly increased. Perifoveal fleck-like abnormalities were observed in fundus AF images in four carriers, and corresponding changes were detected in the outer retinal layers in SD-OCT scans. Thicknesses of the outer retinal layers were within the normal range. Conclusions With few exceptions, individuals heterozygous for ABCA4 mutations and between the ages of 9 and 60 years do not present with elevated qAF. In a small number of carriers, perifoveal fleck-like changes were visible. PMID:26551331

  7. Detection of human brain cancer infiltration ex vivo and in vivo using quantitative optical coherence tomography.

    PubMed

    Kut, Carmen; Chaichana, Kaisorn L; Xi, Jiefeng; Raza, Shaan M; Ye, Xiaobu; McVeigh, Elliot R; Rodriguez, Fausto J; Quiñones-Hinojosa, Alfredo; Li, Xingde

    2015-06-17

    More complete brain cancer resection can prolong survival and delay recurrence. However, it is challenging to distinguish cancer from noncancer tissues intraoperatively, especially at the transitional, infiltrative zones. This is especially critical in eloquent regions (for example, speech and motor areas). This study tested the feasibility of label-free, quantitative optical coherence tomography (OCT) for differentiating cancer from noncancer in human brain tissues. Fresh ex vivo human brain tissues were obtained from 32 patients with grade II to IV brain cancer and 5 patients with noncancer brain pathologies. On the basis of volumetric OCT imaging data, pathologically confirmed brain cancer tissues (both high- and low-grade) had significantly lower optical attenuation values at both cancer core and infiltrated zones when compared with noncancer white matter, and OCT achieved high sensitivity and specificity at an attenuation threshold of 5.5 mm(-1) for brain cancer patients. We also used this attenuation threshold to confirm the intraoperative feasibility of performing in vivo OCT-guided surgery using a murine model harboring human brain cancer. Our OCT system was capable of processing and displaying a color-coded optical property map in real time at a rate of 110 to 215 frames per second, or 1.2 to 2.4 s for an 8- to 16-mm(3) tissue volume, thus providing direct visual cues for cancer versus noncancer areas. Our study demonstrates the translational and practical potential of OCT in differentiating cancer from noncancer tissue. Its intraoperative use may facilitate safe and extensive resection of infiltrative brain cancers and consequently lead to improved outcomes when compared with current clinical standards. PMID:26084803

  8. Detection of Human Brain Cancer Infiltration ex vivo and in vivo Using Quantitative Optical Coherence Tomography*

    PubMed Central

    Kut, Carmen; Chaichana, Kaisorn L.; Xi, Jiefeng; Raza, Shaan M.; Ye, Xiaobu; McVeigh, Elliot R.; Rodriguez, Fausto J.; Quinones-Hinojosa, Alfredo; Li, Xingde

    2015-01-01

    More complete brain cancer resection can prolong survival and delay recurrence. However, it is challenging to distinguish cancer from non-cancer tissues intraoperatively, especially at the transitional, infiltrative zones. This is especially critical in eloquent regions (e.g. speech and motor areas). This study tested the feasibility of label-free, quantitative optical coherence tomography (OCT) for differentiating cancer from non-cancer in human brain tissues. Fresh ex vivo human brain tissues were obtained from 32 patients with grades II-IV brain cancer and 5 patients with non-cancer brain pathologies. Based on volumetric OCT imaging data, pathologically confirmed brain cancer tissues (both high-grade and low-grade) had significantly lower optical attenuation values at both cancer core and infiltrated zones when compared with non-cancer white matter, and OCT achieved high sensitivity and specificity at an attenuation threshold of 5.5 mm-1 for brain cancer patients. We also used this attenuation threshold to confirm the intraoperative feasibility of performing in vivo OCT-guided surgery using a murine model harboring human brain cancer. Our OCT system was capable of processing and displaying a color-coded optical property map in real time at a rate of 110-215 frames per second, or 1.2-2.4 seconds for an 8-16 mm3 tissue volume, thus providing direct visual cues for cancer versus non-cancer areas. Our study demonstrates the translational and practical potential of OCT in differentiating cancer from non-cancer tissue. Its intraoperative use may facilitate safe and extensive resection of infiltrative brain cancers and consequently lead to improved outcomes when compared with current clinical standards. PMID:26084803

  9. Quantitative spectral domain optical coherence tomography thickness parameters in type II diabetes

    PubMed Central

    Gella, Laxmi; Raman, Rajiv; Sharma, Tarun

    2016-01-01

    Purpose: To elucidate the changes in retinal thickness and individual layer thickness in subjects with diabetic retinopathy (DR) using spectral domain optical coherence tomography (SDOCT). Materials and Methods: A total of 251 eyes from 170 subjects were included in this study. The study sample was subdivided into nondiabetic subjects; subjects with diabetes but no DR; subjects with mild, moderate, and severe nonproliferative DR (NPDR); and proliferative DR. Various retinal thickness parameters were assessed using SDOCT. Results: The mean age of the study population was 55.34 ± 9.02 years (range: 32–80 years) and 56.6% of the subjects were males. Men had significantly greater central foveal thickness, central subfield thickness, retinal nerve fiber layer thickness, and retinal thickness in all the quadrants of 3 mm and 6 mm zones compared to women (P < 0.001). Superior (293.11 ± 25.46 vs. 285.25 ± 19.17; P = 0.044) and temporal (282.10 ± 25.26 vs. 272.46 ± 16.21; P = 0.011) quadrants showed an increased retinal thickness in any DR group when compared with diabetic subjects without DR. Photoreceptor layer thickness was significantly reduced in diabetic subjects with no DR when compared with nondiabetic subjects and also in cases of severe NPDR when compared with mild and moderate NPDR. Conclusion: Here, we analyze the quantitative retinal thickness parameters in diabetic subjects using SDOCT. Neuronal degenerative changes such as photoreceptor and retinal pigment epithelial thinning in case of DR are also reported. PMID:27013826

  10. Quantitative optical coherence tomography angiography of choroidal neovascularization in age-related macular degeneration

    PubMed Central

    Jia, Yali; Bailey, Steven T.; Wilson, David J.; Tan, Ou; Klein, Michael L.; Flaxel, Christina J.; Potsaid, Benjamin; Liu, Jonathan J.; Lu, Chen D.; Kraus, Martin F.; Fujimoto, James G.; Huang, David

    2014-01-01

    Purpose To detect and quantify choroidal neovascularization (CNV) in age-related macular degeneration (AMD) patients using optical coherence tomography (OCT) angiography. Design Observational, cross-sectional study. Participants Five normal subjects and five neovascular AMD patients were included. Methods Five eyes with neovascular AMD and five normal age-matched controls were scanned by a high-speed (100,000 A-scans/sec) 1050 nm wavelength swept-source OCT. The macular angiography scan covered a 3×3 mm area and comprised 200×200×8 A-scans acquired in 3.5 sec. Flow was detected using the split-spectrum amplitude-decorrelation angiography (SSADA) algorithm. Motion artifacts were removed by three dimensional (3D) orthogonal registration and merging of 4 scans. The 3D angiography was segmented into 3 layers: inner retina (to show retinal vasculature), outer retina (to identify CNV), and choroid. En face maximum projection was used to obtain 2D angiograms from the 3 layers. CNV area and flow index were computed from the en face OCT angiogram of the outer retinal layer. Flow (decorrelation) and structural data were combined in composite color angiograms for both en face and cross-sectional views. Main Outcome Measurements CNV angiogram, CNV area, and CNV flow index. Results En face OCT angiograms of CNVs showed sizes and locations that were confirmed by fluorescein angiography. OCT angiography provided more distinct vascular network patterns that were less obscured by subretinal hemorrhage. The en face angiograms also showed areas of reduced choroidal flow adjacent to the CNV in all cases and significantly reduced retinal flow in one case. Cross-sectional angiograms were used to visualize CNV location relative to the retinal pigment epithelium and Bruch’s layer and classify type I and type II CNV. A feeder vessel could be identified in one case. Higher flow indexes were associated with larger CNV and type II CNV. Conclusions OCT angiography provides depth

  11. Quantitative airway assessment on computed tomography in patients with alpha1-antitrypsin deficiency.

    PubMed

    Yamashiro, Tsuneo; Matsuoka, Shin; Estépar, Raúl San José; Diaz, Alejandro; Newell, John D; Sandhaus, Robert A; Mergo, Patricia J; Brantly, Mark L; Murayama, Sadayuki; Reilly, John J; Hatabu, Hiroto; Silverman, Edwin K; Washko, George R

    2009-12-01

    The relationship between quantitative airway measurements on computed tomography (CT) and airflow limitation in individuals with severe alpha (1)-antitrypsin deficiency (AATD) is undefined. Thus, we planned to clarify the relationship between CT-based airway indices and airflow limitation in AATD. 52 patients with AATD underwent chest CT and pre-bronchodilator spirometry at three institutions. In the right upper (RUL) and lower (RLL) lobes, wall area percent (WA%) and luminal area (Ai) were measured in the third, fourth, and fifth generations of the bronchi. The severity of emphysema was also calculated in each lobe and expressed as low attenuation area percent (LAA%). Correlations between obtained measurements and FEV(1)% predicted (FEV(1)%P) were evaluated by the Spearman rank correlation test. In RUL, WA% of all generations was significantly correlated with FEV(1)%P (3rd, R = -0.33, p = 0.02; 4th, R = -0.39, p = 0.004; 5th, R = -0.57, p < 0.001; respectively). Ai also showed significant correlations (3rd, R = 0.32, p = 0.02; 4th, R = 0.34, p = 0.01; 5th, R = 0.56, p < 0.001; respectively). Measured correlation coefficients improved when the airway progressed distally from the third to fifth generations. LAA% also correlated with FEV(1)%P (R = -0.51, p < 0.001). In RLL, WA% showed weak correlations with FEV(1)%P in all generations (3rd, R = -0.34, p = 0.01; 4th, R = -0.30, p = 0.03; 5th, R = -0.31, p = 0.03; respectively). Only Ai from the fifth generation significantly correlated with FEV(1)%P in this lobe (R = 0.34, p = 0.01). LAA% strongly correlated with FEV(1)%P (R = -0.71, p < 0.001). We conclude therefore that quantitative airway measurements are significantly correlated with airflow limitation in AATD, particularly in the distal airways of RUL. Emphysema of the lower lung is the predominant component; however, airway disease also has a significant impact on airflow limitation in AATD. PMID:19938971

  12. Quantitative material analysis by dual-energy computed tomography for industrial NDT applications

    NASA Astrophysics Data System (ADS)

    Nachtrab, F.; Weis, S.; Keßling, P.; Sukowski, F.; Haßler, U.; Fuchs, T.; Uhlmann, N.; Hanke, R.

    2011-05-01

    Dual-energy computed tomography (DECT) is an established method in the field of medical CT to obtain quantitative information on a material of interest instead of mean attenuation coefficients only. In the field of industrial X-ray imaging dual-energy techniques have been used to solve special problems on a case-by-case basis rather than as a standard tool. Our goal is to develop an easy-to-use dual-energy solution that can be handled by the average industrial operator without the need for a specialist. We are aiming at providing dual-energy CT as a measurement tool for those cases where qualitative images are not enough and one needs additional quantitative information (e.g. mass density ρ and atomic number Z) about the sample at hand. Our solution is based on an algorithm proposed by Heismann et al. (2003) [1] for application in medical CT . As input data this algorithm needs two CT data sets, one with low (LE) and one with high effective energy (HE). A first order linearization is applied to the raw data, and two volumes are reconstructed thereafter. The dual-energy analysis is done voxel by voxel, using a pre-calculated function F(Z) that implies the parameters of the low and high energy measurement (such as tube voltage, filtration and detector sensitivity). As a result, two volume data sets are obtained, one providing information about the mass density ρ in each voxel, the other providing the effective atomic number Z of the material therein. One main difference between medical and industrial CT is that the range of materials that can be contained in a sample is much wider and can cover the whole range of elements, from hydrogen to uranium. Heismann's algorithm is limited to the range of elements Z=1-30, because for Z>30 the function F(Z) as given by Heismann is not a bijective function anymore. While this still seems very suitable for medical application, it is not enough to cover the complete range of industrial applications. We therefore investigated the

  13. Positron emission tomography response criteria in solid tumours criteria for quantitative analysis of [18F]-fluorodeoxyglucose positron emission tomography with integrated computed tomography for treatment response assessment in metastasised solid tumours: All that glitters is not gold.

    PubMed

    Willemsen, Annelieke E C A B; Vlenterie, Myrella; van Herpen, Carla M L; van Erp, Nielka P; van der Graaf, Winette T A; de Geus-Oei, Lioe-Fee; Oyen, Wim J G

    2016-03-01

    For solid tumours, quantitative analysis of [(18)F]-fluorodeoxyglucose positron emission tomography with integrated computed tomography potentially can have significant value in early response assessment and thereby discrimination between responders and non-responders at an early stage of treatment. Standardised strategies for this analysis have been proposed, and the positron emission tomography response criteria in solid tumours (PERCIST) criteria can be regarded as the current standard to perform quantitative analysis in a research setting, yet is not implemented in daily practice. However, several exceptions and limitations limit the feasibility of PERCIST criteria. In this article, we point out dilemmas that arise when applying proposed criteria like PERCIST on an expansive set of patients with metastasised solid tumours. Clinicians and scientists should be aware of these limitations to prevent that methodological issues impede successful introduction of research data into clinical practice. Therefore, to deliver on the high potential of quantitative imaging, consensus should be reached on a standardised, feasible and clinically useful analysis methodology. This methodology should be applicable in the majority of patients, tumour types and treatments. PMID:26808297

  14. a Dynamic Technique for the Quantitation of Oxygen Utilization Rates Using Positron Emission Tomography

    NASA Astrophysics Data System (ADS)

    Hutchins, Gary Dwight

    The conversion of oxygen to water in oxidative phosphorylation is required for the efficient production of adenosine triphosphate. This process can be monitored externally using oxygen-15 and positron emission tomography to allow estimation of metabolic rate in the human brain. A dynamic technique using ('15)O-O(,2) has been developed and compared to the existing steady state and autoradiographic approaches. These currently employed methods suffer from pitfalls associated with using assumed values for the tissue -blood partition coefficient of water. Computer simulations have been performed demonstrating the underestimation of physiological rates with the steady state technique and the time varying solutions of the autoradiographic approach. Experimental data agrees with the predicted behavior of each of these methods. The new technique requires the estimation of local cerebral blood volume and the tissue-blood partition coefficient value of water. The blood volume, necessary for a blood radioactivity correction, is estimated from the equilibrium distribution of ('15)O-CO. The tissue-blood partition coefficient is calculated using a rapid least squares analysis of ('15)O-H(,2)O dynamic blood flow data. The measured values of blood volume and partition coefficient are assumed to remain invariant with changes in the physiological state of the brain. The metabolic rate is then estimated by fitting the oxygen model to the observed kinetics in a one minute breathhold study. Alternatives to arterial blood sampling have been considered. Expired breath and lung activity concentrations used in conjunction with arterial blood sample data provide the required input functions. A time-of-flight probe has been developed as a non-invasive alternative and some intial measurements with the system are presented. The experimental data are in good agreement with the model predictions supporting the switch to a dynamic technique for the estimation of oxygen utilization rate using ('15

  15. Automatic multi-parametric quantification of the proximal femur with quantitative computed tomography

    PubMed Central

    Bonaretti, Serena; Saeed, Isra; Harnish, Roy; Recker, Robert; Burghardt, Andrew J.; Keyak, Joyce H.; Harris, Tamara; Khosla, Sundeep; Lang, Thomas F.

    2015-01-01

    Background Quantitative computed tomography (QCT) imaging is the basis for multiple assessments of bone quality in the proximal femur, including volumetric bone mineral density (vBMD), tissue volume, estimation of bone strength using finite element modeling (FEM), cortical bone thickness, and computational-anatomy-based morphometry assessments. Methods Here, we present an automatic framework to perform a multi-parametric QCT quantification of the proximal femur. In this framework, the proximal femur is cropped from the bilateral hip scans, segmented using a multi-atlas based segmentation approach, and then assigned volumes of interest through the registration of a proximal femoral template. The proximal femur is then subjected to compartmental vBMD, compartmental tissue volume, FEM bone strength, compartmental surface-based cortical bone thickness, compartmental surface-based vBMD, local surface-based cortical bone thickness, and local surface-based cortical vBMD computations. Consequently, the template registrations together with vBMD and surface-based cortical bone parametric maps enable computational anatomy studies. The accuracy of the segmentation was validated against manual segmentations of 80 scans from two clinical facilities, while the multi-parametric reproducibility was evaluated using repeat scans with repositioning from 22 subjects obtained on CT imaging systems from two manufacturers. Results Accuracy results yielded a mean dice similarity coefficient of 0.976±0.006, and a modified Haussdorf distance of 0.219±0.071 mm. Reproducibility of QCT-derived parameters yielded root mean square coefficients of variation (CVRMS) between 0.89-1.66% for compartmental vBMD; 0.20-1.82% for compartmental tissue volume; 3.51-3.59% for FEM bone strength; 1.89-2.69% for compartmental surface-based cortical bone thickness; and 1.08-2.19% for compartmental surface-based cortical vBMD. For local surface-based assessments, mean CVRMS were between 3.45-3.91% and 2

  16. Quantitative Analysis of Intraventricular Dyssynchrony Using Wall Thickness by Multidetector Computed Tomography

    PubMed Central

    Truong, Quynh A.; Singh, Jagmeet P.; Cannon, Christopher P.; Sarwar, Ammar; Nasir, Khurram; Auricchio, Angelo; Faletra, Francesco F.; Sorgente, Antonio; Conca, Cristina; Moccetti, Tiziano; Handschumacher, Mark; Brady, Thomas J.; Hoffmann, Udo

    2009-01-01

    OBJECTIVES We sought to determine the feasibility of cardiac computed tomography (CT) to detect significant differences in the extent of left ventricular dyssynchrony in heart failure (HF) patients with wide QRS, HF patients with narrow QRS, and age-matched controls. BACKGROUND The degree of mechanical dyssynchrony has been suggested as a predictor of response to cardiac resynchronization therapy. There have been no published reports of dyssynchrony assessment with the use of CT. METHODS Thirty-eight subjects underwent electrocardiogram-gated contrast-enhanced 64-slice multidetector CT. The left ventricular endocardial and epicardial boundaries were delineated from short-axis images reconstructed at 10% phase increments of the cardiac cycle. Global and segmental CT dyssynchrony metrics that used changes in wall thickness, wall motion, and volume over time were assessed for reproducibility. We defined a global metric using changes in wall thickness as the dyssynchrony index (DI). RESULTS The DI was the most reproducible metric (interobserver and intraobserver intraclass correlation coefficients ≥0.94, p < 0.0001) and was used to determine differences between the 3 groups: HF-wide QRS group (ejection fraction [EF] 22 ± 8%, QRS 163 ± 28 ms), HF-narrow QRS (EF 26 ± 7%, QRS 96 ± 11 ms), and age-matched control subjects (EF 64 ± 5%, QRS 87 ± 9 ms). Mean DI was significantly different between the 3 groups (HF-wide QRS: 152 ± 44 ms, HF-narrow QRS: 121 ± 58 ms, and control subjects: 65 ± 12 ms; p < 0.0001) and greater in the HF-wide QRS (p < 0.0001) and HF-narrow QRS (p = 0.005) groups compared with control subjects. We found that DI had a good correlation with 2-dimensional (r = 0.65, p = 0.012) and 3-dimensional (r = 0.68, p = 0.008) echocardiographic dyssynchrony. CONCLUSIONS Quantitative assessment of global CT-derived DI, based on changes in wall thickness over time, is highly reproducible and renders significant differences between subjects most likely to

  17. Quantitative HAADF-STEM tomography of unsupported intermetallic Ga-Pd catalysts

    NASA Astrophysics Data System (ADS)

    Leary, Rowan; Saghi, Zineb; Armbrüster, Marc; Schlögl, Robert; Meurig Thomas, John; Midgley, Paul

    2012-07-01

    HAADF-STEM tomography has been used for characterisation of novel unsupported intermetallic Ga-Pd catalysts, with accompanying analysis by HRTEM and EDXS. Image processing techniques applied to the tomogram have facilitated segmentation and the subsequent extraction of size and shape parameters. The fidelity of the analysis has been critically examined, enabling identification of reconstruction artefacts and thereby more reliable determination of catalytically relevant properties. Further steps towards robust and accurate metrology by electron tomography are discussed.

  18. Nanoparticles as contrast-enhancing agents in optical coherence tomography imaging of the structural components of skin: Quantitative evaluation

    SciTech Connect

    Kirillin, M Yu; Agrba, P D; Kamenskii, V A; Sirotkina, M A; Shiryamova, M V; Zagainova, E V

    2010-08-27

    This work examines the effect of gold nanoshells and titania nanoparticles on the imaging contrast of structural components of skin in optical coherence tomography (OCT). Experimental data are compared to Monte Carlo (MC) simulation results. In experiments with pig skin in vivo, the epidermis - dermis contrast is improved from 0.78 {+-} 0.03 to 0.92 {+-} 0.04 by gold nanoshells applied to the skin surface and from 0.78 {+-} 0.03 to 0.86 {+-} 0.04 by titania nanoparticles. The contrast of glands is enhanced by titania from 0.68 {+-} 0.12 to 0.84 {+-} 0.07. The highest contrast is reached 120 - 150 min after applying gold nanoshells and 160 - 200 min after applying titania. According to the MC simulation results, the contrast of inclusions increases from zero to 0.85 and 0.65, respectively. (optical tomography)

  19. [Dry matter accumulation in rice aboveground part: quantitative simulation].

    PubMed

    Li, Yan-Da; Tang, Liang; Chen, Qing-Chun; Zhang, Yu-Ping; Cao, Wei-Xing; Zhu, Yan

    2010-06-01

    A field experiment with four rice (Oryza sativa L.) cultivars and different nitrogen application rates was conducted, with the dry matter accumulation (DMA) in the cultivars aboveground part measured at their main growth stages. The dynamic model of relative dry matter accumulation (RDMA) was established with the normalized DMA and TEP (product of thermal effectiveness and PAR) from emergence to maturity, and the temporal characteristics of DMA changes was quantitatively analyzed based on the RDMA model. The dynamic changes of the RDMA could be well described with Richards equation, i. e., RDMA = 1.0157/(1 +e(3.6329-7.5907xRTEP)) 1/0.5574 (r = 0.9938). The model was validated with independent field experiment datasets, involving different eco-sites, cultivars, and nitrogen application rates. The RMSE (root mean square error) between the simulated and observed values of DMA at varied RTEP was 0.86 t x hm(-2). According to the two inflexion points of dry matter accumulation rate equation, the whole process of dry matter accumulation could be divided into early, middle, and late phases. The maximum dry matter accumulation rate (AR(max)), relative TEP at AR(max), and relative dry matter accumulation at AR(max) were found to be 2.24, 0.56, and 0.46, respectively. PMID:20873627

  20. Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

    PubMed Central

    2011-01-01

    approach is both quantitative, allowing statistical verification and calibration, and extensible, allowing modification and revision as guided by experimental evidence. The simulation methodology is part of the US EPA Virtual Liver, which is investigating the effects of everyday contaminants on living tissues. Future models will incorporate additional crosstalk surrounding proliferation as well as the putative effects of xenobiotics on these signaling cascades within hepatocytes. PMID:21745399

  1. Estimation of computed tomography dose index in cone beam computed tomography: MOSFET measurements and Monte Carlo simulations.

    PubMed

    Kim, Sangroh; Yoshizumi, Terry; Toncheva, Greta; Yoo, Sua; Yin, Fang-Fang; Frush, Donald

    2010-05-01

    To address the lack of accurate dose estimation method in cone beam computed tomography (CBCT), we performed point dose metal oxide semiconductor field-effect transistor (MOSFET) measurements and Monte Carlo (MC) simulations. A Varian On-Board Imager (OBI) was employed to measure point doses in the polymethyl methacrylate (PMMA) CT phantoms with MOSFETs for standard and low dose modes. A MC model of the OBI x-ray tube was developed using BEAMnrc/EGSnrc MC system and validated by the half value layer, x-ray spectrum and lateral and depth dose profiles. We compared the weighted computed tomography dose index (CTDIw) between MOSFET measurements and MC simulations. The CTDIw was found to be 8.39 cGy for the head scan and 4.58 cGy for the body scan from the MOSFET measurements in standard dose mode, and 1.89 cGy for the head and 1.11 cGy for the body in low dose mode, respectively. The CTDIw from MC compared well to the MOSFET measurements within 5% differences. In conclusion, a MC model for Varian CBCT has been established and this approach may be easily extended from the CBCT geometry to multi-detector CT geometry. PMID:20386198

  2. Thermal tracer tomography: from numerical simulation to field implementation

    NASA Astrophysics Data System (ADS)

    Somogyvári, Márk; Brauchler, Ralf; Bayer, Peter

    2016-04-01

    Choosing heat for subsurface investigations is attractive because changes in temperature can be easily measured, and natural variations are typically slower than the timescale of the experiments. The tomographical setup expands the applicability of such tests to reconstruct the spatial distribution of hydraulic aquifer properties. A new inversion methodology is presented for thermal tracer tomography, using tracer travel times to invert the hydraulic conductivity distribution of the aquifer. If we can assume that heat transport is driven by advection, the travel time of the thermal tracer can be related to the hydraulic parameters of the aquifer. With this assumption other thermal effects such as thermal diffusion or density driven flow appear as noise in the results. To reduce these effects the early time diagnostics of the recorded breakthrough curves are used, focusing on the fastest transport routes between the sources and receivers. The inverse problem of the experiment thus can be formulated as a classical travel time problem, and it can be solved using standard eikonal solver algorithms known from seismic or hydraulic tomography. The method is demonstrated with a high resolution 3-D aquifer analog dataset. The generated 3-D reconstruction reveals the potential of the method, especially in finding the preferential flow paths within the aquifer. Aside from this, the developed method is computationally efficient and can provide results in a fragment of the time required for full-physics model calibration. The method is also tested under field conditions. Four heat tracer injections were performed during a three day field campaign at the Widen field site in northeast Switzerland. Pulse signals were used and the temperature evolution was measured downstream using a distributed measurement system. The preliminary results of the tomographic inversion correspond well with the findings of earlier studies from the field site imaging the same geological features as

  3. Automated quantification of three-dimensional subject motion to monitor image quality in high-resolution peripheral quantitative computed tomography

    NASA Astrophysics Data System (ADS)

    Pauchard, Yves; Ayres, Fábio J.; Boyd, Steven K.

    2011-10-01

    Subject motion during acquisition of high-resolution peripheral quantitative computed tomography (HR-pQCT) results in image artifacts and interferes with quantification of bone architecture used to study bone-related diseases such as osteoporosis. We propose an automatic method to measure physical subject motion that frequently takes place during acquisition. Three measures derived from projection data are proposed to quantify motion artifacts: in-plane translation (εT) and in-plane rotation (εR) utilizing projection moments and longitudinal translation (εz) based on tracking projection profiles. Validation was performed using a phantom containing sections of distal human cadaver radii attached to a mechanical device to precisely control in-plane rotation and longitudinal translation that was intentionally performed during HR-pQCT data acquisition. Motion measured by the new automated technique was compared to the known applied motion, and related to percent errors in morphological parameters quantifying bone properties. It was determined that of the three proposed measures, εT best captured a quantified representation of image quality. εT linearly relates to true physical in-plane translational motion (r2 = 0.95, p<0.001) and is independent from longitudinal translational motion as well as the object being scanned. Additionally, εz captures large longitudinal movements and combines well with εT to fully characterize physical motion artifacts. The magnitude of εT corresponds to morphological parameter error and is an excellent basis to select high-quality images. Morphological parameter errors from these experiments confirmed our earlier computer simulations which showed that increased subject motion resulted in artificially higher trabecular number, and artificially lower bone mineral density and cortical thickness. The magnitude and, notably, the uncertainty of the morphological errors increased with increased physical motion, and this impedes a direct

  4. Compressed Sensing Electron tomography using adaptive dictionaries: a simulation study

    NASA Astrophysics Data System (ADS)

    AlAfeef, A.; Cockshott, P.; MacLaren, I.; McVitie, S.

    2014-06-01

    Electron tomography (ET) is an increasingly important technique for examining the three-dimensional morphologies of nanostructures. ET involves the acquisition of a set of 2D projection images to be reconstructed into a volumetric image by solving an inverse problem. However, due to limitations in the acquisition process this inverse problem is considered ill-posed (i.e., no unique solution exists). Furthermore reconstruction usually suffers from missing wedge artifacts (e.g., star, fan, blurring, and elongation artifacts). Compressed sensing (CS) has recently been applied to ET and showed promising results for reducing missing wedge artifacts caused by limited angle sampling. CS uses a nonlinear reconstruction algorithm that employs image sparsity as a priori knowledge to improve the accuracy of density reconstruction from a relatively small number of projections compared to other reconstruction techniques. However, The performance of CS recovery depends heavily on the degree of sparsity of the reconstructed image in the selected transform domain. Prespecified transformations such as spatial gradients provide sparse image representation, while synthesising the sparsifying transform based on the properties of the particular specimen may give even sparser results and can extend the application of CS to specimens that can not be sparsely represented with other transforms such as Total variation (TV). In this work, we show that CS reconstruction in ET can be significantly improved by tailoring the sparsity representation using a sparse dictionary learning principle.

  5. Feasibility study of endoscopic x-ray luminescence computed tomography: Simulation demonstration and phantom application

    SciTech Connect

    Chen, Xueli; Liang, Jimin; Cao, Xin; Yang, Defu; Chen, Dongmei; Ripoll, Jorge; Tian, Jie

    2013-08-28

    Even though endoscopic fluorescence diffuse optical tomography (eFDOT) exhibits significant potential, currently its application is limited due to the existence of strong autofluorescence and the imaging inaccuracy caused by a very short source-detector distance. Motivated by the emerging X-ray luminescence computed tomography (XLCT) technology, we presented an endoscopic XLCT (eXLCT) methodology. In the methodology, the aperture angle of the objective was incorporated into the forward model, providing a more accurate description of light propagation. Numerical simulation with a heterogeneous geometry and an imaging experiment with a physical phantom were illustrated to demonstrate the feasibility of the presented eXLCT methodology.

  6. Anatomical optical coherence tomography: a safe and effective tool for quantitative long-term monitoring of upper airway size and shape

    NASA Astrophysics Data System (ADS)

    Armstrong, J. J.; Becker, S.; McLaughlin, R. A.; Leigh, M. S.; Williamson, J.; Walsh, J. H.; Hillman, D. R.; Eastwood, P. R.; Sampson, D. D.

    2008-02-01

    Anatomical optical coherence tomography (aOCT) is an endoscopic optical technique that enables continuous, quantitative assessment of hollow organ size and shape in three dimensions. It is a powerful alternative to X-ray computed tomography, magnetic resonance imaging, and video endoscopy for the assessment of gross hollow-organ anatomy. This paper reviews our instrument and its application to the upper and lower airway, and includes a number of new results.

  7. Fast simulation of Proton Induced X-Ray Emission Tomography using CUDA

    NASA Astrophysics Data System (ADS)

    Beasley, D. G.; Marques, A. C.; Alves, L. C.; da Silva, R. C.

    2013-07-01

    A new 3D Proton Induced X-Ray Emission Tomography (PIXE-T) and Scanning Transmission Ion Microscopy Tomography (STIM-T) simulation software has been developed in Java and uses NVIDIA™ Common Unified Device Architecture (CUDA) to calculate the X-ray attenuation for large detector areas. A challenge with PIXE-T is to get sufficient counts while retaining a small beam spot size. Therefore a high geometric efficiency is required. However, as the detector solid angle increases the calculations required for accurate reconstruction of the data increase substantially. To overcome this limitation, the CUDA parallel computing platform was used which enables general purpose programming of NVIDIA graphics processing units (GPUs) to perform computations traditionally handled by the central processing unit (CPU). For simulation performance evaluation, the results of a CPU- and a CUDA-based simulation of a phantom are presented. Furthermore, a comparison with the simulation code in the PIXE-Tomography reconstruction software DISRA (A. Sakellariou, D.N. Jamieson, G.J.F. Legge, 2001) is also shown. Compared to a CPU implementation, the CUDA based simulation is approximately 30× faster.

  8. Quantitative Technique for Comparing Simulant Materials through Figures of Merit

    NASA Technical Reports Server (NTRS)

    Rickman, Doug; Hoelzer, Hans; Fourroux, Kathy; Owens, Charles; McLemore, Carole; Fikes, John

    2007-01-01

    The 1989 workshop report entitled Workshop on Production and Uses of Simulated Lunar Materials and the Lunar Regolith Simulant Materials: Recommendations for Standardization, Production, and Usage, NASA Technical Publication both identified and reinforced a need for a set of standards and requirements for the production and usage of the Lunar simulant materials. As NASA prepares to return to the Moon, and set out to Mars, a set of early requirements have been developed for simulant materials and the initial methods to produce and measure those simulants have been defined. Addressed in the requirements document are: 1) a method for evaluating the quality of any simulant of a regolith, 2) the minimum characteristics for simulants of Lunar regolith, and 3) a method to produce simulants needed for NASA's Exploration mission. As an extension of the requirements document a method to evaluate new and current simulants has been rigorously defined through the mathematics of Figures of Merit (FoM). Requirements and techniques have been developed that allow the simulant provider to compare their product to a standard reference material through Figures of Merit. Standard reference material may be physical material such as the Apollo core samples or material properties predicted for any landing site. The simulant provider is not restricted to providing a single "high fidelity" simulant, which may be costly to produce. The provider can now develop "lower fidelity" simulants for engineering applications such as drilling and mobility applications.

  9. Neutron Radiography and Tomography Investigations of the Secondary Hydriding of Zircaloy-4 during Simulated Loss of Coolant Nuclear Accidents

    NASA Astrophysics Data System (ADS)

    Grosse, Mirco K.; Stuckert, Juri; Steinbrück, Martin; Kaestner, Anders P.; Hartmann, Stefan

    In the framework of the post-test examinations of the large-scale LOCA simulation tests at the fuel rod bundle scale, the hydrogen distributions in specimens prepared from the QUENCH-L0 and -L1 tests were studied by means of neutron radiography and tomography. In order to determine quantitative hydrogen concentrations, both, neutron radiography and tomography were calibrated using cladding tube segments with known hydrogen concentrations. The linear dependence of the total macroscopic neutron cross section with the H/Zr atomic ratio was determined for both methods. The hydrogen distributions in samples prepared from the two tests differ significantly as a first glance to the results obtained for the QUENCH-L1 shows. Whereas clearly visible hydrogen bands were found in samples of the QUENCH-L0 test with a time between burst and quenching of more than 70 s; in some specimens prepared from the QUENCH-L1 test only blurred bands could be detected. The reasons for these different behaviors can be the different times between reaching the temperature maxima and the quenching, as well as bending of the QUENCH-L1 bundle. In the QUENCH-L0 test the bundle was quenched immediately after reaching the maximal temperature. In QUENCH-L1 the hydrogen had about 130 s to diffuse and reach more homogeneous distributions without clear contrasts between the hydrogen bands and the neighboring regions in the neutron images.

  10. Quantitative dopant distributions in GaAs nanowires using atom probe tomography.

    PubMed

    Du, Sichao; Burgess, Timothy; Gault, Baptiste; Gao, Qiang; Bao, Peite; Li, Li; Cui, Xiangyuan; Kong Yeoh, Wai; Liu, Hongwei; Yao, Lan; Ceguerra, Anna V; Hoe Tan, Hark; Jagadish, Chennupati; Ringer, Simon P; Zheng, Rongkun

    2013-09-01

    Controllable doping of semiconductor nanowires is critical to realize their proposed applications, however precise and reliable characterization of dopant distributions remains challenging. In this article, we demonstrate an atomic-resolution three-dimensional elemental mapping of pristine semiconductor nanowires on growth substrates by using atom probe tomography to tackle this major challenge. This highly transferrable method is able to analyze the full diameter of a nanowire, with a depth resolution better than 0.17 nm thanks to an advanced reconstruction method exploiting the specimen's crystallography, and an enhanced chemical sensitivity of better than 8-fold increase in the signal-to-noise ratio. PMID:23489910

  11. Quantitative optical coherence tomography of fluid-filled oral mucosal lesions.

    PubMed

    Adegun, O K; Tomlins, P H; Hagi-Pavli, E; Bader, D L; Fortune, Farida

    2013-09-01

    The decision of selecting the most representative site for the biopsy of fluid-filled lesions can be difficult. This may be attributed to the poor delineation of the correct lesional site by clinical observation alone. In this study, optical coherence tomography is used to quantify the contrast between solid- and fluid-filled lesions by measuring the light intensity change at the tissue-fluid interface (intensity drop). This parameter was measured from sequential axial scans (n ≈ 10(6) per sample) of 3D optical coherence tomography (OCT) datasets from control tissues (n = 14) and fluid-filled lesions (n = 7) and displayed as a 2D-scaled intensity drop (SID) image. The results of the SID image allowed for discrimination, characterisation and extent of a fluid filled region. The differentiation of normal and fluid-filled areas using individual SID values yielded both a sensitivity and specificity of approximately 80 %. OCT complemented by SID analysis provides a potential in vivo clinical tool that would enable non-invasive objective visualisation of the oral mucosa. PMID:22996049

  12. Bone Health Monitoring in Astronauts: Recommended Use of Quantitative Computed Tomography [QCT] for Clinical and Operational Decisions

    NASA Technical Reports Server (NTRS)

    Sibonga, J. D.; Truskowski, P.

    2010-01-01

    This slide presentation reviews the concerns that astronauts in long duration flights might have a greater risk of bone fracture as they age than the general population. A panel of experts was convened to review the information and recommend mechanisms to monitor the health of bones in astronauts. The use of Quantitative Computed Tomography (QCT) scans for risk surveillance to detect the clinical trigger and to inform countermeasure evaluation is reviewed. An added benefit of QCT is that it facilitates an individualized estimation of bone strength by Finite Element Modeling (FEM), that can inform approaches for bone rehabilitation. The use of FEM is reviewed as a process that arrives at a composite number to estimate bone strength, because it integrates multiple factors.

  13. [Quantitative structure characteristics and fractal dimension of Chinese medicine granules measured by synchrotron radiation X-ray computed micro tomography].

    PubMed

    Lu, Xiao-long; Zheng, Qin; Yin, Xian-zhen; Xiao, Guang-qing; Liao, Zu-hua; Yang, Ming; Zhang, Ji-wen

    2015-06-01

    The shape and structure of granules are controlled by the granulation process, which is one of the main factors to determine the nature of the solid dosage forms. In this article, three kinds of granules of a traditional Chinese medicine for improving appetite and promoting digestion, namely, Jianwei Granules, were prepared using granulation technologies as pendular granulation, high speed stirring granulation, and fluidized bed granulation and the powder properties of them were investigated. Meanwhile, synchrotron radiation X-ray computed micro tomography (SR-µCT) was applied to quantitatively determine the irregular internal structures of the granules. The three-dimensional (3D) structure models were obtained by 3D reconstruction, which were more accurately to characterize the three-dimensional structures of the particles through the quantitative data. The models were also used to quantitatively compare the structural differences of granules prepared by different granulation processes with the same formula, so as to characterize how the production process plays a role in the pharmaceutical behaviors of the granules. To focus on the irregularity of the particle structure, the box counting method was used to calculate the fractal dimensions of the granules. The results showed that the fractal dimension is more sensitive to reflect the minor differences in the structure features than the conventional parameters, and capable to specifically distinct granules in structure. It is proved that the fractal dimension could quantitatively characterize the structural information of irregular granules. It is the first time suggested by our research that the fractal dimension difference (Df,c) between two fractal dimension parameters, namely, the volume matrix fractal dimension and the surface matrix fractal dimension, is a new index to characterize granules with irregular structures and evaluate the effects of production processes on the structures of granules as a new

  14. Quantitative technique for robust and noise-tolerant speed measurements based on speckle decorrelation in optical coherence tomography

    PubMed Central

    Uribe-Patarroyo, Néstor; Villiger, Martin; Bouma, Brett E.

    2014-01-01

    Intensity-based techniques in optical coherence tomography (OCT), such as those based on speckle decorrelation, have attracted great interest for biomedical and industrial applications requiring speed or flow information. In this work we present a rigorous analysis of the effects of noise on speckle decorrelation, demonstrate that these effects frustrate accurate speed quantitation, and propose new techniques that achieve quantitative and repeatable measurements. First, we derive the effect of background noise on the speckle autocorrelation function, finding two detrimental effects of noise. We propose a new autocorrelation function that is immune to the main effect of background noise and permits quantitative measurements at high and moderate signal-to-noise ratios. At the same time, this autocorrelation function is able to provide motion contrast information that accurately identifies areas with movement, similar to speckle variance techniques. In order to extend the SNR range, we quantify and model the second effect of background noise on the autocorrelation function through a calibration. By obtaining an explicit expression for the decorrelation time as a function of speed and diffusion, we show how to use our autocorrelation function and noise calibration to measure a flowing liquid. We obtain accurate results, which are validated by Doppler OCT, and demonstrate a very high dynamic range (> 600 mm/s) compared to that of Doppler OCT (±25 mm/s). We also derive the behavior for low flows, and show that there is an inherent non-linearity in speed measurements in the presence of diffusion due to statistical fluctuations of speckle. Our technique allows quantitative and robust measurements of speeds using OCT, and this work delimits precisely the conditions in which it is accurate. PMID:25322018

  15. Semi-quantitative Multispectral Optoacoustic Tomography (MSOT) for volumetric PK imaging of gastric emptying

    PubMed Central

    Morscher, Stefan; Driessen, Wouter H.P.; Claussen, Jing; Burton, Neal C.

    2014-01-01

    A common side effect of medication is gastrointestinal intolerance. Symptoms can include reduced appetite, diarrhea, constipation, GI inflammation, nausea and vomiting. Such effects often have a dramatic impact on compliance with a treatment regimen. Therefore, characterization of GI tolerance is an important step when establishing a novel therapeutic approach. In this study, Multispectral Optoacoustic Tomography (MSOT) is used to monitor gastrointestinal motility by in vivo whole body imaging in mice. MSOT combines high spatial and temporal resolution based on ultrasound detection with strong optical contrast in the near infrared. Animals were given Indocyanine Green (ICG) by oral gavage and imaged by MSOT to observe the fate of ICG in the gastrointestinal tract. Exponential decay of ICG signal was observed in the stomach in good correlation with ex vivo validation. We discuss how kinetic imaging in MSOT allows visualization of parameters unavailable to other imaging methods, both in 2D and 3D. PMID:25431754

  16. Quantitative optical coherence tomography by maximum a-posteriori estimation of signal intensity

    NASA Astrophysics Data System (ADS)

    Chan, Aaron C.; Kurokawa, Kazuhiro; Makita, Shuichi; Hong, Young-Joo; Miyazawa, Arata; Miura, Masahiro; Yasuno, Yoshiaki

    2016-03-01

    A maximum a-posteriori (MAP) estimator for signal amplitude of optical coherence tomography (OCT) is presented. This estimator provides an accurate and low bias estimation of the correct OCT signal amplitude even at very low signal-tonoise ratios. As a result, contrast improvement of retinal OCT images is demonstrated. In addition, this estimation method allows for an estimation reliability to be calculated. By combining the MAP estimator with a previously demonstrated attenuation imaging algorithm, we present attenuation coefficient images of the retina. From the reliability derived from the MAP image one can also determine which regions of the attenuation images are unreliable. From Jones matrix OCT data of the optic nerve head (ONH), we also demonstrate that combining MAP with polarization diversity (PD) OCT images can generate intensity images with fewer birefringence artifacts, resulting in better attenuation images. Analysis of the MAP intensity images shows higher image SNR than averaging.

  17. Quantitative evaluation of hip joint laxity in 22 Border Collies using computed tomography.

    PubMed

    Kishimoto, Miori; Yamada, Kazutaka; Pae, Sa-Hun; Muroya, Naoyoshi; Watarai, Hirokazu; Anzai, Hiroshi; Shimizu, Junichiro; Iwasaki, Toshiroh; Miyake, Yoh-Ichi; Wisner, Erik R

    2009-02-01

    The purpose of this study was to obtain the computed tomography (CT) data for the hip joints of 22 Border Collies. The dorsolateral subluxation (DLS) score, lateral center edge angle (LCEA), dorsal acetabular rim angle (DARA) and center distance (CD) index were measured on the CT images in a weight-bearing position. Radiographic Norberg angle (NA) was also measured. The mean values were 45.7 +/- 10.2% for DLS score, 85.9 degrees +/- 10.3 degrees for LCEA, 18.5 degrees +/- 7.3 degrees for DARA, 0.40 +/- 0.17 for CD index and 102.7 degrees +/- 6.9 degrees for NA. Since the DLS score and LCEA showed strong correlation, combined use of these parameters might improve diagnostic accuracy. We consider CT evaluation in a weight-bearing position to be a useful method for multidirectional evaluation of hips. PMID:19262043

  18. Quantitative optical coherence tomography imaging of intermediate flow defect phenotypes in ciliary physiology and pathophysiology

    NASA Astrophysics Data System (ADS)

    Huang, Brendan K.; Gamm, Ute A.; Jonas, Stephan; Khokha, Mustafa K.; Choma, Michael A.

    2015-03-01

    Cilia-driven fluid flow is a critical yet poorly understood aspect of pulmonary physiology. Here, we demonstrate that optical coherence tomography-based particle tracking velocimetry can be used to quantify subtle variability in cilia-driven flow performance in Xenopus, an important animal model of ciliary biology. Changes in flow performance were quantified in the setting of normal development, as well as in response to three types of perturbations: mechanical (increased fluid viscosity), pharmacological (disrupted serotonin signaling), and genetic (diminished ciliary motor protein expression). Of note, we demonstrate decreased flow secondary to gene knockdown of kif3a, a protein involved in ciliogenesis, as well as a dose-response decrease in flow secondary to knockdown of dnah9, an important ciliary motor protein.

  19. Improving the quantitative accuracy of optical-emission computed tomography by incorporating an attenuation correction: application to HIF1 imaging

    NASA Astrophysics Data System (ADS)

    Kim, E.; Bowsher, J.; Thomas, A. S.; Sakhalkar, H.; Dewhirst, M.; Oldham, M.

    2008-10-01

    Optical computed tomography (optical-CT) and optical-emission computed tomography (optical-ECT) are new techniques for imaging the 3D structure and function (including gene expression) of whole unsectioned tissue samples. This work presents a method of improving the quantitative accuracy of optical-ECT by correcting for the 'self'-attenuation of photons emitted within the sample. The correction is analogous to a method commonly applied in single-photon-emission computed tomography reconstruction. The performance of the correction method was investigated by application to a transparent cylindrical gelatin phantom, containing a known distribution of attenuation (a central ink-doped gelatine core) and a known distribution of fluorescing fibres. Attenuation corrected and uncorrected optical-ECT images were reconstructed on the phantom to enable an evaluation of the effectiveness of the correction. Significant attenuation artefacts were observed in the uncorrected images where the central fibre appeared ~24% less intense due to greater attenuation from the surrounding ink-doped gelatin. This artefact was almost completely removed in the attenuation-corrected image, where the central fibre was within ~4% of the others. The successful phantom test enabled application of attenuation correction to optical-ECT images of an unsectioned human breast xenograft tumour grown subcutaneously on the hind leg of a nude mouse. This tumour cell line had been genetically labelled (pre-implantation) with fluorescent reporter genes such that all viable tumour cells expressed constitutive red fluorescent protein and hypoxia-inducible factor 1 transcription-produced green fluorescent protein. In addition to the fluorescent reporter labelling of gene expression, the tumour microvasculature was labelled by a light-absorbing vasculature contrast agent delivered in vivo by tail-vein injection. Optical-CT transmission images yielded high-resolution 3D images of the absorbing contrast agent, and

  20. Monte Carlo simulation of photonic state tomography: a virtual Hanbury Brown and Twiss correlator

    NASA Astrophysics Data System (ADS)

    Murray, Eoin; Juska, Gediminas; Pelucchi, Emanuele

    2016-05-01

    This paper provides a theoretical background for the simulations of particular quantum optics experiments, namely, photon intensity correlation measurements. A practical example, adapted to polarisation-entangled photon pairs emitted from a quantum dot, is presented. The tool, a virtual Hanbury Brown and Twiss correlator, simulates polarisation-resolved the second-order correlation functions, which then can be used in a photonic state tomography procedure—a full description of a light source’s polarisation state. This educational tool is meant to improve general understanding of such quantum optics experiments.

  1. Absolute quantitation of iodine-123 epidepride kinetics using single-photon emission tomography: comparison with carbon-11 epidepride and positron emission tomography.

    PubMed

    Almeida, P; Ribeiro, M J; Bottlaender, M; Loc'h, C; Langer, O; Strul, D; Hugonnard, P; Grangeat, P; Mazière, B; Bendriem, B

    1999-12-01

    Epidepride labelled with iodine-123 is a suitable probe for the in vivo imaging of striatal and extrastriatal dopamine D2 receptors using single-photon emission tomography (SPET). Recently, this molecule has also been labelled with carbon-11. The goal of this work was to develop a method allowing the in vivo quantification of radioactivity uptake in baboon brain using SPET and to validate it using positron emission tomography (PET). SPET studies were performed in Papio anubis baboons using 123I-epidepride. Emission and transmission measurements were acquired on a dual-headed system with variable head angulation and low-energy ultra-high resolution (LEUHR) collimation. The imaging protocol consisted of one transmission measurement (24 min, heads at 90 degrees), obtained with two sliding line sources of gadolinium-153 prior to injection of 0.21-0.46 GBq of 123I-epidepride, and 12 emission measurements starting 5 min post injection. For scatter correction (SC) we used a dual-window method adapted to 123I. Collimator blurring correction (CBC) was done by deconvolution in Fourier space and attenuation correction (AT) was applied on a preliminary (CBC) filtered back-projection reconstruction using 12 iterations of a preconditioned, regularized minimal residual algorithm. For each reconstruction, a calibration factor was derived from a uniform cylinder filled with a 123I solution of a known radioactivity concentration. Calibration and baboon images were systematically built with the same reconstruction parameters. Uncorrected (UNC) and (AT), (SC + AT) and (SC + CBC + AT) corrected images were compared. PET acquisitions using 0.11-0.44 GBq of 11C-epidepride were performed on the same baboons and used as a reference. The radioactive concentrations expressed in percent of the injected dose per 100 ml (% ID/100 ml) obtained after (SC + CBC + AT) in SPET are in good agreement with those obtained with PET and 11C-epidepride. A method for the in vivo absolute quantitation of 123

  2. Quantitative measurement of local cerebral blood flow in humans by positron computed tomography and /sup 15/O-water

    SciTech Connect

    Huang, S.C.; Carson, R.E.; Hoffman, E.J.; Carson, J.; MacDonald, N.; Barrio, J.R.; Phelps, M.E.

    1983-06-01

    A noninvasive method that employs /sup 15/O-water and positron-computed tomography (PCT) was used to measure quantitative local cerebral blood flow (lCBF) in man. /sup 15/O-Water (about 30-50 mCi) was introduced through a single-breath inhalation of /sup 15/O-carbon dioxide or through an intravenous bolus injection of /sup 15/O-water. A sequence of five 2-min PCT scans was initiated at the time of tracer administration. A series of 15-20 blood samples (1 ml each) was withdrawn from the radial artery of the subject over a period of 10 min. Oxygen-15 radioactivities in the blood samples were immediately counted in a well counter to give an input function, which together with the projection data collected by PCT were processed to provide images of 1CBF and local water distribution volume. The method was found to be convenient to use and gave good-quality images of 1CBF. Quantitative values of 1CBF in images were 59 +/- 11 and 20 +/- 4 ml/min/100 g for gray and white matter, respectively, with a gray-to-white matter ratio of 2.93 and a global flow value of 42 +/- 8 ml/min/100 g. Distribution volume of water was 0.85 +/- 0.03, 0.76 +/- 0.03, and 0.81 +/- 0.02 ml/g respectively, for gray matter, white matter, and whole brain.

  3. Excitation spectroscopy in multispectral optical fluorescence tomography: methodology, feasibility, and computer simulation studies

    PubMed Central

    Chaudhari, Abhijit J; Ahn, Sangtae; Levenson, Richard; Badawi, Ramsey D; Cherry, Simon R; Leahy, Richard M

    2009-01-01

    inhomogeneous mouse atlas using singular value decomposition and analysis of reconstructed spatial resolution versus noise. For simplicity, quantitative results have been shown for one representative fluorescent probe (Alexa 700®) and effects due to tissue autofluorescence have not been taken into account. We also demonstrate the performance of our method for 3D reconstruction of tumors in a simulated mouse model of metastatic human hepatocellular carcinoma. PMID:19590118

  4. Investigation of a quantitative photoacoustic tomography fitting procedure on multiple targets in reflection geometry with diffuse optical measurement assistance

    NASA Astrophysics Data System (ADS)

    Xu, Chen; Kumavor, Patrick D.; Zhu, Quing

    2012-02-01

    Traditional Photoacoustic tomography provides the distribution of absorbed optical energy densities which are the products of the optical absorption coefficients and fluences. However, the absorption coefficient is the only functional parameter that is related to disease diagnosis, such as cancer. In this paper, we report the experimental investigation of an improved fitting procedure which can quantitatively characterize optical absorption coefficients of multiple targets. The original fitting procedure was proposed by us and used for a single target. The fitting procedure included a complete photoacoustic forward model, which incorporated an analytical model of light transport and a model of acoustic propagation. Using the target information from the PAT images and the background information from diffuse optical measurements (DOM), the fitting method minimizes the photoacoustic measurements and forward model data and recovers the target absorption coefficient quantitatively. The fitting errors in the absorption coefficients can reach 20% to 100% if the original fitting procedure is directly used on multiple targets. In our improved fitting method, the ratio between the photoacoustic intensities is introduced and served as extra input to the fitting procedure. As a result, the total number of unknown parameters is reduced and fitting accuracy is improved. The hybrid system used in the experiment combines a 64-channel photoacoustic system with a frequency-domain diffused optical system. The experiment was performed in the reflection geometry suitable for breast imaging. Phantom experiments include the combination of high contrast and low contrast targets with absorption coefficients ranging from 0.07 to 0.28 cm-1 and with different spatial separations. The phantoms were inserted into a chicken breast tissue. The fitting errors of multiple targets were reduced to less than 20% for both high and low contrast targets. These results illustrate the potential application

  5. Radiomorphometric quantitative analysis of vasculature utilizing micro-computed tomography and vessel perfusion in the murine mandible.

    PubMed

    Jing, Xi Lin; Farberg, Aaron S; Monson, Laura A; Donneys, Alexis; Tchanque-Fossuo, Catherine N; Buchman, Steven R

    2012-12-01

    Purpose Biomechanical, densitometric, and histological analyses have been the mainstay for reproducible outcome measures for investigation of new bone formation and osseous healing. Here we report the addition of radiomorphometric vascular analysis as a quantitative measure of vascularity in the murine mandible. To our knowledge this is the first description of using micro-computed tomography (micro-CT) to evaluate the temporal and spatial pattern of angiogenesis in the craniofacial skeleton. Methods The vessel perfusion technique was performed on 10 Sprague-Dawley rats using Microfil (MV-122, Flow Tech; Carver, MA). After decalcification, hemimandibles were imaged using high-resolution micro-CT. Six separate radiomorphometric vascular metrics were calculated. Results Radiomorphometric values were analyzed using three different thresholds on micro-CT. Experimentally, 1000 Hounsfield units was found to be the optimal threshold for analysis to capture the maximal vascular content of the bone. Data from seven hemimandibles were analyzed. Minimal statistical variance in each of the quantitative measures of vascularity resulted in reproducible metrics for each of the radiomorphometric parameters. Conclusions We have demonstrated that micro-CT vascular imaging provides a robust methodology for evaluation of vascular networks in the craniofacial skeleton. This technique provides 3D quantitative data analysis that differs significantly from laser Doppler and microsphere methods, which simply measure flow. This technique is advantageous over labor-intensive 2D conventional analyses using histology and X-ray microangiography. Our data establish the appropriate thresholding for optimal vascular analyses and provide baseline measurements that can be used to analyze the role of angiogenesis in bone regeneration and repair in the craniofacial skeleton. PMID:24294405

  6. Quantitative analysis applied to contrast medium extravasation by using the computed-tomography number within the region of interest

    NASA Astrophysics Data System (ADS)

    Lee, Jae-Seung; Im, In-Chul; Kim, Moon-Jib; Goo, Eun-Hoe; Kim, Sun-Ju; Kim, Kwang; Kwak, Byung-Joon

    2014-02-01

    The present study was carried out to present a method to analyze extravasation quantitatively by measuring the computed tomography (CT) number after determining the region of interest (ROI) in the CT images obtained from patients suspected of extravasation induced by contrast medium auto-injection. To achieve this, we divided the study subjects into a group of patients who incurred extravasation and a group of patients who underwent routine scans without incurring extravasation. The CT numbers at IV sites were obtained as reference values, and CT numbers at extravasation sites and hepatic portal veins, respectively, were obtained as relative values. Thereupon, the predicted time for extravasation ( T EP ) and the predicted ratio for extravasation ( R EP ) of an extravasation site were obtained and analyzed quantitatively. In the case of extravasation induced by a dual auto-injector, the values of the CT numbers were confirmed to be lower and the extravasation site to be enlarged when compared to the extravasation induced by a single autoinjector. This is because the physiological saline introduced after the injection of the contrast agent diluted the concentration of the extravasated contrast agent. Additionally, the T EP caused by the auto-injector was about 40 seconds, and we could perform a precise quantitative assessment of the site suspected of extravasation. In conclusion, the dual auto-injection method, despite its advantage of reducing the volume of contrast agent and improving the quality of images for patients with good vascular integrity, was judged to be likely to increase the risk of extravasation and aggravate outcomes for patients with poor vascular integrity by enlarging extravasation sites.

  7. Quantitative Analysis of Mouse Retinal Layers Using Automated Segmentation of Spectral Domain Optical Coherence Tomography Images

    PubMed Central

    Dysli, Chantal; Enzmann, Volker; Sznitman, Raphael; Zinkernagel, Martin S.

    2015-01-01

    Purpose Quantification of retinal layers using automated segmentation of optical coherence tomography (OCT) images allows for longitudinal studies of retinal and neurological disorders in mice. The purpose of this study was to compare the performance of automated retinal layer segmentation algorithms with data from manual segmentation in mice using the Spectralis OCT. Methods Spectral domain OCT images from 55 mice from three different mouse strains were analyzed in total. The OCT scans from 22 C57Bl/6, 22 BALBc, and 11 C3A.Cg-Pde6b+Prph2Rd2/J mice were automatically segmented using three commercially available automated retinal segmentation algorithms and compared to manual segmentation. Results Fully automated segmentation performed well in mice and showed coefficients of variation (CV) of below 5% for the total retinal volume. However, all three automated segmentation algorithms yielded much thicker total retinal thickness values compared to manual segmentation data (P < 0.0001) due to segmentation errors in the basement membrane. Conclusions Whereas the automated retinal segmentation algorithms performed well for the inner layers, the retinal pigmentation epithelium (RPE) was delineated within the sclera, leading to consistently thicker measurements of the photoreceptor layer and the total retina. Translational Relevance The introduction of spectral domain OCT allows for accurate imaging of the mouse retina. Exact quantification of retinal layer thicknesses in mice is important to study layers of interest under various pathological conditions. PMID:26336634

  8. Small pulmonary vascular alteration and acute exacerbations of COPD: quantitative computed tomography analysis.

    PubMed

    Wang, Zhiyue; Chen, Xuesong; Liu, Kouying; Xie, Weiping; Wang, Hong; Wei, Yongyue; Tang, Lijun; Zhu, Yinsu

    2016-01-01

    The morphologic alterations of pulmonary small vessels measured by computed tomography (CT) have been used to evaluate chronic obstructive pulmonary disease (COPD). However, the relationship between small pulmonary vascular alteration and acute exacerbations of COPD (AECOPD) is not well understood. The aim of this study was to evaluate the cross-sectional area (CSA) of small pulmonary vessel alterations measured on CT images and investigate its relationship with the COPD severity staged by the degree of airflow limitation and the occurrence of AECOPD. We retrospectively reviewed CT scans, clinical characteristics, and pulmonary function test results of 153 patients with COPD. All the patients were divided into AECOPD and non-AECOPD group according to the COPD staging and pulmonary function test results. The percentages of the total CSA less than 5 mm(2) and equal to 5-10 mm(2) over the lung area (%CSA<5 and %CSA5-10, respectively) were measured. The %CSA<5 steadily decreased in relation to the increase of COPD severity. In addition, %CSA<5 of the AECOPD group was significantly lower than that of the non-AECOPD group (0.41±0.13 versus 0.68±0.18, P<0.001), and the optimal cutoff value was 0.56 (sensitivity, 0.863; specificity, 0.731). Therefore, small pulmonary vascular alteration, as measured by %CSA<5, could indicate not only the degree of COPD severity, but also the occurrence of AECOPD. PMID:27578971

  9. Quantitative Computer Tomography for Determining Composition of Microgravity and Ground Based Solid Solutions

    NASA Technical Reports Server (NTRS)

    Gillies, D. C.; Engel, H. P.

    1999-01-01

    Advances in x-ray Computer Tomography (CT) have been led by the medical profession, and by evaluation of industrial products, particularly castings. Porosity can readily be determined as a function of the density of a material, and CT is thus an industrially important NDE tool. Providing high purity, 100% dense standards of pure elements and compounds can be fabricated, the composition of solid solution alloys can be determined by measuring the CT number, which is a function of the absorption of the sample. Average densities across slices 1 mm thick can generally be determined to better than 1 percent. With present technology this spatial sensitivity is less than ideal, but important benefits can nevertheless be obtained by using CT, particularly single crystals, prior to making any destructive assault upon the sample. The sample can in fact be examined prior to removal from the mold within which it has been grown and, in the cases of microgravity flight samples, before removal from the cartridge assembly. This greatly assists the researcher in the characterization of the products, particularly as a guide to cutting and sampling. Examples of work with germanium-silicon alloys and mercury cadmium telluride taken with a radioactive cobalt source will be demonstrated.

  10. A novel 3D absorption correction method for quantitative EDX-STEM tomography.

    PubMed

    Burdet, Pierre; Saghi, Z; Filippin, A N; Borrás, A; Midgley, P A

    2016-01-01

    This paper presents a novel 3D method to correct for absorption in energy dispersive X-ray (EDX) microanalysis of heterogeneous samples of unknown structure and composition. By using STEM-based tomography coupled with EDX, an initial 3D reconstruction is used to extract the location of generated X-rays as well as the X-ray path through the sample to the surface. The absorption correction needed to retrieve the generated X-ray intensity is then calculated voxel-by-voxel estimating the different compositions encountered by the X-ray. The method is applied to a core/shell nanowire containing carbon and oxygen, two elements generating highly absorbed low energy X-rays. Absorption is shown to cause major reconstruction artefacts, in the form of an incomplete recovery of the oxide and an erroneous presence of carbon in the shell. By applying the correction method, these artefacts are greatly reduced. The accuracy of the method is assessed using reference X-ray lines with low absorption. PMID:26484792

  11. Small pulmonary vascular alteration and acute exacerbations of COPD: quantitative computed tomography analysis

    PubMed Central

    Wang, Zhiyue; Chen, Xuesong; Liu, Kouying; Xie, Weiping; Wang, Hong; Wei, Yongyue; Tang, Lijun; Zhu, Yinsu

    2016-01-01

    The morphologic alterations of pulmonary small vessels measured by computed tomography (CT) have been used to evaluate chronic obstructive pulmonary disease (COPD). However, the relationship between small pulmonary vascular alteration and acute exacerbations of COPD (AECOPD) is not well understood. The aim of this study was to evaluate the cross-sectional area (CSA) of small pulmonary vessel alterations measured on CT images and investigate its relationship with the COPD severity staged by the degree of airflow limitation and the occurrence of AECOPD. We retrospectively reviewed CT scans, clinical characteristics, and pulmonary function test results of 153 patients with COPD. All the patients were divided into AECOPD and non-AECOPD group according to the COPD staging and pulmonary function test results. The percentages of the total CSA less than 5 mm2 and equal to 5–10 mm2 over the lung area (%CSA<5 and %CSA5–10, respectively) were measured. The %CSA<5 steadily decreased in relation to the increase of COPD severity. In addition, %CSA<5 of the AECOPD group was significantly lower than that of the non-AECOPD group (0.41±0.13 versus 0.68±0.18, P<0.001), and the optimal cutoff value was 0.56 (sensitivity, 0.863; specificity, 0.731). Therefore, small pulmonary vascular alteration, as measured by %CSA<5, could indicate not only the degree of COPD severity, but also the occurrence of AECOPD. PMID:27578971

  12. Use of ultrafast computed tomography to quantitate regional myocardial perfusion: a preliminary report

    SciTech Connect

    Rumberger, J.A.; Feiring, A.J.; Lipton, M.J.; Higgins, C.B.; Ell, S.R.; Marcus, M.L.

    1987-01-01

    The purpose of this study was to assess the potential for rapid acquisition computed axial tomography (Imatron C-100) to quantify regional myocardial perfusion. Myocardial and left ventricular cavity contrast clearance curves were constructed after injecting nonionic contrast (1 ml/kg over 2 to 3 seconds) into the inferior vena cava of six anesthetized, closed chest dogs (n = 14). Independent myocardial perfusion measurements were obtained by coincident injection of radiolabeled microspheres into the left atrium during control, intermediate and maximal myocardial vasodilation with adenosine (0.5 to 1.0 mg/kg per min, intravenously, respectively). At each flow state, 40 serial short-axis scans of the left ventricle were taken near end-diastole at the midpapillary muscle level. Contrast clearance curves were generated and analyzed from the left ventricular cavity and posterior papillary muscle regions after excluding contrast recirculation and minimizing partial volume effects. The area under the curve (gamma variate function) was determined for a region of interest placed within the left ventricular cavity. Characteristics of contrast clearance data from the posterior papillary muscle region that were evaluated included the peak myocardial opacification, area under the contrast clearance curve and a contrast clearance time defined by the full width/half maximal extent of the clearance curve. Myocardial perfusion (microspheres) ranged from 35 to 450 ml/100 g per min (mean 167 +/- 125).

  13. High-Resolution and Quantitative X-Ray Phase-Contrast Tomography for Mouse Brain Research

    PubMed Central

    Xi, Yan; Lin, Xiaojie; Yuan, Falei; Yang, Guo-Yuan; Zhao, Jun

    2015-01-01

    Imaging techniques for visualizing cerebral vasculature and distinguishing functional areas are essential and critical to the study of various brain diseases. In this paper, with the X-ray phase-contrast imaging technique, we proposed an experiment scheme for the ex vivo mouse brain study, achieving both high spatial resolution and improved soft-tissue contrast. This scheme includes two steps: sample preparation and volume reconstruction. In the first step, we use heparinized saline to displace the blood inside cerebral vessels and then replace it with air making air-filled mouse brain. After sample preparation, X-ray phase-contrast tomography is performed to collect the data for volume reconstruction. Here, we adopt a phase-retrieval combined filtered backprojection method to reconstruct its three-dimensional structure and redesigned the reconstruction kernel. To evaluate its performance, we carried out experiments at Shanghai Synchrotron Radiation Facility. The results show that the air-tissue structured cerebral vasculatures are highly visible with propagation-based phase-contrast imaging and can be clearly resolved in reconstructed cross-images. Besides, functional areas, such as the corpus callosum, corpus striatum, and nuclei, are also clearly resolved. The proposed method is comparable with hematoxylin and eosin staining method but represents the studied mouse brain in three dimensions, offering a potential powerful tool for the research of brain disorders. PMID:26576198

  14. Quantitative imaging of red blood cell velocity invivo using optical coherence Doppler tomography

    NASA Astrophysics Data System (ADS)

    Ren, Hugang; Du, Congwu; Park, Kicheon; Volkow, Nora D.; Pan, Yingtian

    2012-06-01

    We present particle counting ultrahigh-resolution optical Doppler tomography (pc-μODT) that enables accurate imaging of red blood cell velocities (νRBC) of cerebrovascular networks by detecting the Doppler phase transients induced by the passage of a RBC through a capillary. We apply pc-μODT to image the response of capillary νRBC to mild hypercapnia in mouse cortex. The results show that νRBC in normocapnia (νN = 0.72 ± 0.15 mm/s) increased 36.1% ± 5.3% (νH = 0.98 ± 0.29 mm/s) in response to hypercapnia. Due to uncorrected angle effect and low hematocrit (e.g., ˜10%), νRBC directly measured by μODT were markedly underestimated (νN ≈ 0.27 ± 0.03 mm/s, νH ≈ 0.37± 0.05 mm/s). Nevertheless, the measured νRBC increase (35.3%) matched that (36.1% ± 5.3%) by pc-μODT.

  15. In vivo quantitative imaging of normal and cancerous breast tissue using broadband diffuse optical tomography

    PubMed Central

    Wang, Jia; Jiang, Shudong; Li, Zhongze; diFlorio-Alexander, Roberta M.; Barth, Richard J.; Kaufman, Peter A.; Pogue, Brian W.; Paulsen, Keith D.

    2010-01-01

    Purpose: A NIR tomography system that combines frequency domain (FD) and continuous wave (CW) measurements was used to image normal and malignant breast tissues. Methods: FD acquisitions were confined to wavelengths less than 850 nm because of detector limitations, whereas light from longer wavelengths (up to 948 nm) was measured in CW mode with CCD-coupled spectrometer detection. The two data sets were combined and processed in a single spectrally constrained reconstruction to map concentrations of hemoglobin, water, and lipid, as well as scattering parameters in the breast. Results: Chromophore concentrations were imaged in the breasts of nine asymptomatic volunteers to evaluate their intrasubject and intersubject variability. Normal subject data showed physiologically expected trends. Images from three cancer patients indicate that the added CW data is critical to recovering the expected increases in water and decreases in lipid content within malignancies. Contrasts of 1.5 to twofold in hemoglobin and water values were found in cancers. Conclusions:In vivo breast imaging with instrumentation that combines FD and CW NIR data acquisition in a single spectral reconstruction produces more accurate hemoglobin, water, and lipid results relative to FD data alone. PMID:20831079

  16. Quantitative Fourier Domain Optical Coherence Tomography Imaging of the Ocular Anterior Segment

    NASA Astrophysics Data System (ADS)

    McNabb, Ryan Palmer

    Clinical imaging within ophthalmology has had transformative effects on ocular health over the last century. Imaging has guided clinicians in their pharmaceutical and surgical treatments of macular degeneration, glaucoma, cataracts and numerous other pathologies. Many of the imaging techniques currently used are photography based and are limited to imaging the surface of ocular structures. This limitation forces clinicians to make assumptions about the underlying tissue which may reduce the efficacy of their diagnoses. Optical coherence tomography (OCT) is a non-invasive, non-ionizing imaging modality that has been widely adopted within the field of ophthalmology in the last 15 years. As an optical imaging technique, OCT utilizes low-coherence interferometry to produce micron-scale three-dimensional datasets of a tissue's structure. Much of the human body consists of tissues that significantly scatter and attenuate optical signals limiting the imaging depth of OCT in those tissues to only 1-2mm. However, the ocular anterior segment is unique among human tissue in that it is primarily transparent or translucent. This allows for relatively deep imaging of tissue structure with OCT and is no longer limited by the optical scattering properties of the tissue. This goal of this work is to develop methods utilizing OCT that offer the potential to reduce the assumptions made by clinicians in their evaluations of their patients' ocular anterior segments. We achieved this by first developing a method to reduce the effects of patient motion during OCT volume acquisitions allowing for accurate, three dimensional measurements of corneal shape. Having accurate corneal shape measurements then allowed us to determine corneal spherical and astigmatic refractive contribution in a given individual. This was then validated in a clinical study that showed OCT better measured refractive change due to surgery than other clinical devices. Additionally, a method was developed to combine

  17. Quantitative 3D petrography using X-ray tomography 2: Combining information at various resolutions

    SciTech Connect

    Pamukcu, Ayla S.; Gualda, Guilherme A.R.

    2010-12-02

    X-ray tomography is a nondestructive technique that can be used to study rocks and other materials in three dimensions over a wide range of sizes. Samples that range from decimeters to micrometers in size can be analyzed, and micrometer- to centimeter-sized crystals, vesicles, and other particles can be identified and quantified. In many applications, quantification of a large spectrum of sizes is important, but this cannot be easily accomplished using a single tomogram due to a common trade-off between sample size and image resolution. This problem can be circumvented by combining tomograms acquired for a single sample at a variety of resolutions. We have successfully applied this method to obtain crystal size distributions (CSDs) for magnetite, pyroxene + biotite, and quartz + feldspar in Bishop Tuff pumice. Five cylinders of systematically varying size (1-10 mm diameter and height) were analyzed from each of five pumice clasts. Cylinder size is inversely proportional to image resolution, such that resolution ranges from 2.5 to 17 {micro}m/voxel with increasing sample size. This allows quantification of crystals 10-1000 {micro}m in size. We obtained CSDs for each phase in each sample by combining information from all resolutions, each size bin containing data from the resolution that best characterizes crystals of that size. CSDs for magnetite and pyroxene + biotite in late-erupted Bishop pumice obtained using this method are fractal, but do not seem to result from crystal fragmentation. CSDs for quartz + feldspar reveal a population of abundant crystals <35 {micro}m in size, and a population of crystals >50 {micro}m in size, which will be the focus of a separate publication.

  18. 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.

  19. Simultaneous multivessel coronary artery spasm demonstrated by quantitative analysis of thallium-201 single photon emission computed tomography

    SciTech Connect

    Kugiyama, K.; Yasue, H.; Okumura, K.; Minoda, K.; Takaoka, K.; Matsuyama, K.; Kojima, A.; Koga, Y.; Takahashi, M.

    1987-11-01

    Thallium-201 myocardial scintigraphy with quantitative analysis of emission computed tomography was performed during episodes of angina in 19 patients with variant angina and nearly normal coronary arteriographic findings. Eleven patients (group I) were shown by arteriography to have spasm in 2 or more large coronary arteries. Eight patients (group II) had spasm in only 1 coronary artery. In 7 patients in group I, significant diffuse perfusion defects simultaneously appeared in multiple coronary artery regions on the scintigram (group IA). The extent and severity of the perfusion defect as measured by thallium-201 tomography were significantly greater in group IA than in group II (p less than 0.001 and p less than 0.01, respectively). The duration of transient ST-segment elevation during the attack in group IA was significantly longer than in group II (p less than 0.001). The incidence of ventricular arrhythmias, including ventricular tachycardia, or complete atrioventricular block during the anginal attack was significantly higher (p less than 0.05) in group IA than in group II. In all study patients, neither attack nor scintigraphic perfusion defect appeared on the repeat test after oral administration of nifedipine. In conclusion, multivessel coronary artery spasm simultaneously appears and causes the attack in many patients with variant angina and nearly normal coronary arteriographic findings, and myocardial ischemia due to simultaneous multivessel coronary spasm is likely to be more extensive and severe, persist longer and have a higher frequency of potentially dangerous arrhythmias than that due to spasm of only 1 coronary artery.

  20. Quantitative visualization of high-speed 3D turbulent flow structures using holographic interferometric tomography

    NASA Astrophysics Data System (ADS)

    Timmerman, B. H.; Watt, D. W.; Bryanston-Cross, P. J.

    1999-02-01

    Using holographic interferometry the three-dimensional structure of unsteady and large-scale motions within subsonic and transonic turbulent jet flows has been studied. The instantaneous 3D flow structure is obtained by tomographic reconstruction techniques from quantitative phase maps recorded using a rapid-switching, double reference beam, double pulse laser system. The reconstruction of the jets studied here reveal a three-dimensional nature of the flow. In particular an increasing complexity can be seen in the turbulence as the flow progresses from the jet nozzle. Furthermore, a coherent three-dimensional, possibly rotating, structure can be seen to exist within these jets. The type of flow features illustrated here are not just of fundamental importance for understanding the behavior of free jet flows, but are also common to a number of industrial applications, ranging from the combustion flow within an IC engine to the transonic flow through the stages of a gas turbine.

  1. Verification of Scientific Simulations via Hypothesis-Driven Comparative and Quantitative Visualization

    SciTech Connect

    Ahrens, James P; Heitmann, Katrin; Petersen, Mark R; Woodring, Jonathan; Williams, Sean; Fasel, Patricia; Ahrens, Christine; Hsu, Chung-Hsing; Geveci, Berk

    2010-11-01

    This article presents a visualization-assisted process that verifies scientific-simulation codes. Code verification is necessary because scientists require accurate predictions to interpret data confidently. This verification process integrates iterative hypothesis verification with comparative, feature, and quantitative visualization. Following this process can help identify differences in cosmological and oceanographic simulations.

  2. Exploring the Perceptions of College Instructors towards Computer Simulation Software Programs: A Quantitative Study

    ERIC Educational Resources Information Center

    Punch, Raymond J.

    2012-01-01

    The purpose of the quantitative regression study was to explore and to identify relationships between attitudes toward use and perceptions of value of computer-based simulation programs, of college instructors, toward computer based simulation programs. A relationship has been reported between attitudes toward use and perceptions of the value of…

  3. Quantitative Comparison of Commercial and Non-Commercial Metal Artifact Reduction Techniques in Computed Tomography

    PubMed Central

    Wagenaar, Dirk; van der Graaf, Emiel R.; van der Schaaf, Arjen; Greuter, Marcel J. W.

    2015-01-01

    Objectives Typical streak artifacts known as metal artifacts occur in the presence of strongly attenuating materials in computed tomography (CT). Recently, vendors have started offering metal artifact reduction (MAR) techniques. In addition, a MAR technique called the metal deletion technique (MDT) is freely available and able to reduce metal artifacts using reconstructed images. Although a comparison of the MDT to other MAR techniques exists, a comparison of commercially available MAR techniques is lacking. The aim of this study was therefore to quantify the difference in effectiveness of the currently available MAR techniques of different scanners and the MDT technique. Materials and Methods Three vendors were asked to use their preferential CT scanner for applying their MAR techniques. The scans were performed on a Philips Brilliance ICT 256 (S1), a GE Discovery CT 750 HD (S2) and a Siemens Somatom Definition AS Open (S3). The scans were made using an anthropomorphic head and neck phantom (Kyoto Kagaku, Japan). Three amalgam dental implants were constructed and inserted between the phantom’s teeth. The average absolute error (AAE) was calculated for all reconstructions in the proximity of the amalgam implants. Results The commercial techniques reduced the AAE by 22.0±1.6%, 16.2±2.6% and 3.3±0.7% for S1 to S3 respectively. After applying the MDT to uncorrected scans of each scanner the AAE was reduced by 26.1±2.3%, 27.9±1.0% and 28.8±0.5% respectively. The difference in efficiency between the commercial techniques and the MDT was statistically significant for S2 (p=0.004) and S3 (p<0.001), but not for S1 (p=0.63). Conclusions The effectiveness of MAR differs between vendors. S1 performed slightly better than S2 and both performed better than S3. Furthermore, for our phantom and outcome measure the MDT was more effective than the commercial MAR technique on all scanners. PMID:26030821

  4. Optical Coherence Tomography for Quantitative Assessment of Microstructural and Microvascular Alterations in Late Oral Radiation Toxicity

    NASA Astrophysics Data System (ADS)

    Davoudi, Bahar

    More than half of head-and-neck cancer patients undergo radiotherapy at some point during their treatment. Even though the use of conformed therapeutic beams has increased radiation dose localization to the tumor, resulting in more normal tissue sparing, still, in many head-and-neck cancer patients, the healthy tissue of the oral cavity still receives a sizeable amount of radiation. This causes acute and / or late complications in these patients. The latter occur as late as several months or even years after the completion of treatment and are typically associated with severe symptoms. Currently, the clinical method for diagnosing these complications is visual examination of the oral tissue surface. However, it has been well established that such complications originate in subsurface oral tissue layers including its microvasculature. Therefore, to better understand the mechanism of these complications and to be able to diagnose them earlier, there exists a need for subsurface monitoring of the irradiated oral tissue. Histology has been used as such a tool for research purposes; however, its use in clinical diagnosis is limited due to its invasive and hazardous nature. Therefore, in this thesis, I propose to use optical coherence tomography (OCT) as a subsurface, micron-scale resolution optical imaging tool that can provide images of oral tissue subsurface layers down to a depth of 1-2 mm (structural OCT), as well as images demonstrating vessel morphology (speckle variance OCT) and blood flow information (Doppler OCT). This thesis explains the development of an OCT setup and an oral probe to acquire images in-vivo. Moreover, it introduces a software-based quantification platform for extracting specific biologically-meaningful metrics from the structural and vascular OCT images. It then describes the application of the developed imaging and quantification platform in a feasibility clinical study that was performed on 15 late oral radiation toxicity patients and 5 age

  5. Exploring the utility of high resolution "nano-" computed tomography imaging to place quantitative constraints on shell biometric changes in marine pteropods in response to ocean acidification

    NASA Astrophysics Data System (ADS)

    Eagle, R.; Howes, E.; Lischka, S.; Rudolph, R.; Büdenbender, J.; Bijma, J.; Gattuso, J. P.; Riebesell, U.

    2014-12-01

    Understanding and quantifying the response of marine organisms to present and future ocean acidification remains a major challenge encompassing observations on single species in culture and scaling up to the ecosystem and global scale. Understanding calcification changes in culture experiments designed to simulate present and future ocean conditions under potential CO2 emissions scenarios, and especially detecting the likely more subtle changes that may occur prior to the onset of more extreme ocean acidification, depends on the tools available. Here we explore the utility of high-resolution computed tomography (nano-CT) to provide quantitative biometric data on field collected and cultured marine pteropods, using the General Electric Company Phoenix Nanotom S Instrument. The technique is capable of quantitating the whole shell of the organism, allowing shell dimensions to be determined as well as parameters such as average shell thickness, the variation in thickness across the whole shell and in localized areas, total shell volume and surface area and when combined with weight measurements shell density can be calculated. The potential power of the technique is the ability to derive these parameters even on very small organisms less than 1 millimeter in size. Tuning the X-ray strength of the instrument allows organic material to be excluded from the analysis. Through replicate analysis of standards, we assess the reproducibility of data, and by comparison with dimension measurements derived from light microscopy we assess the accuracy of dimension determinations. We present results from historical and modern pteropod populations from the Mediterranean and cultured polar pteropods, resolving statistically significant differences in shell biometrics in both cases that may represent responses to ocean acidification.

  6. Molecular Dynamics and Monte Carlo simulations in the microcanonical ensemble: Quantitative comparison and reweighting techniques.

    PubMed

    Schierz, Philipp; Zierenberg, Johannes; Janke, Wolfhard

    2015-10-01

    Molecular Dynamics (MD) and Monte Carlo (MC) simulations are the most popular simulation techniques for many-particle systems. Although they are often applied to similar systems, it is unclear to which extent one has to expect quantitative agreement of the two simulation techniques. In this work, we present a quantitative comparison of MD and MC simulations in the microcanonical ensemble. For three test examples, we study first- and second-order phase transitions with a focus on liquid-gas like transitions. We present MD analysis techniques to compensate for conservation law effects due to linear and angular momentum conservation. Additionally, we apply the weighted histogram analysis method to microcanonical histograms reweighted from MD simulations. By this means, we are able to estimate the density of states from many microcanonical simulations at various total energies. This further allows us to compute estimates of canonical expectation values. PMID:26450299

  7. In vivo quantitative evaluation of gold nanocages' kinetics in sentinel lymph nodes by photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Cai, Xin; Li, Weiyang; Kim, Chulhong; Yuan, Yuchen; Xia, Younan; Wang, Lihong V.

    2012-02-01

    As a new class of sentinel lymph node (SLN) tracers for photoacoustic (PA) imaging, Au nanocages offer the advantages of noninvasiveness, strong optical absorption in the near-infrared region (for deep penetration), and accumulation in higher concentrations than the initial injected solution. By monitoring the amplitude changes of PA signals in an animal model, we quantified the accumulations of nanocages in SLNs over time. Based on this method, we quantitatively evaluated the kinetics of gold nanocages in SLN in terms of concentration, size, and surface modification. We could detect the SLN at an Au nanocage injection concentration of 50 pM and a dose of 100 μL in vivo. This concentration is about 40 times less than the previously reported value. We also investigated the influence of nanocages' size (50 nm and 30 nm in edge length), and the effects of surface modification (with positive, or neutral, or negative surface charges). The results are helpful to develop this AuNC-based PA imaging system for noninvasive lymph node mapping, providing valuable information about metastatic cancer staging.

  8. Dynamic contrast optical coherence tomography: quantitative measurement of microvascular transit-time distributions in vivo (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Merkle, Conrad W.; Srinivasan, Vivek J.

    2016-03-01

    Transit time is a fundamental microcirculatory parameter that is critical in determining oxygen delivery from capillaries to surrounding tissue. Recently, it was demonstrated theoretically that capillary transit-time heterogeneity potentially leads to non-uniform oxygen extraction in micro-domains. However, in spite of its importance, capillary transit-time distribution has been challenging to quantify comprehensively and efficiently at the microscopic level. Here, we introduce a method, called Dynamic Contrast Optical Coherence Tomography (DyC-OCT), based on dynamic cross-sectional OCT imaging of the kinetics of an intravascular tracer during its passage through the field-of-view. DyC-OCT is used to quantitatively measure the transit-time distribution in microvascular networks in cross-section at the single-capillary level. Transit-time metrics are derived from analysis of the temporal characteristics of the dynamic scattering signal, related to tracer concentration, using indicator-dilution theory. Since DyC-OCT does not require calibration of the optical focus, quantitative accuracy is achieved even deep in highly scattering brain tissue where the focal spot degrades. After direct validation of DyC-OCT against the dilution curves measured using a fluorescent plasma label in the surface pial vessels of a mouse brain, imaged through a thinned-skull, glass coverslip-reinforced cranial window, the laminar transit-time distribution was investigated in microvasculature across the entire depth of the mouse somatosensory cortex. Laminar trends were identified, with the earliest transit times in the middle cortical layers, and the lowest heterogeneity in cortical layer 4. The new DyC-OCT technique affords a novel perspective of microvascular networks, with the unique capability of performing simultaneous measurements of transit-time distributions across cortical laminae.

  9. In situ flash x-ray high-speed computed tomography for the quantitative analysis of highly dynamic processes

    NASA Astrophysics Data System (ADS)

    Moser, Stefan; Nau, Siegfried; Salk, Manfred; Thoma, Klaus

    2014-02-01

    The in situ investigation of dynamic events, ranging from car crash to ballistics, often is key to the understanding of dynamic material behavior. In many cases the important processes and interactions happen on the scale of milli- to microseconds at speeds of 1000 m s-1 or more. Often, 3D information is necessary to fully capture and analyze all relevant effects. High-speed 3D-visualization techniques are thus required for the in situ analysis. 3D-capable optical high-speed methods often are impaired by luminous effects and dust, while flash x-ray based methods usually deliver only 2D data. In this paper, a novel 3D-capable flash x-ray based method, in situ flash x-ray high-speed computed tomography is presented. The method is capable of producing 3D reconstructions of high-speed processes based on an undersampled dataset consisting of only a few (typically 3 to 6) x-ray projections. The major challenges are identified, discussed and the chosen solution outlined. The application is illustrated with an exemplary application of a 1000 m s-1 high-speed impact event on the scale of microseconds. A quantitative analysis of the in situ measurement of the material fragments with a 3D reconstruction with 1 mm voxel size is presented and the results are discussed. The results show that the HSCT method allows gaining valuable visual and quantitative mechanical information for the understanding and interpretation of high-speed events.

  10. Analyzing bone remodeling patterns after total hip arthroplasty using quantitative computed tomography and patient-specific 3D computational models

    PubMed Central

    Arachchi, Shanika; Pitto, Rocco P.; Anderson, Iain A.

    2015-01-01

    Background Computational models in the form of finite element analysis technique that incorporates bone remodeling theories along with DEXA scans has been extensively used in predicting bone remodeling patterns around the implant. However, majority of such studies used generic models. Therefore, the aim of this study is to develop patient-specific finite element models of total hip replacement patients using their quantitative computed tomography (QCT) scans and accurately analyse bone remodelling patterns after total hip arthroplasty (THA). Methods Patient-specific finite element models have been generated using the patients’ QCT scans from a previous clinical follow-up study. The femur was divided into five regions in proximal-distal direction and then further divided into four quadrants for detailed analysis of bone remodeling patterns. Two types of analysis were performed—inter-patient and intra patient to compare them and then the resulting bone remodeling patterns were quantitatively analyzed. Results Our results show that cortical bone density decrease is higher in diaphyseal region over time and the cancellous bone density decreases significantly in metaphyseal region over time. In metaphyseal region, posterior-medial (P-M) quadrant showed high bone loss while diaphyseal regions show high bone loss in anterior-lateral (A-L) quadrant. Conclusions Our study demonstrated that combining QCT with 3D patient-specific models has the ability of monitoring bone density change patterns after THA in much finer details. Future studies include using these findings for the development of a bone remodelling algorithm capable of predicting surgical outcomes for THA patients. PMID:26435921

  11. Quantitative monitoring of subsurface CO2 emplacement and leakage using muon tomography

    NASA Astrophysics Data System (ADS)

    Coleman, M. L.; Kudryavtsev, V.; Spooner, N.; Gluyas, J.; Fung, C.

    2011-12-01

    Monitoring CO2 emplacement and possible leakage is a major challenge; methods, such as repeat seismic surveys, are episodic and expensive. A relevant alternative approach will use detection of cosmic ray muons, which has been used previously in archaeological and geological research as a technique for mapping features hidden underground. We developed a model to test if this concept would work for monitoring CO2 storage and show that muon detection is a viable method. To achieve this we used the well-established MUSUN/MUSIC computer codes to model changes in muon fluxes resulting from the introduction of supercritical CO2 into a simulated sandstone reservoir. Results from our first simulation indicate that we could detect as little as 0.4% change in the mean reservoir density at about 1 km depth, resulting from changing the relative proportions of CO2 and existing brine pore fluid. This change is equivalent to 7% of the pore volume in this particular case. However, other scenarios offer the promise of considerable increase in sensitivity. We will show how practical implementation can be achieved using state of the art drilling technology to place an array of detectors in short-radius side-track horizontal wells beneath the storage site. We conclude that with an appropriate design it will be possible to monitor and image the migration or loss of injected CO2 continuously using cosmic ray muons, a significant step towards implementing widescale CCS safely and help rapid introduction of this essential technology.

  12. Tomography based numerical simulation of the demagnetizing field in soft magnetic composites

    SciTech Connect

    Arzbacher, S.; Petrasch, J.; Amann, P.; Weidenfeller, B.; Loerting, T.; Ostermann, A.

    2015-04-28

    The magneto-static behaviour of soft magnetic composites (SMCs) is investigated using tomography based direct numerical simulation. The microgeometry crucially affects the magnetic properties of the composite since a geometry dependent demagnetizing field is established inside the composite, which lowers the magnetic permeability. We determine the magnetic field information inside the SMC using direct numerical simulation of the magnetic field based on high resolution micro-computed tomography data of the SMC's microstructure as well as artificially generated data made of statistically homogeneous systems of identical fully penetrable spheres and prolate spheroids. Quasi-static electromagnetic behaviour and linear material response are assumed. The 3D magnetostatic Maxwell equations are solved using Whitney finite elements. Simulations show that clustering and percolation behaviour determine the demagnetizing factor of SMCs rather than the particle shape. The demagnetizing factor correlates with the slope of a 2-point probability function at its origin, which is related to the specific surface area of the SMC. Comparison with experimental results indicates that the relatively low permeability of SMCs cannot be explained by demagnetizing effects alone and suggests that the permeability of SMC particles has to be orders of magnitude smaller than the bulk permeability of the particle material.

  13. Tomography based numerical simulation of the demagnetizing field in soft magnetic composites

    NASA Astrophysics Data System (ADS)

    Arzbacher, S.; Amann, P.; Weidenfeller, B.; Loerting, T.; Ostermann, A.; Petrasch, J.

    2015-04-01

    The magneto-static behaviour of soft magnetic composites (SMCs) is investigated using tomography based direct numerical simulation. The microgeometry crucially affects the magnetic properties of the composite since a geometry dependent demagnetizing field is established inside the composite, which lowers the magnetic permeability. We determine the magnetic field information inside the SMC using direct numerical simulation of the magnetic field based on high resolution micro-computed tomography data of the SMC's microstructure as well as artificially generated data made of statistically homogeneous systems of identical fully penetrable spheres and prolate spheroids. Quasi-static electromagnetic behaviour and linear material response are assumed. The 3D magnetostatic Maxwell equations are solved using Whitney finite elements. Simulations show that clustering and percolation behaviour determine the demagnetizing factor of SMCs rather than the particle shape. The demagnetizing factor correlates with the slope of a 2-point probability function at its origin, which is related to the specific surface area of the SMC. Comparison with experimental results indicates that the relatively low permeability of SMCs cannot be explained by demagnetizing effects alone and suggests that the permeability of SMC particles has to be orders of magnitude smaller than the bulk permeability of the particle material.

  14. Quantitative simulation of a magnetospheric substorm. II - Comparison with observations

    NASA Technical Reports Server (NTRS)

    Harel, M.; Wolf, R. A.; Spiro, R. W.; Reiff, P. H.; Chen, C.-K.; Burke, W. J.; Rich, F. J.; Smiddy, M.

    1981-01-01

    Results of the computer simulation of the behavior of the inner magnetosphere during the substorm-type event of September 19, 1976, are discussed. The computed electric fields are found to compare satisfactorily with electric fields measured from S3-2, although there are detailed differences. The three general features on which the model and observations are in good agreement are (1) the magnitude and direction of the high-latitude electric field, (2) the degree to which the low-latitude ionosphere is shielded from the high-latitude convection electric field, and (3) the fact that the poleward electric field on the duskside is significantly larger, on the average, than the equatorward electric field on the dawnside. Simple formulas are presented that give rough estimates of global Joule heating rates from observable parameters.

  15. Theoretical magnetograms based on quantitative simulation of a magnetospheric substorm

    NASA Technical Reports Server (NTRS)

    Chen, C.-K.; Wolf, R. A.; Karty, J. L.; Harel, M.

    1982-01-01

    Substorm currents derived from the Rice University computer simulation of the September 19, 1976 substorm event are used to compute theoretical magnetograms as a function of universal time for various stations, integrating the Biot-Savart law over a maze of about 2700 wires and bands that carry the ring, Birkeland and horizontal ionospheric currents. A comparison of theoretical results with corresponding observations leads to a claim of general agreement, especially for stations at high and middle magnetic latitudes. Model results suggest that the ground magnetic field perturbations arise from complicated combinations of different kinds of currents, and that magnetic field disturbances due to different but related currents cancel each other out despite the inapplicability of Fukushima's (1973) theorem. It is also found that the dawn-dusk asymmetry in the horizontal magnetic field disturbance component at low latitudes is due to a net downward Birkeland current at noon, a net upward current at midnight, and, generally, antisunward-flowing electrojets.

  16. In Vivo Quantitative Assessment of Myocardial Structure, Function, Perfusion and Viability Using Cardiac Micro-computed Tomography

    PubMed Central

    van Deel, Elza; Ridwan, Yanto; van Vliet, J. Nicole; Belenkov, Sasha; Essers, Jeroen

    2016-01-01

    The use of Micro-Computed Tomography (MicroCT) for in vivo studies of small animals as models of human disease has risen tremendously due to the fact that MicroCT provides quantitative high-resolution three-dimensional (3D) anatomical data non-destructively and longitudinally. Most importantly, with the development of a novel preclinical iodinated contrast agent called eXIA160, functional and metabolic assessment of the heart became possible. However, prior to the advent of commercial MicroCT scanners equipped with X-ray flat-panel detector technology and easy-to-use cardio-respiratory gating, preclinical studies of cardiovascular disease (CVD) in small animals required a MicroCT technologist with advanced skills, and thus were impractical for widespread implementation. The goal of this work is to provide a practical guide to the use of the high-speed Quantum FX MicroCT system for comprehensive determination of myocardial global and regional function along with assessment of myocardial perfusion, metabolism and viability in healthy mice and in a cardiac ischemia mouse model induced by permanent occlusion of the left anterior descending coronary artery (LAD). PMID:26967592

  17. In Vivo Quantitative Assessment of Myocardial Structure, Function, Perfusion and Viability Using Cardiac Micro-computed Tomography.

    PubMed

    van Deel, Elza; Ridwan, Yanto; van Vliet, J Nicole; Belenkov, Sasha; Essers, Jeroen

    2016-01-01

    The use of Micro-Computed Tomography (MicroCT) for in vivo studies of small animals as models of human disease has risen tremendously due to the fact that MicroCT provides quantitative high-resolution three-dimensional (3D) anatomical data non-destructively and longitudinally. Most importantly, with the development of a novel preclinical iodinated contrast agent called eXIA160, functional and metabolic assessment of the heart became possible. However, prior to the advent of commercial MicroCT scanners equipped with X-ray flat-panel detector technology and easy-to-use cardio-respiratory gating, preclinical studies of cardiovascular disease (CVD) in small animals required a MicroCT technologist with advanced skills, and thus were impractical for widespread implementation. The goal of this work is to provide a practical guide to the use of the high-speed Quantum FX MicroCT system for comprehensive determination of myocardial global and regional function along with assessment of myocardial perfusion, metabolism and viability in healthy mice and in a cardiac ischemia mouse model induced by permanent occlusion of the left anterior descending coronary artery (LAD). PMID:26967592

  18. Validation of high-resolution gamma-ray computed tomography for quantitative gas holdup measurements in centrifugal pumps

    NASA Astrophysics Data System (ADS)

    Bieberle, André; Schäfer, Thomas; Neumann, Martin; Hampel, Uwe

    2015-09-01

    In this article, the capability of high-resolution gamma-ray computed tomography (HireCT) for quantitative gas-liquid phase distribution measurements in commercially available industrial pumps is experimentally investigated. The object of interest thereby operates under two-phase flow conditions. HireCT System comprises a collimated 137Cs isotopic source, a radiation detector arc with a multi-channel signal processing unit, and a rotary unit enabling CT scans of objects with diameters of up to 700 mm. The accuracy of gas holdup measurements was validated on a sophisticated modular test mockup replicating defined gas-liquid distributions, which are expected in impeller chambers of industrial centrifugal pumps under two-phase operation. Stationary as well as rotation-synchronized CT scanning techniques have been analyzed, which are both used to obtain sharply resolved gas phase distributions in rotating structures as well as non-rotating zones. A measuring accuracy of better than 1% absolute for variously distributed static gas holdups in the rotating frame has been verified with the modular test mockup using HireCT.

  19. An incommensurately modulated structure of η'-phase of Cu(3+x)Si determined by quantitative electron diffraction tomography.

    PubMed

    Palatinus, Lukáš; Klementová, Mariana; Dřínek, Vladislav; Jarošová, Markéta; Petříček, Václav

    2011-04-18

    The diffraction data of η'-Cu(3+x)(Si,Ge) were collected by 3D quantitative electron diffraction tomography on a submicrometer-sized sample, and the structure was solved by the charge-flipping algorithm in superspace. It is shown that the structure is trigonal, and it is incommensurately modulated with two modulation vectors q(1) = (α, α, 1/3) and q(2) = (-2α, α, 1/3), superspace group P31m(α, α, 1/3)000(-2α, α, 1/3)000. The modulation functions of some atoms are very complicated and reach amplitudes comparable with the unit cell dimensions. The modulated structure can be described as sheets of Cu clusters separated by honeycomb layers of mixed Si/Ge positions. The shape of the Cu clusters in the sheets strongly varies with the modulation phase, and the predominant form is an icosahedron. The striving of the Cu layers to form icosahedral clusters is deemed to be the main driving force of the modulation. The combination of methods used in this work can be applied to other structures that are difficult to crystallize in large crystals and opens new perspectives, especially for investigations of aperiodic or otherwise complex metallic alloys. PMID:21438499

  20. Assessment of Bone Mineral Density in Male Patients with Chronic Obstructive Pulmonary Disease by DXA and Quantitative Computed Tomography

    PubMed Central

    Fountoulis, George; Kerenidi, Theodora; Kokkinis, Constantinos; Georgoulias, Panagiotis; Thriskos, Paschal; Gourgoulianis, Konstantinos; Fezoulidis, Ioannis; Vassiou, Katerina

    2016-01-01

    The purpose of this study is to identify the prevalence of osteoporosis in male patients with chronic obstructive pulmonary disease (COPD) by dual-energy X-ray absorptiometry (DXA) and quantitative computed tomography (QCT) and to compare the diagnostic abilities of the above methods. Thirty-seven male patients with established COPD were examined with DXA and standard QCT in lumbar spine, including L1, L2, and L3 vertebrae. T-scores and bone mineral density values were calculated by DXA and QCT method, respectively. Comparative assessment of the findings was performed and statistical analysis was applied. QCT measurements found more COPD patients with impaired bone mineral density compared to DXA, namely, 13 (35.1%) versus 12 (32.4%) patients with osteopenia and 16 (43.2%) versus 9 (16.2%) patients with osteoporosis (p = 0.04). More vertebrae were found with osteoporosis by QCT compared to DXA (p = 0.03). The prevalence of osteoporosis among male patients with COPD is increased and DXA may underestimate this risk. QCT measurements have an improved discriminating ability to identify low BMD compared to DXA measurements because QCT is able to overcome diagnostic pitfalls including aortic calcifications and degenerative spinal osteophytes. PMID:27087809

  1. Assessment of Bone Mineral Density in Male Patients with Chronic Obstructive Pulmonary Disease by DXA and Quantitative Computed Tomography.

    PubMed

    Fountoulis, George; Kerenidi, Theodora; Kokkinis, Constantinos; Georgoulias, Panagiotis; Thriskos, Paschal; Gourgoulianis, Konstantinos; Fezoulidis, Ioannis; Vassiou, Katerina; Vlychou, Marianna

    2016-01-01

    The purpose of this study is to identify the prevalence of osteoporosis in male patients with chronic obstructive pulmonary disease (COPD) by dual-energy X-ray absorptiometry (DXA) and quantitative computed tomography (QCT) and to compare the diagnostic abilities of the above methods. Thirty-seven male patients with established COPD were examined with DXA and standard QCT in lumbar spine, including L1, L2, and L3 vertebrae. T-scores and bone mineral density values were calculated by DXA and QCT method, respectively. Comparative assessment of the findings was performed and statistical analysis was applied. QCT measurements found more COPD patients with impaired bone mineral density compared to DXA, namely, 13 (35.1%) versus 12 (32.4%) patients with osteopenia and 16 (43.2%) versus 9 (16.2%) patients with osteoporosis (p = 0.04). More vertebrae were found with osteoporosis by QCT compared to DXA (p = 0.03). The prevalence of osteoporosis among male patients with COPD is increased and DXA may underestimate this risk. QCT measurements have an improved discriminating ability to identify low BMD compared to DXA measurements because QCT is able to overcome diagnostic pitfalls including aortic calcifications and degenerative spinal osteophytes. PMID:27087809

  2. Quantitative imaging of cerebral blood flow velocity and intracellular motility using dynamic light scattering–optical coherence tomography

    PubMed Central

    Lee, Jonghwan; Radhakrishnan, Harsha; Wu, Weicheng; Daneshmand, Ali; Climov, Mihail; Ayata, Cenk; Boas, David A

    2013-01-01

    This paper describes a novel optical method for label-free quantitative imaging of cerebral blood flow (CBF) and intracellular motility (IM) in the rodent cerebral cortex. This method is based on a technique that integrates dynamic light scattering (DLS) and optical coherence tomography (OCT), named DLS–OCT. The technique measures both the axial and transverse velocities of CBF, whereas conventional Doppler OCT measures only the axial one. In addition, the technique produces a three-dimensional map of the diffusion coefficient quantifying nontranslational motions. In the DLS–OCT diffusion map, we observed high-diffusion spots, whose locations highly correspond to neuronal cell bodies and whose diffusion coefficient agreed with that of the motion of intracellular organelles reported in vitro in the literature. Therefore, the present method has enabled, for the first time to our knowledge, label-free imaging of the diffusion-like motion of intracellular organelles in vivo. As an example application, we used the method to monitor CBF and IM during a brief ischemic stroke, where we observed an induced persistent reduction in IM despite the recovery of CBF after stroke. This result supports that the IM measured in this study represent the cellular energy metabolism-related active motion of intracellular organelles rather than free diffusion of intracellular macromolecules. PMID:23403378

  3. Strategies for displaying computer simulated three-dimensional images from emission computed tomography

    SciTech Connect

    Schlusselberg, D.S.; Simon, T.R.; Smith, W.K.; Woodward, D.J.; Parkey, R.W.

    1985-05-01

    Emission computed tomography (ECT) quantitatively localizes radionuclide tracer distributions within a three-dimensional (3D) volume. Currently available techniques limit the display of this information to series of cross-sectional or rotating images. Such techniques of ten rely on special viewing equipment to synthesize the image series into a volumetric display. The authors have developed new algorithms that generate 3D images of radiotracer distributions using computerized analysis of tomographic data. Imaging strategies including transparent volumes, surface models, color-coded circumferential histograms and transparent slices are combined to produce a single image that contains the quantitative distributional information. While the images can be displayed on most raster-based display devices, they are suitable for archiving and distribution as single image photographs. This choice of formats enhances the value of the technique for communicating scintigraphic information to referring physicians while maintaining the quantitative integrity of the data. The technique has been successfully applied to a variety of ECT examination including brain, heart, liver and bone studies.

  4. Crosshole Tomography, Waveform Inversion, and Anisotropy: A Combined Approach Using Simulated Annealing

    NASA Astrophysics Data System (ADS)

    Afanasiev, M.; Pratt, R. G.; Kamei, R.; McDowell, G.

    2012-12-01

    Crosshole seismic tomography has been used by Vale to provide geophysical images of mineralized massive sulfides in the Eastern Deeps deposit at Voisey's Bay, Labrador, Canada. To date, these data have been processed using traveltime tomography, and we seek to improve the resolution of these images by applying acoustic Waveform Tomography. Due to the computational cost of acoustic waveform modelling, local descent algorithms are employed in Waveform Tomography; due to non-linearity an initial model is required which predicts first-arrival traveltimes to within a half-cycle of the lowest frequency used. Because seismic velocity anisotropy can be significant in hardrock settings, the initial model must quantify the anisotropy in order to meet the half-cycle criterion. In our case study, significant velocity contrasts between the target massive sulfides and the surrounding country rock led to difficulties in generating an accurate anisotropy model through traveltime tomography, and our starting model for Waveform Tomography failed the half-cycle criterion at large offsets. We formulate a new, semi-global approach for finding the best-fit 1-D elliptical anisotropy model using simulated annealing. Through random perturbations to Thompson's ɛ parameter, we explore the L2 norm of the frequency-domain phase residuals in the space of potential anisotropy models: If a perturbation decreases the residuals, it is always accepted, but if a perturbation increases the residuals, it is accepted with the probability P = exp(-(Ei-E)/T). This is the Metropolis criterion, where Ei is the value of the residuals at the current iteration, E is the value of the residuals for the previously accepted model, and T is a probability control parameter, which is decreased over the course of the simulation via a preselected cooling schedule. Convergence to the global minimum of the residuals is guaranteed only for infinitely slow cooling, but in practice good results are obtained from a variety

  5. Validation of a Low Dose Simulation Technique for Computed Tomography Images

    PubMed Central

    Muenzel, Daniela; Koehler, Thomas; Brown, Kevin; Žabić, Stanislav; Fingerle, Alexander A.; Waldt, Simone; Bendik, Edgar; Zahel, Tina; Schneider, Armin; Dobritz, Martin; Rummeny, Ernst J.; Noël, Peter B.

    2014-01-01

    Purpose Evaluation of a new software tool for generation of simulated low-dose computed tomography (CT) images from an original higher dose scan. Materials and Methods Original CT scan data (100 mAs, 80 mAs, 60 mAs, 40 mAs, 20 mAs, 10 mAs; 100 kV) of a swine were acquired (approved by the regional governmental commission for animal protection). Simulations of CT acquisition with a lower dose (simulated 10–80 mAs) were calculated using a low-dose simulation algorithm. The simulations were compared to the originals of the same dose level with regard to density values and image noise. Four radiologists assessed the realistic visual appearance of the simulated images. Results Image characteristics of simulated low dose scans were similar to the originals. Mean overall discrepancy of image noise and CT values was −1.2% (range −9% to 3.2%) and −0.2% (range −8.2% to 3.2%), respectively, p>0.05. Confidence intervals of discrepancies ranged between 0.9–10.2 HU (noise) and 1.9–13.4 HU (CT values), without significant differences (p>0.05). Subjective observer evaluation of image appearance showed no visually detectable difference. Conclusion Simulated low dose images showed excellent agreement with the originals concerning image noise, CT density values, and subjective assessment of the visual appearance of the simulated images. An authentic low-dose simulation opens up opportunity with regard to staff education, protocol optimization and introduction of new techniques. PMID:25247422

  6. Tomography and Simulation of Microstructure Evolution of a Closed-Cell Polymer Foam in Compression

    SciTech Connect

    Daphalapurkar, N.P.; Hanan, J.C.; Phelps, N.B.; Bale, H.; Lu, H.

    2010-10-25

    Closed-cell foams in compression exhibit complex deformation characteristics that remain incompletely understood. In this paper the microstructural evolution of closed-cell polymethacrylimide foam was simulated in compression undergoing elastic, compaction, and densification stages. The three-dimensional microstructure of the foam is determined using Micro-Computed Tomography ({micro}-CT), and is converted to material points for simulations using the material point method (MPM). The properties of the cell-walls are determined from nanoindentation on the wall of the foam. MPM simulations captured the three stages of deformations in foam compression. Features of the microstructures from simulations are compared qualitatively with the in-situ observations of the foam under compression using {micro}-CT. The stress-strain curve simulated from MPM compares reasonably with the experimental results. Based on the results from {micro}-CT and MPM simulations, it was found that elastic buckling of cell-walls occurs even in the elastic regime of compression. Within the elastic region, less than 35% of the cell-wall material carries the majority of the compressive load. In the experiment, a shear band was observed as a result of collapse of cells in a weak zone. From this collapsed weak zone a compaction (collapse) wave was seen traveling which eventually lead to the collapse of the entire foam cell-structure. Overall, this methodology will allow prediction of material properties for microstructures driving the optimization of processing and performance in foam materials.

  7. Theoretical magnetograms based on quantitative simulation of a magnetospheric substorm

    SciTech Connect

    Chen, C.; Wolf, R.A.; Harel, M.; Karty, J.L.

    1982-08-01

    Using substorm currents derived from the Rice computer simulation of the substorm event of September 19, 1976, we have computed theoretical magnetograms as a function of universal time for various stations. A theoretical Dst has also been computed. Our computed magnetograms were obtained by integrating the Biot-Savart law over a maze of approximately 2700 wires and bands that carry the ring currents, the Birkeland currents, and the horizontal ionospheric currents. Ground currents and dynamo currents were neglected. Computed contributions to the magnetic field perturbation from eleven different kinds of currents are displayed (e.g., ring currents, northern hemisphere Birkeland currents). First, overall agreement of theory and data is generally satisfactory, especially for stations at high and mid-magnetic latitudes. Second, model results suggest that the ground magnetic field perturbations arise from very complicated combinations of different kinds of currents and that the magnetic field disturbances due to different but related currents often cancel each other, despite the fact that complicated inhomogeneous conductivities in our model prevent rigorous application of Fukushima's theorem. Third, both the theoretical and observed Dst decrease during the expansion phase of the substorm, but data indicate that Dst relaxes back toward its initial value within about an hour after the peak of the substorm. Fourth, the dawn-dusk asymmetry in the horizontal component of magnetic field disturbance at low latitudes in a substorm is essentially due to a net downward Birkeland current at noon, net upward current at midnight, and generally antisunward flowing electrojets; it is not due to a physical partial ring current injected into the duskside of the inner magnetosphere.

  8. Numerical simulation of x-ray luminescence optical tomography for small-animal imaging.

    PubMed

    Li, Changqing; Martínez-Dávalos, Arnulfo; Cherry, Simon R

    2014-04-01

    X-ray luminescence optical tomography (XLOT) is an emerging hybrid imaging modality in which x-ray excitable particles (phosphor particles) emit optical photons when stimulated with a collimated x-ray beam. XLOT can potentially combine the high sensitivity of optical imaging with the high spatial resolution of x-ray imaging. For reconstruction of XLOT data, we compared two reconstruction algorithms, conventional filtered backprojection (FBP) and a new algorithm, x-ray luminescence optical tomography with excitation priors (XLOT-EP), in which photon propagation is modeled with the diffusion equation and the x-ray beam positions are used as reconstruction priors. Numerical simulations based on dose calculations were used to validate the proposed XLOT imaging system and the reconstruction algorithms. Simulation results showed nanoparticle concentrations reconstructed with XLOT-EP are much less dependent on scan depth than those obtained with FBP. Measurements at just two orthogonal projections are sufficient for XLOT-EP to reconstruct an XLOT image for simple source distributions. The heterogeneity of x-ray energy deposition is included in the XLOT-EP reconstruction and improves the reconstruction accuracy, suggesting that there is a need to calculate the x-ray energy distribution for experimental XLOT imaging. PMID:24695846

  9. Recent advances in 3D computed tomography techniques for simulation and navigation in hepatobiliary pancreatic surgery.

    PubMed

    Uchida, Masafumi

    2014-04-01

    A few years ago it could take several hours to complete a 3D image using a 3D workstation. Thanks to advances in computer science, obtaining results of interest now requires only a few minutes. Many recent 3D workstations or multimedia computers are equipped with onboard 3D virtual patient modeling software, which enables patient-specific preoperative assessment and virtual planning, navigation, and tool positioning. Although medical 3D imaging can now be conducted using various modalities, including computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasonography (US) among others, the highest quality images are obtained using CT data, and CT images are now the most commonly used source of data for 3D simulation and navigation image. If the 2D source image is bad, no amount of 3D image manipulation in software will provide a quality 3D image. In this exhibition, the recent advances in CT imaging technique and 3D visualization of the hepatobiliary and pancreatic abnormalities are featured, including scan and image reconstruction technique, contrast-enhanced techniques, new application of advanced CT scan techniques, and new virtual reality simulation and navigation imaging. PMID:24464989

  10. Micro computed tomography and CFD simulation of drop deposition on gas diffusion layers

    NASA Astrophysics Data System (ADS)

    Guilizzoni, M.; Santini, M.; Lorenzi, M.; Knisel, V.; Fest-Santini, S.

    2014-11-01

    Fuel cells are electrochemical power generation system which may achieve high energy efficiencies with environmentally friendly emissions. Among the different types, Proton Exchange Membrane fuel cells (PEMFC) seem at present one of the most promising choices. A very important component of a PEMFC is the gas diffusion layer (GDL), which has the primary role of managing water in the cell, allowing reactant gases transport to the catalyst layer while keeping the membrane correctly hydrated and preventing electrode flooding. Therefore, GDLs have to be porous and very hydrophobic. Carbon clothes or carbon papers coated with a hydrophobizing agent - typically a fluoropolymer - are used. Given the complex chemistry and morphology of the GDLs, wettability analyses on them present some critical issues when using the conventional contact angle measurement techniques. In this paper, the deposition of a drop on a GDL (produced using polytetrafluoroethylene-co-perfluoroalcoxy vinyl ether as the fluorinated polymer) was investigated by means of micro computed tomography (microCT) and numerical simulation. The microCT facility operational at the University of Bergamo was used to acquire a 3D tomography of a water drop deposed on a sample GDL. The reconstructed drop dataset allows thorough understanding of the real drop shape, of its contact area and contact line. The GDL dataset was used to create a realistic mesh for the numerical simulation of the drop deposition, which was performed using the OpenFOAM® interFOAM solver.

  11. Design and simulation of superconducting Lorentz Force Electrical Impedance Tomography (LFEIT)

    NASA Astrophysics Data System (ADS)

    Shen, Boyang; Fu, Lin; Geng, Jianzhao; Zhang, Xiuchang; Zhang, Heng; Dong, Qihuan; Li, Chao; Li, Jing; Coombs, T. A.

    2016-05-01

    Lorentz Force Electrical Impedance Tomography (LFEIT) is a hybrid diagnostic scanner with strong capability for biological imaging, particularly in cancer and haemorrhages detection. This paper presents the design and simulation of a novel combination: a superconducting magnet together with LFEIT system. Superconducting magnets can generate magnetic field with high intensity and homogeneity, which could significantly enhance the imaging performance. The modelling of superconducting magnets was carried out using Finite Element Method (FEM) package, COMSOL Multiphysics, which was based on Partial Differential Equation (PDE) model with H-formulation coupling B-dependent critical current density and bulk approximation. The mathematical model for LFEIT system was built based on the theory of magneto-acoustic effect. The magnetic field properties from magnet design were imported into the LFEIT model. The basic imaging of electrical signal was developed using MATLAB codes. The LFEIT model simulated two samples located in three different magnetic fields with varying magnetic strength and homogeneity.

  12. Quantitative validation of carbon-fiber laminate low velocity impact simulations

    SciTech Connect

    English, Shawn A.; Briggs, Timothy M.; Nelson, Stacy M.

    2015-09-26

    Simulations of low velocity impact with a flat cylindrical indenter upon a carbon fiber fabric reinforced polymer laminate are rigorously validated. Comparison of the impact energy absorption between the model and experiment is used as the validation metric. Additionally, non-destructive evaluation, including ultrasonic scans and three-dimensional computed tomography, provide qualitative validation of the models. The simulations include delamination, matrix cracks and fiber breaks. An orthotropic damage and failure constitutive model, capable of predicting progressive damage and failure, is developed in conjunction and described. An ensemble of simulations incorporating model parameter uncertainties is used to predict a response distribution which is then compared to experimental output using appropriate statistical methods. Lastly, the model form errors are exposed and corrected for use in an additional blind validation analysis. The result is a quantifiable confidence in material characterization and model physics when simulating low velocity impact in structures of interest.

  13. Quantitative validation of carbon-fiber laminate low velocity impact simulations

    DOE PAGESBeta

    English, Shawn A.; Briggs, Timothy M.; Nelson, Stacy M.

    2015-09-26

    Simulations of low velocity impact with a flat cylindrical indenter upon a carbon fiber fabric reinforced polymer laminate are rigorously validated. Comparison of the impact energy absorption between the model and experiment is used as the validation metric. Additionally, non-destructive evaluation, including ultrasonic scans and three-dimensional computed tomography, provide qualitative validation of the models. The simulations include delamination, matrix cracks and fiber breaks. An orthotropic damage and failure constitutive model, capable of predicting progressive damage and failure, is developed in conjunction and described. An ensemble of simulations incorporating model parameter uncertainties is used to predict a response distribution which ismore » then compared to experimental output using appropriate statistical methods. Lastly, the model form errors are exposed and corrected for use in an additional blind validation analysis. The result is a quantifiable confidence in material characterization and model physics when simulating low velocity impact in structures of interest.« less

  14. Direct reconstruction in CT-analogous pharmacokinetic diffuse fluorescence tomography: two-dimensional simulative and experimental validations

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Zhang, Yanqi; Zhang, Limin; Li, Jiao; Zhou, Zhongxing; Zhao, Huijuan; Gao, Feng

    2016-04-01

    We present a generalized strategy for direct reconstruction in pharmacokinetic diffuse fluorescence tomography (DFT) with CT-analogous scanning mode, which can accomplish one-step reconstruction of the indocyanine-green pharmacokinetic-rate images within in vivo small animals by incorporating the compartmental kinetic model into an adaptive extended Kalman filtering scheme and using an instantaneous sampling dataset. This scheme, compared with the established indirect and direct methods, eliminates the interim error of the DFT inversion and relaxes the expensive requirement of the instrument for obtaining highly time-resolved date-sets of complete 360 deg projections. The scheme is validated by two-dimensional simulations for the two-compartment model and pilot phantom experiments for the one-compartment model, suggesting that the proposed method can estimate the compartmental concentrations and the pharmacokinetic-rates simultaneously with a fair quantitative and localization accuracy, and is well suitable for cost-effective and dense-sampling instrumentation based on the highly-sensitive photon counting technique.

  15. Direct reconstruction in CT-analogous pharmacokinetic diffuse fluorescence tomography: two-dimensional simulative and experimental validations.

    PubMed

    Wang, Xin; Zhang, Yanqi; Zhang, Limin; Li, Jiao; Zhou, Zhongxing; Zhao, Huijuan; Gao, Feng

    2016-04-30

    We present a generalized strategy for direct reconstruction in pharmacokinetic diffuse fluorescence tomography (DFT) with CT-analogous scanning mode, which can accomplish one-step reconstruction of the indocyanine-green pharmacokinetic-rate images within in vivo small animals by incorporating the compartmental kinetic model into an adaptive extended Kalman filtering scheme and using an instantaneous sampling dataset. This scheme, compared with the established indirect and direct methods, eliminates the interim error of the DFT inversion and relaxes the expensive requirement of the instrument for obtaining highly time-resolved date-sets of complete 360 deg projections. The scheme is validated by two-dimensional simulations for the two-compartment model and pilot phantom experiments for the one-compartment model, suggesting that the proposed method can estimate the compartmental concentrations and the pharmacokinetic-rates simultaneously with a fair quantitative and localization accuracy, and is well suitable for cost-effective and dense-sampling instrumentation based on the highly-sensitive photon counting technique. PMID:27093958

  16. Differentiation of Calcium Oxalate Monohydrate and Calcium Oxalate Dihydrate Stones Using Quantitative Morphological Information from Micro-Computerized and Clinical Computerized Tomography

    PubMed Central

    Duan, Xinhui; Qu, Mingliang; Wang, Jia; Trevathan, James; Vrtiska, Terri; Williams, James C.; Krambeck, Amy; Lieske, John; McCollough, Cynthia

    2014-01-01

    Purpose We differentiated calcium oxalate monohydrate and calcium oxalate dihydrate kidney stones using micro and clinical computerized tomography images. Materials and Methods A total of 22 calcium oxalate monohydrate and 15 calcium oxalate dihydrate human kidney stones were scanned using a commercial micro-computerized tomography scanner with a pixel size of 7 to 23 μm. Under an institutional review board approved protocol, image data on 10 calcium oxalate monohydrate and 9 calcium oxalate dihydrate stones greater than 5 mm were retrieved from a total of 80 patients who underwent clinical dual energy computerized tomography for clinical indications and had stones available for infrared spectroscopic compositional analysis. Micro and clinical computerized tomography images were processed using in-house software, which quantified stone surface morphology with curvature based calculations. A shape index was generated as a quantitative shape metric to differentiate calcium oxalate monohydrate from calcium oxalate dihydrate stones. Statistical tests were used to test the performance of the shape index. Results On micro-computerized tomography images the shape index of calcium oxalate monohydrate and calcium oxalate dihydrate stones significantly differed (ROC curve AUC 0.92, p <0.0001). At the optimal cutoff sensitivity was 0.93 and specificity was 0.91. On clinical computerized tomography images a significant morphological difference was also detected (p = 0.007). AUC, sensitivity and specificity were 0.90, 1 and 0.73, respectively. Conclusions On micro and clinical computerized tomography images a morphological difference was detectable in calcium oxalate monohydrate and calcium oxalate dihydrate stones larger than 5 mm. The shape index is a highly promising method that can distinguish calcium oxalate monohydrate and calcium oxalate dihydrate stones with reasonable accuracy. PMID:23142201

  17. Computed Tomography Angiography of Carotid Arteries and Vertebrobasilar System: A Simulation Study for Radiation Dose Reduction.

    PubMed

    Kramer, Manuel; Ellmann, Stephan; Allmendinger, Thomas; Eller, Achim; Kammerer, Ferdinand; May, Matthias S; Baigger, João F; Uder, Michael; Lell, Michael M

    2015-07-01

    Computed tomography angiography (CTA) of carotid arteries and vertebrobasilar system is a standardized procedure with excellent image quality, but radiation exposure remains a matter of concern. The aim of this study is to examine to what extent radiation dose can be lowered in relation to a standard protocol by simulating examinations with lower tube currents applying a dedicated software.Lower tube current was simulated by a dedicated noise insertion and reconstruction software (ReconCT). In a phantom study, true scans were performed with different dose protocols and compared to the results of simulated dose reductions of the same degree, respectively. In a patient study, 30 CTAs of supra-aortic vessels were reconstructed at a level of 100%, 75%, 50%, and 25% of the initial dose. Objective and subjective image analyses were performed.No significant noise differences between true scans and simulated scans of mimicked contrasted vessels were found. In the patient study, the quality scores of the 4 dose groups differed statistically significant; this difference vanished for the comparison of the 100% and 75% datasets after dichotomization into the categories of diagnostic and nondiagnostic image quality (P = .50).This study suggests an easy-to-implement method of simulating CTAs of carotid arteries and vertebrobasilar system with lower tube current for dose reduction by artificially adding noise to the original raw data. Lowering the radiation dose in a moderate extent to 75% of the original dose levels does not significantly alter the diagnostic image quality. PMID:26131822

  18. Magnetoacoustic tomography with magnetic induction (MAT-MI) for breast tumor imaging: numerical modeling and simulation

    NASA Astrophysics Data System (ADS)

    Zhou, Lian; Li, Xu; Zhu, Shanan; He, Bin

    2011-04-01

    Magnetoacoustic tomography with magnetic induction (MAT-MI) was recently introduced as a noninvasive electrical conductivity imaging approach with high spatial resolution close to ultrasound imaging. In this study, we test the feasibility of the MAT-MI method for breast tumor imaging using numerical modeling and computer simulation. Using the finite element method, we have built three-dimensional numerical breast models with varieties of embedded tumors for this simulation study. In order to obtain an accurate and stable forward solution that does not have numerical errors caused by singular MAT-MI acoustic sources at conductivity boundaries, we first derive an integral forward method for calculating MAT-MI acoustic sources over the entire imaging volume. An inverse algorithm for reconstructing the MAT-MI acoustic source is also derived with spherical measurement aperture, which simulates a practical setup for breast imaging. With the numerical breast models, we have conducted computer simulations under different imaging parameter setups and all the results suggest that breast tumors that have large conductivity in contrast to the surrounding tissue as reported in the literature may be readily detected in the reconstructed MAT-MI images. In addition, our simulations also suggest that the sensitivity of imaging breast tumors using the presented MAT-MI setup depends more on the tumor location and the conductivity contrast between the tumor and its surrounding tissue than on the tumor size.

  19. Pitch control margin at high angle of attack - Quantitative requirements (flight test correlation with simulation predictions)

    NASA Technical Reports Server (NTRS)

    Lackey, J.; Hadfield, C.

    1992-01-01

    Recent mishaps and incidents on Class IV aircraft have shown a need for establishing quantitative longitudinal high angle of attack (AOA) pitch control margin design guidelines for future aircraft. NASA Langley Research Center has conducted a series of simulation tests to define these design guidelines. Flight test results have confirmed the simulation studies in that pilot rating of high AOA nose-down recoveries were based on the short-term response interval in the forms of pitch acceleration and rate.

  20. Optical distortion correction in optical coherence tomography for quantitative ocular anterior segment by three-dimensional imaging.

    PubMed

    Ortiz, Sergio; Siedlecki, Damian; Grulkowski, Ireneusz; Remon, Laura; Pascual, Daniel; Wojtkowski, Maciej; Marcos, Susana

    2010-02-01

    A method for three-dimensional 3-D optical distortion (refraction) correction on anterior segment Optical Coherence Tomography (OCT) images has been developed. The method consists of 3-D ray tracing through the different surfaces, following denoising, segmentation of the surfaces, Delaunay representation of the surfaces, and application of fan distortion correction. The correction has been applied theoretically to realistic computer eye models, and experimentally to OCT images of: an artificial eye with a Polymethyl Methacrylate (PMMA) cornea and an intraocular lens (IOL), an enucleated porcine eye, and a human eye in vivo obtained from two OCT laboratory set-ups (time domain and spectral). Data are analyzed in terms of surface radii of curvature and asphericity. Comparisons are established between the reference values for the surfaces (nominal values in the computer model; non-contact profilometric measurements for the artificial eye; Scheimpflug imaging for the real eyes in vivo and vitro). The results from the OCT data were analyzed following the conventional approach of dividing the optical path by the refractive index, after application of 2-D optical correction, and 3-D optical correction (in all cases after fan distortion correction). The application of 3-D optical distortion correction increased significantly both the accuracy of the radius of curvature estimates and particularly asphericity of the surfaces, with respect to conventional methods of OCT image analysis. We found that the discrepancies of the radii of curvature estimates from 3-D optical distortion corrected OCT images are less than 1% with respect to nominal values. Optical distortion correction in 3-D is critical for quantitative analysis of OCT anterior segment imaging, and allows accurate topography of the internal surfaces of the eye. PMID:20174107

  1. Quantitative computed tomography of lung parenchyma in patients with emphysema: analysis of higher-density lung regions

    NASA Astrophysics Data System (ADS)

    Lederman, Dror; Leader, Joseph K.; Zheng, Bin; Sciurba, Frank C.; Tan, Jun; Gur, David

    2011-03-01

    Quantitative computed tomography (CT) has been widely used to detect and evaluate the presence (or absence) of emphysema applying the density masks at specific thresholds, e.g., -910 or -950 Hounsfield Unit (HU). However, it has also been observed that subjects with similar density-mask based emphysema scores could have varying lung function, possibly indicating differences of disease severity. To assess this possible discrepancy, we investigated whether density distribution of "viable" lung parenchyma regions with pixel values > -910 HU correlates with lung function. A dataset of 38 subjects, who underwent both pulmonary function testing and CT examinations in a COPD SCCOR study, was assembled. After the lung regions depicted on CT images were automatically segmented by a computerized scheme, we systematically divided the lung parenchyma into different density groups (bins) and computed a number of statistical features (i.e., mean, standard deviation (STD), skewness of the pixel value distributions) in these density bins. We then analyzed the correlations between each feature and lung function. The correlation between diffusion lung capacity (DLCO) and STD of pixel values in the bin of -910HU <= PV < -750HU was -0.43, as compared with a correlation of -0.49 obtained between the post-bronchodilator ratio (FEV1/FVC) measured by the forced expiratory volume in 1 second (FEV1) dividing the forced vital capacity (FVC) and the STD of pixel values in the bin of -1024HU <= PV < -910HU. The results showed an association between the distribution of pixel values in "viable" lung parenchyma and lung function, which indicates that similar to the conventional density mask method, the pixel value distribution features in "viable" lung parenchyma areas may also provide clinically useful information to improve assessments of lung disease severity as measured by lung functional tests.

  2. Quantitative determination of the mineral distribution in different collagen zones of calcifying tendon using high voltage electron microscopic tomography

    NASA Technical Reports Server (NTRS)

    McEwen, B. F.; Song, M. J.; Landis, W. J.

    1991-01-01

    High voltage electron microscopic tomography was used to make the first quantitative determination of the distribution of mineral between different regions of collagen fibrils undergoing early calcification in normal leg tendons of the domestic turkey, Meleagris gallopavo. The tomographic 3-D reconstruction was computed from a tilt series of 61 different views spanning an angular range of +/- 60 degrees in 2 degrees intervals. Successive applications of an interactive computer operation were used to mask the collagen banding pattern of either hole or overlap zones into separate versions of the reconstruction. In such 3-D volumes, regions specified by the mask retained their original image density while the remaining volume was set to background levels. This approach was also applied to the mineral crystals present in the same volumes to yield versions of the 3-D reconstructions that were masked for both the crystal mass and the respective collagen zones. Density profiles from these volumes contained a distinct peak corresponding only to the crystal mass. A comparison of the integrated density of this peak from each profile established that 64% of the crystals observed were located in the collagen hole zones and 36% were found in the overlap zones. If no changes in crystal stability occur once crystals are formed, this result suggests the possibilities that nucleation of mineral is preferentially and initially associated with the hole zones, nucleation occurs more frequently in the hole zones, the rate of crystal growth is more rapid in the hole zones, or a combination of these alternatives. All lead to the conclusion that the overall accumulation of mineral mass is predominant in the collagen hole zones compared to overlap zones during early collagen fibril calcification.

  3. Comparison of frequency domain optical coherence tomography and quantitative coronary angiography for the assessment of coronary lesions

    NASA Astrophysics Data System (ADS)

    Zafar, Haroon; Sharif, Faisal; Leahy, Martin J.

    2014-03-01

    Quantitative coronary angiography (QCA) has been used as a standard technique for the evaluation of coronary artery disease for many years. Intracoronary optical coherence tomography (OCT) offers higher resolution, faster image acquisition speeds and greater sensitivity than the intravascular ultrasound (IVUS). Recently developed frequency domain OCT (FD-OCT) systems overcome many technical limitations of conventional time domain OCT systems (TDOCT). The main objective of this study was to compare the FD-OCT and QCA measurements for the assessment of coronary lesions. A total of 21 stenoses in 18 patients were analysed using QCA and FD-OCT. The average minimum lumen diameter (MLD) and percent lumen area stenosis (%AS) by QCA were 1.52+/-0.44 mm and 68+/-9% respectively. The average MLD and %AS by FD-OCT were 1.32+/-0.38 mm and 63+/-14% respectively. There was a moderate but significant correlation between QCA and FD-OCT measured MLD (r = 0.5, p < 0.01) and %AS (r = 0.56, p < 0.01). Bland-Altman analysis showed that the mean differences between the QCA and FD-OCT measurements were 0.18+/-0.81 (limits of agreement: -0.63 to 0.99) for MLD and 4.4+/-22.8 (limits of agreement: -18.4 to 27.2) for %AS. The root mean square error (RMSE) between the QCA and FD-OCT measured MLD and %AS was +/-0.44 mm and +/-12.1% respectively.

  4. Role of quantitative computed tomography texture analysis in the differentiation of primary lung cancer and granulomatous nodules

    PubMed Central

    Thornhill, Rebecca; Sethi-Virmani, Vineeta; Souza, Carolina A.; Bayanati, Hamid; Gupta, Ashish; Maziak, Donna

    2016-01-01

    Background Texture analysis is a computer tool that enables quantification of gray-level patterns, pixel interrelationships, and spectral properties of an image. It can enhance visual methods of image analysis. Primary lung cancer and granulomatous nodules have identical CT imaging features. The purpose of this study was to assess the sensitivity and specificity of CT texture analysis in differentiating lung cancer and granulomas. Methods This retrospective study evaluated 55 patients with primary lung cancer and granulomatous nodules who had contrast-enhanced (CE) and/or non-contrast-enhanced (NCE) CT within 3 months of biopsy. Textural features were extracted from 61 nodules. Mann-Whitney U tests were used to compare values for nodules. Receiver operating characteristic (ROC) curves were constructed and the area under the curve (AUC) calculated with histopathology as outcome. Combinations of features were entered as predictors in logistic regression models and optimal threshold criteria were used to estimate sensitivity and specificity. Results The model generated by sum of squares, sum difference, and sum entropy features for NCE CT yielded 88% sensitivity and 92% specificity (AUC =0.90±0.06, P<0.0001). For nodules with fluorodeoxyglucose positron emission tomography (FDG-PET)/CT, sensitivity for detection of lung cancer was 79.2% (CI: 57.8–92.9%), specificity was 38.5% (CI: 13.9–68.4%) and accuracy was 64.8%. Conclusions Quantitative CT texture analysis has the potential to differentiate primary lung cancer and granulomatous lesions. PMID:26981450

  5. Population-Stratified Analysis of Bone Mineral Density Distribution in Cervical and Lumbar Vertebrae of Chinese from Quantitative Computed Tomography

    PubMed Central

    Zhang, Yong; Zhou, Zhuang; Wu, Cheng'ai; Zhao, Danhui; Wang, Chao; Cai, Wei; Wang, Ling; Duanmu, Yangyang; Zhang, Chenxin; Tian, Wei

    2016-01-01

    Objective To investigate the bone mineral density (BMD) of cervical vertebrae in a population-stratified manner and correlate with that of the lumbar vertebrae. Materials and Methods Five hundred and ninety-eight healthy volunteers (254 males, 344 females), ranging from 20 to 64 years of age, were recruited for volumetric BMD (vBMD) measurements by quantitative computed tomography. Basic information (age, height, weight, waistline, and hipline), and vBMD of the cervical and lumbar vertebrae (C2–7 and L2–4) were recorded. Comparisons among sex, age groups and different levels of vertebrae were analyzed using analysis of variance. Linear regression was performed for relevance of different vertebral levels. Results The vBMD of cervical and lumbar vertebrae was higher in females than males in each age group. The vBMD of the cervical and lumbar vertebrae in males and the vBMD of lumbar vertebrae in females decreased with aging. In each age group, the vBMD of the cervical vertebrae was higher than that of the lumbar vertebrae with gradual decreases from C2 to C7 except for C3; moreover, the vBMD of C6 and C7 was significantly different from that of C2–5. Correlations of vBMD among different cervical vertebrae (females: r = 0.62–0.94; males: r = 0.63–0.94) and lumbar vertebrae (males: r = 0.93–0.98; females: r = 0.82–0.97) were statistically significant at each age group. Conclusion The present study provided normative data of cervical vertebrae in an age- and sex-stratified manner. Sex differences in vBMD prominently vary with age, which can be helpful to design a more comprehensive pre-operative surgical plan. PMID:27587947

  6. Quantitation of the reconstruction quality of a four-dimensional computed tomography process for lung cancer patients

    SciTech Connect

    Lu Wei; Parikh, Parag J.; El Naqa, Issam M.; Nystrom, Michelle M.; Hubenschmidt, James P.; Wahab, Sasha H.; Mutic, Sasa; Singh, Anurag K.; Christensen, Gary E.; Bradley, Jeffrey D.; Low, Daniel A.

    2005-04-01

    We have developed a four-dimensional computed tomography (4D CT) technique for mapping breathing motion in radiotherapy treatment planning. A multislice CT scanner (1.5 mm slices) operated in cine mode was used to acquire 12 contiguous slices in each couch position for 15 consecutive scans (0.5 s rotation, 0.25 s between scans) while the patient underwent simultaneous quantitative spirometry measurements to provide a sorting metric. The spirometry-sorted scans were used to reconstruct a 4D data set. A critical factor for 4D CT is quantifying the reconstructed data set quality which we measure by correlating the metric used relative to internal-object motion. For this study, the internal air content within the lung was used as a surrogate for internal motion measurements. Thresholding and image morphological operations were applied to delineate the air-containing tissues (lungs, trachea) from each CT slice. The Hounsfield values were converted to the internal air content (V). The relationship between the air content and spirometer-measured tidal volume ({nu}) was found to be quite linear throughout the lungs and was used to estimate the overall accuracy and precision of tidal volume-sorted 4D CT. Inspection of the CT-scan air content as a function of tidal volume showed excellent correlations (typically r>0.99) throughout the lung volume. Because of the discovered linear relationship, the ratio of internal air content to tidal volume was indicative of the fraction of air change in each couch position. Theoretically, due to air density differences within the lung and in room, the sum of these ratios would equal 1.11. For 12 patients, the mean value was 1.08{+-}0.06, indicating the high quality of spirometry-based image sorting. The residual of a first-order fit between {nu} and V was used to estimate the process precision. For all patients, the precision was better than 8%, with a mean value of 5.1%{+-}1.9%. This quantitative analysis highlights the value of using

  7. SU-E-QI-16: Reproducibility of Computed Tomography Quantitative Structural Features Using the FDA Thoracic Phantom Image Database

    SciTech Connect

    Budzevich, M; Grove, O; Balagurunathan, Y; Gu, Y; Wang, H; Oliver, J; Latifi, K; Zhang, G; Dilling, T; Gillies, R; Moros, E; Lee, H.

    2014-06-15

    Purpose: To assess the reproducibility of quantitative structural features using images from the computed tomography thoracic FDA phantom database under different scanning conditions. Methods: Development of quantitative image features to describe lesion shape and size, beyond conventional RECIST measures, is an evolving area of research in need of benchmarking standards. Gavrielides et al. (2010) scanned a FDA-developed thoracic phantom with nodules of various Hounsfield units (HU) values, shapes and sizes close to vascular structures using several scanners and varying scanning conditions/parameters; these images are in the public domain. We tested six structural features, namely, Convexity, Perimeter, Major Axis, Minor Axis, Extent Mean and Eccentricity, to characterize lung nodules. Convexity measures lesion irregularity referenced to a convex surface. Previously, we showed it to have prognostic value in lung adenocarcinoma. The above metrics and RECIST measures were evaluated on three spiculated (8mm/-300HU, 12mm/+30HU and 15mm/+30HU) and two non-spiculated (8mm/+100HU and 10mm/+100HU) nodules (from layout 2) imaged at three different mAs values: 25, 100 and 200 mAs; on a Phillips scanner (16-slice Mx8000-IDT; 3mm slice thickness). The nodules were segmented semi-automatically using a commercial software tool; the same HU range was used for all nodules. Results: Analysis showed convexity having the lowest maximum coefficient of variation (MCV): 1.1% and 0.6% for spiculated and non-spiculated nodules, respectively, much lower compared to RECIST Major and Minor axes whose MCV were 10.1% and 13.4% for spiculated, and 1.9% and 2.3% for non-spiculated nodules, respectively, across the various mAs. MCVs were consistently larger for speculated nodules. In general, the dependence of structural features on mAs (noise) was low. Conclusion: The FDA phantom CT database may be used for benchmarking of structural features for various scanners and scanning conditions; we used

  8. Quantitative evaluation of atlas-based high-density diffuse optical tomography for imaging of the human visual cortex

    PubMed Central

    Wu, Xue; Eggebrecht, Adam T.; Ferradal, Silvina L; Culver, Joseph P.; Dehghani, Hamid

    2014-01-01

    Image recovery in diffuse optical tomography (DOT) of the human brain often relies on accurate models of light propagation within the head. In the absence of subject specific models for image reconstruction, the use of atlas based models are showing strong promise. Although there exists some understanding in the use of some limited rigid model registrations in DOT, there has been a lack of a detailed analysis between errors in geometrical accuracy, light propagation in tissue and subsequent errors in dynamic imaging of recovered focal activations in the brain. In this work 11 different rigid registration algorithms, across 24 simulated subjects, are evaluated for DOT studies in the visual cortex. Although there exists a strong correlation (R2 = 0.97) between geometrical surface error and internal light propagation errors, the overall variation is minimal when analysing recovered focal activations in the visual cortex. While a subject specific mesh gives the best results with a 1.2 mm average location error, no single algorithm provides errors greater than 4.5 mm. This work demonstrates that the use of rigid algorithms for atlas based imaging is a promising route when subject specific models are not available. PMID:25426318

  9. Validation of a novel technique for creating simulated radiographs using computed tomography datasets.

    PubMed

    Mendoza, Patricia; d'Anjou, Marc-André; Carmel, Eric N; Fournier, Eric; Mai, Wilfried; Alexander, Kate; Winter, Matthew D; Zwingenberger, Allison L; Thrall, Donald E; Theoret, Christine

    2014-01-01

    Understanding radiographic anatomy and the effects of varying patient and radiographic tube positioning on image quality can be a challenge for students. The purposes of this study were to develop and validate a novel technique for creating simulated radiographs using computed tomography (CT) datasets. A DICOM viewer (ORS Visual) plug-in was developed with the ability to move and deform cuboidal volumetric CT datasets, and to produce images simulating the effects of tube-patient-detector distance and angulation. Computed tomographic datasets were acquired from two dogs, one cat, and one horse. Simulated radiographs of different body parts (n = 9) were produced using different angles to mimic conventional projections, before actual digital radiographs were obtained using the same projections. These studies (n = 18) were then submitted to 10 board-certified radiologists who were asked to score visualization of anatomical landmarks, depiction of patient positioning, realism of distortion/magnification, and image quality. No significant differences between simulated and actual radiographs were found for anatomic structure visualization and patient positioning in the majority of body parts. For the assessment of radiographic realism, no significant differences were found between simulated and digital radiographs for canine pelvis, equine tarsus, and feline abdomen body parts. Overall, image quality and contrast resolution of simulated radiographs were considered satisfactory. Findings from the current study indicated that radiographs simulated using this new technique are comparable to actual digital radiographs. Further studies are needed to apply this technique in developing interactive tools for teaching radiographic anatomy and the effects of varying patient and tube positioning. PMID:24219133

  10. Note on quantitatively correct simulations of the kinetic beam-plasma instability

    SciTech Connect

    Lotov, K. V.; Timofeev, I. V.; Mesyats, E. A.; Snytnikov, A. V.; Vshivkov, V. A.

    2015-02-15

    A large number of model particles are shown necessary for quantitatively correct simulations of the kinetic beam-plasma instability with the clouds-in-cells method. The required number of particles scales inversely with the expected growth rate, as only a narrow interval of beam velocities is resonant with the wave in the kinetic regime.

  11. Induced current electrical impedance tomography system: experimental results and numerical simulations.

    PubMed

    Zlochiver, Sharon; Radai, M Michal; Abboud, Shimon; Rosenfeld, Moshe; Dong, Xiu-Zhen; Liu, Rui-Gang; You, Fu-Sheng; Xiang, Hai-Yan; Shi, Xue-Tao

    2004-02-01

    In electrical impedance tomography (EIT), measurements of developed surface potentials due to applied currents are used for the reconstruction of the conductivity distribution. Practical implementation of EIT systems is known to be problematic due to the high sensitivity to noise of such systems, leading to a poor imaging quality. In the present study, the performance of an induced current EIT (ICEIT) system, where eddy current is applied using magnetic induction, was studied by comparing the voltage measurements to simulated data, and examining the imaging quality with respect to simulated reconstructions for several phantom configurations. A 3-coil, 32-electrode ICEIT system was built, and an iterative modified Newton-Raphson algorithm was developed for the solution of the inverse problem. The RMS norm between the simulated and the experimental voltages was found to be 0.08 +/- 0.05 mV (<3%). Two regularization methods were implemented and compared: the Marquardt regularization and the Laplacian regularization (a bounded second-derivative regularization). While the Laplacian regularization method was found to be preferred for simulated data, it resulted in distinctive spatial artifacts for measured data. The experimental reconstructed images were found to be indicative of the angular positioning of the conductivity perturbations, though the radial sensitivity was low, especially when using the Marquardt regularization method. PMID:15005319

  12. Optical coherence tomography images simulated with an analytical solution of Maxwell's equations for cylinder scattering

    NASA Astrophysics Data System (ADS)

    Brenner, Thomas; Reitzle, Dominik; Kienle, Alwin

    2016-04-01

    An algorithm for the simulation of image formation in Fourier domain optical coherence tomography (OCT) for an infinitely long cylinder is presented. The analytical solution of Maxwell's equations for light scattering by a single cylinder is employed for the case of perpendicular incidence to calculate OCT images. The A-scans and the time-resolved scattered intensities are compared to geometrical optics results calculated with a ray tracing approach. The reflection peaks, including the whispering gallery modes, are identified. Additionally, the Debye series expansion is employed to identify single peaks in the OCT A-scans. Furthermore, a Gaussian beam is implemented in order to simulate lateral scanning over the cylinder for two-dimensional B-scans. The fields are integrated over a certain angular range to simulate a detection aperture. In addition, the solution for light scattering by layered cylinders is employed and the various layers are identified in the resulting OCT image. Overall, the simulations in this work show that OCT images do not always display the real surface of investigated samples.

  13. A quantitative parameter-free prediction of simulated crystal nucleation times

    SciTech Connect

    Aga, Rachel S; Morris, James R; Hoyt, Jeffrey John; Mendelev, Mikhail I.

    2006-01-01

    We present direct comparisons between simulated crystal-nucleation times and theoretical predictions using a model of aluminum, and demonstrate that a quantitative prediction can be made. All relevant thermodynamic properties of the system are known, making the agreement of our simulation data with nucleation theories free of any adjustable parameters. The role of transient nucleation is included in the classical nucleation theory approach, and shown to be necessary to understand the observed nucleation times. The calculations provide an explanation on why nucleation is difficult to observe in simulations at moderate undercoolings. Even when the simulations are significantly larger than the critical nucleus, and when simulation times are sufficiently long, at moderate undercoolings the small concentration of critical nuclei makes the probability of the nucleation low in molecular dynamics simulations.

  14. Organ doses for reference adult male and female undergoing computed tomography estimated by Monte Carlo simulations

    SciTech Connect

    Lee, Choonsik; Kim, Kwang Pyo; Long, Daniel; Fisher, Ryan; Tien, Chris; Simon, Steven L.; Bouville, Andre; Bolch, Wesley E.

    2011-03-15

    Purpose: To develop a computed tomography (CT) organ dose estimation method designed to readily provide organ doses in a reference adult male and female for different scan ranges to investigate the degree to which existing commercial programs can reasonably match organ doses defined in these more anatomically realistic adult hybrid phantomsMethods: The x-ray fan beam in the SOMATOM Sensation 16 multidetector CT scanner was simulated within the Monte Carlo radiation transport code MCNPX2.6. The simulated CT scanner model was validated through comparison with experimentally measured lateral free-in-air dose profiles and computed tomography dose index (CTDI) values. The reference adult male and female hybrid phantoms were coupled with the established CT scanner model following arm removal to simulate clinical head and other body region scans. A set of organ dose matrices were calculated for a series of consecutive axial scans ranging from the top of the head to the bottom of the phantoms with a beam thickness of 10 mm and the tube potentials of 80, 100, and 120 kVp. The organ doses for head, chest, and abdomen/pelvis examinations were calculated based on the organ dose matrices and compared to those obtained from two commercial programs, CT-EXPO and CTDOSIMETRY. Organ dose calculations were repeated for an adult stylized phantom by using the same simulation method used for the adult hybrid phantom. Results: Comparisons of both lateral free-in-air dose profiles and CTDI values through experimental measurement with the Monte Carlo simulations showed good agreement to within 9%. Organ doses for head, chest, and abdomen/pelvis scans reported in the commercial programs exceeded those from the Monte Carlo calculations in both the hybrid and stylized phantoms in this study, sometimes by orders of magnitude. Conclusions: The organ dose estimation method and dose matrices established in this study readily provides organ doses for a reference adult male and female for different

  15. Organ doses for reference adult male and female undergoing computed tomography estimated by Monte Carlo simulations

    PubMed Central

    Lee, Choonsik; Kim, Kwang Pyo; Long, Daniel; Fisher, Ryan; Tien, Chris; Simon, Steven L.; Bouville, Andre; Bolch, Wesley E.

    2011-01-01

    Purpose: To develop a computed tomography (CT) organ dose estimation method designed to readily provide organ doses in a reference adult male and female for different scan ranges to investigate the degree to which existing commercial programs can reasonably match organ doses defined in these more anatomically realistic adult hybrid phantoms Methods: The x-ray fan beam in the SOMATOM Sensation 16 multidetector CT scanner was simulated within the Monte Carlo radiation transport code MCNPX2.6. The simulated CT scanner model was validated through comparison with experimentally measured lateral free-in-air dose profiles and computed tomography dose index (CTDI) values. The reference adult male and female hybrid phantoms were coupled with the established CT scanner model following arm removal to simulate clinical head and other body region scans. A set of organ dose matrices were calculated for a series of consecutive axial scans ranging from the top of the head to the bottom of the phantoms with a beam thickness of 10 mm and the tube potentials of 80, 100, and 120 kVp. The organ doses for head, chest, and abdomen∕pelvis examinations were calculated based on the organ dose matrices and compared to those obtained from two commercial programs, CT-EXPO and CTDOSIMETRY. Organ dose calculations were repeated for an adult stylized phantom by using the same simulation method used for the adult hybrid phantom. Results: Comparisons of both lateral free-in-air dose profiles and CTDI values through experimental measurement with the Monte Carlo simulations showed good agreement to within 9%. Organ doses for head, chest, and abdomen∕pelvis scans reported in the commercial programs exceeded those from the Monte Carlo calculations in both the hybrid and stylized phantoms in this study, sometimes by orders of magnitude. Conclusions: The organ dose estimation method and dose matrices established in this study readily provides organ doses for a reference adult male and female for

  16. Imaging the tympanic membrane oscillation ex vivo with Doppler optical coherence tomography during simulated Eustachian catarrh

    NASA Astrophysics Data System (ADS)

    Kirsten, Lars; Burkhardt, Anke; Golde, Jonas; Walther, Julia; Stoppe, Thomas; Bornitz, Matthias; Kemper, Max; Zahnert, Thomas; Koch, Edmund

    2015-07-01

    Recently, optical coherence tomography (OCT) was utilized in multiple studies for structural and functional imaging of the middle ear and the tympanic membrane. Since Doppler OCT allows both, the spatially resolved measurement of the tympanic membrane oscillation and high-resolution imaging, it is regarded as a promising tool for future in vivo applications. In this study, Doppler OCT is utilized for the visualization of the tympanic membrane oscillation in temporal bones with simulated Eustachian catarrh, which was realized by generating a depression in the tympanic cavity. The transfer function, meaning the oscillation amplitude normalized to the applied sound pressure, is measured frequency resolved in the range from 0.5 kHz to 6 kHz and with a lateral spatial resolution of 0.4 mm. Typical oscillation patterns could be observed in case of ambient pressure in the tympanic cavity. Under depression the characteristic oscillation patterns were observed with widely congruent appearance but at higher frequencies.

  17. 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.

  18. Noninvasive imaging of hemoglobin concentration and oxygen saturation for detection of osteoarthritis in the finger joints using multispectral three-dimensional quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Sun, Yao; Sobel, Eric; Jiang, Huabei

    2013-05-01

    We present quantitative imaging of hemoglobin concentration and oxygen saturation in in vivo finger joints and evaluate the feasibility of detecting osteoarthritis (OA) in the hand using three-dimensional (3D) multispectral quantitative photoacoustic tomography (3D qPAT). The results show that both the anatomical structures and quantitative chromophore concentrations (oxy-hemoglobin and deoxy-hemoglobin) of different joint tissues (hard phalanges and soft cartilage/synovial fluid between phalanges) can be imaged in vivo with the multispectral 3D qPAT. Enhanced hemoglobin concentrations and dropped oxygen saturations in osteoarthritic phalanges and soft joint tissues in joint cavities have been observed. This study indicates that the multispectral 3D qPAT is a promising approach to detect the angiogenesis and hypoxia associated with OA disease and a potential clinical tool for early OA detection in the finger joints.

  19. Rapid quantitative pharmacodynamic imaging by a novel method: theory, simulation testing and proof of principle.

    PubMed

    Black, Kevin J; Koller, Jonathan M; Miller, Brad D

    2013-01-01

    Pharmacological challenge imaging has mapped, but rarely quantified, the sensitivity of a biological system to a given drug. We describe a novel method called rapid quantitative pharmacodynamic imaging. This method combines pharmacokinetic-pharmacodynamic modeling, repeated small doses of a challenge drug over a short time scale, and functional imaging to rapidly provide quantitative estimates of drug sensitivity including EC 50 (the concentration of drug that produces half the maximum possible effect). We first test the method with simulated data, assuming a typical sigmoidal dose-response curve and assuming imperfect imaging that includes artifactual baseline signal drift and random error. With these few assumptions, rapid quantitative pharmacodynamic imaging reliably estimates EC 50 from the simulated data, except when noise overwhelms the drug effect or when the effect occurs only at high doses. In preliminary fMRI studies of primate brain using a dopamine agonist, the observed noise level is modest compared with observed drug effects, and a quantitative EC 50 can be obtained from some regional time-signal curves. Taken together, these results suggest that research and clinical applications for rapid quantitative pharmacodynamic imaging are realistic. PMID:23940831

  20. Computed tomography with a low-intensity proton flux: results of a Monte Carlo simulation study

    NASA Astrophysics Data System (ADS)

    Schulte, Reinhard W.; Klock, Margio C. L.; Bashkirov, Vladimir; Evseev, Ivan G.; de Assis, Joaquim T.; Yevseyeva, Olga; Lopes, Ricardo T.; Li, Tianfang; Williams, David C.; Wroe, Andrew J.; Schelin, Hugo R.

    2004-10-01

    Conformal proton radiation therapy requires accurate prediction of the Bragg peak position. This problem may be solved by using protons rather than conventional x-rays to determine the relative electron density distribution via proton computed tomography (proton CT). However, proton CT has its own limitations, which need to be carefully studied before this technique can be introduced into routine clinical practice. In this work, we have used analytical relationships as well as the Monte Carlo simulation tool GEANT4 to study the principal resolution limits of proton CT. The GEANT4 simulations were validated by comparing them to predictions of the Bethe Bloch theory and Tschalar's theory of energy loss straggling, and were found to be in good agreement. The relationship between phantom thickness, initial energy, and the relative electron density uncertainty was systematically investigated to estimate the number of protons and dose needed to obtain a given density resolution. The predictions of this study were verified by simulating the performance of a hypothetical proton CT scanner when imaging a cylindrical water phantom with embedded density inhomogeneities. We show that a reasonable density resolution can be achieved with a relatively small number of protons, thus providing a possible dose advantage over x-ray CT.

  1. Hybrid simulation of scatter intensity in industrial cone-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Thierry, R.; Miceli, A.; Hofmann, J.; Flisch, A.; Sennhauser, U.

    2009-01-01

    A cone-beam computed tomography (CT) system using a 450 kV X-ray tube has been developed to challenge the three-dimensional imaging of parts of the automotive industry in short acquisition time. Because the probability of detecting scattered photons is high regarding the energy range and the area of detection, a scattering correction becomes mandatory for generating reliable images with enhanced contrast detectability. In this paper, we present a hybrid simulator for the fast and accurate calculation of the scattering intensity distribution. The full acquisition chain, from the generation of a polyenergetic photon beam, its interaction with the scanned object and the energy deposit in the detector is simulated. Object phantoms can be spatially described in form of voxels, mathematical primitives or CAD models. Uncollided radiation is treated with a ray-tracing method and scattered radiation is split into single and multiple scattering. The single scattering is calculated with a deterministic approach accelerated with a forced detection method. The residual noisy signal is subsequently deconvoluted with the iterative Richardson-Lucy method. Finally the multiple scattering is addressed with a coarse Monte Carlo (MC) simulation. The proposed hybrid method has been validated on aluminium phantoms with varying size and object-to-detector distance, and found in good agreement with the MC code Geant4. The acceleration achieved by the hybrid method over the standard MC on a single projection is approximately of three orders of magnitude.

  2. The use of isodose levels to interpret radiation induced lung injury: a quantitative analysis of computed tomography changes

    PubMed Central

    Knoll, Miriam A.; Sheu, Ren Dih; Knoll, Abraham D.; Kerns, Sarah L.; Lo, Yeh-Chi; Rosenzweig, Kenneth E.

    2016-01-01

    Background Patients treated with stereotactic body radiation therapy (SBRT) for lung cancer are often found to have radiation-induced lung injury (RILI) surrounding the treated tumor. We investigated whether treatment isodose levels could predict RILI. Methods Thirty-seven lung lesions in 32 patients were treated with SBRT and received post-treatment follow up (FU) computed tomography (CT). Each CT was fused with the original simulation CT and treatment isodose levels were overlaid. The RILI surrounding the treated lesion was contoured. The RILI extension index [fibrosis extension index (FEI)] was defined as the volume of RILI extending outside a given isodose level relative to the total volume of RILI and was expressed as a percentage. Results Univariate analysis revealed that the planning target volume (PTV) was positively correlated with RILI volume at FU: correlation coefficient (CC) =0.628 and P<0.0001 at 1st FU; CE =0.401 and P=0.021 at 2nd FU; CE =0.265 and P=0.306 at 3rd FU. FEI −40 Gy at 1st FU was significantly positively correlated with FEI −40 Gy at subsequent FU’s (CC =0.689 and P=6.5×10−5 comparing 1st and 2nd FU; 0.901 and P=0.020 comparing 2nd and 3rd FU. Ninety-six percent of the RILI was found within the 20 Gy isodose line. Sixty-five percent of patients were found to have a decrease in RILI on the second 2nd CT. Conclusions We have shown that RILI evolves over time and 1st CT correlates well with subsequent CTs. Ninety-six percent of the RILI can be found to occur within the 20 Gy isodose lines, which may prove beneficial to radiologists attempting to distinguish recurrence vs. RILI. PMID:26981453

  3. Quantitative analysis of doped/undoped ZnO nanomaterials using laser assisted atom probe tomography: Influence of the analysis parameters

    NASA Astrophysics Data System (ADS)

    Amirifar, Nooshin; Lardé, Rodrigue; Talbot, Etienne; Pareige, Philippe; Rigutti, Lorenzo; Mancini, Lorenzo; Houard, Jonathan; Castro, Celia; Sallet, Vincent; Zehani, Emir; Hassani, Said; Sartel, Corine; Ziani, Ahmed; Portier, Xavier

    2015-12-01

    In the last decade, atom probe tomography has become a powerful tool to investigate semiconductor and insulator nanomaterials in microelectronics, spintronics, and optoelectronics. In this paper, we report an investigation of zinc oxide nanostructures using atom probe tomography. We observed that the chemical composition of zinc oxide is strongly dependent on the analysis parameters used for atom probe experiments. It was observed that at high laser pulse energies, the electric field at the specimen surface is strongly dependent on the crystallographic directions. This dependence leads to an inhomogeneous field evaporation of the surface atoms, resulting in unreliable measurements. We show that the laser pulse energy has to be well tuned to obtain reliable quantitative chemical composition measurements of undoped and doped ZnO nanomaterials.

  4. Quantitative analysis of doped/undoped ZnO nanomaterials using laser assisted atom probe tomography: Influence of the analysis parameters

    SciTech Connect

    Amirifar, Nooshin; Lardé, Rodrigue Talbot, Etienne; Pareige, Philippe; Rigutti, Lorenzo; Mancini, Lorenzo; Houard, Jonathan; Castro, Celia; Sallet, Vincent; Zehani, Emir; Hassani, Said; Sartel, Corine; Ziani, Ahmed; Portier, Xavier

    2015-12-07

    In the last decade, atom probe tomography has become a powerful tool to investigate semiconductor and insulator nanomaterials in microelectronics, spintronics, and optoelectronics. In this paper, we report an investigation of zinc oxide nanostructures using atom probe tomography. We observed that the chemical composition of zinc oxide is strongly dependent on the analysis parameters used for atom probe experiments. It was observed that at high laser pulse energies, the electric field at the specimen surface is strongly dependent on the crystallographic directions. This dependence leads to an inhomogeneous field evaporation of the surface atoms, resulting in unreliable measurements. We show that the laser pulse energy has to be well tuned to obtain reliable quantitative chemical composition measurements of undoped and doped ZnO nanomaterials.

  5. Low resolution brain electromagnetic tomography in a realistic geometry head model: a simulation study

    NASA Astrophysics Data System (ADS)

    Ding, Lei; Lai, Yuan; He, Bin

    2005-01-01

    It is of importance to localize neural sources from scalp recorded EEG. Low resolution brain electromagnetic tomography (LORETA) has received considerable attention for localizing brain electrical sources. However, most such efforts have used spherical head models in representing the head volume conductor. Investigation of the performance of LORETA in a realistic geometry head model, as compared with the spherical model, will provide useful information guiding interpretation of data obtained by using the spherical head model. The performance of LORETA was evaluated by means of computer simulations. The boundary element method was used to solve the forward problem. A three-shell realistic geometry (RG) head model was constructed from MRI scans of a human subject. Dipole source configurations of a single dipole located at different regions of the brain with varying depth were used to assess the performance of LORETA in different regions of the brain. A three-sphere head model was also used to approximate the RG head model, and similar simulations performed, and results compared with the RG-LORETA with reference to the locations of the simulated sources. Multi-source localizations were discussed and examples given in the RG head model. Localization errors employing the spherical LORETA, with reference to the source locations within the realistic geometry head, were about 20-30 mm, for four brain regions evaluated: frontal, parietal, temporal and occipital regions. Localization errors employing the RG head model were about 10 mm over the same four brain regions. The present simulation results suggest that the use of the RG head model reduces the localization error of LORETA, and that the RG head model based LORETA is desirable if high localization accuracy is needed.

  6. Fine grid computer simulation of QRS-T and criteria for the quantitation of regional ischemia.

    PubMed

    Selvester, R H; Solomon, J C; Tolan, G D

    1987-10-01

    A comprehensive fine grid simulation of excitation and recovery (QRS-T), realistic cardiac and torso anatomy, and electrophysiologic properties has been developed that produces a total body surface electrocardiogram (ECG) as output. The simulation leads to the specific hypothesis that additional leads on the upper and lower torso, and on the back, are required to optimize the quantitation and localization of regional ischemia and infarction. Criteria in the STT portion of the ECG for quantitating the severity of the ischemia were developed and presented. The combination of the leads in which the STT changes occur and the severity of the STT change provide a testable set of hypotheses for predicting the severity of ischemia, the probable coronary perfusion bed involved, the severity of the perfusion defect, and the severity of the proximal coronary obstruction. PMID:3694084

  7. Radiation doses in cone-beam breast computed tomography: A Monte Carlo simulation study

    SciTech Connect

    Yi Ying; Lai, Chao-Jen; Han Tao; Zhong Yuncheng; Shen Youtao; Liu Xinming; Ge Shuaiping; You Zhicheng; Wang Tianpeng; Shaw, Chris C.

    2011-02-15

    Purpose: In this article, we describe a method to estimate the spatial dose variation, average dose and mean glandular dose (MGD) for a real breast using Monte Carlo simulation based on cone beam breast computed tomography (CBBCT) images. We present and discuss the dose estimation results for 19 mastectomy breast specimens, 4 homogeneous breast models, 6 ellipsoidal phantoms, and 6 cylindrical phantoms. Methods: To validate the Monte Carlo method for dose estimation in CBBCT, we compared the Monte Carlo dose estimates with the thermoluminescent dosimeter measurements at various radial positions in two polycarbonate cylinders (11- and 15-cm in diameter). Cone-beam computed tomography (CBCT) images of 19 mastectomy breast specimens, obtained with a bench-top experimental scanner, were segmented and used to construct 19 structured breast models. Monte Carlo simulation of CBBCT with these models was performed and used to estimate the point doses, average doses, and mean glandular doses for unit open air exposure at the iso-center. Mass based glandularity values were computed and used to investigate their effects on the average doses as well as the mean glandular doses. Average doses for 4 homogeneous breast models were estimated and compared to those of the corresponding structured breast models to investigate the effect of tissue structures. Average doses for ellipsoidal and cylindrical digital phantoms of identical diameter and height were also estimated for various glandularity values and compared with those for the structured breast models. Results: The absorbed dose maps for structured breast models show that doses in the glandular tissue were higher than those in the nearby adipose tissue. Estimated average doses for the homogeneous breast models were almost identical to those for the structured breast models (p=1). Normalized average doses estimated for the ellipsoidal phantoms were similar to those for the structured breast models (root mean square (rms

  8. Wolter X-Ray Microscope Computed Tomography Ray-Trace Model with Preliminary Simulation Results

    SciTech Connect

    Jackson, J A

    2006-02-27

    It is proposed to build a Wolter X-ray Microscope Computed Tomography System in order to characterize objects to sub-micrometer resolution. Wolter Optics Systems use hyperbolic, elliptical, and/or parabolic mirrors to reflect x-rays in order to focus or magnify an image. Wolter Optics have been used as telescopes and as microscopes. As microscopes they have been used for a number of purposes such as measuring emission x-rays and x-ray fluoresce of thin biological samples. Standard Computed Tomography (CT) Systems use 2D radiographic images, from a series of rotational angles, acquired by passing x-rays through an object to reconstruct a 3D image of the object. The x-ray paths in a Wolter X-ray Microscope will be considerably different than those of a standard CT system. There is little information about the 2D radiographic images that can be expected from such a system. There are questions about the quality, resolution and focusing range of an image created with such a system. It is not known whether characterization information can be obtained from these images and whether these 2D images can be reconstructed to 3D images of the object. A code has been developed to model the 2D radiographic image created by an object in a Wolter X-ray Microscope. This code simply follows the x-ray through the object and optics. There is no modeling at this point of other effects, such as scattering, reflection losses etc. Any object, of appropriate size, can be used in the model code. A series of simulations using a number of different objects was run to study the effects of the optics. The next step will be to use this model to reconstruct an object from the simulated data. Funding for the project ended before this goal could be accomplished. The following documentation includes: (1) background information on current X-ray imaging systems, (2) background on Wolter Optics, (3) description of the Wolter System being used, (4) purpose, limitations and development of the modeling

  9. Improved importance sampling for Monte Carlo simulation of time-domain optical coherence tomography.

    PubMed

    Lima, Ivan T; Kalra, Anshul; Sherif, Sherif S

    2011-01-01

    We developed an importance sampling based method that significantly speeds up the calculation of the diffusive reflectance due to ballistic and to quasi-ballistic components of photons scattered in turbid media: Class I diffusive reflectance. These components of scattered photons make up the signal in optical coherence tomography (OCT) imaging. We show that the use of this method reduces the computation time of this diffusive reflectance in time-domain OCT by up to three orders of magnitude when compared with standard Monte Carlo simulation. Our method does not produce a systematic bias in the statistical result that is typically observed in existing methods to speed up Monte Carlo simulations of light transport in tissue. This fast Monte Carlo calculation of the Class I diffusive reflectance can be used as a tool to further study the physical process governing OCT signals, e.g., obtain the statistics of the depth-scan, including the effects of multiple scattering of light, in OCT. This is an important prerequisite to future research to increase penetration depth and to improve image extraction in OCT. PMID:21559120

  10. FEM-based simulation of a fluorescence tomography experiment using anatomical MR images

    NASA Astrophysics Data System (ADS)

    Ren, Wuwei; Elmer, Andreas; Augath, Mark-Aurel; Rudin, Markus

    2016-03-01

    A hybrid system combining fluorescence molecular tomography (FMT) and magnetic resonance imaging (MRI) is attractive for preclinical imaging as it allows fusion of molecular information derived from FMT and anatomical reference data derived from MRI. We have previously developed such a system and demonstrated its performance in biological applications. For reconstruction slab geometry with homogeneous optical parameters was assumed, which led to undesirable artifacts. In order to exploit the power of the hybrid system, the use of MRI derived anatomical information, as a constraint for FMT reconstruction, appears logical. Heterogeneity of tissues and irregular surface derived from MRI can be accounted for by generating a mesh using the finite element method (FEM), and attributing optical parameters to individual mesh points. We have established a forward simulation tool based on TOAST++ to mimic an FMT experiment. MRI images were recorded on a 9.4T MR scanner using a T1-weighted pulse sequence. The voxelized dataset was processed by iso2mesh to yield a 3D-mesh. Four steps of FMT simulation were included: 1) Assignment of optical properties, 2) Specification of boundary conditions and generation of 3) excitation and 4) emission maps. FEM-derived results were compared with those obtained using the analytical solution of Green's function and with experimental data with a single fluorescent inclusion in a silicon phantom. Once, the forward modeling method is properly validated it will be used as a central element of a reconstruction algorithm for analyzing data derived from a hybrid FMT/MRI setup.

  11. Simulation of broad spectral bandwidth emitters at 1060 nm for optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Tooley, I. G.; Childs, D. T. D.; Stevens, B. J.; Groom, K. M.; Hogg, R. A.

    2016-03-01

    The simulation of broad spectral bandwidth light sources (semiconductor optical amplifiers (SOA) and superluminescent diodes (SLD)) for application in ophthalmic optical coherence tomography is reported. The device requirements and origin of key device parameters are outlined, and a range of single and double InGaAs/GaAs quantum well (QW) active elements are simulated with a view to application in different OCT embodiments. We confirm that utilising higher order optical transitions is beneficial for single QW SOAs, but may introduce deleterious spectral modulation in SLDs. We show how an addition QW may be introduced to eliminate this spectral modulation, but that this results in a reduction of the gain spectrum width. We go on to explore double QW structures where the roles of the two QWs are reversed, with the narrow QW providing long wavelength emission and gain. We show how this modification in the density of states results in a significant increase in gain-spectrum width for a given current.

  12. Quantitative agent-based firm dynamics simulation with parameters estimated by financial and transaction data analysis

    NASA Astrophysics Data System (ADS)

    Ikeda, Yuichi; Souma, Wataru; Aoyama, Hideaki; Iyetomi, Hiroshi; Fujiwara, Yoshi; Kaizoji, Taisei

    2007-03-01

    Firm dynamics on a transaction network is considered from the standpoint of econophysics, agent-based simulations, and game theory. In this model, interacting firms rationally invest in a production facility to maximize net present value. We estimate parameters used in the model through empirical analysis of financial and transaction data. We propose two different methods ( analytical method and regression method) to obtain an interaction matrix of firms. On a subset of a real transaction network, we simulate firm's revenue, cost, and fixed asset, which is the accumulated investment for the production facility. The simulation reproduces the quantitative behavior of past revenues and costs within a standard error when we use the interaction matrix estimated by the regression method, in which only transaction pairs are taken into account. Furthermore, the simulation qualitatively reproduces past data of fixed assets.

  13. Celiac plexus block: an anatomical study and simulation using computed tomography*

    PubMed Central

    Pereira, Gabriela Augusta Mateus; Lopes, Paulo Tadeu Campos; dos Santos, Ana Maria Pujol Vieira; Pozzobon, Adriane; Duarte, Rodrigo Dias; Cima, Alexandre da Silveira; Massignan, Ângela

    2014-01-01

    Objective To analyze anatomical variations associated with celiac plexus complex by means of computed tomography simulation, assessing the risk for organ injury as the transcrural technique is utilized. Materials and Methods One hundred eight transaxial computed tomography images of abdomen were analyzed. The aortic-vertebral, celiac trunk (CeT)-vertebral, CeT-aortic and celiac-aortic-vertebral topographical relationships were recorded. Two needle insertion pathways were drawn on each of the images, at right and left, 9 cm and 4.5 cm away from the midline. Transfixed vital organs and gender-related associations were recorded. Results Aortic-vertebral - 45.37% at left and 54.62% in the middle; CeT-vertebral - T12, 36.11%; T12-L1, 32.4%; L1, 27.77%; T11-T12, 2.77%; CeT-aortic - 53.7% at left and 46.3% in the middle; celiac-aortic-vertebral - L-l, 22.22%; M-m, 23.15%; L-m, 31.48%; M-l, 23.15%. Neither correspondence on the right side nor significant gender-related associations were observed. Conclusion Considering the wide range of abdominal anatomical variations and the characteristics of needle insertion pathways, celiac plexus block should not be standardized. Imaging should be performed prior to the procedure in order to reduce the risks for injuries or for negative outcomes to patients. Gender-related anatomical variations involved in celiac plexus block should be more deeply investigated, since few studies have addressed the subject. PMID:25741102

  14. Quantitative analysis of voids in percolating structures in two-dimensional N-body simulations

    NASA Technical Reports Server (NTRS)

    Harrington, Patrick M.; Melott, Adrian L.; Shandarin, Sergei F.

    1993-01-01

    We present in this paper a quantitative method for defining void size in large-scale structure based on percolation threshold density. Beginning with two-dimensional gravitational clustering simulations smoothed to the threshold of nonlinearity, we perform percolation analysis to determine the large scale structure. The resulting objective definition of voids has a natural scaling property, is topologically interesting, and can be applied immediately to redshift surveys.

  15. Treatment of advanced solid tumours with NSAIDs: Correlation of quantitative monitoring of circulating tumour cells and positron emission tomography-computed tomography imaging

    PubMed Central

    Willecke-Hochmuth, Regina; Pachmann, Katharina; Drevs, Joachim

    2016-01-01

    The detection and characterisation of tumour-derived circulating epithelial tumor cells (CETCs) or circulating tumor cells (CTCs) have been a main focus of basic oncological research over previous years. Numerous studies in the past decade have shown that CTCs are a promising tool for the estimation of the risk for metastatic relapse. The present observational study describes treatment results using tumour imaging and the quantification of CTCs. A group of 14 patients with advanced carcinomas was followed during their anticancer treatments. CTC numbers were serially detected and treatment success was estimated by positron emission tomography-computed tomography. A connection was found between tumour remission and a decreasing CTC count in 83%, a connection between stable disease and stable CTC numbers in 78% and a connection between progressive disease (PD) and an increase in CTC count in 50% of cases. In the patients with PD, an incomplete response was observed affecting the CTCs, but not the solid region of the tumour. As a result of this study, it may be concluded that patients with solid tumours benefit from serial quantification of CTCs in addition to imaging, as this combination of techniques provides a more sensitive result than imaging alone. PMID:27588120

  16. Quantitative Assessment of Optical Coherence Tomography Imaging Performance with Phantom-Based Test Methods And Computational Modeling

    NASA Astrophysics Data System (ADS)

    Agrawal, Anant

    Optical coherence tomography (OCT) is a powerful medical imaging modality that uniquely produces high-resolution cross-sectional images of tissue using low energy light. Its clinical applications and technological capabilities have grown substantially since its invention about twenty years ago, but efforts have been limited to develop tools to assess performance of OCT devices with respect to the quality and content of acquired images. Such tools are important to ensure information derived from OCT signals and images is accurate and consistent, in order to support further technology development, promote standardization, and benefit public health. The research in this dissertation investigates new physical and computational models which can provide unique insights into specific performance characteristics of OCT devices. Physical models, known as phantoms, are fabricated and evaluated in the interest of establishing standardized test methods to measure several important quantities relevant to image quality. (1) Spatial resolution is measured with a nanoparticle-embedded phantom and model eye which together yield the point spread function under conditions where OCT is commonly used. (2) A multi-layered phantom is constructed to measure the contrast transfer function along the axis of light propagation, relevant for cross-sectional imaging capabilities. (3) Existing and new methods to determine device sensitivity are examined and compared, to better understand the detection limits of OCT. A novel computational model based on the finite-difference time-domain (FDTD) method, which simulates the physics of light behavior at the sub-microscopic level within complex, heterogeneous media, is developed to probe device and tissue characteristics influencing the information content of an OCT image. This model is first tested in simple geometric configurations to understand its accuracy and limitations, then a highly realistic representation of a biological cell, the retinal

  17. Imaging hemorrhagic stroke with magnetic induction tomography: realistic simulation and evaluation.

    PubMed

    Chen, Yinan; Yan, Ming; Chen, Dayu; Hamsch, Matthias; Liu, Hui; Jin, Hua; Vauhkonen, Marko; Igney, Claudia H; Kahlert, Joachim; Wang, Yuanyuan

    2010-06-01

    Magnetic induction tomography (MIT) is a noncontact method for detecting the internal conductivity distribution of an object. This technology has the potential to be used in the biomedical area to check bio-impedance change inside the human body, for example to detect hemorrhage in the human brain. In this study the hemorrhagic stroke detectability with a 16-channel MIT system operating at 10 MHz was evaluated. Since the conductivity distribution is changed by the hemorrhagic stroke as well as the squeezed brain tissue around the stroke, deformation of the brain tissue is also considered and simulated with the help of a FEM-based linear bio-mechanical model in this paper. To simulate the raw measurement data as realistically as possible, the noise estimated from the experimental MIT system with hypothesis testing methods at 95% confidence level is added to the simulated measurements. Stroke images of 600 noisy samples for each detection assignment are reconstructed by the one-step Tikhonov-regularized inverse eddy current solution. Under the statistical framework, the detection failure is in control of a high false negative rate which represents a large artifact visualized in the reconstruction domain. The qualitative detectability of 18 detecting assignments, with three hemorrhagic positions (shallow, medial and center of the cerebrum) and two volume values (10 ml and 20 ml), overlaid by noise with three levels (standard deviation of phase change at 5 x 10(-3) degrees , 2.5 x 10(-3) degrees , 10 x 10(-3) degrees ), are investigated. These detecting assignments are compared with each other to find out which volumes of deformed spherical hemorrhagic stroke can be detected by the modeled MIT system. PMID:20453292

  18. A Simulation Framework for Quantitative Validation of Artefact Correction in Diffusion MRI.

    PubMed

    Graham, Mark S; Drobnjak, Ivana; Zhang, Hui

    2015-01-01

    In this paper we demonstrate a simulation framework that enables the direct and quantitative comparison of post-processing methods for diffusion weighted magnetic resonance (DW-MR) images. DW-MR datasets are employed in a range of techniques that enable estimates of local microstructure and global connectivity in the brain. These techniques require full alignment of images across the dataset, but this is rarely the case. Artefacts such as eddy-current (EC) distortion and motion lead to misalignment between images, which compromise the quality of the microstructural measures obtained from them. Numerous methods and software packages exist to correct these artefacts, some of which have become de-facto standards, but none have been subject to rigorous validation. The ultimate aim of these techniques is improved image alignment, yet in the literature this is assessed using either qualitative visual measures or quantitative surrogate metrics. Here we introduce a simulation framework that allows for the direct, quantitative assessment of techniques, enabling objective comparisons of existing and future methods. DW-MR datasets are generated using a process that is based on the physics of MRI acquisition, which allows for the salient features of the images and their artefacts to be reproduced. We demonstrate the application of this framework by testing one of the most commonly used methods for EC correction, registration of DWIs to b = 0, and reveal the systematic bias this introduces into corrected datasets. PMID:26221709

  19. Quantitative and rapid estimations of human sub-surface skin mass using ultra-high-resolution spectral domain optical coherence tomography.

    PubMed

    Kuo, Wen-Chuan; Kuo, Yue-Ming; Wen, Su-Ying

    2016-04-01

    Non-invasive and quantitative estimations for the delineation of sub-surface tumor margins could greatly aid in the early detection and monitoring of the morphological appearances of tumor growth, ensure complete tumor excision without the unnecessary sacrifice of healthy tissue, and facilitate post-operative follow-up for recurrence. In this study, a high-speed, non-invasive, and ultra-high-resolution spectral domain optical coherence tomography (UHR-SDOCT) imaging platform was developed for the quantitative measurement of human sub-surface skin mass. With a proposed robust, semi-automatic analysis, the system can rapidly quantify lesion area and shape regularity by an en-face-oriented algorithm. Various sizes of nylon sutures embedded in pork skin were used first as a phantom to verify the accuracy of our algorithm, and then in vivo, feasibility was proven using benign human angiomas and pigmented nevi. Clinically, this is the first step towards an automated skin lesion measurement system. In vivo optical coherence tomography (OCT) image of angioma (A). Thin red arrows point to a blood vessel (BV). PMID:25755214

  20. Semiautomated analysis of optical coherence tomography crystalline lens images under simulated accommodation

    NASA Astrophysics Data System (ADS)

    Kim, Eon; Ehrmann, Klaus; Uhlhorn, Stephen; Borja, David; Arrieta-Quintero, Esdras; Parel, Jean-Marie

    2011-05-01

    Presbyopia is an age related, gradual loss of accommodation, mainly due to changes in the crystalline lens. As part of research efforts to understand and cure this condition, ex vivo, cross-sectional optical coherence tomography images of crystalline lenses were obtained by using the Ex-Vivo Accommodation Simulator (EVAS II) instrument and analyzed to extract their physical and optical properties. Various filters and edge detection methods were applied to isolate the edge contour. An ellipse is fitted to the lens outline to obtain central reference point for transforming the pixel data into the analysis coordinate system. This allows for the fitting of a high order equation to obtain a mathematical description of the edge contour, which obeys constraints of continuity as well as zero to infinite surface slopes from apex to equator. Geometrical parameters of the lens were determined for the lens images captured at different accommodative states. Various curve fitting functions were developed to mathematically describe the anterior and posterior surfaces of the lens. Their differences were evaluated and their suitability for extracting optical performance of the lens was assessed. The robustness of these algorithms was tested by analyzing the same images repeated times.

  1. Microwave tomography of extremities: 2. Functional fused imaging of flow reduction and simulated compartment syndrome

    NASA Astrophysics Data System (ADS)

    Semenov, Serguei; Kellam, James; Nair, Bindu; Williams, Thomas; Quinn, Michael; Sizov, Yuri; Nazarov, Alexei; Pavlovsky, Andrey

    2011-04-01

    Medical imaging has recently expanded into the dual- or multi-modality fusion of anatomical and functional imaging modalities. This significantly improves the diagnostic power while simultaneously increasing the cost of already expensive medical devices or investigations and decreasing their mobility. We are introducing a novel imaging concept of four-dimensional (4D) microwave tomographic (MWT) functional imaging: three dimensional (3D) in the spatial domain plus one dimensional (1D) in the time, functional dynamic domain. Instead of a fusion of images obtained by different imaging modalities, 4D MWT fuses absolute anatomical images with dynamic, differential images of the same imaging technology. The approach was successively validated in animal experiments with short-term arterial flow reduction and a simulated compartment syndrome in an initial simplified experimental setting using a dedicated MWT system. The presented fused images are not perfect as MWT is a novel imaging modality at its early stage of the development and ways of reading reconstructed MWT images need to be further studied and understood. However, the reconstructed fused images present clear evidence that microwave tomography is an emerging imaging modality with great potentials for functional imaging.

  2. Monte Carlo simulation of an x-ray luminescence optical tomography scanner prototype

    SciTech Connect

    Rosas-González, S. E-mail: arnulfo@fisica.unam.mx; Martínez-Dávalos, A. E-mail: arnulfo@fisica.unam.mx; Rodríguez-Villafuerte, M. E-mail: arnulfo@fisica.unam.mx; Murrieta-Rodríguez, T. E-mail: arnulfo@fisica.unam.mx

    2014-11-07

    In this work we report the calculation of the deposited energy distribution produced by an x-ray luminescence optical tomography (XLOT) system in a phantom containing different concentrations of Gd{sub 2}O{sub 2}S:Eu nanoparticles. The calculations were performed via Monte Carlo simulation considering spectra from a W target x-ray tube operating between 30 and 90 kVp, with 1.0 mm Al added filtration. CT and XLOT tomographic images were reconstructed from the same data. The results show that XLOT has better detectability than CT alone, that the dose scales linearly with kVp for a fixed concentration of Gd{sub 2}O{sub 2}S:Eu and air-kerma rate, the scattered radiation contribution to the total dose and signal is about 20% and that the dose ratio for a 3 mm diameter insert containing 10 mg/ml Gd{sub 2}O{sub 2}S embedded in a 30 mm diameter water phantom is 6:1. This ratio drops to less than 2:1 for a 1 mg/ml concentration. Finally we show that the method of conjugate images can be used to correct for artifacts due to attenuation effects in XLOT images.

  3. Microwave tomography of extremities: 2) Functional fused imaging of flow reduction and simulated compartment syndrome

    PubMed Central

    Semenov, Serguei; Kellam, James; Nair, Bindu; Williams, Thomas; Quinn, Michael; Sizov, Yuri; Nazarov, Alexei; Pavlovsky, Andrey

    2011-01-01

    Medical imaging has recently expanded into the dual- or multi-modality fusion of anatomical and functional imaging modalities. This significantly improves the diagnostic power while simultaneously increasing the cost of an already expensive medical devices or investigations and decreasing their mobility. We are introducing a novel imaging concept of four-dimensional (4D) Microwave Tomographic (MWT) functional imaging: three-dimensional (3D) in spatial domain plus one-dimension (1D) in the time, functional dynamic domain. Instead of a fusion of images obtained by different imaging modalities, 4D MWT fuses absolute anatomical images with dynamic, differential images of the same imaging technology. The approach was successively validated in animal experiments with short term arterial flow reduction and a simulated compartment syndrome in an initial simplified experimental setting using dedicated microwave tomographic system. The presented fused images are not perfect as MWT is a novel imaging modality at its early stage of the development and ways of reading of reconstructed MWT images need to be further studied and understood. However, the reconstructed fused images present clear evidence that microwave tomography is an emerging imaging modality with great potentials for functional imaging. PMID:21364266

  4. Microwave tomography of extremities: 2. Functional fused imaging of flow reduction and simulated compartment syndrome.

    PubMed

    Semenov, Serguei; Kellam, James; Nair, Bindu; Williams, Thomas; Quinn, Michael; Sizov, Yuri; Nazarov, Alexei; Pavlovsky, Andrey

    2011-04-01

    Medical imaging has recently expanded into the dual- or multi-modality fusion of anatomical and functional imaging modalities. This significantly improves the diagnostic power while simultaneously increasing the cost of already expensive medical devices or investigations and decreasing their mobility. We are introducing a novel imaging concept of four-dimensional (4D) microwave tomographic (MWT) functional imaging: three dimensional (3D) in the spatial domain plus one dimensional (1D) in the time, functional dynamic domain. Instead of a fusion of images obtained by different imaging modalities, 4D MWT fuses absolute anatomical images with dynamic, differential images of the same imaging technology. The approach was successively validated in animal experiments with short-term arterial flow reduction and a simulated compartment syndrome in an initial simplified experimental setting using a dedicated MWT system. The presented fused images are not perfect as MWT is a novel imaging modality at its early stage of the development and ways of reading reconstructed MWT images need to be further studied and understood. However, the reconstructed fused images present clear evidence that microwave tomography is an emerging imaging modality with great potentials for functional imaging. PMID:21364266

  5. Robust tomography of microwave resonator arrays for quantum simulation with light

    NASA Astrophysics Data System (ADS)

    Lachapelle, Aman; Owens, John C.; Ma, Ruichao; Simon, Jonathan; Schuster, David

    We are interested in using a bottom-up approach to create topologically non-trivial states of light via Hamiltonian engineering in coupled microwave cavities. Characterization and reduction of disorder is paramount to realizing and studying idealized many-body Hamiltonians. Our tight-binding lattices are made of arrays of evanescently coupled three-dimensional microwave resonators. From the spectroscopic response measured at specific lattice sites, we develop methods to fully map out the underlying tight-binding Hamiltonian, including onsite energies, nearest-neighbor couplings and the local dissipation on all sites. We show that for a 1D system, one reflection measurement off of the site at the end of the chain is sufficient, while for 2D only measurements along one edge of the system is sufficient for complete tomography of the lattice Hamiltonian. The transmission between neighboring sites also reveals the phase of the tunnel coupling, thereby allow direct measurement of the flux in lattices with time-reversal breaking synthetic gauge fields. These methods can be readily applied to many other physical systems for the characterization of quantum processes or the validation of quantum simulators.

  6. EVALUATION OF SIMULATED BONE LESION IN THE HEAD OF THE MANDIBLE BY USING MULTISLICE COMPUTED TOMOGRAPHY

    PubMed Central

    Utumi, Estevam Rubens; Perrella, Andréia; Albuquerque, Marco Antonio Portela; Adde, Carlos Alberto; Rocha, Rodney Garcia; Cavalcanti, Marcelo Gusmão Paraíso

    2009-01-01

    Conventional radiography has shown limitation in acquiring image of the ATM region, thus, computed tomography (CT) scanning has been the best option to the present date for diagnosis, surgical planning and treatment of bone lesions, owing to its specific properties. Objective: The aim of the study was to evaluate images of simulated bone lesions at the head of the mandible by multislice CT. Material and methods: Spherical lesions were made with dental spherical drills (sizes 1, 3, and 6) and were evaluated by using multislice CT (64 rows), by two observers in two different occasions, deploying two protocols: axial, coronal, and sagittal images, and parasagittal images for pole visualization (anterior, lateral, posterior, medial and superior). Acquired images were then compared with those lesions in the dry mandible (gold standard) to evaluate the specificity and sensibility of both protocols. Statistical methods included: Kappa statistics, validity test and chi-square test. Results demonstrated the advantage of associating axial, coronal, and sagittal slices with parasagittal slices for lesion detection at the head of the mandible. Results: There was no statistically significant difference between the types of protocols regarding a particular localization of lesions at the poles. Conclusions: Protocols for the assessment of the head of the mandible were established to improve the visualization of alterations of each of the poles of the mandible's head. The anterior and posterior poles were better visualized in lateral-medial planes while lateral, medial and superior poles were better visualized in the anterior-posterior plane. PMID:19936536

  7. Conceptual detector development and Monte Carlo simulation of a novel 3D breast computed tomography system

    NASA Astrophysics Data System (ADS)

    Ziegle, Jens; Müller, Bernhard H.; Neumann, Bernd; Hoeschen, Christoph

    2016-03-01

    A new 3D breast computed tomography (CT) system is under development enabling imaging of microcalcifications in a fully uncompressed breast including posterior chest wall tissue. The system setup uses a steered electron beam impinging on small tungsten targets surrounding the breast to emit X-rays. A realization of the corresponding detector concept is presented in this work and it is modeled through Monte Carlo simulations in order to quantify first characteristics of transmission and secondary photons. The modeled system comprises a vertical alignment of linear detectors hold by a case that also hosts the breast. Detectors are separated by gaps to allow the passage of X-rays towards the breast volume. The detectors located directly on the opposite side of the gaps detect incident X-rays. Mechanically moving parts in an imaging system increase the duration of image acquisition and thus can cause motion artifacts. So, a major advantage of the presented system design is the combination of the fixed detectors and the fast steering electron beam which enable a greatly reduced scan time. Thereby potential motion artifacts are reduced so that the visualization of small structures such as microcalcifications is improved. The result of the simulation of a single projection shows high attenuation by parts of the detector electronics causing low count levels at the opposing detectors which would require a flat field correction, but it also shows a secondary to transmission ratio of all counted X-rays of less than 1 percent. Additionally, a single slice with details of various sizes was reconstructed using filtered backprojection. The smallest detail which was still visible in the reconstructed image has a size of 0.2mm.

  8. Business Scenario Evaluation Method Using Monte Carlo Simulation on Qualitative and Quantitative Hybrid Model

    NASA Astrophysics Data System (ADS)

    Samejima, Masaki; Akiyoshi, Masanori; Mitsukuni, Koshichiro; Komoda, Norihisa

    We propose a business scenario evaluation method using qualitative and quantitative hybrid model. In order to evaluate business factors with qualitative causal relations, we introduce statistical values based on propagation and combination of effects of business factors by Monte Carlo simulation. In propagating an effect, we divide a range of each factor by landmarks and decide an effect to a destination node based on the divided ranges. In combining effects, we decide an effect of each arc using contribution degree and sum all effects. Through applied results to practical models, it is confirmed that there are no differences between results obtained by quantitative relations and results obtained by the proposed method at the risk rate of 5%.

  9. Tomographic reconstruction of melanin structures of optical coherence tomography via the finite-difference time-domain simulation

    NASA Astrophysics Data System (ADS)

    Huang, Shi-Hao; Wang, Shiang-Jiu; Tseng, Snow H.

    2015-03-01

    Optical coherence tomography (OCT) provides high resolution, cross-sectional image of internal microstructure of biological tissue. We use the Finite-Difference Time-Domain method (FDTD) to analyze the data acquired by OCT, which can help us reconstruct the refractive index of the biological tissue. We calculate the refractive index tomography and try to match the simulation with the data acquired by OCT. Specifically, we try to reconstruct the structure of melanin, which has complex refractive indices and is the key component of human pigment system. The results indicate that better reconstruction can be achieved for homogenous sample, whereas the reconstruction is degraded for samples with fine structure or with complex interface. Simulation reconstruction shows structures of the Melanin that may be useful for biomedical optics applications.

  10. Biomedical implications of dental-ceramic defects investigated by numerical simulation, radiographic, microcomputer tomography, and time-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Sinescu, Cosmin; Negrutiu, Meda Lavinia; Ionita, Ciprian; Marsavina, Liviu; Negru, Radu; Topala, Florin; Petrescu, Emanuela; Rominu, Roxana; Fabriky, Mihai; Bradu, Adrian; Rominu, Mihai; Podoleanu, Adrian Gh.

    2011-10-01

    Imagistic investigation of the metal-ceramic crowns and fixed partial prostheses represent a very important issue in nowadays dentistry. At this time, in dental office, it is difficult or even impossible to evaluate a metal ceramic crown or bridge before setting it in the oral cavity. The possibilities of ceramic fractures are due to small fracture lines or material defects inside the esthetic layers. Material and methods: In this study 25 metal ceramic crowns and fixed partial prostheses were investigated by radiographic method (Rx), micro computer tomography (MicroCT) and optical coherence tomography (OCT) working in Time Domain, at 1300 nm. The OCT system contains two interferometers and one scanner. For each incident analysis a stuck made of 100 slices was obtain. These slices were used in order to obtain a 3D model of the ceramic interface. After detecting the presence and the positions of the ceramic defects the numerical simulation method was used to estimate the biomechanical effect of the masticatory forces on fractures propagations in ceramic materials. Results: For all the dental ceramic defects numerical simulation analysis was performed. The simulation of crack propagation shows that the crack could initiate from the upper, lower or both parts of the defect and propagates through the ceramic material where tensile stress field is present. RX and MicroCT are very powerful instruments that provide a good characterization of the dental construct. It is important to observe the reflections due to the metal infrastructure that could affect the evaluation of the metal ceramic crowns and bridges. The OCT investigations could complete the imagistic evaluation of the dental construct by offering important information when it is need it.

  11. Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs

    PubMed Central

    Sonnaert, Maarten; Kerckhofs, Greet; Papantoniou, Ioannis; Van Vlierberghe, Sandra; Boterberg, Veerle; Dubruel, Peter; Luyten, Frank P.; Schrooten, Jan; Geris, Liesbet

    2015-01-01

    To progress the fields of tissue engineering (TE) and regenerative medicine, development of quantitative methods for non-invasive three dimensional characterization of engineered constructs (i.e. cells/tissue combined with scaffolds) becomes essential. In this study, we have defined the most optimal staining conditions for contrast-enhanced nanofocus computed tomography for three dimensional visualization and quantitative analysis of in vitro engineered neo-tissue (i.e. extracellular matrix containing cells) in perfusion bioreactor-developed Ti6Al4V constructs. A fractional factorial ‘design of experiments’ approach was used to elucidate the influence of the staining time and concentration of two contrast agents (Hexabrix and phosphotungstic acid) and the neo-tissue volume on the image contrast and dataset quality. Additionally, the neo-tissue shrinkage that was induced by phosphotungstic acid staining was quantified to determine the operating window within which this contrast agent can be accurately applied. For Hexabrix the staining concentration was the main parameter influencing image contrast and dataset quality. Using phosphotungstic acid the staining concentration had a significant influence on the image contrast while both staining concentration and neo-tissue volume had an influence on the dataset quality. The use of high concentrations of phosphotungstic acid did however introduce significant shrinkage of the neo-tissue indicating that, despite sub-optimal image contrast, low concentrations of this staining agent should be used to enable quantitative analysis. To conclude, design of experiments allowed us to define the most optimal staining conditions for contrast-enhanced nanofocus computed tomography to be used as a routine screening tool of neo-tissue formation in Ti6Al4V constructs, transforming it into a robust three dimensional quality control methodology. PMID:26076131

  12. Monte Carlo simulation of simultaneous radiation detection in the hybrid tomography system ClearPET-XPAD3/CT

    NASA Astrophysics Data System (ADS)

    Dávila, H. Olaya; Sevilla, A. C.; Castro, H. F.; Martínez, S. A.

    2016-07-01

    Using the Geant4 based simulation framework SciFW1, a detailed simulation was performed for a detector array in the hybrid tomography prototype for small animals called ClearPET / XPAD, which was built in the Centre de Physique des Particules de Marseille. The detector system consists of an array of phoswich scintillation detectors: LSO (Lutetium Oxy-ortosilicate doped with cerium Lu2SiO5:Ce) and LuYAP (Lutetium Ortoaluminate of Yttrium doped with cerium Lu0.7Y0.3AlO3:Ce) for Positron Emission Tomography (PET) and hybrid pixel detector XPAD for Computed Tomography (CT). Simultaneous acquisition of deposited energy and the corresponding time - position for each recorded event were analyzed, independently, for both detectors. interference between detection modules for PET and CT. Information about amount of radiation reaching each phoswich crystal and XPAD detector using a phantom in order to study the effectiveness by radiation attenuation and influence the positioning of the radioactive source 22Na was obtained. The simulation proposed will improve distribution of detectors rings and interference values will be taken into account in the new versions of detectors.

  13. A computer simulation study of soft tissue characterization using low-frequency ultrasonic tomography.

    PubMed

    Goncharsky, A V; Romanov, S Y; Seryozhnikov, S Y

    2016-04-01

    We investigate the potential of using ultrasonic diffraction tomography technique for characterization of biological tissues. Unlike most of other studies where ultrasonic tomography operates at frequencies higher than 1 MHz, low-frequency tomography uses lower frequencies on the order of 0.3-0.5 MHz. Such a choice is due to low attenuation at these frequencies, resulting in higher precision of input data. In this paper we explore transmission and reflection schemes for both 2D (layer-by-layer) and 3D tomography. We treat inverse tomography problems as coefficient inverse problems for the wave equation. The time-domain algorithms employed for solving the inverse problem of low-frequency tomography focus on the use of GPU clusters. The results obtained show that a spatial resolution of about 2-3mm can be achieved when operating at the wavelength of about 5mm even using a stationary 3D scheme with a few fixed sources and no rotating elements. The study primarily focuses on determining the performance limits of ultrasonic tomography devices currently designed for breast cancer diagnosis. PMID:26836291

  14. Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations.

    PubMed

    Rizzetto, Simone; Priami, Corrado; Csikász-Nagy, Attila

    2015-10-01

    Despite recent progress in proteomics most protein complexes are still unknown. Identification of these complexes will help us understand cellular regulatory mechanisms and support development of new drugs. Therefore it is really important to establish detailed information about the composition and the abundance of protein complexes but existing algorithms can only give qualitative predictions. Herein, we propose a new approach based on stochastic simulations of protein complex formation that integrates multi-source data--such as protein abundances, domain-domain interactions and functional annotations--to predict alternative forms of protein complexes together with their abundances. This method, called SiComPre (Simulation based Complex Prediction), achieves better qualitative prediction of yeast and human protein complexes than existing methods and is the first to predict protein complex abundances. Furthermore, we show that SiComPre can be used to predict complexome changes upon drug treatment with the example of bortezomib. SiComPre is the first method to produce quantitative predictions on the abundance of molecular complexes while performing the best qualitative predictions. With new data on tissue specific protein complexes becoming available SiComPre will be able to predict qualitative and quantitative differences in the complexome in various tissue types and under various conditions. PMID:26492574

  15. Integrated scanning laser ophthalmoscopy and optical coherence tomography for quantitative multimodal imaging of retinal degeneration and autofluorescence

    NASA Astrophysics Data System (ADS)

    Issaei, Ali; Szczygiel, Lukasz; Hossein-Javaheri, Nima; Young, Mei; Molday, L. L.; Molday, R. S.; Sarunic, M. V.

    2011-03-01

    Scanning Laser Ophthalmoscopy (SLO) and Coherence Tomography (OCT) are complimentary retinal imaging modalities. Integration of SLO and OCT allows for both fluorescent detection and depth- resolved structural imaging of the retinal cell layers to be performed in-vivo. System customization is required to image rodents used in medical research by vision scientists. We are investigating multimodal SLO/OCT imaging of a rodent model of Stargardt's Macular Dystrophy which is characterized by retinal degeneration and accumulation of toxic autofluorescent lipofuscin deposits. Our new findings demonstrate the ability to track fundus autofluorescence and retinal degeneration concurrently.

  16. Quantitative comparison of contrast and imaging depth of ultrahigh-resolution optical coherence tomography images in 800–1700 nm wavelength region

    PubMed Central

    Ishida, Shutaro; Nishizawa, Norihiko

    2012-01-01

    We investigated the wavelength dependence of imaging depth and clearness of structure in ultrahigh-resolution optical coherence tomography over a wide wavelength range. We quantitatively compared the optical properties of samples using supercontinuum sources at five wavelengths, 800 nm, 1060 nm, 1300 nm, 1550 nm, and 1700 nm, with the same system architecture. For samples of industrially used homogeneous materials with low water absorption, the attenuation coefficients of the samples were fitted using Rayleigh scattering theory. We confirmed that the systems with the longer-wavelength sources had lower scattering coefficients and less dependence on the sample materials. For a biomedical sample, we observed wavelength dependence of the attenuation coefficient, which can be explained by absorption by water and hemoglobin. PMID:22312581

  17. A method for volume determination of the orbit and its contents by high resolution axial tomography and quantitative digital image analysis.

    PubMed Central

    Cooper, W C

    1985-01-01

    The various congenital and acquired conditions which alter orbital volume are reviewed. Previous investigative work to determine orbital capacity is summarized. Since these studies were confined to postmortem evaluations, the need for a technique to measure orbital volume in the living state is presented. A method for volume determination of the orbit and its contents by high-resolution axial tomography and quantitative digital image analysis is reported. This procedure has proven to be accurate (the discrepancy between direct and computed measurements ranged from 0.2% to 4%) and reproducible (greater than 98%). The application of this method to representative clinical problems is presented and discussed. The establishment of a diagnostic system versatile enough to expand the usefulness of computerized axial tomography and polytomography should add a new dimension to ophthalmic investigation and treatment. Images FIGURE 8 FIGURE 9 FIGURE 10 A FIGURE 10 B FIGURE 11 A FIGURE 11 B FIGURE 12 FIGURE 13 FIGURE 14 FIGURE 15 FIGURE 16 FIGURE 17 FIGURE 18 FIGURE 19 FIGURE 20 FIGURE 21 FIGURE 22 FIGURE 23 FIGURE 24 FIGURE 25 FIGURE 26 A FIGURE 26 B FIGURE 27 FIGURE 28 FIGURE 29 FIGURE 30 FIGURE 31 FIGURE 32 PMID:3938582

  18. Nondestructive and quantitative characterization of TRU and LLW mixed-waste using active and passive gamma-ray spectrometry and computed tomography

    SciTech Connect

    Camp, D.C.; Martz, H.E.

    1991-11-12

    The technology being proposed by LLNL is an Active and Passive Computed Tomography (A P CT) Drum Scanner for contact-handled (CH) wastes. It combines the advantages offered by two well-developed nondestructive assay technologies: gamma-ray spectrometry and computed tomography (CT). Coupled together, these two technologies offer to nondestructively and quantitatively characterize mixed- wastes forms. Gamma-ray spectroscopy uses one or more external radiation detectors to passively and nondestructively measure the energy spectrum emitted from a closed container. From the resulting spectrum one can identify most radioactivities detected, be they transuranic isotopes, mixed-fission products, activation products or environmental radioactivities. Spectral libraries exist at LLNL for all four. Active (A) or transmission CT is a well-developed, nondestructive medical and industrial technique that uses an external-radiation beam to map regions of varying attenuation within a container. Passive (P) or emission CT is a technique mainly developed for medical application, e.g., single-photon emission CT. Nondestructive industrial uses of PCT are under development and just coming into use. This report discuses work on the A P CT Drum Scanner at LLNL.

  19. Effects of propranolol and nifedipine on exercise-induced attack in patients variant angina: assessment by exercise thallium-201 myocardial scintigraphy with quantitative rotational tomography

    SciTech Connect

    Kugiyama, K.; Yasue, H.; Horio, Y.; Morikami, Y.; Fujii, H.; Koga, Y.; Kojima, A.; Takahashi, M.

    1986-08-01

    To examine the effects of propranolol and nifedipine on exercise-induced attack in patients with variant angina, exercise /sup 201/Tl myocardial scintigraphy with quantitative analysis by emission-computed tomography was performed in 20 patients with variant angina after oral propranolol (80 mg), nifedipine (20 mg), and placebo. Exercise-induced attack occurred in 11 patients on placebo, in 14 on propranolol, and in none on nifedipine. The exercise duration was significantly shorter in those on propranolol (p less than .05), but significantly longer in patients on nifedipine (p less than .05) than in those on placebo. The peak rate-pressure product was significantly lower in patients on propranolol (p less than .01), but did not change in those on nifedipine, as compared with that in patients on placebo. The size of the perfusion defect as measured by /sup 201/Tl tomography was significantly greater in patients on propranolol (p less than .05), but significantly less in those on nifedipine (p less than .01) than in those on placebo. In conclusion, propranolol does not suppress but rather may aggravate exercise-induced attack in patients with variant angina, while nifedipine suppresses it. This unfavorable effect of propranolol on exercise-induced attack in patients with variant angina is likely to be due to a reduction of regional myocardial blood flow.

  20. Effect of nitroglycerin on coronary collateral function during exercise evaluated by quantitative analysis of thallium-201 single photon emission computed tomography

    SciTech Connect

    Aoki, M.; Sakai, K.; Koyanagi, S.; Takeshita, A.; Nakamura, M. )

    1991-05-01

    A noninfarcted, entirely collateral-dependent myocardial region provides an opportunity to assess the effect of nitroglycerin on coronary collateral function during exercise. Stress thallium-201 computed tomography was performed in seven patients with effort angina and no history of myocardial infarction, both before and after nitroglycerin (0.3 mg). All patients had single-vessel disease with total or subtotal (99% with delay) occlusion of proximal left anterior descending coronary artery and well-developed collaterals. The pressure-rate product, mean blood pressure, and heart rate at peak exercise did not differ before and after nitroglycerin. The size of the perfusion defect and the severity of ischemia during exercise estimated by quantitative analysis of thallium-201 single photon emission computed tomography were significantly less after nitroglycerin administration (extent score: 23 +/- 17 vs 7 +/- 9, p less than 0.01; severity score: 20 +/- 22 vs 3 +/- 4, p less than 0.05). The pressure-rate products at peak exercise did not differ before and after nitroglycerin, which suggested that the reduction in perfusion defect size was unlikely to be the result of decreased myocardial oxygen consumption. These results suggest that nitroglycerin improved coronary collateral function during exercise and thus prevented exercise-induced myocardial ischemia.

  1. Quantitative evaluation of ozone and selected climate parameters in a set of EMAC simulations

    NASA Astrophysics Data System (ADS)

    Righi, M.; Eyring, V.; Gottschaldt, K.-D.; Klinger, C.; Frank, F.; Jöckel, P.; Cionni, I.

    2014-10-01

    Four simulations with the ECHAM/MESSy Atmospheric Chemistry (EMAC) model have been evaluated with the Earth System Model Validation Tool (ESMValTool) to identify differences in simulated ozone and selected climate parameters that resulted from (i) different setups of the EMAC model (nudged vs. free-running) and (ii) different boundary conditions (emissions, sea surface temperatures (SSTs) and sea-ice concentrations (SICs)). To assess the relative performance of the simulations, quantitative performance metrics are calculated consistently for the climate parameters and ozone. This is important for the interpretation of the evaluation results since biases in climate can impact on biases in chemistry and vice versa. The observational datasets used for the evaluation include ozonesonde and aircraft data, meteorological reanalyses and satellite measurements. The results from a previous EMAC evaluation of a model simulation with weak nudging towards realistic meteorology in the troposphere have been compared to new simulations with different model setups and updated emission datasets in free-running timeslice and nudged Quasi Chemistry-Transport Model (QCTM) mode. The latter two configurations are particularly important for chemistry-climate projections and for the quantification of individual sources (e.g. transport sector) that lead to small chemical perturbations of the climate system, respectively. With the exception of some specific features which are detailed in this study, no large differences that could be related to the different setups of the EMAC simulations (nudged vs. free-running) were found, which offers the possibility to evaluate and improve the overall model with the help of shorter nudged simulations. The main differences between the two setups is a better representation of the tropospheric and stratospheric temperature in the nudged simulations, which also better reproduce stratospheric water vapour concentrations, due to the improved simulation of

  2. Predicting the image noise level of prospective ECG-triggered coronary computed tomography angiography: quantitative measurement of thoracic component versus body mass index.

    PubMed

    Kim, Hyeongmin; Park, Chul Hwan; Han, Kyung Hwa; Kim, Tae Hoon

    2015-12-01

    We evaluated the feasibility of using quantitatively measured thoracic components, as compared to body mass index (BMI), for predicting the image noise of coronary computed tomography angiography (CCTA). One hundred subjects (M:F = 64:36; mean age, 55 ± 8.8 years) who underwent prospective electrocardiography-gated CCTA and low-dose chest computed tomography (CT) were analyzed retrospectively. The image noise of the CCTA was determined by the standard deviation of the attenuation value in a region of interest on the aortic root level. On the low-dose chest CT, the areas of the thoracic components were measured at the aortic root level. An auto-segmentation technique with the following threshold levels was used: quantitatively measured area of total thorax [QMAtotal: -910 to 1000 Hounsfield units (HU)], lung (QMAlung: -910 to -200 HU), fat (QMAfat: -200 to 0 HU), muscle (QMAmuscle: 0-300 HU), soft tissue (fat + muscle, QMAsoft tissue: -200 to 300 HU), bone (QMAbone: 300-1000 HU) and solid tissue (fat + muscle + bone, QMAsolid tissue: -200 to 1000 HU). The relationship between image noise and variable biometric parameters including QMA was analyzed, and the linear correlation coefficients were used as indicators of the strength of association. Among the variable biometric parameters, including BMI, QMAsolid tissue showed the highest correlation coefficient with image noise in all subjects (r = 0.804), males (r = 0.716), females (r = 0.889), the overweight (r = 0.556), and the non-overweight subgroups (r = 0.783). QMAsolid tissue can be used as a potential surrogate predictor of the image noise level in low tube voltage CCTA. PMID:26507324

  3. Curved Beam Computed Tomography based Structural Rigidity Analysis of Bones with Simulated Lytic Defect: A Comparative Study with Finite Element Analysis.

    PubMed

    Oftadeh, R; Karimi, Z; Villa-Camacho, J; Tanck, E; Verdonschot, N; Goebel, R; Snyder, B D; Hashemi, H N; Vaziri, A; Nazarian, A

    2016-01-01

    In this paper, a CT based structural rigidity analysis (CTRA) method that incorporates bone intrinsic local curvature is introduced to assess the compressive failure load of human femur with simulated lytic defects. The proposed CTRA is based on a three dimensional curved beam theory to obtain critical stresses within the human femur model. To test the proposed method, ten human cadaveric femurs with and without simulated defects were mechanically tested under axial compression to failure. Quantitative computed tomography images were acquired from the samples, and CTRA and finite element analysis were performed to obtain the failure load as well as rigidities in both straight and curved cross sections. Experimental results were compared to the results obtained from FEA and CTRA. The failure loads predicated by curved beam CTRA and FEA are in agreement with experimental results. The results also show that the proposed method is an efficient and reliable method to find both the location and magnitude of failure load. Moreover, the results show that the proposed curved CTRA outperforms the regular straight beam CTRA, which ignores the bone intrinsic curvature and can be used as a useful tool in clinical practices. PMID:27585495

  4. Curved Beam Computed Tomography based Structural Rigidity Analysis of Bones with Simulated Lytic Defect: A Comparative Study with Finite Element Analysis

    PubMed Central

    Oftadeh, R.; Karimi, Z.; Villa-Camacho, J.; Tanck, E.; Verdonschot, N.; Goebel, R.; Snyder, B. D.; Hashemi, H. N.; Vaziri, A.; Nazarian, A.

    2016-01-01

    In this paper, a CT based structural rigidity analysis (CTRA) method that incorporates bone intrinsic local curvature is introduced to assess the compressive failure load of human femur with simulated lytic defects. The proposed CTRA is based on a three dimensional curved beam theory to obtain critical stresses within the human femur model. To test the proposed method, ten human cadaveric femurs with and without simulated defects were mechanically tested under axial compression to failure. Quantitative computed tomography images were acquired from the samples, and CTRA and finite element analysis were performed to obtain the failure load as well as rigidities in both straight and curved cross sections. Experimental results were compared to the results obtained from FEA and CTRA. The failure loads predicated by curved beam CTRA and FEA are in agreement with experimental results. The results also show that the proposed method is an efficient and reliable method to find both the location and magnitude of failure load. Moreover, the results show that the proposed curved CTRA outperforms the regular straight beam CTRA, which ignores the bone intrinsic curvature and can be used as a useful tool in clinical practices. PMID:27585495

  5. Quantitative evaluation of ozone and selected climate parameters in a set of EMAC simulations

    NASA Astrophysics Data System (ADS)

    Righi, M.; Eyring, V.; Gottschaldt, K.-D.; Klinger, C.; Frank, F.; Jöckel, P.; Cionni, I.

    2015-03-01

    Four simulations with the ECHAM/MESSy Atmospheric Chemistry (EMAC) model have been evaluated with the Earth System Model Validation Tool (ESMValTool) to identify differences in simulated ozone and selected climate parameters that resulted from (i) different setups of the EMAC model (nudged vs. free-running) and (ii) different boundary conditions (emissions, sea surface temperatures (SSTs) and sea ice concentrations (SICs)). To assess the relative performance of the simulations, quantitative performance metrics are calculated consistently for the climate parameters and ozone. This is important for the interpretation of the evaluation results since biases in climate can impact on biases in chemistry and vice versa. The observational data sets used for the evaluation include ozonesonde and aircraft data, meteorological reanalyses and satellite measurements. The results from a previous EMAC evaluation of a model simulation with nudging towards realistic meteorology in the troposphere have been compared to new simulations with different model setups and updated emission data sets in free-running time slice and nudged quasi chemistry-transport model (QCTM) mode. The latter two configurations are particularly important for chemistry-climate projections and for the quantification of individual sources (e.g., the transport sector) that lead to small chemical perturbations of the climate system, respectively. With the exception of some specific features which are detailed in this study, no large differences that could be related to the different setups (nudged vs. free-running) of the EMAC simulations were found, which offers the possibility to evaluate and improve the overall model with the help of shorter nudged simulations. The main differences between the two setups is a better representation of the tropospheric and stratospheric temperature in the nudged simulations, which also better reproduce stratospheric water vapor concentrations, due to the improved simulation of

  6. Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions.

    PubMed

    Olivieri, Giorgia; Parry, Krista M; Powell, Cedric J; Tobias, Douglas J; Brown, Matthew A

    2016-04-21

    Over the past decade, energy-dependent ambient pressure X-ray photoelectron spectroscopy(XPS) has emerged as a powerful analytical probe of the ion spatial distributions at the vapor (vacuum)-aqueous electrolyteinterface. These experiments are often paired with complementary molecular dynamics (MD) simulations in an attempt to provide a complete description of the liquidinterface. There is, however, no systematic protocol that permits a straightforward comparison of the two sets of results. XPS is an integrated technique that averages signals from multiple layers in a solution even at the lowest photoelectron kinetic energies routinely employed, whereas MD simulations provide a microscopic layer-by-layer description of the solution composition near the interface. Here, we use the National Institute of Standards and Technology database for the Simulation of Electron Spectra for Surface Analysis (SESSA) to quantitatively interpret atom-density profiles from MD simulations for XPS signal intensities using sodium and potassium iodide solutions as examples. We show that electron inelastic mean free paths calculated from a semi-empirical formula depend strongly on solution composition, varying by up to 30% between pure water and concentrated NaI. The XPS signal thus arises from different information depths in different solutions for a fixed photoelectron kinetic energy. XPS signal intensities are calculated using SESSA as a function of photoelectron kinetic energy (probe depth) and compared with a widely employed ad hoc method. SESSA simulations illustrate the importance of accounting for elastic-scattering events at low photoelectron kinetic energies (<300 eV) where the ad hoc method systematically underestimates the preferential enhancement of anions over cations. Finally, some technical aspects of applying SESSA to liquidinterfaces are discussed. PMID:27389231

  7. Cortical neuron activation induced by electromagnetic stimulation: a quantitative analysis via modelling and simulation.

    PubMed

    Wu, Tiecheng; Fan, Jie; Lee, Kim Seng; Li, Xiaoping

    2016-02-01

    Previous simulation works concerned with the mechanism of non-invasive neuromodulation has isolated many of the factors that can influence stimulation potency, but an inclusive account of the interplay between these factors on realistic neurons is still lacking. To give a comprehensive investigation on the stimulation-evoked neuronal activation, we developed a simulation scheme which incorporates highly detailed physiological and morphological properties of pyramidal cells. The model was implemented on a multitude of neurons; their thresholds and corresponding activation points with respect to various field directions and pulse waveforms were recorded. The results showed that the simulated thresholds had a minor anisotropy and reached minimum when the field direction was parallel to the dendritic-somatic axis; the layer 5 pyramidal cells always had lower thresholds but substantial variances were also observed within layers; reducing pulse length could magnify the threshold values as well as the variance; tortuosity and arborization of axonal segments could obstruct action potential initiation. The dependence of the initiation sites on both the orientation and the duration of the stimulus implies that the cellular excitability might represent the result of the competition between various firing-capable axonal components, each with a unique susceptibility determined by the local geometry. Moreover, the measurements obtained in simulation intimately resemble recordings in physiological and clinical studies, which seems to suggest that, with minimum simplification of the neuron model, the cable theory-based simulation approach can have sufficient verisimilitude to give quantitatively accurate evaluation of cell activities in response to the externally applied field. PMID:26719168

  8. Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions

    NASA Astrophysics Data System (ADS)

    Olivieri, Giorgia; Parry, Krista M.; Powell, Cedric J.; Tobias, Douglas J.; Brown, Matthew A.

    2016-04-01

    Over the past decade, energy-dependent ambient pressure X-ray photoelectron spectroscopy (XPS) has emerged as a powerful analytical probe of the ion spatial distributions at the vapor (vacuum)-aqueous electrolyte interface. These experiments are often paired with complementary molecular dynamics (MD) simulations in an attempt to provide a complete description of the liquid interface. There is, however, no systematic protocol that permits a straightforward comparison of the two sets of results. XPS is an integrated technique that averages signals from multiple layers in a solution even at the lowest photoelectron kinetic energies routinely employed, whereas MD simulations provide a microscopic layer-by-layer description of the solution composition near the interface. Here, we use the National Institute of Standards and Technology database for the Simulation of Electron Spectra for Surface Analysis (SESSA) to quantitatively interpret atom-density profiles from MD simulations for XPS signal intensities using sodium and potassium iodide solutions as examples. We show that electron inelastic mean free paths calculated from a semi-empirical formula depend strongly on solution composition, varying by up to 30% between pure water and concentrated NaI. The XPS signal thus arises from different information depths in different solutions for a fixed photoelectron kinetic energy. XPS signal intensities are calculated using SESSA as a function of photoelectron kinetic energy (probe depth) and compared with a widely employed ad hoc method. SESSA simulations illustrate the importance of accounting for elastic-scattering events at low photoelectron kinetic energies (<300 eV) where the ad hoc method systematically underestimates the preferential enhancement of anions over cations. Finally, some technical aspects of applying SESSA to liquid interfaces are discussed.

  9. Quantitative assessment of rat corneal thickness and morphology during stem cell therapy by high-speed optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Lal, Cerine; McGrath, James; Subhash, Hrebesh; Rani, Sweta; Ritter, Thomas; Leahy, Martin

    2016-03-01

    Optical Coherence Tomography (OCT) is a non-invasive 3 dimensional optical imaging modality that enables high resolution cross sectional imaging in biological tissues and materials. Its high axial and lateral resolution combined with high sensitivity, imaging depth and wide field of view makes it suitable for wide variety of high resolution medical imaging applications at clinically relevant speed. With the advent of swept source lasers, the imaging speed of OCT has increased considerably in recent years. OCT has been used in ophthalmology to study dynamic changes occurring in the cornea and iris, thereby providing physiological and pathological changes that occur within the anterior segment structures such as in glaucoma, during refractive surgery, lamellar keratoplasty and corneal diseases. In this study, we assess the changes in corneal thickness in the anterior segment of the eye during wound healing process in a rat corneal burn model following stem cell therapy using high speed swept source OCT.

  10. Quantitative Three-Dimensional Imaging of Lipid, Protein, and Water Contents via X-Ray Phase-Contrast Tomography.

    PubMed

    Willner, Marian; Viermetz, Manuel; Marschner, Mathias; Scherer, Kai; Braun, Christian; Fingerle, Alexander; Noël, Peter; Rummeny, Ernst; Pfeiffer, Franz; Herzen, Julia

    2016-01-01

    X-ray phase-contrast computed tomography is an emerging imaging technology with powerful capabilities for three-dimensional (3D) visualization of weakly absorbing objects such as biological soft tissues. This technique is an extension of existing X-ray applications because conventional attenuation-contrast images are simultaneously acquired. The complementary information provided by both the contrast modalities suggests that enhanced material characterization is possible when performing combined data analysis. In this study, we describe how protein, lipid, and water concentrations in each 3D voxel can be quantified by vector decomposition. Experimental results of dairy products, porcine fat and rind, and different human soft tissue types are presented. The results demonstrate the potential of phase-contrast imaging as a new analysis tool. The 3D representations of protein, lipid, and water contents open up new opportunities in the fields of biology, medicine, and food science. PMID:27003308

  11. Quantitative Three-Dimensional Imaging of Lipid, Protein, and Water Contents via X-Ray Phase-Contrast Tomography

    PubMed Central

    Willner, Marian; Viermetz, Manuel; Marschner, Mathias; Scherer, Kai; Braun, Christian; Fingerle, Alexander; Noël, Peter; Rummeny, Ernst; Pfeiffer, Franz; Herzen, Julia

    2016-01-01

    X-ray phase-contrast computed tomography is an emerging imaging technology with powerful capabilities for three-dimensional (3D) visualization of weakly absorbing objects such as biological soft tissues. This technique is an extension of existing X-ray applications because conventional attenuation-contrast images are simultaneously acquired. The complementary information provided by both the contrast modalities suggests that enhanced material characterization is possible when performing combined data analysis. In this study, we describe how protein, lipid, and water concentrations in each 3D voxel can be quantified by vector decomposition. Experimental results of dairy products, porcine fat and rind, and different human soft tissue types are presented. The results demonstrate the potential of phase-contrast imaging as a new analysis tool. The 3D representations of protein, lipid, and water contents open up new opportunities in the fields of biology, medicine, and food science. PMID:27003308

  12. Measuring the accuracy and precision of quantitative coronary angiography using a digitally simulated test phantom

    NASA Astrophysics Data System (ADS)

    Morioka, Craig A.; Whiting, James S.; LeFree, Michelle T.

    1998-06-01

    Quantitative coronary angiography (QCA) diameter measurements have been used as an endpoint measurement in clinical studies involving therapies to reduce coronary atherosclerosis. The accuracy and precision of the QCA measure can affect the sample size and study conclusions of a clinical study. Measurements using x-ray test phantoms can underestimate the precision and accuracy of the actual arteries in clinical digital angiograms because they do not contain complex patient structures. Determining the clinical performance of QCA algorithms under clinical conditions is difficult because: (1) no gold standard test object exists in clinical images, (2) phantom images do not have any structured background noise. We purpose the use of computer simulated arteries as a replacement for traditional angiographic test phantoms to evaluate QCA algorithm performance.

  13. Introducing Simulated Cellular Architecture to the Quantitative Analysis of Fluorescent Microscopy

    PubMed Central

    DePristo, Mark A.; Chang, Lynne; Vale, Ronald D.; Khan, Shahid M.; Lipkow, Karen

    2009-01-01

    Biological cells are complex and highly dynamic: Many macromolecules are organized in loose assemblies, clusters or highly structured complexes, others exist most of the time as freely diffusing monomers. They move between regions and compartments through diffusion and enzyme-mediated transport, within a heavily crowded cytoplasm. To make sense of this complexity, computational models, and, in turn, quantitative in vivo data are needed. An array of fluorescent microscopy methods is available, but due to the inherent noise and complexity inside the cell, they are often hard to interpret. Using the example of fluorescence recovery after photobleaching (FRAP) and the bacterial chemotaxis system, we are here introducing detailed spatial simulations as a new approach in analysing such data. PMID:19628003

  14. Validation of quantitative attenuation and backscattering coefficient measurements by optical coherence tomography in the concentration-dependent and multiple scattering regime.

    PubMed

    Almasian, Mitra; Bosschaart, Nienke; van Leeuwen, Ton G; Faber, Dirk J

    2015-12-01

    Optical coherence tomography (OCT) has the potential to quantitatively measure optical properties of tissue such as the attenuation coefficient and backscattering coefficient. However, to obtain reliable values for strong scattering tissues, accurate consideration of the effects of multiple scattering and the nonlinear relation between the scattering coefficient and scatterer concentration (concentration-dependent scattering) is required. We present a comprehensive model for the OCT signal in which we quantitatively account for both effects, as well as our system parameters (confocal point spread function and sensitivity roll-off). We verify our model with experimental data from controlled phantoms of monodisperse silica beads (scattering coefficients between 1 and 30  mm(−1) and scattering anisotropy between 0.4 and 0.9). The optical properties of the phantoms are calculated using Mie theory combined with the Percus–Yevick structure factor to account for concentration-dependent scattering. We demonstrate excellent agreement between the OCT attenuation and backscattering coefficient predicted by our model and experimentally derived values. We conclude that this model enables us to accurately model OCT-derived parameters (i.e., attenuation and backscattering coefficients) in the concentration-dependent and multiple scattering regime for spherical monodisperse samples. PMID:26720868

  15. Optical coherence tomography based microangiography for quantitative monitoring of structural and vascular changes in a rat model of acute uveitis in vivo: a preliminary study

    NASA Astrophysics Data System (ADS)

    Choi, Woo June; Pepple, Kathryn L.; Zhi, Zhongwei; Wang, Ruikang K.

    2015-01-01

    Uveitis models in rodents are important in the investigation of pathogenesis in human uveitis and the development of appropriate therapeutic strategies for treatment. Quantitative monitoring of ocular inflammation in small animal models provides an objective metric to assess uveitis progression and/or therapeutic effects. We present a new application of optical coherence tomography (OCT) and OCT-based microangiography (OMAG) to a rat model of acute anterior uveitis induced by intravitreal injection of a killed mycobacterial extract. OCT/OMAG is used to provide noninvasive three-dimensional imaging of the anterior segment of the eyes prior to injection (baseline) and two days post-injection (peak inflammation) in rats with and without steroid treatments. OCT imaging identifies characteristic structural and vascular changes in the anterior segment of the inflamed animals when compared to baseline images. Characteristics of inflammation identified include anterior chamber cells, corneal edema, pupillary membranes, and iris vasodilation. In contrast, no significant difference from the control is observed for the steroid-treated eye. These findings are compared with the histology assessment of the same eyes. In addition, quantitative measurements of central corneal thickness and iris vessel diameter are determined. This pilot study demonstrates that OCT-based microangiography promises to be a useful tool for the assessment and management of uveitis in vivo.

  16. Disturbances in the cerebral perfusion of human immune deficiency virus-1 seropositive asymptomatic subjects: A quantitative tomography study of 18 cases

    SciTech Connect

    Tran Dinh, Y.R.; Mamo, H.; Cervoni, J.; Caulin, C.; Saimot, A.C. , Paris )

    1990-10-01

    Quantitative measurements of cerebral blood flow (CBF) by xenon-133 ({sup 133}Xe) tomography, together with magnetic resonance imaging (MRI), electroencephalography (EEG), psychometric tests, and laboratory analyses were performed on 18 human immunodeficiency virus 1 (HIV-1) seropositive asymptomatic subjects. Abnormalities of cerebral perfusion were observed in 16 cases (88%). These abnormalities were particularly frequent in the frontal regions (77% of cases). MRI demonstrated leucoencephalopathy in only two cases. EEG showed only induced diffuse abnormalities in two cases. Psychometric tests showed restricted moderate disturbances in 55% of patients. These disturbances mostly concerned those sectors involved in cognitive functions and memorization. These results indicate that quantitative measurements of CBF by {sup 133}Xe-SPECT is capable of detecting abnormalities of cerebral perfusion at a very early stage (Phase II) of HIV-1 infection. These abnormalities are indications of disturbances resulting from unidentified metabolic or vascular lesions. This technique appears to be superior to MRI at this stage of the disease's development. It could provide objective information leading to earlier treatment, and prove useful in evaluating potential antiviral chemotherapy.

  17. Quantitative thallium-201 single-photon emission computed tomography during maximal pharmacologic coronary vasodilation with adenosine for assessing coronary artery disease

    SciTech Connect

    Nishimura, S.; Mahmarian, J.J.; Boyce, T.M.; Verani, M.S. )

    1991-09-01

    The diagnostic value of maximal pharmacologic coronary vasodilation with intravenously administered adenosine in conjunction with thallium-201 single-photon emission computed tomography (SPECT) for detection of coronary artery disease was investigated in 101 consecutive patients who had concomitant coronary arteriography. Tomographic images were assessed visually and from computer-quantified polar maps of the thallium-201 distribution. Significant coronary artery disease, defined as greater than 50% luminal diameter stenosis, was present in 70 patients. The sensitivity for detecting patients with coronary artery disease using quantitative analysis was 87% in the total group, 82% in patients without myocardial infarction and 96% in those with prior myocardial infarction; the specificity was 90%. The sensitivity for diagnosing coronary artery disease in patients without infarction with single-, double-and triple-vessel disease was 76%, 86% and 90%, respectively. All individual stenoses were identified in 68% of patients with double-vessel disease and in 65% of those with triple-vessel disease. The extent of the perfusion defects, as quantified by polar maps, was directly related to the extent of coronary artery disease. In conclusion, quantitative thallium-201 SPECT during adenosine infusion has high sensitivity and specificity for diagnosing the presence of coronary artery disease, localizing the anatomic site of coronary stenosis and identifying the majority of affected vascular regions in patients with multivessel involvement.

  18. A 3D reconstruction solution to ultrasound Joule heat density tomography based on acousto-electric effect: a simulation study

    NASA Astrophysics Data System (ADS)

    Yang, R.; Song, A.; Li, X. D.; Lu, Y.; Yan, R.; Xu, B.; Li, X.

    2014-10-01

    A 3D reconstruction solution to ultrasound Joule heat density tomography based on acousto-electric effect by deconvolution is proposed for noninvasive imaging of biological tissue. Compared with ultrasound current source density imaging, ultrasound Joule heat density tomography doesn't require any priori knowledge of conductivity distribution and lead fields, so it can gain better imaging result, more adaptive to environment and with wider application scope. For a general 3D volume conductor with broadly distributed current density field, in the AE equation the ultrasound pressure can't simply be separated from the 3D integration, so it is not a common modulation and basebanding (heterodyning) method is no longer suitable to separate Joule heat density from the AE signals. In the proposed method the measurement signal is viewed as the output of Joule heat density convolving with ultrasound wave. As a result, the internal 3D Joule heat density can be reconstructed by means of Wiener deconvolution. A series of computer simulations set for breast cancer imaging applications, with consideration of ultrasound beam diameter, noise level, conductivity contrast, position dependency and size of simulated tumors, have been conducted to evaluate the feasibility and performance of the proposed reconstruction method. The computer simulation results demonstrate that high spatial resolution 3D ultrasound Joule heat density imaging is feasible using the proposed method, and it has potential applications to breast cancer detection and imaging of other organs.

  19. A qualitative and quantitative analysis of radiation dose and image quality of computed tomography images using adaptive statistical iterative reconstruction.

    PubMed

    Hussain, Fahad Ahmed; Mail, Noor; Shamy, Abdulrahman M; Suliman, Alghamdi; Saoudi, Abdelhamid

    2016-01-01

    Image quality is a key issue in radiology, particularly in a clinical setting where it is important to achieve accurate diagnoses while minimizing radiation dose. Some computed tomography (CT) manufacturers have introduced algorithms that claim significant dose reduction. In this study, we assessed CT image quality produced by two reconstruction algorithms provided with GE Healthcare's Discovery 690 Elite positron emission tomography (PET) CT scanner. Image quality was measured for images obtained at various doses with both conventional filtered back-projection (FBP) and adaptive statistical iterative reconstruction (ASIR) algorithms. A stan-dard CT dose index (CTDI) phantom and a pencil ionization chamber were used to measure the CT dose at 120 kVp and an exposure of 260 mAs. Image quality was assessed using two phantoms. CT images of both phantoms were acquired at tube voltage (kV) of 120 with exposures ranging from 25 mAs to 400 mAs. Images were reconstructed using FBP and ASIR ranging from 10% to 100%, then analyzed for noise, low-contrast detectability, contrast-to-noise ratio (CNR), and modulation transfer function (MTF). Noise was 4.6 HU in water phantom images acquired at 260 mAs/FBP 120 kV and 130 mAs/50% ASIR 120 kV. The large objects (fre-quency < 7 lp/cm) retained fairly acceptable image quality at 130 mAs/50% ASIR, compared to 260 mAs/FBP. The application of ASIR for small objects (frequency >7 lp/cm) showed poor visibility compared to FBP at 260 mAs and even worse for images acquired at less than 130 mAs. ASIR blending more than 50% at low dose tends to reduce contrast of small objects (frequency >7 lp/cm). We concluded that dose reduction and ASIR should be applied with close attention if the objects to be detected or diagnosed are small (frequency > 7 lp/cm). Further investigations are required to correlate the small objects (frequency > 7 lp/cm) to patient anatomy and clinical diagnosis. PMID:27167261

  20. Organ doses for reference pediatric and adolescent patients undergoing computed tomography estimated by Monte Carlo simulation

    SciTech Connect

    Lee, Choonsik; Kim, Kwang Pyo; Long, Daniel J.; Bolch, Wesley E.

    2012-04-15

    Purpose: To establish an organ dose database for pediatric and adolescent reference individuals undergoing computed tomography (CT) examinations by using Monte Carlo simulation. The data will permit rapid estimates of organ and effective doses for patients of different age, gender, examination type, and CT scanner model. Methods: The Monte Carlo simulation model of a Siemens Sensation 16 CT scanner previously published was employed as a base CT scanner model. A set of absorbed doses for 33 organs/tissues normalized to the product of 100 mAs and CTDI{sub vol} (mGy/100 mAs mGy) was established by coupling the CT scanner model with age-dependent reference pediatric hybrid phantoms. A series of single axial scans from the top of head to the feet of the phantoms was performed at a slice thickness of 10 mm, and at tube potentials of 80, 100, and 120 kVp. Using the established CTDI{sub vol}- and 100 mAs-normalized dose matrix, organ doses for different pediatric phantoms undergoing head, chest, abdomen-pelvis, and chest-abdomen-pelvis (CAP) scans with the Siemens Sensation 16 scanner were estimated and analyzed. The results were then compared with the values obtained from three independent published methods: CT-Expo software, organ dose for abdominal CT scan derived empirically from patient abdominal circumference, and effective dose per dose-length product (DLP). Results: Organ and effective doses were calculated and normalized to 100 mAs and CTDI{sub vol} for different CT examinations. At the same technical setting, dose to the organs, which were entirely included in the CT beam coverage, were higher by from 40 to 80% for newborn phantoms compared to those of 15-year phantoms. An increase of tube potential from 80 to 120 kVp resulted in 2.5-2.9-fold greater brain dose for head scans. The results from this study were compared with three different published studies and/or techniques. First, organ doses were compared to those given by CT-Expo which revealed dose

  1. Reconstruction of the blood flow pattern by tomography of the acoustic nonlinearity parameter: Computer simulation and physical experiment

    NASA Astrophysics Data System (ADS)

    Burov, V. A.; Evtukhov, S. N.; Rumyantseva, O. D.

    2008-09-01

    A method is proposed for reconstructing the distribution of the total blood flow velocity vector from the data obtained within the nonlinear parameter tomography scheme. The method calculates the Doppler shift of the combination frequency with the use of the spectral analysis of the combination signal and the moving target selection procedure. Results of numerical simulations are presented, and possibilities of practical application of the method are discussed. A physical experiment is carried out. The results of this experiment are found to be in good agreement with the theory and the numerical model.

  2. SIMULATION STUDY FOR GASEOUS FLUXES FROM AN AREA SOURCE USING COMPUTED TOMOGRAPHY AND OPTICAL REMOTE SENSING

    EPA Science Inventory

    The paper presents a new approach to quantifying emissions from fugitive gaseous air pollution sources. Computed tomography (CT) and path-integrated optical remote sensing (PI-ORS) concentration data are combined in a new field beam geometry. Path-integrated concentrations are ...

  3. Absolute Quantitation of Myocardial Blood Flow in Human Subjects with or without Myocardial Ischemia using Dynamic Flurpiridaz F 18 Positron Emission Tomography

    PubMed Central

    Packard, René R. S.; Huang, Sung-Cheng; Dahlbom, Magnus; Czernin, Johannes; Maddahi, Jamshid

    2015-01-01

    Absolute quantitation of myocardial blood flow (MBF) by positron emission tomography (PET) is an established method of analyzing coronary artery disease (CAD) but subject to the various shortcomings of available radiotracers. Flurpiridaz F 18 is a novel PET radiotracer which exhibits properties of an ideal tracer. Methods A new absolute perfusion quantitation method with Flurpiridaz was developed, taking advantage of the early kinetics and high first-pass extraction by the myocardium of this radiotracer, and the first in human measurements of MBF performed in 7 normal subjects and 8 patients with documented CAD. PET images with time-activity curves were acquired at rest and during adenosine stress. Results In normal subjects, regional MBF between coronary artery territories did not differ significantly, leading to a mean global MBF of 0.73 mL/min/g at rest and 2.53 mL/min/g during stress, with a mean global myocardial flow reserve (MFR) of 3.70. CAD vascular territories with <50% stenosis demonstrated a mean MBF of 0.73 at rest and 2.02 during stress, leading to a mean MFR of 2.97. CAD vascular territories with ≥50% stenosis exhibited a mean MBF of 0.86 at rest and 1.43 during stress, leading to a mean MFR of 1.86. Differences in stress MBF and MFR between normal and CAD territories, as well as between <50% and ≥50% stenosis vascular territories, were significant (P<0.01). Conclusion Absolute quantitation of MBF in humans with the novel PET radiotracer Flurpiridaz is feasible over a wide range of cardiac flow in the presence or absence of stress-inducible myocardial ischemia. The significant decrease in stress MBF and ensuing MFR in CAD territories allows a clear distinction between vascular territories exhibiting stress-inducible myocardial ischemia and those with normal perfusion. PMID:25071096

  4. Quantitative EEG and Low-Resolution Electromagnetic Tomography (LORETA) Imaging of Patients Undergoing Methadone Treatment for Opiate Addiction.

    PubMed

    Wang, Grace Y; Kydd, Robert R; Russell, Bruce R

    2016-07-01

    Methadone maintenance treatment (MMT) has been used as a treatment for opiate dependence since the mid-1960s. Evidence suggests that methadone binds to mu opiate receptors as do other opiates and induces changes in neurophysiological function. However, little is known, about how neural activity within the higher frequency gamma band (>30 Hz) while at rest changes in those stabilized on MMT despite its association with the excitation-inhibition balance within pyramidal-interneuron networks. Our study investigated differences in resting gamma power (37-41 Hz) between patients undergoing MMT for opiate dependence, illicit opiate users, and healthy controls subjects. Electroencephalographic data were recorded from 26 sites according to the international 10-20 system. Compared with the healthy controls subjects, people either undergoing MMT (mean difference [MD] = 0.32, 95% CI = 0.09-0.55, P < .01) or currently using illicit opiates (MD = 0.31, 95% CI = 0.06-0.56, P = .01) exhibited significant increased gamma power. The sLORETA (standardized low-resolution electromagnetic tomography) between-group comparison revealed dysfunctional neuronal activity in the occipital, parietal, and frontal lobes in the patients undergoing MMT. A more severe profile of dysfunction was observed in those using illicit opiates. Our findings suggest that long-term exposure to opioids is associated with disrupted resting state network, which may be reduced after MMT. PMID:26002855

  5. Quantitative imaging of gold nanoparticle distribution in a tumor-bearing mouse using benchtop x-ray fluorescence computed tomography

    PubMed Central

    Manohar, Nivedh; Reynoso, Francisco J.; Diagaradjane, Parmeswaran; Krishnan, Sunil; Cho, Sang Hyun

    2016-01-01

    X-ray fluorescence computed tomography (XFCT) is a technique that can identify, quantify, and locate elements within objects by detecting x-ray fluorescence (characteristic x-rays) stimulated by an excitation source, typically derived from a synchrotron. However, the use of a synchrotron limits practicality and accessibility of XFCT for routine biomedical imaging applications. Therefore, we have developed the ability to perform XFCT on a benchtop setting with ordinary polychromatic x-ray sources. Here, we report our postmortem study that demonstrates the use of benchtop XFCT to accurately image the distribution of gold nanoparticles (GNPs) injected into a tumor-bearing mouse. The distribution of GNPs as determined by benchtop XFCT was validated using inductively coupled plasma mass spectrometry. This investigation shows drastically enhanced sensitivity and specificity of GNP detection and quantification with benchtop XFCT, up to two orders of magnitude better than conventional x-ray CT. The results also reaffirm the unique capabilities of benchtop XFCT for simultaneous determination of the spatial distribution and concentration of nonradioactive metallic probes, such as GNPs, within the context of small animal imaging. Overall, this investigation identifies a clear path toward in vivo molecular imaging using benchtop XFCT techniques in conjunction with GNPs and other metallic probes. PMID:26912068

  6. Quantitative imaging of gold nanoparticle distribution in a tumor-bearing mouse using benchtop x-ray fluorescence computed tomography

    NASA Astrophysics Data System (ADS)

    Manohar, Nivedh; Reynoso, Francisco J.; Diagaradjane, Parmeswaran; Krishnan, Sunil; Cho, Sang Hyun

    2016-02-01

    X-ray fluorescence computed tomography (XFCT) is a technique that can identify, quantify, and locate elements within objects by detecting x-ray fluorescence (characteristic x-rays) stimulated by an excitation source, typically derived from a synchrotron. However, the use of a synchrotron limits practicality and accessibility of XFCT for routine biomedical imaging applications. Therefore, we have developed the ability to perform XFCT on a benchtop setting with ordinary polychromatic x-ray sources. Here, we report our postmortem study that demonstrates the use of benchtop XFCT to accurately image the distribution of gold nanoparticles (GNPs) injected into a tumor-bearing mouse. The distribution of GNPs as determined by benchtop XFCT was validated using inductively coupled plasma mass spectrometry. This investigation shows drastically enhanced sensitivity and specificity of GNP detection and quantification with benchtop XFCT, up to two orders of magnitude better than conventional x-ray CT. The results also reaffirm the unique capabilities of benchtop XFCT for simultaneous determination of the spatial distribution and concentration of nonradioactive metallic probes, such as GNPs, within the context of small animal imaging. Overall, this investigation identifies a clear path toward in vivo molecular imaging using benchtop XFCT techniques in conjunction with GNPs and other metallic probes.

  7. Quantitative imaging of gold nanoparticle distribution in a tumor-bearing mouse using benchtop x-ray fluorescence computed tomography.

    PubMed

    Manohar, Nivedh; Reynoso, Francisco J; Diagaradjane, Parmeswaran; Krishnan, Sunil; Cho, Sang Hyun

    2016-01-01

    X-ray fluorescence computed tomography (XFCT) is a technique that can identify, quantify, and locate elements within objects by detecting x-ray fluorescence (characteristic x-rays) stimulated by an excitation source, typically derived from a synchrotron. However, the use of a synchrotron limits practicality and accessibility of XFCT for routine biomedical imaging applications. Therefore, we have developed the ability to perform XFCT on a benchtop setting with ordinary polychromatic x-ray sources. Here, we report our postmortem study that demonstrates the use of benchtop XFCT to accurately image the distribution of gold nanoparticles (GNPs) injected into a tumor-bearing mouse. The distribution of GNPs as determined by benchtop XFCT was validated using inductively coupled plasma mass spectrometry. This investigation shows drastically enhanced sensitivity and specificity of GNP detection and quantification with benchtop XFCT, up to two orders of magnitude better than conventional x-ray CT. The results also reaffirm the unique capabilities of benchtop XFCT for simultaneous determination of the spatial distribution and concentration of nonradioactive metallic probes, such as GNPs, within the context of small animal imaging. Overall, this investigation identifies a clear path toward in vivo molecular imaging using benchtop XFCT techniques in conjunction with GNPs and other metallic probes. PMID:26912068

  8. Quantitative analysis of hydrogen in SiO2/SiN/SiO2 stacks using atom probe tomography

    NASA Astrophysics Data System (ADS)

    Kunimune, Yorinobu; Shimada, Yasuhiro; Sakurai, Yusuke; Inoue, Masao; Nishida, Akio; Han, Bin; Tu, Yuan; Takamizawa, Hisashi; Shimizu, Yasuo; Inoue, Koji; Yano, Fumiko; Nagai, Yasuyoshi; Katayama, Toshiharu; Ide, Takashi

    2016-04-01

    We have demonstrated that it is possible to reproducibly quantify hydrogen concentration in the SiN layer of a SiO2/SiN/SiO2 (ONO) stack structure using ultraviolet laser-assisted atom probe tomography (APT). The concentration of hydrogen atoms detected using APT increased gradually during the analysis, which could be explained by the effect of hydrogen adsorption from residual gas in the vacuum chamber onto the specimen surface. The amount of adsorbed hydrogen in the SiN layer was estimated by analyzing another SiN layer with an extremely low hydrogen concentration (<0.2 at. %). Thus, by subtracting the concentration of adsorbed hydrogen, the actual hydrogen concentration in the SiN layer was quantified as approximately 1.0 at. %. This result was consistent with that obtained by elastic recoil detection analysis (ERDA), which confirmed the accuracy of the APT quantification. The present results indicate that APT enables the imaging of the three-dimensional distribution of hydrogen atoms in actual devices at a sub-nanometer scale.

  9. Frontonasal and craniofrontonasal dysplasia: preoperative quantitative description of the cranio-orbito-zygomatic region based on computed and conventional tomography.

    PubMed

    Moffat, S M; Posnick, J C; Pron, G E; Armstrong, D C

    1994-03-01

    The unoperated crano-orbito-zygomatic complex of 18 children (mean 4.7 years) with frontonasal dysplasia (FND) and 12 children (mean 1.1 years) with crainofrontonasal dysplasia (CFND) was quantified by 15 standard measurements performed on either computed tomography scans or facial tomograms. The results were compared with age-matched control values. In the FND group, the mean anterior interorbital and mid-interorbital distances were significantly increased at 148% and 118% of normal, and in the CFND patients, at 177% and 140% of normal. Excessive medial orbital wall protrusion (mean, 145% of normal in FND and 177% in CFND), shortened zygomatic arch lengths (mean, 94% of normal in FND and 91% in CFND), and reduced cephalic lengths (mean, 96% of normal in FND and 83% in CFND) were all observed. An expanded interzygomatic buttress distance was documented only in the CFND group, at 11% of normal. The clinical presentation of craniofacial deformities such as FND and CFND can be objectively described by a numerical analysis of the bony pathology. PMID:8186226

  10. Quantitative assessment of diffuse optical tomography sensitivity to the cerebral cortex using a whole-head probe

    NASA Astrophysics Data System (ADS)

    Perdue, Katherine L.; Fang, Qianqian; Diamond, Solomon G.

    2012-05-01

    We quantify the variability in diffuse optical tomography (DOT) sensitivity over the cortical surface in eight young adult subjects. We use the 10/5 electroencephalography system as a basis for our whole-head optical high-density probe design. The contrast-to-noise ratio (CNR) is calculated along with the percentage of the cortex that is above a CNR = 0 dB threshold. We also quantify the effect of including vasculature on the forward model and list our assumptions that allow us to estimate light penetration depth in the head. We show that using the 10/5 system for the optical probe design allows for the measurement of 37% of the cortical surface on average, with a mean CNR in the visible region of 5.5 dB. Certain anatomical regions, such as the lateral occipital cortex, had a very high percentage above the CNR threshold, while other regions such as the cingulate cortex were not measurable. Vasculature blocked optical sensitivity over 1% of the cortex. Cortical coverage was positively correlated with intracranial volume and relative cerebrospinal fluid volume, and negatively correlated with relative scalp volume and skull volume. These contributions allow experimenters to understand how anatomical variation in a subject population may impact DOT or functional near-infrared spectroscopy measurements.

  11. Quantitative orientation preference and susceptibility to space motion sickness simulated in a virtual reality environment.

    PubMed

    Chen, Wei; Chao, Jian-Gang; Chen, Xue-Wen; Wang, Jin-Kun; Tan, Cheng

    2015-04-01

    Orientation preference should appear when variable weightings of spatial orientation cues are used between individuals. It is possible that astronauts' orientation preferences could be a potential predictor for susceptibility to space motion sickness (SMS). The present study was conducted to confirm this relationship on Earth by quantifying orientation preferences and simulating SMS in a virtual reality environment. Two tests were carried out. The first was to quantitatively determine one's orientation preference. Thirty-two participants' vision and body cue preferences were determined by measuring perceptual up (PU) orientations. The ratio of vision and body vector (ROVB) was used as the indicator of one's orientation preference. The second test was to visually induce motion sickness symptoms that represent similar sensory conflicts as SMS using a virtual reality environment. Relationships between ROVB values and motion sickness scores were analyzed, which revealed cubic functions by using optimal fits. According to ROVB level, participants were divided into three groups - body group, vision group, and confusion group - and the factor of gender was further considered as a covariate in the analysis. Consistent differences in motion sickness scores were observed between the three groups. Thus, orientation preference had a significant relationship with susceptibility to simulated SMS symptoms. This knowledge could assist with astronaut selection and might be a useful countermeasure when developing new preflight trainings. PMID:25647233

  12. Quantitative analysis of bone and soft tissue by micro-computed tomography: applications to ex vivo and in vivo studies

    PubMed Central

    Campbell, Graeme M; Sophocleous, Antonia

    2014-01-01

    Micro-computed tomography (micro-CT) is a high-resolution imaging modality that is capable of analysing bone structure with a voxel size on the order of 10 μm. With the development of in vivo micro-CT, where disease progression and treatment can be monitored in a living animal over a period of time, this modality has become a standard tool for preclinical assessment of bone architecture during disease progression and treatment. For meaningful comparison between micro-CT studies, it is essential that the same parameters for data acquisition and analysis methods be used. This protocol outlines the common procedures that are currently used for sample preparation, scanning, reconstruction and analysis in micro-CT studies. Scan and analysis methods for trabecular and cortical bone are covered for the femur, tibia, vertebra and the full neonate body of small rodents. The analysis procedures using the software provided by ScancoMedical and Bruker are discussed, and the routinely used bone architectural parameters are outlined. This protocol also provides a section dedicated to in vivo scanning and analysis, which covers the topics of anaesthesia, radiation dose and image registration. Because of the expanding research using micro-CT to study other skeletal sites, as well as soft tissues, we also provide a review of current techniques to examine the skull and mandible, adipose tissue, vasculature, tumour severity and cartilage. Lists of recommended further reading and literature references are included to provide the reader with more detail on the methods described. PMID:25184037

  13. Quantitative analysis of the impact of three tillage systems on soil structure using X-ray tomography

    NASA Astrophysics Data System (ADS)

    Le Couteulx, Alexis; Pérès, Guénola; Wolf, Cédric; Hallaire, Vincent

    2015-04-01

    Soil structure is a dynamic property that can be altered by various structuring processes. Among other processes, there are soil tillage, soil organisms (e.g. earthworm bioturbation) and climate (e.g. freeze-thaw cycles). In cultivated fields, it is often acknowledged that soil tillage is a main structuring process, indeed in a very short time soil tillage can drastically altered soil structure. Despite this, the direct effect of tillage on soil structure through the mechanical action of tillage tools is seldom studied. Thus, this study aims at describing the effect of tillage tools used in three different tillage systems (ploughing, surface tillage and direct seedling). Their effect on soil structure is analysed by X-ray computed tomography (CT). In our study, the ploughing and surface tillage systems consist in two tillage actions at different times: first the ploughing or the use of a tined tool and then the sowing combined with a rotary harrow. On the contrary, there is only one tillage action under the direct seedling system: the sowing. Soil columns were taken before and after each tillage action and then analysed by CT (spatial resolution of 0.3x0.3x0.1 mm). We first analysed the macroporosity and noticeably root and earthworm burrow paths. Algorithms developped in other studies to analyse earthworm burrows allowed us to measure the length, volume, continuity and branching rate of these paths. First results show that there are very few paths in the tilled layer after ploughing and surface tillage. These paths are short, seldom connected to soil surface and mainly in dense aggregates suggesting that they can weakly improve soil water conductivity. Under direct seedling, we observed that there is a disturbed volume around the seed furrow that removed several paths but this impact is weaker than after the other tillage tools. Acquired knowledges will be used to build a model that accounts for the impact of tillage practices and earthworm bioturbation on soil

  14. Quantitative comparison of dose distribution in radiotherapy plans using 2D gamma maps and X-ray computed tomography

    PubMed Central

    Balosso, Jacques

    2016-01-01

    Background The advanced dose calculation algorithms implemented in treatment planning system (TPS) have remarkably improved the accuracy of dose calculation especially the modeling of electrons transport in the low density medium. The purpose of this study is to evaluate the use of 2D gamma (γ) index to quantify and evaluate the impact of the calculation of electrons transport on dose distribution for lung radiotherapy. Methods X-ray computed tomography images were used to calculate the dose for twelve radiotherapy treatment plans. The doses were originally calculated with Modified Batho (MB) 1D density correction method, and recalculated with anisotropic analytical algorithm (AAA), using the same prescribed dose. Dose parameters derived from dose volume histograms (DVH) and target coverage indices were compared. To compare dose distribution, 2D γ-index was applied, ranging from 1%/1 mm to 6%/6 mm. The results were displayed using γ-maps in 2D. Correlation between DVH metrics and γ passing rates was tested using Spearman’s rank test and Wilcoxon paired test to calculate P values. Results the plans generated with AAA predicted more heterogeneous dose distribution inside the target, with P<0.05. However, MB overestimated the dose predicting more coverage of the target by the prescribed dose. The γ analysis showed that the difference between MB and AAA could reach up to ±10%. The 2D γ-maps illustrated that AAA predicted more dose to organs at risks, as well as lower dose to the target compared to MB. Conclusions Taking into account of the electrons transport on radiotherapy plans showed a significant impact on delivered dose and dose distribution. When considering the AAA represent the true cumulative dose, a readjusting of the prescribed dose and an optimization to protect the organs at risks should be taken in consideration in order to obtain the better clinical outcome. PMID:27429908

  15. Quantitative measurement of biological substances in daily-life environment with the little-finger-size one-shot spectroscopic tomography

    NASA Astrophysics Data System (ADS)

    Ishida, Akane; Sato, Shun; Nakada, Sho; Suzuki, Satoru; Abeygunawardhana, P. K. W.; Wada, Kenji; Nishiyama, Akira; Ishimaru, Ichiro

    2014-02-01

    In daily-life environment, the quantitative measurement of biological substances, such as the blood glucose level in the human skin, is strongly required to realize the non-invasive healthcare apparatus. Fourier-spectroscopic-tomography of the little-finger-size with high time-resolution and with the strong robustness for mechanical vibrations is proposed. The proposed method is a kind of near-common-path interferometer with spatial phase-shift method. We install the transmission-type relative-inclined phase-shifter on the optical Fourier transform plane of the infinity corrected optical system. The phase shifter is constructed with the cuboid and wedge prisms to give the relative phase-shift spatially between each half-flux of the objective beams. The interferograms from each single-bright-point on an objective surface in a line are formed as fringe patterns on 2-dimensional imaging array devices. And because the proposed method is based on the imaging optics, only emitted rays from a focal plane can contribute forming of interferograms. Thus, the measurement plane can be limited onto the focal plane only. From the spectroscopic tomography, only at a localized vessel area in human skins, we can get the pinpointed near-infrared spectroscopic data. And we can expect the improvement of the determination precision, because a Fourier spectroscopic-character is acquired from multiple intensity data in accordance with amount of phase-shift. From the statistical point of view, the gradation of detector is improved with the square root of sample number, based on t-distribution. We constructed the statistical model to assure the determination accuracy, and demonstrated the feasibility of the glucose sensor using liquid cells.

  16. Contrasting properties of gold nanoparticles for optical coherence tomography: phantom, in vivo studies and Monte Carlo simulation.

    PubMed

    Zagaynova, E V; Shirmanova, M V; Kirillin, M Yu; Khlebtsov, B N; Orlova, A G; Balalaeva, I V; Sirotkina, M A; Bugrova, M L; Agrba, P D; Kamensky, V A

    2008-09-21

    The possibility of using silica-gold nanoshells with 150 nm silica core size and 25 nm thick gold shell as contrasting agents for optical coherence tomography (OCT) is analyzed. Experiments on agar biotissue phantoms showed that the penetration of nanoshells into the phantoms increases the intensity of the optical coherence tomography (OCT) signal and the brightness of the corresponding areas of the OCT image. In vivo experiments on rabbit skin demonstrated that the application of nanoshells onto the skin provides significant contrasting of the borders between the areas containing nanoshells and those without. This effect of nanoshells on skin in vivo is manifested by the increase in intensity of the OCT signal in superficial parts of the skin, boundary contrast between superficial and deep dermis and contrast of hair follicles and glands. The presence of nanoshells in the skin was confirmed by electron microscopy. Monte Carlo simulations of OCT images confirmed the possibility of contrasting skin-layer borders and structures by the application of gold nanoshells. The Monte Carlo simulations were performed for two skin models and exhibit effects of nanoparticles similar to those obtained in the experimental part of the study, thus proving that the effects originate exactly from the presence of nanoparticles. PMID:18711247

  17. Accuracy in contouring of small and low contrast lesions: Comparison between diagnostic quality computed tomography scanner and computed tomography simulation scanner-A phantom study

    SciTech Connect

    Ho, Yick Wing; Wong, Wing Kei Rebecca; Yu, Siu Ki; Lam, Wai Wang; Geng Hui

    2012-01-01

    To evaluate the accuracy in detection of small and low-contrast regions using a high-definition diagnostic computed tomography (CT) scanner compared with a radiotherapy CT simulation scanner. A custom-made phantom with cylindrical holes of diameters ranging from 2-9 mm was filled with 9 different concentrations of contrast solution. The phantom was scanned using a 16-slice multidetector CT simulation scanner (LightSpeed RT16, General Electric Healthcare, Milwaukee, WI) and a 64-slice high-definition diagnostic CT scanner (Discovery CT750 HD, General Electric Healthcare). The low-contrast regions of interest (ROIs) were delineated automatically upon their full width at half maximum of the CT number profile in Hounsfield units on a treatment planning workstation. Two conformal indexes, CI{sub in}, and CI{sub out}, were calculated to represent the percentage errors of underestimation and overestimation in the automated contours compared with their actual sizes. Summarizing the conformal indexes of different sizes and contrast concentration, the means of CI{sub in} and CI{sub out} for the CT simulation scanner were 33.7% and 60.9%, respectively, and 10.5% and 41.5% were found for the diagnostic CT scanner. The mean differences between the 2 scanners' CI{sub in} and CI{sub out} were shown to be significant with p < 0.001. A descending trend of the index values was observed as the ROI size increases for both scanners, which indicates an improved accuracy when the ROI size increases, whereas no observable trend was found in the contouring accuracy with respect to the contrast levels in this study. Images acquired by the diagnostic CT scanner allow higher accuracy on size estimation compared with the CT simulation scanner in this study. We recommend using a diagnostic CT scanner to scan patients with small lesions (<1 cm in diameter) for radiotherapy treatment planning, especially for those pending for stereotactic radiosurgery in which accurate delineation of small

  18. Use of Relative vs Fixed Offset Distance to Define Region of Interest at the Distal Radius and Tibia in High-Resolution Peripheral Quantitative Computed Tomography.

    PubMed

    Shanbhogue, Vikram V; Hansen, Stinus; Halekoh, Ulrich; Brixen, Kim

    2015-01-01

    Although the region of interest in high-resolution peripheral quantitative computed tomography, defined based on the manufacturer's protocol for in vivo scanning, provides consistency and is practically convenient, it does not take into account possible variation in morphology in the regions adjacent to the measurement site. This study aimed at compare the morphologic variation in measurements using the standard fixed offset distance to define the distal starting slice against those obtained by using a relative measurement position scaled to the individual bone length at the distal radius and tibia in normal healthy adult subjects. A total of 40 healthy adult subjects (median height, 175.3 cm; range: 150.0-196.0 cm) were included in the study. High-resolution peripheral quantitative computed tomography at the distal radius and tibia was performed in all subjects, the region of interest defined by, first, the standard measurement protocol, where the most distal CT slice was 9.5 mm and 22.5 mm from the end plate of the radius and tibia, respectively, and second, the relative measurement method, where the most distal CT slice was at 4% and 7% of the radial and tibial lengths, respectively. Volumetric densities and microarchitectural parameters were compared between the 2 methods. Measurements of the total and cortical volumetric density and cortical thickness at the radius and tibia and cortical porosity, trabecular volumetric density, and trabecular number at the tibia were significantly different between the 2 methods (all p < 0.001). The predicted morphologic variation with varying measurement position was substantial at both the radius (up to 34%) and the tibia (up to 36%). A lack of consideration to height (and in turn the bone lengths) in the standard patient protocol could lead to the introduction of systematic errors in radial and tibial measurements. Although this may not be of particular significance in longitudinal studies in the same individual, it

  19. Quantitative comparison of functional magnetic resonance imaging with positron emission tomography using a force-related paradigm.

    PubMed

    Dettmers, C; Connelly, A; Stephan, K M; Turner, R; Friston, K J; Frackowiak, R S; Gadian, D G

    1996-12-01

    The intention of our study was to compare functional magnetic resonance imaging (fMRI) with positron emission tomography (PET). We used the same force-related motor paradigm for both techniques, which allows for quantification of stimulus intensity. Regional cerebral blood flow (rCBF) was determined with PET in six male subjects (age 30 +/- 3) using the slow bolus injection technique and oxygen-15-labeled water. Scans were collected during six different conditions: at rest and during repetitive Morse key press at 1 Hz, with the right index finger at a range of different forces. In a second series of experiments fMRI data were acquired under similar conditions in six volunteers in a single slice parallel to and 51 +/- 3 mm dorsal to the anterior and posterior commissure (AC-PC). A conventional 1.5-T clinical magnetic resonance (MR) system and the FLASH technique were used. The data obtained in both series of experiments were subjected to the same statistical analyses. Statistical parametric maps (SPM) were generated by two different approaches: a correlation between peak force and rCBF or fMRI signal and using a categorical comparison of force exerted with rest. SPMs were coregistered with anatomical MR images. PET and fMRI measurements demonstrated activation in the primary motor cortex (M1) and posterior supplementary motor cortex in all subjects. Correlation analysis demonstrated foci in the M1 in four subjects with PET and in only one subject with fMRI. Locations of activation peaks differed by 2 to 8 mm between imaging methods. The relationship between fMRI signal or rCBF and peak force was logarithmic. The maximum increase in fMRI signal was 5.0% +/- 0.9 at 60% of the maximum voluntary contraction while the corresponding increase in rCBF was 13.7% +/- 1.2. The ratio of percentage rCBF change to percentage fMRI signal change was very similar across all force levels. The high degree of correspondence between PET and fMRI data provides good cross-validation for

  20. The Humphrey optical coherence tomography scanner: quantitative analysis and reproducibility study of the normal human retinal nerve fibre layer

    PubMed Central

    Jones, A.; Sheen, N.; North, R.; Morgan, J.

    2001-01-01

    BACKGROUND/AIMS—To determine the reproducibility of the Humphrey optical coherence tomography scanner (OCT), software version 5.0, for measurement of retinal nerve fibre layer (RNFL) thickness in normal subjects and to compare OCT measurements with published histological thickness of the human RNFL.
METHODS—Three independent measurements were obtained at each session for one eye from 15 normal subjects with a mean age of 30.8 (SD 10.9) years. Scans were taken in the peripapillary retina using the default setting (1.74 mm radius from centre of the optic disc) and were repeated 1 week later. Additional scans were obtained at the optic nerve head (ONH) margin overlying the scleral rim, for comparison with available histological data on the human RNFL.
RESULTS—For the 1.74 mm circular scan, the mean coefficient of variation (COV) for the global RNFL thickness measurement was 5% (SD 3%). This increased to 8% (3%) for quadrant measurements and to 9% (3%) with further subdivision into 12 segments. Significant differences (p<0.05) between sessions were only found when the data were divided into segments. The mean RNFL thickness for the 1.74 mm scan was 127.87 (9.81) µm. The RNFL was maximal at the superior disc pole, 161.44 µm (14.8), and minimal at the temporal pole, 83.1 (12.8) µm. Peak thickness values occurred superior temporal and inferior temporal to the vertical axis. RNFL thickness for every sector of the disc was greatest at the margin of the optic disc (mean 185.79 µm; SD 32.61). Although the variation in RNFL thickness around the disc follows published histology data, the OCT underestimates RNFL thickness by an average of 37% (SD 11; range 21-48%).
CONCLUSION—The OCT provides reproducible measurement of the retinal structures that are consistent with the properties of the RNFL. However, comparison with available studies of RNFL thickness in the human suggests that in its present form, the OCT underestimates RNFL thickness. Further

  1. Hybrid deterministic and stochastic x-ray transport simulation for transmission computed tomography with advanced detector noise model

    NASA Astrophysics Data System (ADS)

    Popescu, Lucretiu M.

    2016-03-01

    We present a model for simulation of noisy X-ray computed tomography data sets. The model is made of two main components, a photon transport simulation component that generates the noiseless photon field incident on the detector, and a detector response model that takes as input the incident photon field parameters and given the X-ray source intensity and exposure time can generate noisy data sets, accordingly. The photon transport simulation component combines direct ray-tracing of polychromatic X-rays for calculation of transmitted data, with Monte Carlo simulation for calculation of the scattered-photon data. The Monte Carlo scatter simulation is accelerated by implementing particle splitting and importance sampling variance reduction techniques. The detector-incident photon field data are stored as energy expansion coefficients on a refined grid that covers the detector area. From these data the detector response model is able to generate noisy detector data realizations, by reconstituting the main parameters that describe each detector element response in statistical terms, including spatial correlations. The model is able to generate very fast, on the fly, CT data sets corresponding to different radiation doses, as well as detector response characteristics, facilitating data management in extensive optimization studies by reducing the computation time and storage space demands.

  2. Phase contrast imaging X-ray computed tomography: quantitative characterization of human patellar cartilage matrix with topological and geometrical features

    NASA Astrophysics Data System (ADS)

    Nagarajan, Mahesh B.; Coan, Paola; Huber, Markus B.; Diemoz, Paul C.; Wismüller, Axel

    2014-03-01

    Current assessment of cartilage is primarily based on identification of indirect markers such as joint space narrowing and increased subchondral bone density on x-ray images. In this context, phase contrast CT imaging (PCI-CT) has recently emerged as a novel imaging technique that allows a direct examination of chondrocyte patterns and their correlation to osteoarthritis through visualization of cartilage soft tissue. This study investigates the use of topological and geometrical approaches for characterizing chondrocyte patterns in the radial zone of the knee cartilage matrix in the presence and absence of osteoarthritic damage. For this purpose, topological features derived from Minkowski Functionals and geometric features derived from the Scaling Index Method (SIM) were extracted from 842 regions of interest (ROI) annotated on PCI-CT images of healthy and osteoarthritic specimens of human patellar cartilage. The extracted features were then used in a machine learning task involving support vector regression to classify ROIs as healthy or osteoarthritic. Classification performance was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC). The best classification performance was observed with high-dimensional geometrical feature vectors derived from SIM (0.95 ± 0.06) which outperformed all Minkowski Functionals (p < 0.001). These results suggest that such quantitative analysis of chondrocyte patterns in human patellar cartilage matrix involving SIM-derived geometrical features can distinguish between healthy and osteoarthritic tissue with high accuracy.

  3. Quantitative assessment of optical properties in healthy cartilage and repair tissue by optical coherence tomography and histology (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Jansen, Sanne M. A.; Cernohorsky, Paul; de Bruin, Daniel M.; van der Pol, Edwin; Savci-Heijink, Cemile D.; Strackee, Simon D.; Faber, Dirk J.; van Leeuwen, Ton G.

    2016-02-01

    Quantification of the OCT signal is an important step toward clinical implementation of a diagnostic tool in cartilage imaging. Discrimination of structural cartilage differences in patients with osteoarthritis is critical, yet challenging. This study assesses the variation in the optical attenuation coefficient (μOCT) between healthy cartilage, repair tissue, bone and layers within repair tissue in a controlled setting. OCT and histology was used to assess goat talus articular surfaces in which central osteochondral defects were created. Exact matches of OCT and histology were selected for research. μOCT measurements were taken from healthy cartilage, repair tissue and bone. Measured μOCT in healthy cartilage was higher compared to both repair tissue and bone tissue. Two possible mechanisms for the difference in attenuation were investigated. We studied morphological parameters in terms of nucleus count, nucleus size and inter-nucleus distance. Collagen content in healthy cartilage and repair tissue was assessed using polarization microscopy. Quantitative analysis of the nuclei did not demonstrate a difference in nucleus size and count between healthy cartilage and repair tissue. In healthy cartilage, cells were spaced farther apart and had a lower variation in local nuclear density compared to repair tissue. Polarization microscopy suggested higher collagen content in healthy cartilage compared to repair tissue. μOCT measurements can distinguish between healthy cartilage, repair tissue and bone. Results suggest that cartilage OCT attenuation measurements could be of great impact in clinical diagnostics of osteoarthritis.

  4. Treatment of subclinical hypothyroidism does not affect bone mass as determined by dual-energy X-ray absorptiometry, peripheral quantitative computed tomography and quantitative bone ultrasound in Spanish women

    PubMed Central

    Roncero-Martin, Raul; Calderon-Garcia, Julian F.; Santos-Vivas, Mercedes; Vera, Vicente; Martínez-Alvárez, Mariana; Rey-Sanchez, Purificación

    2015-01-01

    Introduction The results of studies examining the influence of subclinical hypothyroidism (SCH) and levothyroxine (L-T4) replacement therapy on bone have generated considerable interest but also controversy. The present research aims to evaluate the effects of L-T4 treatment on different skeletal sites in women. Material and methods A group of 45 premenopausal (mean age: 43.62 ±6.65 years) and 180 postmenopausal (mean age: 59.51 ±7.90 years) women with SCH who were undergoing L-T4 replacement therapy for at least 6 months were compared to 58 pre- and 180 postmenopausal women with SCH (untreated) matched for age. The mean doses of L-T4 were 90.88 ±42.59 µg/day in the premenopausal women and 86.35 ±34.11 µg/day in the postmenopausal women. Bone measurements were obtained using quantitative bone ultrasound (QUS) for the phalanx, dual-energy X-ray absorptiometry (DXA) for the lumbar spine and hip, and peripheral quantitative computed tomography (pQCT) for the non-dominant distal forearm. Results No differences were observed between patients and untreated controls in these bone measurements except in the bone mineral density (BMD) of the spine (p = 0.0214) in postmenopausal women, which was greater in treated women than in untreated controls. Conclusions Our results indicate that adequate metabolic control through replacement treatment with L-T4 in pre- and postmenopausal women does not affect bone mass. PMID:26528344

  5. Quantitative study of fluctuation effects by fast lattice Monte Carlo simulations: Compression of grafted homopolymers

    SciTech Connect

    Zhang, Pengfei; Wang, Qiang

    2014-01-28

    Using fast lattice Monte Carlo (FLMC) simulations [Q. Wang, Soft Matter 5, 4564 (2009)] and the corresponding lattice self-consistent field (LSCF) calculations, we studied a model system of grafted homopolymers, in both the brush and mushroom regimes, in an explicit solvent compressed by an impenetrable surface. Direct comparisons between FLMC and LSCF results, both of which are based on the same Hamiltonian (thus without any parameter-fitting between them), unambiguously and quantitatively reveal the fluctuations/correlations neglected by the latter. We studied both the structure (including the canonical-ensemble averages of the height and the mean-square end-to-end distances of grafted polymers) and thermodynamics (including the ensemble-averaged reduced energy density and the related internal energy per chain, the differences in the Helmholtz free energy and entropy per chain from the uncompressed state, and the pressure due to compression) of the system. In particular, we generalized the method for calculating pressure in lattice Monte Carlo simulations proposed by Dickman [J. Chem. Phys. 87, 2246 (1987)], and combined it with the Wang-Landau–Optimized Ensemble sampling [S. Trebst, D. A. Huse, and M. Troyer, Phys. Rev. E 70, 046701 (2004)] to efficiently and accurately calculate the free energy difference and the pressure due to compression. While we mainly examined the effects of the degree of compression, the distance between the nearest-neighbor grafting points, the reduced number of chains grafted at each grafting point, and the system fluctuations/correlations in an athermal solvent, the θ-solvent is also considered in some cases.

  6. Altered myocardial perfusion in patients with angina pectoris or silent ischemia during exercise as assessed by quantitative thallium-201 single-photon emission computed tomography

    SciTech Connect

    Mahmarian, J.J.; Pratt, C.M.; Cocanougher, M.K.; Verani, M.S. )

    1990-10-01

    The extent of abnormally perfused myocardium was compared in patients with and without chest pain during treadmill exercise from a large, relatively low-risk consecutive patient population (n = 356) referred for quantitative thallium-201 single-photon emission computed tomography (SPECT). All patients had concurrent coronary angiography. Patients were excluded if they had prior coronary angioplasty or bypass surgery. Tomographic images were assessed visually and from computer-generated polar maps. Chest pain during exercise was as frequent in patients with normal coronary arteries (12%) as in those with significant (greater than 50% stenosis) coronary artery disease (CAD) (14%). In the 219 patients with significant CAD, silent ischemia was fivefold more common than symptomatic ischemia (83% versus 17%, p = 0.0001). However, there were no differences in the extent, severity, or distribution of coronary stenoses in patients with silent or symptomatic ischemia. Our major observation was that the extent of quantified SPECT perfusion defects was nearly identical in patients with (20.9 +/- 15.9%) and without (20.5 +/- 15.6%) exertional chest pain. The sensitivity for detecting the presence of CAD was significantly improved with quantitative SPECT compared with stress electrocardiography (87% versus 65%, p = 0.0001). Although scintigraphic and electrocardiographic evidence of exercise-induced ischemia were comparable in patients with chest pain (67% versus 73%, respectively; p = NS), SPECT was superior to stress electrocardiography for detecting silent myocardial ischemia. The majority of patients in this study with CAD who developed ischemia during exercise testing were asymptomatic, although they exhibited an angiographic profile and extent of abnormally perfused myocardium similar to those of patients with symptomatic ischemia.

  7. Quantitative cerebral perfusion assessment using microscope-integrated analysis of intraoperative indocyanine green fluorescence angiography versus positron emission tomography in superficial temporal artery to middle cerebral artery anastomosis

    PubMed Central

    Kobayashi, Shinya; Ishikawa, Tatsuya; Tanabe, Jun; Moroi, Junta; Suzuki, Akifumi

    2014-01-01

    Background: Intraoperative qualitative indocyanine green (ICG) angiography has been used in cerebrovascular surgery. Hyperperfusion may lead to neurological complications after superficial temporal artery to middle cerebral artery (STA-MCA) anastomosis. The purpose of this study is to quantitatively evaluate intraoperative cerebral perfusion using microscope-integrated dynamic ICG fluorescence analysis, and to assess whether this value predicts hyperperfusion syndrome (HPS) after STA-MCA anastomosis. Methods: Ten patients undergoing STA-MCA anastomosis due to unilateral major cerebral artery occlusive disease were included. Ten patients with normal cerebral perfusion served as controls. The ICG transit curve from six regions of interest (ROIs) on the cortex, corresponding to ROIs on positron emission tomography (PET) study, was recorded. Maximum intensity (IMAX), cerebral blood flow index (CBFi), rise time (RT), and time to peak (TTP) were evaluated. Results: RT/TTP, but not IMAX or CBFi, could differentiate between control and study subjects. RT/TTP correlated (|r| = 0.534-0.807; P < 0.01) with mean transit time (MTT)/MTT ratio in the ipsilateral to contralateral hemisphere by PET study. Bland–Altman analysis showed a wide limit of agreement between RT and MTT and between TTP and MTT. The ratio of RT before and after bypass procedures was significantly lower in patients with postoperative HPS than in patients without postoperative HPS (0.60 ± 0.032 and 0.80 ± 0.056, respectively; P = 0.017). The ratio of TTP was also significantly lower in patients with postoperative HPS than in patients without postoperative HPS (0.64 ± 0.081 and 0.85 ± 0.095, respectively; P = 0.017). Conclusions: Time-dependent intraoperative parameters from the ICG transit curve provide quantitative information regarding cerebral circulation time with quality and utility comparable to information obtained by PET. These parameters may help predict the occurrence of postoperative HPS. PMID

  8. 3-D imaging and quantitative comparison of human dentitions and simulated bite marks.

    PubMed

    Blackwell, S A; Taylor, R V; Gordon, I; Ogleby, C L; Tanijiri, T; Yoshino, M; Donald, M R; Clement, J G

    2007-01-01

    This study presents a technique developed for 3-D imaging and quantitative comparison of human dentitions and simulated bite marks. A sample of 42 study models and the corresponding bites, made by the same subjects in acrylic dental wax, were digitised by laser scanning. This technique allows image comparison of a 3-D dentition with a 3-D bite mark, eliminating distortion due to perspective as experienced in conventional photography. Cartesian co-ordinates of a series of landmarks were used to describe the dentitions and bite marks, and a matrix was created to compare all possible combinations of matches and non-matches using cross-validation techniques. An algorithm, which estimated the probability of a dentition matching its corresponding bite mark, was developed. A receiver operating characteristic graph illustrated the relationship between values for specificity and sensitivity. This graph also showed for this sample that 15% of non-matches could not be distinguished from the true match, translating to a 15% probability of falsely convicting an innocent person. PMID:16391946

  9. Quantitative multi-agent models for simulating protein release from PLGA bioerodible nano- and microspheres.

    PubMed

    Barat, Ana; Crane, Martin; Ruskin, Heather J

    2008-09-29

    Using poly(lactide-co-glycolide) (PLGA) particles for drug encapsulation and delivery has recently gained considerable popularity for a number of reasons. An advantage in one sense, but a drawback of PLGA use in another, is that drug delivery systems made of this material can provide a wide range of dissolution profiles, due to their internal structure and properties related to particles' manufacture. The advantages of enriching particulate drug design experimentation with computer models, are evident with simulations used to predict and optimize design, as well as indicate choice of best manufacturing parameters. In the present work, we seek to understand the phenomena observed for PLGA micro- and nanospheres, through Cellular Automata (CA) agent-based Monte Carlo (MC) models. Systems are studied both over large temporal scales (capturing slow erosion of PLGA) and for various spatial configurations (capturing initial as well as dynamic morphology). The major strength of this multi-agent approach is to observe dissolution directly, by monitoring the emergent behaviour: the dissolution profile manifested, as a sphere erodes. Different problematic aspects of the modelling process are discussed in details in this paper. The models were tested on experimental data from literature, demonstrating very good performance. Quantitative discussion is provided throughout the text in order to make a demonstration of the use in practice of the proposed model. PMID:18436414

  10. Quantitative Simulations of MST Visual Receptive Field Properties Using a Template Model of Heading Estimation

    NASA Technical Reports Server (NTRS)

    Stone, Leland S.; Perrone, J. A.

    1997-01-01

    We previously developed a template model of primate visual self-motion processing that proposes a specific set of projections from MT-like local motion sensors onto output units to estimate heading and relative depth from optic flow. At the time, we showed that that the model output units have emergent properties similar to those of MSTd neurons, although there was little physiological evidence to test the model more directly. We have now systematically examined the properties of the model using stimulus paradigms used by others in recent single-unit studies of MST: 1) 2-D bell-shaped heading tuning. Most MSTd neurons and model output units show bell-shaped heading tuning. Furthermore, we found that most model output units and the finely-sampled example neuron in the Duffy-Wurtz study are well fit by a 2D gaussian (sigma approx. 35deg, r approx. 0.9). The bandwidth of model and real units can explain why Lappe et al. found apparent sigmoidal tuning using a restricted range of stimuli (+/-40deg). 2) Spiral Tuning and Invariance. Graziano et al. found that many MST neurons appear tuned to a specific combination of rotation and expansion (spiral flow) and that this tuning changes little for approx. 10deg shifts in stimulus placement. Simulations of model output units under the same conditions quantitatively replicate this result. We conclude that a template architecture may underlie MT inputs to MST.

  11. Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study

    PubMed Central

    Abdallah, Jihad M; Goffinet, Bruno; Cierco-Ayrolles, Christine; Pérez-Enciso, Miguel

    2003-01-01

    Recently, the use of linkage disequilibrium (LD) to locate genes which affect quantitative traits (QTL) has received an increasing interest, but the plausibility of fine mapping using linkage disequilibrium techniques for QTL has not been well studied. The main objectives of this work were to (1) measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and (2) investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or biallelic marker loci. The test of association between a marker and QTL and the power of the test were calculated based on single-marker regression analysis. The results show the presence of substantial linkage disequilibrium with closely linked marker loci after 100 to 200 generations of random mating. Although the power to test the association with a frequent QTL of large effect was satisfactory, the power was low for the QTL with a small effect and/or low frequency. More powerful, multi-locus methods may be required to map low frequent QTL with small genetic effects, as well as combining both linkage and linkage disequilibrium information. The results also showed that multiallelic markers are more useful than biallelic markers to detect linkage disequilibrium and association at an equal distance. PMID:12939203

  12. Quantitative cerebral blood flow measurements using N-isopropyl-(iodine 123) p-iodoamphetamine and single photon emission computed tomography with rotating gamma camera

    SciTech Connect

    Matsuda, H.; Seki, H.; Sumiya, H.; Tsuji, S.; Tonami, N.; Hisada, K.; Fujii, H.; Kobayashi, H.

    1986-01-01

    Sixty regional cerebral blood flow measurements were performed on 4 normal volunteers, 7 epileptics, and 40 cerebrovascular disorders using intravenously injected N-isopropyl-(I-123)p-iodoamphetamine (123I-IMP) and single photon emission computed tomography with rotating gamma camera. Arterial blood sampling was combined for obtaining absolute blood flow values. The brain activity distributions of the tomographic image from 30 min after injection, when brain activity reached a plateau, were corrected to represent 5-min reference values with the use of the monitored entire brain's time-activity curve. Brain mean blood flow values ranged from 54 to 63, 34 to 59, and 20 to 60 ml/100 g/min, in normal volunteers, epileptics, and subjects with cerebrovascular disorders, respectively. Brain mean /sup 123/I-IMP uptake corrected for injection dose did not correlate with these absolute flow values. This quantitative method is especially useful for diagnosing diffuse flow reductions, which were observed in 8 (14%) of 56 studies in the patients.

  13. Challenges and Approaches to Quantitative Therapy Response Assessment in Glioblastoma Multiforme Using the Novel Apoptosis Positron Emission Tomography Tracer F-18 ML-101

    PubMed Central

    Oborski, Matthew J; Laymon, Charles M; Qian, Yongxian; Lieberman, Frank S; Nelson, Arden D; Mountz, James M

    2014-01-01

    Evaluation of cancer-therapy efficacy at early time points is necessary for realizing the goal of delivering maximally effective treatment. Molecular imaging with carefully selected tracers and methodologies can provide the means for realizing this ability. Many therapies are aimed at inducing apoptosis in malignant tissue; thus, the ability to quantify apoptosis in vivo may be a fruitful approach. Apoptosis rate changes occur on a fast time scale, potentially allowing correspondingly rapid decisions regarding therapy value. However, quantification of tissue status based on apoptosis imaging is complicated by this time scale and by the spatial heterogeneity of the process. Using the positron emission tomography (PET) tracer 2-(5-fluoro-pentyl)-2-methyl-malonic acid (F-18 ML-10), we present methods of voxelwise analysis yielding quantitative measures of apoptosis changes, parametric apoptosis change images, and graphical representation of apoptotic features. A method of deformable registration to account for anatomic changes between scan time points is also demonstrated. Overall apoptotic rates deduced from imaging depend on tumor density and the specific rate of apoptosis, a situation resulting in an ambiguity in the source of observed image-based changes. The ambiguity may be resolved through multimodality imaging. An example of intracellular sodium magnetic resonance imaging coupled with F-18 ML-10 PET is provided. PMID:24772214

  14. Interim 18F-fluorodeoxyglucose positron emission tomography in diffuse large B-cell lymphoma: qualitative or quantitative interpretation--where do we stand?

    PubMed

    Meignan, Michel; Itti, Emmanuel; Gallamini, Andrea; Haioun, Corinne

    2009-11-01

    Interim 18F-fluorodeoxyglucose positron emission tomography performed early during the course of therapy in diffuse large B-cell lymphoma is highly predictive of outcome and now used in many clinical trials to validate risk-adapted strategies. However, interpretation criteria of interim PET are not yet appropriately defined for the evaluation of tumor response and chemosensitivity. From the results of our studies, a quantitative approach based on SUV(max) reduction between baseline PET (PET0) and interim PET demonstrated a higher predictive value than visual analysis when PET was performed at two cycles (PET2) but was equivalent to visual analysis at four cycles (PET4). The SUV(max) reduction index at PET2 seems to be the best predictor of the response compared to clinical or molecular prognostic indices. When visual analysis is necessary, the use of an online independent reading network may solve the interobserver variability, but the hurdles of visual analysis deserve an international validation study to confirm the newly proposed criteria. PMID:19863178

  15. Fracture Risk Assessment in Older Adults Using a Combination of Selected Quantitative Computed Tomography Bone Measures: A Subanalysis of the Age, Gene/Environment Susceptibility-Reykjavik Study

    PubMed Central

    Rianon, Nahid J.; Lang, Thomas F.; Siggeirsdottir, Kristin; Sigurdsson, Gunnar; Eiriksdottir, Gudny; Sigurdsson, Sigurdur; Jonsson, Brynjolfur Y.; Garcia, Melissa; Yu, Binbing; Kapadia, Asha S.; Taylor, Wendell C.; Selwyn, Beatrice J.; Gudnason, Vilmundur; Launer, Lenore J.; Harris, Tamara B.

    2016-01-01

    Bone mineral density (BMD) and geometric bone measures are individually associated with prevalent osteoporotic fractures. Whether an aggregate of these measures would better associate with fractures has not been examined. We examined relationships between self-reported fractures and selected bone measures acquired by quantitative computerized tomography (QCT), a composite bone score, and QCT-acquired dual-energy X-ray absorptiometry–like total femur BMD in 2110 men and 2682 women in the Age, Gene/Environment Susceptibility-Reykjavik Study. The combined bone score was generated by summing gender-specific Z-scores for 4 QCT measures: vertebral trabecular BMD, femur neck cortical thickness, femur neck trabecular BMD, and femur neck minimal cross-sectional area. Except for the latter measure, lower scores for QCT measures, singly and combined, showed positive (p < 0.05) associations with fractures. Results remained the same in stratified models for participants not taking bone-promoting medication. In women on bone-promoting medication, greater femur neck cortical thickness and trabecular BMD were significantly associated with fracture status. However, the association between fracture and combined bone score was not stronger than the associations between fracture and individual measures or total femur BMD. Thus, the selected measures did not all similarly associate with fracture status and did not appear to have an additive effect on fracture status. PMID:23562129

  16. Quantitative analysis of the reconstruction errors of the currently popular algorithm of magnetic resonance electrical property tomography at the interfaces of adjacent tissues.

    PubMed

    Duan, Song; Xu, Chao; Deng, Guanhua; Wang, Jiajia; Liu, Feng; Xin, Sherman Xuegang

    2016-06-01

    This work quantitatively analyzed the reconstruction errors (REs) of electrical property (EP) images using a currently popular algorithm of magnetic resonance electrical property tomography (MREPT), which occurred along the tissue interfaces. Transmitted magnetic fields B1+ were acquired at 3 T using a birdcage coil loaded with a phantom consisting of various adjacent tissues. Homogeneous Helmholtz was employed to calculate the EP maps by Laplacian computation of central differences. The maps of absolute REs (aREs) and relative REs (rREs) were calculated. The maximum and mean rREs, in addition to rRE distributions at the interfaces, were presented. Reconstructed EP maps showed various REs along different interface boundaries. Among all the investigated tissue interfaces, the kidney-fat interface presented the maximum mean rREs for both conductivity and relative permittivity. The minimum mean rRE of conductivity was observed at the spleen-muscle interface, and the minimum mean rRE of relative permittivity was detected along the lung-heart interface. The mean rREs ranged from 0.3986 to 36.11 for conductivity and 0.2218 to 11.96 for relative permittivity. Overall, this research indicates that different REs occur at various tissue boundaries, as shown by the currently popular algorithm of MREPT. Thus, REs should be considered when applying MREPT to reconstruct the EP distributions inside the human body. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27037715

  17. Quantitative assessment of selective in-plane shielding of tissues in computed tomography through evaluation of absorbed dose and image quality.

    PubMed

    Geleijns, J; Salvadó Artells, M; Veldkamp, W J H; López Tortosa, M; Calzado Cantera, A

    2006-10-01

    This study aimed at assessment of efficacy of selective in-plane shielding in adults by quantitative evaluation of the achieved dose reduction and image quality. Commercially available accessories for in-plane shielding of the eye lens, thyroid and breast, and an anthropomorphic phantom were used for the evaluation of absorbed dose and image quality. Organ dose and total energy imparted were assessed by means of a Monte Carlo technique taking into account tube voltage, tube current, and scanner type. Image quality was quantified as noise in soft tissue. Application of the lens shield reduced dose to the lens by 27% and to the brain by 1%. The thyroid shield reduced thyroid dose by 26%; the breast shield reduced dose to the breasts by 30% and to the lungs by 15%. Total energy imparted (unshielded/shielded) was 88/86 mJ for computed tomography (CT) brain, 64/60 mJ for CT cervical spine, and 289/260 mJ for CT chest scanning. An increase in image noise could be observed in the ranges were bismuth shielding was applied. The observed reduction of organ dose and total energy imparted could be achieved more efficiently by a reduction of tube current. The application of in-plane selective shielding is therefore discouraged. PMID:16604323

  18. Impact of Dynamic Specimen Shape Evolution on the Atom Probe Tomography Results of Doped Epitaxial Oxide Multilayers: Comparison of Experiment and Simulation

    SciTech Connect

    Madaan, Nitesh; Bao, Jie; Nandasiri, Manjula I.; Xu, Zhijie; Thevuthasan, Suntharampillai; Devaraj, Arun

    2015-08-31

    The experimental atom probe tomography results from two different specimen orientations (top-down and side-ways) of a high oxygen ion conducting Samaria-doped-ceria/Scandia-stabilized-zirconia multilayer thin film solid oxide fuel cell electrolyte was correlated with level-set method based field evaporation simulations for the same specimen orientations. This experiment-theory correlation explains the dynamic specimen shape evolution and ion trajectory aberrations that can induce density artifacts in final reconstruction leading to inaccurate estimation of interfacial intermixing. This study highlights the need and importance of correlating experimental results with field evaporation simulations when using atom probe tomography for studying oxide heterostructure interfaces.

  19. Estimate of transport properties of porous media by microfocus X-ray computed tomography and random walk simulation

    NASA Astrophysics Data System (ADS)

    Nakashima, Yoshito; Watanabe, Yoshinori

    2002-12-01

    The transport properties (porosity, surface-to-volume ratio of the pore space, diffusion coefficient, and permeability) of a porous medium were calculated by image analysis and random walk simulation using the digital image data on the pore structure of a bead pack (diameter 2.11 mm). A theory developed for laboratory experiments of nuclear magnetic resonance was applied to the random walk simulation. The three-dimensional data set (2563 voxels) of the bead pack was obtained by microfocus X-ray computed tomography at a spatial resolution of 0.053 mm. An original cluster labeling program, Kai3D.m, was used to estimate the porosity and surface-to-volume ratio. The surface-to-volume ratio and diffusion coefficient were calculated by an original random walk program, RW3D.m. The calculations were completed on a personal computer in reasonable time (≤13 hours). The permeability was estimated by substituting the results of Kai3D.m and RW3D.m into the Kozeny-Carman equation. The results for the porosity, surface-to-volume ratio, and diffusion coefficient were within 5-8% of measured values, whereas the calculated permeability involved an error of 35%. The promising results of the present study indicate that it is possible to estimate the permeability of porous media with reasonable accuracy by the diffusometry and random walk simulation. Because, in principle, the diffusometry could be performed by proton nuclear magnetic resonance logging, the method of estimating the transport properties presented here is applicable to the in situ measurement of strata. We open the original Mathematica® programs (Kai3D.m and RW3D.m) used to calculate the porosity, surface-to-volume ratio, and diffusion coefficient at the authors' home page to facilitate the personal-computer-based study of porous media using X-ray computed tomography.

  20. Dual-energy X-ray absorptiometry, peripheral quantitative computed tomography, and micro-computed tomography techniques are discordant for bone density and geometry measurements in the guinea pig.

    PubMed

    Mak, Ivy L; DeGuire, Jason R; Lavery, Paula; Agellon, Sherry; Weiler, Hope A

    2016-05-01

    This study aims to examine agreement among bone mineral content (BMC) and density (BMD) estimates obtained using dual-energy X-ray absorptiometry (DXA), peripheral quantitative computed tomography (pQCT), and micro-computed tomography (μCT) against high-resolution μCT and bone ash of the guinea pig femur. Middle-aged (n = 40, 86 weeks) male guinea pigs underwent in vivo followed by ex vivo DXA (Hologic QDR 4500A) scanning for intact and excised femur BMC and areal density. To assess bone architecture and strength, excised femurs were scanned on pQCT (Stratec XCT 2000L) as well as on two μCT scanners (LaTheta LCT-200; Skyscan 1174), followed by three-point bending test. Reproducibility was determined using triplicate scans; and agreement assessed using Bland-Altman plots with reference methods being high-resolution μCT (Skyscan) for BMD and bone ashing for BMC. All techniques showed satisfactory ex vivo precision (CV 0.05-4.3 %). However, bias compared to the reference method was highest (207.5 %) in trabecular bone volume fraction (BV/TV) measured by LaTheta, and unacceptable in most total femur and cortical bone measurements. Volumetric BMD (vBMD) and BV/TV derived by LaTheta and pQCT at the distal metaphysis were biased from the Skyscan by an average of 49.3 and 207.5 %, respectively. Variability of vBMD, BV/TV and cross-sectional area at the diaphysis ranged from -5.5 to 30.8 %. LaTheta best quantified total femur BMC with an upper bias of 3.3 %. The observed differences among imaging techniques can be attributable to inherent dissimilarity in construction design, calibration, segmentation and scanning resolution used. These bone imaging tools are precise but are not comparable, at least when assessing guinea pig bones. PMID:26058491

  1. The use of a dynamic real-time jaw tracking device and cone beam computed tomography simulation

    PubMed Central

    He, Shushu; Kau, Chung How; Liao, Lina; Kinderknecht, Keith; Ow, Andrew; Saleh, Tayem Abou

    2016-01-01

    Background: The aim was to introduce and preliminarily evaluate a new software application, SICAT Function, which can directly combine and merge three-dimensional cone beam computed tomography (CBCT) and electronic SICAT jaw motion tracking (JMT) data. Methods: A detailed description of the methods and dynamic clinical simulation of mandibular movements of a patient are demonstrated. Functional jaw movements on 3 days were recorded by JMT tracking system. The simulation was performed by merging CBCT and JMT data in the software SICAT Function suite. The condylar position simulated by SICAT Function suite was compared with real condyle position showed by a CBCT of the patient. Results: The incisor ranges of functional movements were displayed by JMT tracking system. The visualization of patient-specific mandibular movement including the translation of the condyles was displayed after data merge. The recordings of mandibular movements of the patient were similar on 3 different days. The condylar position simulated by SICAT was coincident with real condyle position by CBCT data with the same amount of mouth opening. Conclusions: The SICAT Function software is a system capable of measuring and visualizing patient-specific jaw movement relative to the patient-specific anatomy of the jaw. Further studies are needed to validate its accuracy and its potential for future use. PMID:27563619

  2. Use of 3-D magnetic resonance electrical impedance tomography in detecting human cerebral stroke: a simulation study*

    PubMed Central

    Gao, Nuo; Zhu, Shan-an; He, Bin

    2005-01-01

    We have developed a new three dimensional (3-D) conductivity imaging approach and have used it to detect human brain conductivity changes corresponding to acute cerebral stroke. The proposed Magnetic Resonance Electrical Impedance Tomography (MREIT) approach is based on the J-Substitution algorithm and is expanded to imaging 3-D subject conductivity distribution changes. Computer simulation studies have been conducted to evaluate the present MREIT imaging approach. Simulations of both types of cerebral stroke, hemorrhagic stroke and ischemic stroke, were performed on a four-sphere head model. Simulation results showed that the correlation coefficient (CC) and relative error (RE) between target and estimated conductivity distributions were 0.9245±0.0068 and 8.9997%±0.0084%, for hemorrhagic stroke, and 0.6748±0.0197 and 8.8986%±0.0089%, for ischemic stroke, when the SNR (signal-to-noise radio) of added GWN (Gaussian White Noise) was 40. The convergence characteristic was also evaluated according to the changes of CC and RE with different iteration numbers. The CC increases and RE decreases monotonously with the increasing number of iterations. The present simulation results show the feasibility of the proposed 3-D MREIT approach in hemorrhagic and ischemic stroke detection and suggest that the method may become a useful alternative in clinical diagnosis of acute cerebral stroke in humans. PMID:15822161

  3. Biomechanical effects of teriparatide in women with osteoporosis treated previously with alendronate and risedronate: results from quantitative computed tomography-based finite element analysis of the vertebral body.

    PubMed

    Chevalier, Yan; Quek, Evelyn; Borah, Babul; Gross, Gary; Stewart, John; Lang, Thomas; Zysset, Philippe

    2010-01-01

    Previous antiresorptive treatment may influence the anabolic response to teriparatide. The OPTAMISE (Open-label Study to Determine How Prior Therapy with Alendronate or Risedronate in Postmenopausal Women with Osteoporosis Influences the Clinical Effectiveness of Teriparatide) study reported greater increases in biochemical markers of bone turnover and volumetric bone mineral density (BMD) when 12 months of teriparatide treatment was preceded by 2 years or more of risedronate versus alendronate treatment. The objective of this study was to use quantitative computed tomography (CT)-based nonlinear finite element modeling to evaluate how prior therapy with alendronate or risedronate in postmenopausal women with osteoporosis influences the biomechanical effectiveness of teriparatide. Finite element models of the L1 vertebra were created from quantitative CT scans, acquired before and after 12 months of therapy with teriparatide, from 171 patients from the OPTAMISE study. These models were subjected to uniaxial compression. Total BMD-derived bone volume fraction (BV/TV(d), i.e., bone volume [BV]/total volume [TV]), estimated from quantitative CT-based volumetric BMD, vertebral stiffness, and failure load (strength) were calculated for each time measurement point. The results of this study demonstrated that 12 months of treatment with teriparatide following prior treatment with either risedronate or alendronate increased BMD-derived BV/TV(d), the predicted vertebral stiffness, and failure load. However, the effects of teriparatide were more pronounced in patients treated previously with risedronate, which is consistent with the findings of the OPTAMISE study. The mean (+/-standard error) increase in stiffness was greater in the prior risedronate group than the prior alendronate group (24.6+/-3.2% versus 14.4+/-2.8%, respectively; p=0.0073). Similarly, vertebral failure load increased by 27.2+/-3.5% in the prior risedronate group versus 15.3+/-3.1% in the prior

  4. Prediction of beam hardening artefacts in computed tomography using Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Thomsen, M.; Knudsen, E. B.; Willendrup, P. K.; Bech, M.; Willner, M.; Pfeiffer, F.; Poulsen, M.; Lefmann, K.; Feidenhans'l, R.

    2015-01-01

    We show how radiological images of both single and multi material samples can be simulated using the Monte Carlo simulation tool McXtrace and how these images can be used to make a three dimensional reconstruction. Good numerical agreement between the X-ray attenuation coefficient in experimental and simulated data can be obtained, which allows us to use simulated projections in the linearisation procedure for single material samples and in that way reduce beam hardening artefacts. The simulations can be used to predict beam hardening artefacts in multi material samples with complex geometry, illustrated with an example. Linearisation requires knowledge about the X-ray transmission at varying sample thickness, but in some cases homogeneous calibration phantoms are hard to manufacture, which affects the accuracy of the calibration. Using simulated data overcomes the manufacturing problems and in that way improves the calibration.

  5. Discordance between Prevalent Vertebral Fracture and Vertebral Strength Estimated by the Finite Element Method Based on Quantitative Computed Tomography in Patients with Type 2 Diabetes Mellitus

    PubMed Central

    2015-01-01

    Background Bone fragility is increased in patients with type 2 diabetes mellitus (T2DM), but a useful method to estimate bone fragility in T2DM patients is lacking because bone mineral density alone is not sufficient to assess the risk of fracture. This study investigated the association between prevalent vertebral fractures (VFs) and the vertebral strength index estimated by the quantitative computed tomography-based nonlinear finite element method (QCT-based nonlinear FEM) using multi-detector computed tomography (MDCT) for clinical practice use. Research Design and Methods A cross-sectional observational study was conducted on 54 postmenopausal women and 92 men over 50 years of age, all of whom had T2DM. The vertebral strength index was compared in patients with and without VFs confirmed by spinal radiographs. A standard FEM procedure was performed with the application of known parameters for the bone material properties obtained from nondiabetic subjects. Results A total of 20 women (37.0%) and 39 men (42.4%) with VFs were identified. The vertebral strength index was significantly higher in the men than in the women (P<0.01). Multiple regression analysis demonstrated that the vertebral strength index was significantly and positively correlated with the spinal bone mineral density (BMD) and inversely associated with age in both genders. There were no significant differences in the parameters, including the vertebral strength index, between patients with and without VFs. Logistic regression analysis adjusted for age, spine BMD, BMI, HbA1c, and duration of T2DM did not indicate a significant relationship between the vertebral strength index and the presence of VFs. Conclusion The vertebral strength index calculated by QCT-based nonlinear FEM using material property parameters obtained from nondiabetic subjects, whose risk of fracture is lower than that of T2DM patients, was not significantly associated with bone fragility in patients with T2DM. This discordance

  6. Quantitative parameters to compare image quality of non-invasive coronary angiography with 16-slice, 64-slice and dual-source computed tomography.

    PubMed

    Burgstahler, Christof; Reimann, Anja; Brodoefel, Harald; Daferner, Ulrike; Herberts, Tina; Tsiflikas, Ilias; Thomas, Christoph; Drosch, Tanja; Schroeder, Stephen; Heuschmid, Martin

    2009-03-01

    Multi-slice computed tomography (MSCT) is a non-invasive modality to visualize coronary arteries with an overall good image quality. Improved spatial and temporal resolution of 64-slice and dual-source computed tomography (DSCT) scanners are supposed to have a positive impact on diagnostic accuracy and image quality. However, quantitative parameters to compare image quality of 16-slice, 64-slice MSCT and DSCT are missing. A total of 256 CT examinations were evaluated (Siemens, Sensation 16: n = 90; Siemens Sensation 64: n = 91; Siemens Definition: n = 75). Mean Hounsfield units (HU) were measured in the cavum of the left ventricle (LV), the ascending aorta (Ao), the left ventricular myocardium (My) and the proximal part of the left main (LM), the left anterior descending artery (LAD), the right coronary artery (RCA) and the circumflex artery (CX). Moreover, the ratio of intraluminal attenuation (HU) to myocardial attenuation was assessed for all coronary arteries. Clinical data [body mass index (BMI), gender, heart rate] were accessible for all patients. Mean attenuation (CA) of the coronary arteries was significantly higher for DSCT in comparison to 64- and 16-slice MSCT within the RCA [347 +/- 13 vs. 254 +/- 14 (64-MSCT) vs. 233 +/- 11 (16-MSCT) HU], LM (362 +/- 11/275 +/- 12/262 +/- 9), LAD (332 +/- 17/248 +/- 19/219 +/- 14) and LCX (310 +/- 12/210 +/- 13/221 +/- 10, all p < 0.05), whereas there was no significant difference between DSCT and 64-MSCT for the LV, the Ao and My. Heart rate had a significant impact on CA ratio in 16-slice and 64-slice CT only (p < 0.05). BMI had no impact on the CA ratio in DSCT only (p < 0.001). Improved spatial and temporal resolution of dual-source CT is associated with better opacification of the coronary arteries and a better contrast with the myocardium, which is independent of heart rate. In comparison to MSCT, opacification of the coronary arteries at DSCT is not affected by BMI. The main advantage of DSCT lies with the

  7. Dendritic Growth in Mg-Based Alloys: Phase-Field Simulations and Experimental Verification by X-ray Synchrotron Tomography

    NASA Astrophysics Data System (ADS)

    Wang, Mingyue; Xu, Yanjin; Zheng, Qiwei; Wu, Sujun; Jing, Tao; Chawla, Nikhilesh

    2014-05-01

    Changes in polycrystalline dendritic growth patterns during solidification result in a variety of solidified dendritic structures and morphologies. These microstructural changes are induced by a variety of effects such as the random distribution of nucleation sites and orientations, the interaction of growing individual dendritic grains, and effects of solid-liquid interfacial energy anisotropy. Here, we have studied the formation of the complicated and diverse dendrite morphologies both experimentally, by electron backscatter diffraction and by X-ray tomography; and numerically by three-dimensional phase-field simulations. Three binary magnesium alloys were considered in this study: Mg-Al, Mg-Zn, and Mg-Sn alloys. We show that the solidification microstructure can be attributed to the following factors: The interaction of the growing dendrites, the anisotropy of the growth, and the distribution and initial random orientations of nucleation sites.

  8. Quantitative evaluation of simulated human enamel caries kinetics using photothermal radiometry and modulated luminescence

    NASA Astrophysics Data System (ADS)

    Hellen, Adam; Mandelis, Andreas; Finer, Yoav; Amaechi, Bennett T.

    2011-03-01

    Photothermal radiometry and modulated luminescence (PTR-LUM) is a non-destructive methodology applied toward the detection, monitoring and quantification of dental caries. The purpose of this study was to evaluate the efficacy of PTRLUM to detect incipient caries lesions and quantify opto-thermophysical properties as a function of treatment time. Extracted human molars (n=15) were exposed to an acid demineralization gel (pH 4.5) for 10 or 40 days in order to simulate incipient caries lesions. PTR-LUM frequency scans (1 Hz - 1 kHz) were performed prior to and during demineralization. Transverse Micro-Radiography (TMR) analysis followed at treatment conclusion. A coupled diffusephoton- density-wave and thermal-wave theoretical model was applied to PTR experimental amplitude and phase data across the frequency range of 4 Hz - 354 Hz, to quantitatively evaluate changes in thermal and optical properties of sound and demineralized enamel. Excellent fits with small residuals were observed experimental and theoretical data illustrating the robustness of the computational algorithm. Increased scattering coefficients and poorer thermophysical properties were characteristic of demineralized lesion bodies. Enhanced optical scattering coefficients of demineralized lesions resulted in poorer luminescence yield due to scattering of both incident and converted luminescent photons. Differences in the rate of lesion progression for the 10-day and 40-day samples points to a continuum of surface and diffusion controlled mechanism of lesion formation. PTR-LUM sensitivity to changes in tooth mineralization coupled with opto-thermophysical property extraction illustrates the technique's potential for non-destructive quantification of enamel caries.

  9. A quantitative exposure model simulating human norovirus transmission during preparation of deli sandwiches.

    PubMed

    Stals, Ambroos; Jacxsens, Liesbeth; Baert, Leen; Van Coillie, Els; Uyttendaele, Mieke

    2015-03-01

    Human noroviruses (HuNoVs) are a major cause of food borne gastroenteritis worldwide. They are often transmitted via infected and shedding food handlers manipulating foods such as deli sandwiches. The presented study aimed to simulate HuNoV transmission during the preparation of deli sandwiches in a sandwich bar. A quantitative exposure model was developed by combining the GoldSim® and @Risk® software packages. Input data were collected from scientific literature and from a two week observational study performed at two sandwich bars. The model included three food handlers working during a three hour shift on a shared working surface where deli sandwiches are prepared. The model consisted of three components. The first component simulated the preparation of the deli sandwiches and contained the HuNoV reservoirs, locations within the model allowing the accumulation of NoV and the working of intervention measures. The second component covered the contamination sources being (1) the initial HuNoV contaminated lettuce used on the sandwiches and (2) HuNoV originating from a shedding food handler. The third component included four possible intervention measures to reduce HuNoV transmission: hand and surface disinfection during preparation of the sandwiches, hand gloving and hand washing after a restroom visit. A single HuNoV shedding food handler could cause mean levels of 43±18, 81±37 and 18±7 HuNoV particles present on the deli sandwiches, hands and working surfaces, respectively. Introduction of contaminated lettuce as the only source of HuNoV resulted in the presence of 6.4±0.8 and 4.3±0.4 HuNoV on the food and hand reservoirs. The inclusion of hand and surface disinfection and hand gloving as a single intervention measure was not effective in the model as only marginal reductions of HuNoV levels were noticeable in the different reservoirs. High compliance of hand washing after a restroom visit did reduce HuNoV presence substantially on all reservoirs. The

  10. Efficient scatter model for simulation of ultrasound images from computed tomography data

    NASA Astrophysics Data System (ADS)

    D'Amato, J. P.; Lo Vercio, L.; Rubi, P.; Fernandez Vera, E.; Barbuzza, R.; Del Fresno, M.; Larrabide, I.

    2015-12-01

    Background and motivation: Real-time ultrasound simulation refers to the process of computationally creating fully synthetic ultrasound images instantly. Due to the high value of specialized low cost training for healthcare professionals, there is a growing interest in the use of this technology and the development of high fidelity systems that simulate the acquisitions of echographic images. The objective is to create an efficient and reproducible simulator that can run either on notebooks or desktops using low cost devices. Materials and methods: We present an interactive ultrasound simulator based on CT data. This simulator is based on ray-casting and provides real-time interaction capabilities. The simulation of scattering that is coherent with the transducer position in real time is also introduced. Such noise is produced using a simplified model of multiplicative noise and convolution with point spread functions (PSF) tailored for this purpose. Results: The computational efficiency of scattering maps generation was revised with an improved performance. This allowed a more efficient simulation of coherent scattering in the synthetic echographic images while providing highly realistic result. We describe some quality and performance metrics to validate these results, where a performance of up to 55fps was achieved. Conclusion: The proposed technique for real-time scattering modeling provides realistic yet computationally efficient scatter distributions. The error between the original image and the simulated scattering image was compared for the proposed method and the state-of-the-art, showing negligible differences in its distribution.

  11. Signal simulation and signal processing for multiple reference optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Neuhaus, Kai; Subhash, Hrebesh; Dsouza, Roshan; Hogan, Josh; Wilson, Carol; Leahy, Martin

    2015-03-01

    The generation of a synthetic MR-OCT signal is presented and compared to a real acquired signal. Multiple reference optical coherence tomography (MR-OCT) is a novel time-domain interferometric system. The MR-OCT principle is adding a partial mirror to extend the axial scan range, which effectively extends the scan depth for imaging. The actuation of the scan mirror required for time-domain OCT, was demonstrated to operate with a low cost miniature voice coil, such as a speaker extracted from a smartphone or CD/DVD pick-up system. Building a compact and cost-effective optical imaging system will enable affordable medical diagnosis at low-resource setting applications. The partial mirror recirculates multiple reflections (orders) into the interferometric system and the increase of optical path delay does increase the beat frequency of the interference signal. The synthesis of such an interference signal using a numerical method is described in this manuscript.

  12. Improving image segmentation performance and quantitative analysis via a computer-aided grading methodology for optical coherence tomography retinal image analysis

    NASA Astrophysics Data System (ADS)

    Cabrera Debuc, Delia; Salinas, Harry M.; Ranganathan, Sudarshan; Tátrai, Erika; Gao, Wei; Shen, Meixiao; Wang, Jianhua; Somfai, Gábor M.; Puliafito, Carmen A.

    2010-07-01

    We demonstrate quantitative analysis and error correction of optical coherence tomography (OCT) retinal images by using a custom-built, computer-aided grading methodology. A total of 60 Stratus OCT (Carl Zeiss Meditec, Dublin, California) B-scans collected from ten normal healthy eyes are analyzed by two independent graders. The average retinal thickness per macular region is compared with the automated Stratus OCT results. Intergrader and intragrader reproducibility is calculated by Bland-Altman plots of the mean difference between both gradings and by Pearson correlation coefficients. In addition, the correlation between Stratus OCT and our methodology-derived thickness is also presented. The mean thickness difference between Stratus OCT and our methodology is 6.53 μm and 26.71 μm when using the inner segment/outer segment (IS/OS) junction and outer segment/retinal pigment epithelium (OS/RPE) junction as the outer retinal border, respectively. Overall, the median of the thickness differences as a percentage of the mean thickness is less than 1% and 2% for the intragrader and intergrader reproducibility test, respectively. The measurement accuracy range of the OCT retinal image analysis (OCTRIMA) algorithm is between 0.27 and 1.47 μm and 0.6 and 1.76 μm for the intragrader and intergrader reproducibility tests, respectively. Pearson correlation coefficients demonstrate R2>0.98 for all Early Treatment Diabetic Retinopathy Study (ETDRS) regions. Our methodology facilitates a more robust and localized quantification of the retinal structure in normal healthy controls and patients with clinically significant intraretinal features.

  13. Lean mass and fat mass have differing associations with bone microarchitecture assessed by high resolution peripheral quantitative computed tomography in men and women from the Hertfordshire Cohort Study.

    PubMed

    Edwards, Mark H; Ward, Kate A; Ntani, Georgia; Parsons, Camille; Thompson, Jennifer; Sayer, Avan A; Dennison, Elaine M; Cooper, Cyrus

    2015-12-01

    Understanding the effects of muscle and fat on bone is increasingly important in the optimisation of bone health. We explored relationships between bone microarchitecture and body composition in older men and women from the Hertfordshire Cohort Study. 175 men and 167 women aged 72-81 years were studied. High resolution peripheral quantitative computed tomography (HRpQCT) images (voxel size 82 μm) were acquired from the non-dominant distal radius and tibia with a Scanco XtremeCT scanner. Standard morphological analysis was performed for assessment of macrostructure, densitometry, cortical porosity and trabecular microarchitecture. Body composition was assessed using dual energy X-ray absorptiometry (DXA) (Lunar Prodigy Advanced). Lean mass index (LMI) was calculated as lean mass divided by height squared and fat mass index (FMI) as fat mass divided by height squared. The mean (standard deviation) age in men and women was 76 (3) years. In univariate analyses, tibial cortical area (p<0.01), cortical thickness (p<0.05) and trabecular number (p<0.01) were positively associated with LMI and FMI in both men and women. After mutual adjustment, relationships between cortical area and thickness were only maintained with LMI [tibial cortical area, β (95% confidence interval (CI)): men 6.99 (3.97,10.01), women 3.59 (1.81,5.38)] whereas trabecular number and density were associated with FMI. Interactions by sex were found, including for the relationships of LMI with cortical area and FMI with trabecular area in both the radius and tibia (p<0.05). In conclusion, LMI and FMI appeared to show independent relationships with bone microarchitecture. Further studies are required to confirm the direction of causality and explore the mechanisms underlying these tissue-specific associations. PMID:26187195

  14. Mineral content of vertebral trabecular bone: accuracy of dual energy quantitative computed tomography evaluated against neutron activation analysis and flame atomic absorption spectrometry.

    PubMed

    Louis, O; Van den Winkel, P; Covens, P; Schoutens, A; Osteaux, M

    1994-01-01

    The goal of this study was to evaluate the accuracy of preprocessing dual energy quantitative computed tomography (QCT) for assessment of trabecular bone mineral content (BMC) in lumbar vertebrae. The BMC of 49 lumbar vertebrae taken from 16 cadavers was measured using dual energy QCT with advanced software and hardware capabilities, including an automated definition of the trabecular region of interest (ROI). The midvertebral part of each vertebral body was embedded in a polyester resin and, subsequently, an experimental ROI was cut out using a scanjet image transmission procedure and a computer-assisted milling machine in order to mimic the ROI defined on QCT. After low temperature ashing, the experimental ROIs reduced to a bone powder were submitted to either nondestructive neutron activation analysis (n = 49) or to flame atomic absorption spectrometry (n = 45). BMC obtained with neutron activation analysis was closely related (r = 0.896) to that derived from atomic absorption spectrometry, taken as the gold standard, with, however, a slight overestimation. BMC values measured by QCT were highly correlated with those assessed using the two reference methods, all correlation coefficients being > 0.841. The standard errors of the estimate ranged 47.4-58.9 mg calcium hydroxyapatite in the regressions of BMC obtained with reference methods against BMC assessed by single energy QCT, 47.1-51.9 in the regressions involving dual energy QCT. We conclude that the trabecular BMC of lumbar vertebrae can be accurately measured by QCT and that the superiority in accuracy of dual energy is moderate, which is possible a characteristic of the preprocessing method. PMID:8024849

  15. Cluster analysis of bone microarchitecture from high resolution peripheral quantitative computed tomography demonstrates two separate phenotypes associated with high fracture risk in men and women.

    PubMed

    Edwards, M H; Robinson, D E; Ward, K A; Javaid, M K; Walker-Bone, K; Cooper, C; Dennison, E M

    2016-07-01

    Osteoporosis is a major healthcare problem which is conventionally assessed by dual energy X-ray absorptiometry (DXA). New technologies such as high resolution peripheral quantitative computed tomography (HRpQCT) also predict fracture risk. HRpQCT measures a number of bone characteristics that may inform specific patterns of bone deficits. We used cluster analysis to define different bone phenotypes and their relationships to fracture prevalence and areal bone mineral density (BMD). 177 men and 159 women, in whom fracture history was determined by self-report and vertebral fracture assessment, underwent HRpQCT of the distal radius and femoral neck DXA. Five clusters were derived with two clusters associated with elevated fracture risk. "Cluster 1" contained 26 women (50.0% fractured) and 30 men (50.0% fractured) with a lower mean cortical thickness and cortical volumetric BMD, and in men only, a mean total and trabecular area more than the sex-specific cohort mean. "Cluster 2" contained 20 women (50.0% fractured) and 14 men (35.7% fractured) with a lower mean trabecular density and trabecular number than the sex-specific cohort mean. Logistic regression showed fracture rates in these clusters to be significantly higher than the lowest fracture risk cluster [5] (p<0.05). Mean femoral neck areal BMD was significantly lower than cluster 5 in women in cluster 1 and 2 (p<0.001 for both), and in men, in cluster 2 (p<0.001) but not 1 (p=0.220). In conclusion, this study demonstrates two distinct high risk clusters in both men and women which may differ in etiology and response to treatment. As cluster 1 in men does not have low areal BMD, these men may not be identified as high risk by conventional DXA alone. PMID:27130873

  16. Correlation of X-Ray Computed Tomography with Quantitative Nuclear Magnetic Resonance Methods for Pre-Clinical Measurement of Adipose and Lean Tissues in Living Mice

    PubMed Central

    Metzinger, Matthew N.; Miramontes, Bernadette; Zhou, Peng; Liu, Yueying; Chapman, Sarah; Sun, Lucy; Sasser, Todd A.; Duffield, Giles E.; Stack, M. Sharon; Leevy, W. Matthew

    2014-01-01

    Numerous obesity studies have coupled murine models with non-invasive methods to quantify body composition in longitudinal experiments, including X-ray computed tomography (CT) or quantitative nuclear magnetic resonance (QMR). Both microCT and QMR have been separately validated with invasive techniques of adipose tissue quantification, like post-mortem fat extraction and measurement. Here we report a head-to-head study of both protocols using oil phantoms and mouse populations to determine the parameters that best align CT data with that from QMR. First, an in vitro analysis of oil/water mixtures was used to calibrate and assess the overall accuracy of microCT vs. QMR data. Next, experiments were conducted with two cohorts of living mice (either homogenous or heterogeneous by sex, age and genetic backgrounds) to assess the microCT imaging technique for adipose tissue segmentation and quantification relative to QMR. Adipose mass values were obtained from microCT data with three different resolutions, after which the data were analyzed with different filter and segmentation settings. Strong linearity was noted between the adipose mass values obtained with microCT and QMR, with optimal parameters and scan conditions reported herein. Lean tissue (muscle, internal organs) was also segmented and quantified using the microCT method relative to the analogous QMR values. Overall, the rigorous calibration and validation of the microCT method for murine body composition, relative to QMR, ensures its validity for segmentation, quantification and visualization of both adipose and lean tissues. PMID:25299952

  17. A quantitative index of regional blood flow in canine myocardium derived noninvasively with N-13 ammonia and dynamic positron emission tomography

    SciTech Connect

    Nienaber, C.A.; Ratib, O.; Gambhir, S.S.; Krivokapich, J.; Huang, S.C.; Phelps, M.E.; Schelbert, H.R. )

    1991-01-01

    To derive a quantitative index of regional myocardial blood flow, the arterial input function of the flow tracer N-13 ammonia and the regional myocardial N-13 activity concentrations were noninvasively determined in 29 experiments in eight dogs. N-13 ammonia was administered intravenously and cross-sectional images were acquired dynamically using an ECAT III positron emission tomograph with an effective in-plane resolution of 13.46 mm full-width half-maximum. Time-activity curves were derived from the serial images by assigning regions of interest to the left ventricular myocardium and left ventricular blood pool. Tracer net extractions were estimated from the myocardial time-activity concentrations at various times after tracer injection and the integral of the arterial input function. Myocardial blood flow was altered by intravenous dipyridamole, morphine, propranolol and partial or complete occlusion of the left anterior descending coronary artery, and ranged from 9 to 860 ml/min per 100 g. Estimates of tracer net extractions were most accurate when determined from the myocardial N-13 activity concentrations at 60 s divided by the integral of the arterial input function to that time. These estimates correlated with regional myocardial blood flows determined independently by the microsphere technique by y = x (1 - 0.64(e-114/x); SEE = 22.9; r = 0.94). First pass extraction fractions of N-13 ammonia determined noninvasively with this approach declined with higher flows in a nonlinear fashion and were similar to those determined invasively by direct intracoronary N-13 ammonia injections. The findings indicate that an accurate index of regional myocardial blood flow can be obtained noninvasively by high temporal sampling of arterial and myocardial tracer activity concentrations with positron emission tomography.

  18. Quantitative Genetics and Functional–Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization

    PubMed Central

    Letort, Véronique; Mahe, Paul; Cournède, Paul-Henry; de Reffye, Philippe; Courtois, Brigitte

    2008-01-01

    Background and Aims Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental stresses is characterized by both architectural and functional plasticity, recent attempts to integrate biological knowledge into genetics models have mainly concerned specific physiological processes or crop models without architecture, and thus may prove limited when studying genotype × environment interactions. Consequently, this paper presents a simulation study introducing genetics into a functional–structural growth model, which gives access to more fundamental traits for quantitative trait loci (QTL) detection and thus to promising tools for yield optimization. Methods The GREENLAB model was selected as a reasonable choice to link growth model parameters to QTL. Virtual genes and virtual chromosomes were defined to build a simple genetic model that drove the settings of the species-specific parameters of the model. The QTL Cartographer software was used to study QTL detection of simulated plant traits. A genetic algorithm was implemented to define the ideotype for yield maximization based on the model parameters and the associated allelic combination. Key Results and Conclusions By keeping the environmental factors constant and using a virtual population with a large number of individuals generated by a Mendelian genetic model, results for an ideal case could be simulated. Virtual QTL detection was compared in the case of phenotypic traits – such as cob weight – and when traits were model parameters, and was found to be more accurate in the latter case. The practical interest of this approach is illustrated by calculating the parameters (and the corresponding genotype) associated with yield optimization of a GREENLAB maize model. The paper discusses the potentials of GREENLAB to represent environment × genotype

  19. The application of Monte Carlo simulation to the design of collimators for single photon emission computed tomography

    NASA Astrophysics Data System (ADS)

    Cullum, Ian Derek

    Single photon emission computed tomography offers the potential for quantification of the uptake of radiopharmaceuticals in-vivo. This thesis investigates some of the factors which limit the accuracy of these methods for measurements in the human brain and investigates how the errors can be reduced. Modifications to data collection devices rather than image reconstruction techniques are studied. To assess the impact of errors on images, a set of computer generated test objects were developed. These included standard Anger and Phelps phantoms and a series of slices of the human brain taken from an atlas of transmission tomography. System design involves a balance between resolution and noise in the image. The optimal resolution depends on the data collection system, the uptake characteristics of the radiopharmaceutical and object size. A method to determine this resolution was developed and showed a single-slice system employing focused, probe detectors to offer greater potential for quantification in the brain than systems based on multiple Anger gamma cameras. A collimation system must be designed to achieve the required resolution. Classical, geometric design is not satisfactory in the presence of scattering materials. For this reason a Monte Carlo simulation allowing flexible choice of collimator parameters and source distribution was developed. The simulation was fully tested and then used to predict the performance of collimators for probe and camera based systems. These assessments were carried out for the 'worst case source' which was a concept developed and validated to allow faster prediction of collimator performance. In essence the geometry of this source is such as to allow a resolution measurement to be made which represents the worst value expected from the system. The effect of changes in collimation on image quality was assessed using the computer phantoms and simulation of the data acquisition process on the singleslice system. These data were

  20. Simulation tools for two-dimensional experiments in x-ray computed tomography using the FORBILD head phantom

    NASA Astrophysics Data System (ADS)

    Yu, Zhicong; Noo, Frédéric; Dennerlein, Frank; Wunderlich, Adam; Lauritsch, Günter; Hornegger, Joachim

    2012-07-01

    Mathematical phantoms are essential for the development and early stage evaluation of image reconstruction algorithms in x-ray computed tomography (CT). This note offers tools for computer simulations using a two-dimensional (2D) phantom that models the central axial slice through the FORBILD head phantom. Introduced in 1999, in response to a need for a more robust test, the FORBILD head phantom is now seen by many as the gold standard. However, the simple Shepp-Logan phantom is still heavily used by researchers working on 2D image reconstruction. Universal acceptance of the FORBILD head phantom may have been prevented by its significantly higher complexity: software that allows computer simulations with the Shepp-Logan phantom is not readily applicable to the FORBILD head phantom. The tools offered here address this problem. They are designed for use with Matlab®, as well as open-source variants, such as FreeMat and Octave, which are all widely used in both academia and industry. To get started, the interested user can simply copy and paste the codes from this PDF document into Matlab® M-files.

  1. Simulation tools for two-dimensional experiments in x-ray computed tomography using the FORBILD head phantom.

    PubMed

    Yu, Zhicong; Noo, Frédéric; Dennerlein, Frank; Wunderlich, Adam; Lauritsch, Günter; Hornegger, Joachim

    2012-07-01

    Mathematical phantoms are essential for the development and early stage evaluation of image reconstruction algorithms in x-ray computed tomography (CT). This note offers tools for computer simulations using a two-dimensional (2D) phantom that models the central axial slice through the FORBILD head phantom. Introduced in 1999, in response to a need for a more robust test, the FORBILD head phantom is now seen by many as the gold standard. However, the simple Shepp-Logan phantom is still heavily used by researchers working on 2D image reconstruction. Universal acceptance of the FORBILD head phantom may have been prevented by its significantly higher complexity: software that allows computer simulations with the Shepp-Logan phantom is not readily applicable to the FORBILD head phantom. The tools offered here address this problem. They are designed for use with Matlab®, as well as open-source variants, such as FreeMat and Octave, which are all widely used in both academia and industry. To get started, the interested user can simply copy and paste the codes from this PDF document into Matlab® M-files. PMID:22713335

  2. Scatter correction for kilovoltage cone-beam computed tomography (CBCT) images using Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Jarry, G.; Graham, S. A.; Jaffray, D. A.; Moseley, D. J.; Verhaegen, F.

    2006-03-01

    In this work Monte Carlo (MC) simulations are used to correct kilovoltage (kV) cone-beam computed tomographic (CBCT) projections for scatter radiation. All images were acquired using a kV CBCT bench-top system composed of an x-ray tube, a rotation stage and a flat-panel imager. The EGSnrc MC code was used to model the system. BEAMnrc was used to model the x-ray tube while a modified version of the DOSXYZnrc program was used to transport the particles through various phantoms and score phase space files with identified scattered and primary particles. An analytical program was used to read the phase space files and produce image files. The scatter correction was implemented by subtracting Monte Carlo predicted scatter distribution from measured projection images; these projection images were then reconstructed. Corrected reconstructions showed an important improvement in image quality. Several approaches to reduce the simulation time were tested. To reduce the number of simulated scatter projections, the effect of varying the projection angle on the scatter distribution was evaluated for different geometries. It was found that the scatter distribution does not vary significantly over a 30-degree interval for the geometries tested. It was also established that increasing the size of the voxels in the voxelized phantom does not affect the scatter distribution but reduces the simulation time. Different techniques to smooth the scatter distribution were also investigated.

  3. Assessment of Image Processing and Resolution on Permeability and Drainage Simulations Through 3D Pore-networks Obtained Using X-ray Computed Tomography

    NASA Astrophysics Data System (ADS)

    Mills, G.; Willson, C. S.; Thompson, K. E.; Rivers, M. L.

    2013-12-01

    Typically, continuum-scale flow parameters are obtained through laboratory experiments. Over the past several years, image-based modeling, which is a direct simulation of flow through the structural arrangements of the voids and solids obtained using X-ray computed tomography (XCT) in a sample porous medium, has become a reliable technique for predicting certain flow parameters. Even though XCT is capable of resolving micron-level details, the voxel resolution of the reconstructed image is still dependent upon a number of factors, including the sample size, X-ray energy and XCT beamline setup. Thus, each imaging experiment requires a tradeoff between the sample size that can be imaged, the voxel resolution, and the length scale of the pore space that can be extracted. In addition, the geometric and topological properties of the void space and 3D pore network structure are dictated by the image processing and the choice of pore network generation method. In this research, image-based pore network models are used to quantitatively assess the impact of image resolution, image processing and the choice of pore network generation methods on simulated parameters. A 5 mm diameter and ~15 mm in length Berea sandstone core was scanned two times. First, a ~12 mm long section of the entire cross-section was scanned at 4.1 micron voxel resolution; next, a ~1.4 mm diameter and ~4.12 mm length section within the 1st domain was scanned at 1 micron voxel resolution. The resulting 3D datasets were filtered and segmented into solid and void space. The low resolution image was filtered and segmented using two different approaches in order to evaluate the potential of each approach in identifying the different solid phases in the original 16 bit dataset. A set of networks were created by varying the pore density on both the high and low resolution datasets in order to assess the impact of these factors on flow simulations. Single-phase permeability and a two-phase drainage pore

  4. Verification of the time evolution of cosmological simulations via hypothesis-driven comparative and quantitative visualization

    SciTech Connect

    Hsu, Chung-hsing; Ahrens, James P; Heitmann, Katrin

    2009-01-01

    We describe a visualization assisted process for the verification of cosmological simulation codes. The need for code verification stems from the requirement for very accurate predictions in order to interpret observational data confidently. We compare different simulation algorithms in order to reliably predict differences in simulation results and understand their dependence on input parameter settings.

  5. Frequency and Clinical Significance of Previously Undetected Incidental Findings Detected on Computed Tomography Simulation Scans for Breast Cancer Patients

    SciTech Connect

    Nakamura, Naoki; Tsunoda, Hiroko; Takahashi, Osamu; Kikuchi, Mari; Honda, Satoshi; Shikama, Naoto; Akahane, Keiko; Sekiguchi, Kenji

    2012-11-01

    Purpose: To determine the frequency and clinical significance of previously undetected incidental findings found on computed tomography (CT) simulation images for breast cancer patients. Methods and Materials: All CT simulation images were first interpreted prospectively by radiation oncologists and then double-checked by diagnostic radiologists. The official reports of CT simulation images for 881 consecutive postoperative breast cancer patients from 2009 to 2010 were retrospectively reviewed. Potentially important incidental findings (PIIFs) were defined as any previously undetected benign or malignancy-related findings requiring further medical follow-up or investigation. For all patients in whom a PIIF was detected, we reviewed the clinical records to determine the clinical significance of the PIIF. If the findings from the additional studies prompted by a PIIF required a change in management, the PIIF was also recorded as a clinically important incidental finding (CIIF). Results: There were a total of 57 (6%) PIIFs. The 57 patients in whom a PIIF was detected were followed for a median of 17 months (range, 3-26). Six cases of CIIFs (0.7% of total) were detected. Of the six CIIFs, three (50%) cases had not been noted by the radiation oncologist until the diagnostic radiologist detected the finding. On multivariate analysis, previous CT examination was an independent predictor for PIIF (p = 0.04). Patients who had not previously received chest CT examinations within 1 year had a statistically significantly higher risk of PIIF than those who had received CT examinations within 6 months (odds ratio, 3.54; 95% confidence interval, 1.32-9.50; p = 0.01). Conclusions: The rate of incidental findings prompting a change in management was low. However, radiation oncologists appear to have some difficulty in detecting incidental findings that require a change in management. Considering cost, it may be reasonable that routine interpretations are given to those who have not

  6. Multi-component Cu-Strengthened Steel Welding Simulations: Atom Probe Tomography and Synchrotron X-ray Diffraction Analyses

    NASA Astrophysics Data System (ADS)

    Hunter, Allen H.; Farren, Jeffrey D.; DuPont, John N.; Seidman, David N.

    2015-07-01

    An experimental steel with the composition Fe-1.39Cu-2.70Ni-0.58Al-0.48Mn-0.48Si-0.065Nb-0.05C (wt pct) or alternatively Fe-1.43Cu-2.61Ni-1.21Al-0.48Mn-0.98Si-0.039Nb-0.23C (at. pct) has been developed at Northwestern University, which has both high toughness and high strength after quenching and aging treatments. Simulated heat-affected zone (HAZ) samples are utilized to analyze the microstructures typically obtained after gas metal arc welding (GMAW). Dissolution within the HAZ of cementite (Fe3C) and NbC (F.C.C.) is revealed using synchrotron X-ray diffraction, while dissolution of Cu precipitates is measured employing local electrode atom probe tomography. The results are compared to Thermo-Calc equilibrium calculations. Comparison of measured Cu precipitate radii, number density, and volume fraction with similar measurements from a GMAW sample suggests that the cooling rate in the simulations is faster than in the experimental GMAW sample, resulting in significantly less Cu precipitate nucleation and growth during the cooling part of the weld thermal cycle. The few Cu precipitates detected in the simulated samples are primarily located on grain boundaries resulting from heterogeneous nucleation. The dissolution of NbC precipitates and the resultant austenite coarsening in the highest-temperature sample, coupled with a rapid cooling rate, results in the growth of bainite, and an increase in the strength of the matrix in the absence of significant Cu precipitation.

  7. Simulations and phantom evaluations of magnetic resonance electrical impedance tomography (MREIT) for breast cancer detection

    NASA Astrophysics Data System (ADS)

    Sadleir, Rosalind J.; Sajib, Saurav Z. K.; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

    2013-05-01

    MREIT is a new imaging modality that can be used to reconstruct high-resolution conductivity images of the human body. Since conductivity values of cancerous tissues in the breast are significantly higher than those of surrounding normal tissues, breast imaging using MREIT may provide a new noninvasive way of detecting early stage of cancer. In this paper, we present results of experimental and numerical simulation studies of breast MREIT. We built a realistic three-dimensional model of the human breast connected to a simplified model of the chest including the heart and evaluated the ability of MREIT to detect cancerous anomalies in a background material with similar electrical properties to breast tissue. We performed numerical simulations of various scenarios in breast MREIT including assessment of the effects of fat inclusions and effects related to noise levels, such as changing the amplitude of injected currents, effect of added noise and number of averages. Phantom results showed straightforward detection of cancerous anomalies in a background was possible with low currents and few averages. The simulation results showed it should be possible to detect a cancerous anomaly in the breast, while restricting the maximal current density in the heart below published levels for nerve excitation.

  8. An approach for measuring the spatial orientations of a computed-tomography simulation system.

    PubMed

    Wu, Meng Chia; Ramaseshan, Ramani

    2014-01-01

    The quality assurance tests for measuring the spatial orientations between tabletop, external patient positioning lasers, couch longitudinal moving direction, and imaging plane in a CT simulation system are a complicated and time-consuming process. We proposed a simple and efficient approach to acquire the angular deviations of spatial orientations between these components. An in-house cross-jig was used in this study. We found a relationship between the orientations of the jig's arms shown on the CT images and the orientations of the components in a CT simulator. We verified this relationship with 16 misalignment orientations of known errors, to simulate all possible deviation situations. Generally, the tabletop and external lasers system are mounted separately in a CT simulation system; the former is on the couch trail, the later is on the wall and ceiling. They are independent to each other and will cause different effects on CT images. We only need two scans to acquire the angular deviations of our system: i) when aligning the cross-jig with tabletop, we can check the orientations between the tabletop, couch longitudinal moving direction, and imaging plane; ii) while aligning the cross-jig with the external axial lasers, we will know the angular deviation between the lasers, couch longitudinal moving direction, and imaging plane. The CT simulator had been carefully examined by performing the QA procedures recommended by the AAPM Task Group 66. The measurements of the spatial orientations using the proposed method agree well with TG 66 recommendations. However, the time taken to perform the QA using our method is considerably shorter than the method described in TG 66--5 minutes versus 30 minutes. The deliberate misalignment orientations tests with known errors were detected successfully by our in-house analysis program. The maximum difference between the known errors and the measured angles is only 0.07°. We determined that the relationship between the

  9. Impact of dynamic specimen shape evolution on the atom probe tomography results of doped epitaxial oxide multilayers: Comparison of experiment and simulation

    SciTech Connect

    Madaan, Nitesh; Nandasiri, Manjula; Devaraj, Arun; Bao, Jie; Xu, Zhijie; Thevuthasan, Suntharampillai

    2015-08-31

    The experimental atom probe tomography (APT) results from two different specimen orientations (top-down and sideways) of a high oxygen ion conducting Samaria-doped-ceria/Scandia-stabilized-zirconia multilayer thin film solid oxide fuel cell electrolyte was compared with level-set method based field evaporation simulations for the same specimen orientations. This experiment-simulation comparison explains the dynamic specimen shape evolution and ion trajectory aberrations that can induce density artifacts in final reconstruction, leading to inaccurate estimation of interfacial intermixing. This study highlights the importance of comparing experimental results with field evaporation simulations when using APT to study oxide heterostructure interfaces.

  10. The association between a quantitative computed tomography (CT) measurement of cerebral edema and outcomes in post-cardiac arrest – a validation study

    PubMed Central

    Cristia, Cristal; Ho, Mai-Lan; Levy, Sean; Andersen, Lars W.; Perman, Sarah M.; Giberson, Tyler; Salciccoli, Justin; Saindon, Brian Z.; Cocchi, Michael N.; Donnino, Michael W.

    2014-01-01

    Aim Previous studies have examined the association between quantitative computed tomography (CT) measures of cerebral edema and patient outcomes. It has been reported that a calculated gray matter to white matter attenuation ratio (GWR) of < 1.2 indicates a near 100% non-survivable injury post-cardiac arrest. The objective of the current study was to validate whether a GWR < 1.2 reliably indicates poor survival post-cardiac arrest. We also sought to determine the inter-rater variability among reviewers, and examine the utility of a novel GWR measurement to facilitate easier practical use. Methods We performed a retrospective analysis of post-cardiac arrest patients admitted to a single center from 2008 to 2012. Inclusion criteria were age ≥ 18 years, non-traumatic arrest, and available CT imaging within 24 hours after ROSC. Three independent physician reviewers from different specialties measured CT attenuation of pre-specified gray and white matter areas for GWR calculations. Results Out of 171 consecutive patients, 90 met the study inclusion criteria. Thirteen patients were excluded for technical reasons and/or significant additional pathology, leaving 77 head CT scans for evaluation. Median age was 66 years and 63% were male. In-hospital mortality was 65% and 70% of patients received therapeutic hypothermia. For the validation measurement, the intra-class correlation coefficient was 0.70. In our dataset, a GWR below 1.2 did not accurately predict mortality or poor neurological outcome (sensitivity 0.56–0.62 and specificity 0.63–0.81). A score below 1.1 predicted a near 100% mortality but was not a sensitive metric (sensitivity 0.14–0.20 and specificity 0.96–1.00). Similar results were found for the exploratory model. Conclusion A GWR < 1.2 on CT imaging within 24 hours after cardiac arrest was moderately specific for poor neurologic outcome and mortality. Based on our data, a threshold GWR < 1.1 may be a safer cut-off to identify patients with low

  11. A Quantitative Analysis of the Effect of Simulation on Medication Administration in Nursing Students

    ERIC Educational Resources Information Center

    Scudmore, Casey

    2013-01-01

    Medication errors are a leading cause of injury and death in health care, and nurses are the last line of defense for patient safety. Nursing educators must develop curriculum to effectively teach nursing students to prevent medication errors and protect the public. The purpose of this quantitative, quasi-experimental study was to determine if…

  12. Can You Repeat That Please?: Using Monte Carlo Simulation in Graduate Quantitative Research Methods Classes

    ERIC Educational Resources Information Center

    Carsey, Thomas M.; Harden, Jeffrey J.

    2015-01-01

    Graduate students in political science come to the discipline interested in exploring important political questions, such as "What causes war?" or "What policies promote economic growth?" However, they typically do not arrive prepared to address those questions using quantitative methods. Graduate methods instructors must…

  13. Quantitative modeling of the equilibration of two-phase solid-liquid Fe by atomistic simulations on diffusive time scales

    NASA Astrophysics Data System (ADS)

    Asadi, Ebrahim; Asle Zaeem, Mohsen; Nouranian, Sasan; Baskes, Michael I.

    2015-01-01

    In this paper, molecular dynamics (MD) simulations based on the modified-embedded atom method (MEAM) and a phase-field crystal (PFC) model are utilized to quantitatively investigate the solid-liquid properties of Fe. A set of second nearest-neighbor MEAM parameters for high-temperature applications are developed for Fe, and the solid-liquid coexisting approach is utilized in MD simulations to accurately calculate the melting point, expansion in melting, latent heat, and solid-liquid interface free energy, and surface anisotropy. The required input properties to determine the PFC model parameters, such as liquid structure factor and fluctuations of atoms in the solid, are also calculated from MD simulations. The PFC parameters are calculated utilizing an iterative procedure from the inputs of MD simulations. The solid-liquid interface free energy and surface anisotropy are calculated using the PFC simulations. Very good agreement is observed between the results of our calculations from MEAM-MD and PFC simulations and the available modeling and experimental results in the literature. As an application of the developed model, the grain boundary free energy of Fe is calculated using the PFC model and the results are compared against experiments.

  14. Optimization of beam quality for photon-counting spectral computed tomography in head imaging: simulation study.

    PubMed

    Chen, Han; Xu, Cheng; Persson, Mats; Danielsson, Mats

    2015-10-01

    Head computed tomography (CT) plays an important role in the comprehensive evaluation of acute stroke. Photon-counting spectral detectors, as promising candidates for use in the next generation of x-ray CT systems, allow for assigning more weight to low-energy x-rays that generally contain more contrast information. Most importantly, the spectral information can be utilized to decompose the original set of energy-selective images into several basis function images that are inherently free of beam-hardening artifacts, a potential advantage for further improving the diagnosis accuracy. We are developing a photon-counting spectral detector for CT applications. The purpose of this work is to determine the optimal beam quality for material decomposition in two head imaging cases: nonenhanced imaging and K-edge imaging. A cylindrical brain tissue of 16-cm diameter, coated by a 6-mm-thick bone layer and 2-mm-thick skin layer, was used as a head phantom. The imaging target was a 5-mm-thick blood vessel centered in the head phantom. In K-edge imaging, two contrast agents, iodine and gadolinium, with the same concentration ([Formula: see text]) were studied. Three parameters that affect beam quality were evaluated: kVp settings (50 to 130 kVp), filter materials ([Formula: see text] to 83), and filter thicknesses [0 to 2 half-value layer (HVL)]. The image qualities resulting from the varying x-ray beams were compared in terms of two figures of merit (FOMs): squared signal-difference-to-noise ratio normalized by brain dose ([Formula: see text]) and that normalized by skin dose ([Formula: see text]). For nonenhanced imaging, the results show that the use of the 120-kVp spectrum filtered by 2 HVL copper ([Formula: see text]) provides the best performance in both FOMs. When iodine is used in K-edge imaging, the optimal filter is 2 HVL iodine ([Formula: see text]) and the optimal kVps are 60 kVp in terms of [Formula: see text] and 75 kVp in terms of [Formula: see text]. A

  15. Hydraulic Tomography and Heat Transport Simulation as a Combined Method for the Highly Resolved Characterization of Geothermal Systems

    NASA Astrophysics Data System (ADS)

    Hu, R.; Oberdorfer, P.; Paerisch, P.; Brauchler, R.; Holzbecher, E.; Ptak, T.; Sauter, M.

    2012-12-01

    Recently, more and more concepts for the combination of solar thermal systems and ground-coupled heat pump systems are being proposed by companies and system manufacturers. In this study, this thermal process is simulated, for which the spatial distribution of the subsurface hydraulic parameters is required. However, it is difficult to reconstruct a natural heterogeneous aquifer with high spatial resolution. Hence, an investigation approach is utilized, which is based on the combination of hydraulic tomography and numerical simulation. This approach allows us to simulate the heat transfer in the subsurface based on a highly resolved aquifer reconstruction. Traditional hydraulic tests, e.g. pumping tests, can provide averaged hydraulic parameters only for relatively large volumes, thus the transport-relevant small-scale variability of hydraulic parameters can not be determined. In this study, two inversion methods for the characterization of the aquifer are used to determine the spatial distribution of hydraulic parameters: (1) hydraulic travel time inversion, which determines diffusivity (D) and (2) hydraulic attenuation inversion, which determines specific storage (Ss). Both inversions are based on the transformation of the groundwater flow equation into a form of the Eikonal equation that can be computationally solved efficiently with particle-tracking or ray-tracing techniques. Subsequently, the spatial distribution of hydraulic conductivity (K) can be determined indirectly, based on the ratio of K = D × Ss. The data set used for the inversions consists of 16 short-term pumping tests (lasting approximately 5 min each) with a tomographical configuration in an approximately 40m thick marl-/clay-stone aquifer between two 3" wells. The distance between the two wells is 2.9 m. Subsequently different independent hydraulic tests, i.e. the flow meter test and fluid injection logging are also carried out for the validation of the combined inversions. At the test site

  16. A Quantitative Dynamic Simulation of Bremia lactucae Airborne Conidia Concentration above a Lettuce Canopy.

    PubMed

    Fall, Mamadou Lamine; Van der Heyden, Hervé; Carisse, Odile

    2016-01-01

    Lettuce downy mildew, caused by the oomycete Bremia lactucae Regel, is a major threat to lettuce production worldwide. Lettuce downy mildew is a polycyclic disease driven by airborne spores. A weather-based dynamic simulation model for B. lactucae airborne spores was developed to simulate the aerobiological characteristics of the pathogen. The model was built using the STELLA platform by following the system dynamics methodology. The model was developed using published equations describing disease subprocesses (e.g., sporulation) and assembled knowledge of the interactions among pathogen, host, and weather. The model was evaluated with four years of independent data by comparing model simulations with observations of hourly and daily airborne spore concentrations. The results show an accurate simulation of the trend and shape of B. lactucae temporal dynamics of airborne spore concentration. The model simulated hourly and daily peaks in airborne spore concentrations. More than 95% of the simulation runs, the daily-simulated airborne conidia concentration was 0 when airborne conidia were not observed. Also, the relationship between the simulated and the observed airborne spores was linear. In more than 94% of the simulation runs, the proportion of the linear variation in the hourly-observed values explained by the variation in the hourly-simulated values was greater than 0.7 in all years except one. Most of the errors came from the deviation from the 1:1 line, and the proportion of errors due to the model bias was low. This model is the only dynamic model developed to mimic the dynamics of airborne inoculum and represents an initial step towards improved lettuce downy mildew understanding, forecasting and management. PMID:26953691

  17. A Quantitative Dynamic Simulation of Bremia lactucae Airborne Conidia Concentration above a Lettuce Canopy

    PubMed Central

    Fall, Mamadou Lamine; Van der Heyden, Hervé; Carisse, Odile

    2016-01-01

    Lettuce downy mildew, caused by the oomycete Bremia lactucae Regel, is a major threat to lettuce production worldwide. Lettuce downy mildew is a polycyclic disease driven by airborne spores. A weather-based dynamic simulation model for B. lactucae airborne spores was developed to simulate the aerobiological characteristics of the pathogen. The model was built using the STELLA platform by following the system dynamics methodology. The model was developed using published equations describing disease subprocesses (e.g., sporulation) and assembled knowledge of the interactions among pathogen, host, and weather. The model was evaluated with four years of independent data by comparing model simulations with observations of hourly and daily airborne spore concentrations. The results show an accurate simulation of the trend and shape of B. lactucae temporal dynamics of airborne spore concentration. The model simulated hourly and daily peaks in airborne spore concentrations. More than 95% of the simulation runs, the daily-simulated airborne conidia concentration was 0 when airborne conidia were not observed. Also, the relationship between the simulated and the observed airborne spores was linear. In more than 94% of the simulation runs, the proportion of the linear variation in the hourly-observed values explained by the variation in the hourly-simulated values was greater than 0.7 in all years except one. Most of the errors came from the deviation from the 1:1 line, and the proportion of errors due to the model bias was low. This model is the only dynamic model developed to mimic the dynamics of airborne inoculum and represents an initial step towards improved lettuce downy mildew understanding, forecasting and management. PMID:26953691

  18. Evaluation of radiation dose to organs during kilovoltage cone-beam computed tomography using Monte Carlo simulation.

    PubMed

    Son, Kihong; Cho, Seungryong; Kim, Jin Sung; Han, Youngyih; Ju, Sang Gyu; Choi, Doo Ho

    2014-01-01

    Image-guided techniques for radiation therapy have improved the precision of radiation delivery by sparing normal tissues. Cone-beam computed tomography (CBCT) has emerged as a key technique for patient positioning and target localization in radiotherapy. Here, we investigated the imaging radiation dose delivered to radiosensitive organs of a patient during CBCT scan. The 4D extended cardiac-torso (XCAT) phantom and Geant4 Application for Tomographic Emission (GATE) Monte Carlo (MC) simulation tool were used for the study. A computed tomography dose index (CTDI) standard polymethyl methacrylate (PMMA) phantom was used to validate the MC-based dosimetric evaluation. We implemented an MC model of a clinical on-board imager integrated with the Trilogy accelerator. The MC model's accuracy was validated by comparing its weighted CTDI (CTDIw) values with those of previous studies, which revealed good agreement. We calculated the absorbed doses of various human organs at different treatment sites such as the head-and-neck, chest, abdomen, and pelvis regions, in both standard CBCT scan mode (125 kVp, 80 mA, and 25 ms) and low-dose scan mode (125 kVp, 40 mA, and 10 ms). In the former mode, the average absorbed doses of the organs in the head and neck and chest regions ranged 4.09-8.28 cGy, whereas those of the organs in the abdomen and pelvis regions were 4.30-7.48 cGy. In the latter mode, the absorbed doses of the organs in the head and neck and chest regions ranged 1.61-1.89 cGy, whereas those of the organs in the abdomen and pelvis region ranged between 0.79-1.85 cGy. The reduction in the radiation dose in the low-dose mode compared to the standard mode was about 20%, which is in good agreement with previous reports. We opine that the findings of this study would significantly facilitate decisions regarding the administration of extra imaging doses to radiosensitive organs. PMID:24710444

  19. The development and potential of inverse simulation for the quantitative assessment of helicopter handling qualities

    NASA Technical Reports Server (NTRS)

    Bradley, Roy; Thomson, Douglas G.

    1993-01-01

    In this paper it is proposed that inverse simulation can make a positive contribution to the study of handling qualities. It is shown that mathematical descriptions of the MTEs (Mission Task Elements) defined in ADS-33C may be used to drive an inverse simulation thereby generating, from an appropriate mathematical model, the controls and states of a subject helicopter flying it. By presenting the results of such simulations it is shown that, in the context of inverse simulation, the attitude quickness parameters given in ADS-33C are independent of vehicle configuration. An alternative quickness parameter, associated with the control displacements required to fly the MTE is proposed, and some preliminary results are presented.

  20. A Quantitative Investigation of Entrainment and Detrainment in Numerically Simulated Convective Clouds. Pt. 2; Simulations of Cumulonimbus Clouds

    NASA Technical Reports Server (NTRS)

    Cohen, Charles

    1998-01-01

    Deep cumulonimbus clouds are simulated using a model that makes accurate diagnoses of entrainment and detrainment rates and of the properties of entrained and detrained air. Clouds generated by a variety of initial thermodynamic soundings are compared. In the simulations, updraft entrainment rates are large near and above cloud base, through the entire depth of the conditionally unstable layer. Stronger updrafts in a more unstable environment are better able to entrain relatively undisturbed environmental air, while weaker updrafts can entrain only air that has been modified by the clouds. When the maximum buoyancy is large, the updraft includes parcels with a wide range of buoyancies, while weaker clouds are more horizontally uniform. Strong downdrafts originate from levels at which updrafts detrain, and their mass flux depends on the mass flux of the updraft. The magnitude of mixing between cloud and environment, not the entrainment rate, varies inversely with the cloud radius. How much of the mixed air is entrained depends on the buoyancy.

  1. Tomography using multiple wavelengths in digital holography: method, simulations, and experiments

    NASA Astrophysics Data System (ADS)

    Montfort, Frédéric; Charrière, Florian; Colomb, Tristan; Kuehn, Jonas; Cuche, Etienne; Depeursinge, Christian

    2006-04-01

    In this paper we present a method for tomographic imaging using multiple wavelengths in digital holographic microscopy. This method is based on the recording at different wavelengths equally separated in the k-domain, in off-axis geometry, of the interference between a reference wave and an object wave reflected by a microscopic sample and magnified by a microscope objective. A couple charged device (CCD) camera records consecutively the resulting holograms, which are then numerically reconstructed to obtain their resulting wavefront. Those wavefronts are then summed. The result of this operation is a constructive addition of complex waves in the selected plane and destructive addition in the others. Varying the plane of interest enables the scan the object in depth. For the presented simulations and experiments, twenty wavelengths are used in the 480-700 nm range. An object consisting of irregularly stairs with heights of 375, 525, 975, 1200 and 1275 nm is reconstructed. Its lateral dimensions are 250 × 250 microns. The results show clearly a 3D imaging technique with axial resolution under the micron.

  2. A novel image processing and measurement system applied to quantitative analysis of simulated tooth root canal shape

    NASA Astrophysics Data System (ADS)

    Yong, Tao; Yong, Wei; Jin, Guofan; Gao, Xuejun

    2005-02-01

    Dental pulp is located in root canal of tooth. To modern root canal therapy, "Root canal preparation" is the main means to debride dental pulp infection. The shape of root canal will be changed after preparation, so, when assessing the preparation instruments and techniques, the root canal shaping ability especially the apical offset is very important factor. In this paper, a novel digital image processing and measurement system is designed and applied to quantitative analysis of simulated canal shape. By image pretreatment, feature extraction, registration and fusion, the variation of the root canals' characteristics (before and after preparation) can be accurately compared and measured, so as to assess the shaping ability of instruments. When the scanning resolution is 1200dpi or higher, the registration and measurement precision of the system can achieve 0.021mm or higher. The performance of the system is tested by a series of simulated root canals and stainless steel K-files.

  3. Simulation of 3D MRI brain images for quantitative evaluation of image segmentation algorithms

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Obladen, Thorsten; Sabri, Osama; Buell, Udalrich

    2000-06-01

    To model the true shape of MRI brain images, automatically classified T1-weighted 3D MRI images (gray matter, white matter, cerebrospinal fluid, scalp/bone and background) are utilized for simulation of grayscale data and imaging artifacts. For each class, Gaussian distribution of grayscale values is assumed, and mean and variance are computed from grayscale images. A random generator fills up the class images with Gauss-distributed grayscale values. Since grayscale values of neighboring voxels are not correlated, a Gaussian low-pass filtering is done, preserving class region borders. To simulate anatomical variability, a Gaussian distribution in space with user-defined mean and variance can be added at any user-defined position. Several imaging artifacts can be added: (1) to simulate partial volume effects, every voxel is averaged with neighboring voxels if they have a different class label; (2) a linear or quadratic bias field can be added with user-defined strength and orientation; (3) additional background noise can be added; and (4) artifacts left over after spoiling can be simulated by adding a band with increasing/decreasing grayscale values. With this method, realistic-looking simulated MRI images can be produced to test classification and segmentation algorithms regarding accuracy and robustness even in the presence of artifacts.

  4. Quantitative Comparison Between Reduced Description PIC (RPIC) and full PIC Simulations of Laser-Plasma Instabilities

    NASA Astrophysics Data System (ADS)

    Dodd, E. S.; Barnes, D. C.; Bezzerides, B.; Dubois, D. F.; Vu, H. X.

    2003-10-01

    RPIC is a reduced-description PIC code designed to investigate laser-plasma instabilities (LPI) in physical systems with vastly-different time scales prevalent under ICF conditions(H.X. Vu, B. Bezzerides, D.F. DuBois, J. Comp. Phys. 156), 12 (1999)., typically studied with the extended Zakharov model. Comparisons between the extended Zakharov model and RPIC were presented in a series of papers(K.Y. Sanbonmatsu, H.X. Vu, D.F. DuBois, and B. Bezzerides, Phys. Rev. Lett. 82), 932 (1999); K.Y. Sanbonmatsu, H.X. Vu, B. Bezzerides, and D.F. DuBois, Phys. Plasmas. 7, 1723,2824 (2000)., where quantitative agreements are obtained in the fluid and quasi-linear regime. In the kinetic regime where particle trapping is important, differences were found. The RPIC model itself is limited, e.g., Langmuir wave frequency harmonics are neglected. Our goal is two fold in comparing RPIC with full PIC in 1-d. First, advantages of RPIC over full PIC will be quantitatively assessed. Second, for strong laser drives, harmonics may be important to LPI physics. We would like to establish the regime of validity for RPIC, and to assess if the regimes where RPIC fails is of interest to ICF indirect drive.

  5. Three-dimensional imaging of copper pillars using x-ray tomography within a scanning electron microscope: A simulation study based on synchrotron data

    NASA Astrophysics Data System (ADS)

    Martin, N.; Bertheau, J.; Bleuet, P.; Charbonnier, J.; Hugonnard, P.; Laloum, D.; Lorut, F.; Tabary, J.

    2013-02-01

    While microelectronic devices are frequently characterized with surface-sensitive techniques having nanometer resolution, interconnections used in 3D integration require 3D imaging with high penetration depth and deep sub-micrometer spatial resolution. X-ray tomography is well adapted to this situation. In this context, the purpose of this study is to assess a versatile and turn-key tomographic system allowing for 3D x-ray nanotomography of copper pillars. The tomography tool uses the thin electron beam of a scanning electron microscope (SEM) to provoke x-ray emission from specific metallic targets. Then, radiographs are recorded while the sample rotates in a conventional cone beam tomography scheme that ends up with 3D reconstructions of the pillar. Starting from copper pillars data, collected at the European Synchrotron Radiation Facility, we build a 3D numerical model of a copper pillar, paying particular attention to intermetallics. This model is then used to simulate physical radiographs of the pillar using the geometry of the SEM-hosted x-ray tomography system. Eventually, data are reconstructed and it is shown that the system makes it possible the quantification of 3D intermetallics volume in copper pillars. The paper also includes a prospective discussion about resolution issues.

  6. Three-dimensional imaging of copper pillars using x-ray tomography within a scanning electron microscope: A simulation study based on synchrotron data

    SciTech Connect

    Martin, N.; Bertheau, J.; Charbonnier, J.; Hugonnard, P.; Lorut, F.; Bleuet, P.; Tabary, J.; Laloum, D.

    2013-02-15

    While microelectronic devices are frequently characterized with surface-sensitive techniques having nanometer resolution, interconnections used in 3D integration require 3D imaging with high penetration depth and deep sub-micrometer spatial resolution. X-ray tomography is well adapted to this situation. In this context, the purpose of this study is to assess a versatile and turn-key tomographic system allowing for 3D x-ray nanotomography of copper pillars. The tomography tool uses the thin electron beam of a scanning electron microscope (SEM) to provoke x-ray emission from specific metallic targets. Then, radiographs are recorded while the sample rotates in a conventional cone beam tomography scheme that ends up with 3D reconstructions of the pillar. Starting from copper pillars data, collected at the European Synchrotron Radiation Facility, we build a 3D numerical model of a copper pillar, paying particular attention to intermetallics. This model is then used to simulate physical radiographs of the pillar using the geometry of the SEM-hosted x-ray tomography system. Eventually, data are reconstructed and it is shown that the system makes it possible the quantification of 3D intermetallics volume in copper pillars. The paper also includes a prospective discussion about resolution issues.

  7. A quantitative method for evaluating numerical simulation accuracy of time-transient Lamb wave propagation with its applications to selecting appropriate element size and time step.

    PubMed

    Wan, Xiang; Xu, Guanghua; Zhang, Qing; Tse, Peter W; Tan, Haihui

    2016-01-01

    Lamb wave technique has been widely used in non-destructive evaluation (NDE) and structural health monitoring (SHM). However, due to the multi-mode characteristics and dispersive nature, Lamb wave propagation behavior is much more complex than that of bulk waves. Numerous numerical simulations on Lamb wave propagation have been conducted to study its physical principles. However, few quantitative studies on evaluating the accuracy of these numerical simulations were reported. In this paper, a method based on cross correlation analysis for quantitatively evaluating the simulation accuracy of time-transient Lamb waves propagation is proposed. Two kinds of error, affecting the position and shape accuracies are firstly identified. Consequently, two quantitative indices, i.e., the GVE (group velocity error) and MACCC (maximum absolute value of cross correlation coefficient) derived from cross correlation analysis between a simulated signal and a reference waveform, are proposed to assess the position and shape errors of the simulated signal. In this way, the simulation accuracy on the position and shape is quantitatively evaluated. In order to apply this proposed method to select appropriate element size and time step, a specialized 2D-FEM program combined with the proposed method is developed. Then, the proper element size considering different element types and time step considering different time integration schemes are selected. These results proved that the proposed method is feasible and effective, and can be used as an efficient tool for quantitatively evaluating and verifying the simulation accuracy of time-transient Lamb wave propagation. PMID:26315506

  8. The use of molecular sieves to simulate hot lesions in (18)F-fluorodeoxyglucose--positron emission tomography imaging.

    PubMed

    Matheoud, R; Secco, C; Ridone, S; Inglese, E; Brambilla, M

    2008-04-21

    We investigated the use of a kind of zeolite, the Bowie chabazite, to produce radioactive sources of different shapes, dimensions and activity concentrations that can be used for lesion simulation in positron emission tomography (PET) imaging. The (18)F-fluorodeoxyglucose ((18)F-FDG) uptake of a group of 12 zeolites was studied as a function of their weight (120-1,520 mg) and of the activity concentration of the (18)F-FDG solution (1-37 MBq ml(-1)), using a multiple linear regression model. The reproducibility, homogeneity and stability over time of the (18)F-FDG uptake were assessed. The fit of the regression model is good (r(2) = 0.83). This relation allows the production of zeolites of a desired (18)F-FDG activity using knowledge of the concentration of the soaking solution and the weight of the zeolite. The reproducibility of the (18)F-FDG uptake after heating the zeolites is elevated (CV% = 3.68). The almost complete regeneration of the zeolites allows us to reuse them in successive experiments. The stability of the (18)F-FDG uptake on zeolites is far from ideal. When placed in a saline solution the 'activated' zeolites release the (18)F-FDG with an effective half-time of 53 min. The sealing of the zeolites in plastic film bags has been demonstrated to be effective in preventing any release of (18)F-FDG. These features, together with their variable dimensions and shapes, make them ideal (18)F-FDG sources with a fixed target-to-background ratio that can be placed anywhere in a phantom to study lesion detectability in PET imaging. PMID:18379022

  9. Computer simulations to estimate organ doses from clinically validated cardiac, neuro, and pediatric protocols for multiple detector computed tomography scanners

    NASA Astrophysics Data System (ADS)

    Ghita, Monica

    Recent advances in Computed Tomography (CT) technology, particularly that of multiple detector CT (MDCT) scanning, have provided increased utilization and more diverse clinical applications including more advanced vascular and cardiac exams, perfusion imaging, and screening exams. Notwithstanding the benefits to the patient undergoing a CT study, the fundamental concern in radiation protection is the minimization of the radiation exposure delivered as well as the implementation of structures to prevent inappropriate ordering and clinical use of these advanced studies. This research work developed a computational methodology for routine clinical use to assess patient organ doses from MDCT scanners. To support the methodology, a computer code (DXS-Diagnostic X-ray Spectra) was developed to accurately and conveniently generate x-ray spectra in the diagnostic energy range (45-140 keV). The two accepted standard radiation transport calculation methods namely, deterministic and Monte Carlo, have been preliminarily investigated for their capability and readiness to support the proposed goal of the work. Thorough tests demonstrated that the lack of appropriate discrete photon interaction coefficients in the aforementioned diagnostic energy range impedes the applicability of the deterministic approach to routine clinical use; improvements in the multigroup treatment may make it more viable. Thus, the open source Monte Carlo code, MCNP5, was adapted to appropriately model an MDCT scan. For this, a new method, entirely based on routine clinical CT measurements, was developed and validated to generate an "equivalent source and filtration" model that obviates the need of proprietary information for a given CT scanner. Computer simulations employing the Monte Carlo methodology and UF's tomographic human phantoms were performed to assess, compare, and optimize pediatric, cardiac and neuro-imaging protocols for the new 320-slice scanner at Shands/UF based on dose considerations

  10. Quantitative investigation of the effect of the extra-cerebral vasculature in diffuse optical imaging: a simulation study

    PubMed Central

    Dehaes, Mathieu; Gagnon, Louis; Lesage, Frédéric; Pélégrini-Issac, Mélanie; Vignaud, Alexandre; Valabrègue, Romain; Grebe, Reinhard; Wallois, Fabrice; Benali, Habib

    2011-01-01

    Diffuse optical imaging (DOI) is a non invasive technique allowing the recovery of hemodynamic changes in the brain. Due to the diffusive nature of photon propagation in turbid media and the fact that cerebral tissues are located around 1.5 cm under the adult human scalp, DOI measurements are subject to partial volume errors. DOI measurements are also sensitive to large pial vessels because oxygenated and deoxygenated hemoglobin are the dominant chromophores in the near infrared window. In this study, the effect of the extra-cerebral vasculature in proximity of the sagittal sinus was investigated for its impact on DOI measurements simulated over the human adult visual cortex. Numerical Monte Carlo simulations were performed on two specific models of the human head derived from magnetic resonance imaging (MRI) scans. The first model included the extra-cerebral vasculature in which constant hemoglobin concentrations were assumed while the second did not. The screening effect of the vasculature was quantified by comparing recovered hemoglobin changes from each model for different optical arrays and regions of activation. A correction factor accounting for the difference between the recovered and the simulated hemoglobin changes was computed in each case. The results show that changes in hemoglobin concentration are better estimated when the extra-cerebral vasculature is modeled and the correction factors obtained in this case were at least 1.4-fold lower. The effect of the vasculature was also examined in a high-density diffuse optical tomography configuration. In this case, the difference between changes in hemoglobin concentration recovered with each model was reduced down to 10%. PMID:21412472

  11. Quantitative comparison of electron temperature fluctuations to nonlinear gyrokinetic simulations in C-Mod Ohmic L-mode discharges

    NASA Astrophysics Data System (ADS)

    Sung, C.; White, A. E.; Mikkelsen, D. R.; Greenwald, M.; Holland, C.; Howard, N. T.; Churchill, R.; Theiler, C.

    2016-04-01

    Long wavelength turbulent electron temperature fluctuations (kyρs < 0.3) are measured in the outer core region (r/a > 0.8) of Ohmic L-mode plasmas at Alcator C-Mod [E. S. Marmar et al., Nucl. Fusion 49, 104014 (2009)] with a correlation electron cyclotron emission diagnostic. The relative amplitude and frequency spectrum of the fluctuations are compared quantitatively with nonlinear gyrokinetic simulations using the GYRO code [J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] in two different confinement regimes: linear Ohmic confinement (LOC) regime and saturated Ohmic confinement (SOC) regime. When comparing experiment with nonlinear simulations, it is found that local, electrostatic ion-scale simulations (kyρs ≲ 1.7) performed at r/a ˜ 0.85 reproduce the experimental ion heat flux levels, electron temperature fluctuation levels, and frequency spectra within experimental error bars. In contrast, the electron heat flux is robustly under-predicted and cannot be recovered by using scans of the simulation inputs within error bars or by using global simulations. If both the ion heat flux and the measured temperature fluctuations are attributed predominantly to long-wavelength turbulence, then under-prediction of electron heat flux strongly suggests that electron scale turbulence is important for transport in C-Mod Ohmic L-mode discharges. In addition, no evidence is found from linear or nonlinear simulations for a clear transition from trapped electron mode to ion temperature gradient turbulence across the LOC/SOC transition, and also there is no evidence in these Ohmic L-mode plasmas of the "Transport Shortfall" [C. Holland et al., Phys. Plasmas 16, 052301 (2009)].

  12. Quantitative investigations of quantum coherence for a light-harvesting protein at conditions simulating photosynthesis.

    PubMed

    Turner, Daniel B; Dinshaw, Rayomond; Lee, Kyung-Koo; Belsley, Michael S; Wilk, Krystyna E; Curmi, Paul M G; Scholes, Gregory D

    2012-04-14

    Recent measurements using two-dimensional electronic spectroscopy (2D ES) have shown that the initial dynamic response of photosynthetic proteins can involve quantum coherence. We show how electronic coherence can be differentiated from vibrational coherence in 2D ES. On that basis we conclude that both electronic and vibrational coherences are observed in the phycobiliprotein light-harvesting complex PC645 from Chroomonas sp. CCMP270 at ambient temperature. These light-harvesting antenna proteins of the cryptophyte algae are suspended in the lumen, where the pH drops significantly under sustained illumination by sunlight. Here we measured 2D ES of PC645 at increasing levels of acidity to determine if the change in pH affects the quantum coherence; quantitative analysis reveals that the dynamics are insensitive to the pH change. PMID:22374579

  13. Evaluation of Fourier Transform Profilometry for Quantitative Waste Volume Determination under Simulated Hanford Tank Conditions

    SciTech Connect

    Etheridge, J.A.; Jang, P.R.; Leone, T.; Long, Z.; Norton, O.P.; Okhuysen, W.P.; Monts, D.L.; Coggins, T.L.

    2008-07-01

    The Hanford Site is currently in the process of an extensive effort to empty and close its radioactive single-shell and double-shell waste storage tanks. Before this can be accomplished, it is necessary to know how much residual material is left in a given waste tank and the chemical makeup of the residue. The objective of Mississippi State University's Institute for Clean Energy Technology's (ICET) efforts is to develop, fabricate, and deploy inspection tools for the Hanford waste tanks that will (1) be remotely operable; (2) provide quantitative information on the amount of wastes remaining; and (3) provide information on the spatial distribution of chemical and radioactive species of interest. A collaborative arrangement has been established with the Hanford Site to develop probe-based inspection systems for deployment in the waste tanks. ICET is currently developing an in-tank inspection system based on Fourier Transform Profilometry, FTP. FTP is a non-contact, 3-D shape measurement technique. By projecting a fringe pattern onto a target surface and observing its deformation due to surface irregularities from a different view angle, FTP is capable of determining the height (depth) distribution (and hence volume distribution) of the target surface, thus reproducing the profile of the target accurately under a wide variety of conditions. Hence FTP has the potential to be utilized for quantitative determination of residual wastes within Hanford waste tanks. We are conducting a multi-stage performance evaluation of FTP in order to document the accuracy, precision, and operator dependence (minimal) of FTP under conditions similar to those that can be expected to pertain within Hanford waste tanks. The successive stages impose aspects that present increasing difficulty and increasingly more accurate approximations of in-tank environments. In this paper, we report our investigations of the dependence of the analyst upon FTP volume determination results and of the

  14. Quantitative evaluation of specific vulnerability to nitrate for groundwater resource protection based on process-based simulation model.

    PubMed

    Huan, Huan; Wang, Jinsheng; Zhai, Yuanzheng; Xi, Beidou; Li, Juan; Li, Mingxiao

    2016-04-15

    It has been proved that groundwater vulnerability assessment is an effective tool for groundwater protection. Nowadays, quantitative assessment methods for specific vulnerability are scarce due to limited cognition of complicated contaminant fate and transport processes in the groundwater system. In this paper, process-based simulation model for specific vulnerability to nitrate using 1D flow and solute transport model in the unsaturated vadose zone is presented for groundwater resource protection. For this case study in Jilin City of northeast China, rate constants of denitrification and nitrification as well as adsorption constants of ammonium and nitrate in the vadose zone were acquired by laboratory experiments. The transfer time at the groundwater table t50 was taken as the specific vulnerability indicator. Finally, overall vulnerability was assessed by establishing the relationship between groundwater net recharge, layer thickness and t50. The results suggested that the most vulnerable regions of Jilin City were mainly distributed in the floodplain of Songhua River and Mangniu River. The least vulnerable areas mostly appear in the second terrace and back of the first terrace. The overall area of low, relatively low and moderate vulnerability accounted for 76% of the study area, suggesting the relatively low possibility of suffering nitrate contamination. In addition, the sensitivity analysis showed that the most sensitive factors of specific vulnerability in the vadose zone included the groundwater net recharge rate, physical properties of soil medium and rate constants of nitrate denitrification. By validating the suitability of the process-based simulation model for specific vulnerability and comparing with index-based method by a group of integrated indicators, more realistic and accurate specific vulnerability mapping could be acquired by the process-based simulation model acquiring. In addition, the advantages, disadvantages, constraint conditions and

  15. Quantitative simulation of a magnetospheric substorm. I - Model logic and overview

    NASA Technical Reports Server (NTRS)

    Harel, M.; Wolf, R. A.; Reiff, P. H.; Spiro, R. W.; Burke, W. J.; Rich, F. J.; Smiddy, M.

    1981-01-01

    Results of a comprehensive computer simulation of the behavior of the earth's inner magnetosphere during a substorm-type event are reported. It is pointed out that the computer model self-consistently computes electric fields, currents, and plasma distributions and velocities in the inner-magnetosphere/ionosphere system; parallel electric fields and ionospheric neutral winds, however, are not included. The basic equations of the model are derived, and the inputs are described. An overview of the results is also given. The first appendix contains derivations of general, useful laws of bounce-averaged gradient, curvature, and E x B drifts in a plasma with isotropic pitch angle distribution. The second appendix gives a description of the numerical method used in the simulation.

  16. A Quantitative Investigation of Entrainment and Detrainment in Numerically Simulated Convective Clouds. Pt. 1; Model Development

    NASA Technical Reports Server (NTRS)

    Cohen, Charles

    1998-01-01

    A method is developed which uses numerical tracers to make accurate diagnoses of entraimnent and detrainment rates and of the properties of the entrained and detrained air in numerically simulated clouds. The numerical advection scheme is modified to make it nondispersive, as required by the use of the tracers. Tests of the new method are made, and an appropriate definition of clouds is selected. Distributions of mixing fractions in the model consistently show maximums at the end points, for nearly undilute environmental air or nearly undilute cloud air, with a uniform distribution between. The cumulonimbus clouds simulated here entrain air that had been substantially changed by the clouds, and detrained air that is not necessarily representative of the cloud air at the same level.

  17. Kinetics simulation of luminol chemiluminescence based on quantitative analysis of photons generated in electrochemical oxidation.

    PubMed

    Koizumi, Yozo; Nosaka, Yoshio

    2013-08-22

    The kinetics of electrogenerated chemiluminescence (ECL) of luminol at a gold electrode in alkaline solution was investigated by measuring the absolute number of photons emitted in an integrating sphere. The ECL efficiency as the ratio of photon to electric charge was 0.0004 in cyclic voltammography and 0.0005 in chronoamperometry. By numerically solving the rate equations based on a diffusion layer model, the observed time profile of the luminescence intensity could be successfully simulated from the oxidation current of luminol in the chronoamperometry. In the simulation, the rate constant for the oxidation of luminol by superoxide radicals in alkaline solution was determined to be 6 × 10(5) M(-1) s(-1). The present methodology and the achievement could be widely applicable to various analytical techniques using chemiluminescence. PMID:23879304

  18. A Quantitative Analysis of Aqueous Nanofilm Rupture by Molecular Dynamic Simulation

    SciTech Connect

    Peng, Tiefeng; Nguyen, Anh V.; Peng, Hong; Dang, Liem X.

    2012-01-26

    In this study, we used molecular dynamic (MD) simulations of the rupture process for a water film to define and determine the critical rupture time (CRT). This new approach could be an important method for authentically defining and determining the rupture point of a water film and associated phenomena. We were able to generically predict the CRT and the critical thickness of the water film. Then, we studied the effect of ions on the film rupture process. Our results showed that addition of sodium chloride did not significantly affect on the stability of the water film. Results from MD simulations, when compared with results from experimental measurements, can provide insights into the film rupture process.

  19. Quantitative Comparison of the Variability in Observed and Simulated Shortwave Reflectance

    NASA Technical Reports Server (NTRS)

    Roberts, Yolanda, L.; Pilewskie, P.; Kindel, B. C.; Feldman, D. R.; Collins, W. D.

    2013-01-01

    The Climate Absolute Radiance and Refractivity Observatory (CLARREO) is a climate observation system that has been designed to monitor the Earth's climate with unprecedented absolute radiometric accuracy and SI traceability. Climate Observation System Simulation Experiments (OSSEs) have been generated to simulate CLARREO hyperspectral shortwave imager measurements to help define the measurement characteristics needed for CLARREO to achieve its objectives. To evaluate how well the OSSE-simulated reflectance spectra reproduce the Earth s climate variability at the beginning of the 21st century, we compared the variability of the OSSE reflectance spectra to that of the reflectance spectra measured by the Scanning Imaging Absorption Spectrometer for Atmospheric Cartography (SCIAMACHY). Principal component analysis (PCA) is a multivariate decomposition technique used to represent and study the variability of hyperspectral radiation measurements. Using PCA, between 99.7%and 99.9%of the total variance the OSSE and SCIAMACHY data sets can be explained by subspaces defined by six principal components (PCs). To quantify how much information is shared between the simulated and observed data sets, we spectrally decomposed the intersection of the two data set subspaces. The results from four cases in 2004 showed that the two data sets share eight (January and October) and seven (April and July) dimensions, which correspond to about 99.9% of the total SCIAMACHY variance for each month. The spectral nature of these shared spaces, understood by examining the transformed eigenvectors calculated from the subspace intersections, exhibit similar physical characteristics to the original PCs calculated from each data set, such as water vapor absorption, vegetation reflectance, and cloud reflectance.

  20. Quantitative analysis and simulation of land use changes in the Pearl River Delta, China

    NASA Astrophysics Data System (ADS)

    Zhang, Honghui; Zeng, Yongnian; Zou, Bin; Xiao, Pengfeng; Hu, Deyong; Peng, Jianchao

    2007-06-01

    This paper analyzes and simulates the land use changes in the Pearl River Delta, China, using Longgang City as a case study. The region has pioneered the nation in economic development and urbanization process. Tremendous land use changes have been witnessed since the economic reform in 1978. Land use changes are analyzed and simulated by using stochastic cellular automata model, land use trajectories analysis, spatial indices and multi-temporal TM images of Longgang City (TM1987, TM1991, TM1995, TM1999, TM2003, TM2005) in order to understand how urbanization has transformed the non-urban land to urban land and estimate the consequent environment and ecological impacts in this region. The analysis and simulation results show that urban land continues to sprawl along road and fringe of towns, and concomitant to this development is the loss of agricultural land, orchards and fish ponds. This study provides new evidence with spatial details about the uneven land development in the Pearl River Delta.

  1. Multiple-illumination photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Barber, Quinn M.; Zemp, Roger J.

    2016-03-01

    Previously we described the potential for multiple illumination photoacoustic tomography to provide quantitative reconstructions, however this work used only simulated data. We have developed a custom photoacoustic-ultrasound tomography system capable of multiple illuminations and parallel acquisition from a 256 element 5 MHz transducer ring array with 8-cm diameter. The multiple illumination scheme uses a free-space light delivery geometry where a rotational stage scans a pulsed laser beam onto different incident locations around the sample. For each illumination location a photoacoustic image is reconstructed using a modified backprojection algorithm. Images from different source locations have the potential to be combined to form an improved deep-tissue image using our previously developed iterative algorithms. We complement the photoacoustic imaging data with unique ultrasound imaging data. Most previous ultrasound tomography methods have used migration algorithms, iterative ray-based analysis, wave-equation modeling, or frequency-based algorithms that all demand large amounts of data and computational power. We propose a new UST method that offers isotropic resolution, provides scattering contrast, as well as the potential for measuring ultrasound scattering anisotropy and decoupling density and compressibility contributions. The imaging system is driven by a Verasonics scan engine and programmed for both ultrasound and photoacoustic imaging modes. Resolution has been measured to be 150 μm for ultrasound and 200 μm for photoacoustic images. Imaging capabilities are demonstrated on phantoms with custom-tailored ultrasound scattering and optical properties, as well as in murine models.

  2. A method based on Monte Carlo simulations and voxelized anatomical atlases to evaluate and correct uncertainties on radiotracer accumulation quantitation in beta microprobe studies in the rat brain

    NASA Astrophysics Data System (ADS)

    Pain, F.; Dhenain, M.; Gurden, H.; Routier, A. L.; Lefebvre, F.; Mastrippolito, R.; Lanièce, P.

    2008-10-01

    The β-microprobe is a simple and versatile technique complementary to small animal positron emission tomography (PET). It relies on local measurements of the concentration of positron-labeled molecules. So far, it has been successfully used in anesthetized rats for pharmacokinetics experiments and for the study of brain energetic metabolism. However, the ability of the technique to provide accurate quantitative measurements using 18F, 11C and 15O tracers is likely to suffer from the contribution of 511 keV gamma rays background to the signal and from the contribution of positrons from brain loci surrounding the locus of interest. The aim of the present paper is to provide a method of evaluating several parameters, which are supposed to affect the quantification of recordings performed in vivo with this methodology. We have developed realistic voxelized phantoms of the rat whole body and brain, and used them as input geometries for Monte Carlo simulations of previous β-microprobe reports. In the context of realistic experiments (binding of 11C-Raclopride to D2 dopaminergic receptors in the striatum; local glucose metabolic rate measurement with 18F-FDG and H2O15 blood flow measurements in the somatosensory cortex), we have calculated the detection efficiencies and corresponding contribution of 511 keV gammas from peripheral organs accumulation. We confirmed that the 511 keV gammas background does not impair quantification. To evaluate the contribution of positrons from adjacent structures, we have developed β-Assistant, a program based on a rat brain voxelized atlas and matrices of local detection efficiencies calculated by Monte Carlo simulations for several probe geometries. This program was used to calculate the 'apparent sensitivity' of the probe for each brain structure included in the detection volume. For a given localization of a probe within the brain, this allows us to quantify the different sources of beta signal. Finally, since stereotaxic accuracy is

  3. In operando monitoring of the state of charge and species distribution in zinc air batteries using X-ray tomography and model-based simulations.

    PubMed

    Arlt, Tobias; Schröder, Daniel; Krewer, Ulrike; Manke, Ingo

    2014-10-28

    A novel combination of in operando X-ray tomography and model-based analysis of zinc air batteries is introduced. Using this approach the correlation between the three-dimensional morphological properties of the electrode - on the one hand - and the electrochemical properties of the battery - on the other hand is revealed. In detail, chemical dissolution of zinc particles and the electrode volume were investigated non-destructively during battery operation by X-ray tomography (applying a spatial resolution of 9 μm), while simulation yielded cell potentials of each electrode and allows for the prediction of long-term operation behavior. Furthermore, the analysis of individual zinc particles revealed an electrochemical dissolution process that can be explained using an adapted shrinking-core model. PMID:25220061

  4. The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

    PubMed Central

    Kamerlin, Shina C. L.; Warshel, Arieh

    2012-01-01

    Recent years have seen dramatic improvements in computer power, allowing ever more challenging problems to be approached. In light of this, it is imperative to have a quantitative model for examining chemical reactivity, both in the condensed phase and in solution, as well as to accurately quantify physical organic chemistry (particularly as experimental approaches can often be inconclusive). Similarly, computational approaches allow for great progress in studying enzyme catalysis, as they allow for the separation of the relevant energy contributions to catalysis. Due to the complexity of the problems that need addressing, there is a need for an approach that can combine reliability with an ability to capture complex systems in order to resolve long-standing controversies in a unique way. Herein, we will demonstrate that the empirical valence bond (EVB) approach provides a powerful way to connect the classical concepts of physical organic chemistry to the actual energies of enzymatic reactions by means of computation. Additionally, we will discuss the proliferation of this approach, as well as attempts to capture its basic chemistry and repackage it under different names. We believe that the EVB approach is the most powerful tool that is currently available for studies of chemical processes in the condensed phase in general and enzymes in particular, particularly when trying to explore the different proposals about the origin of the catalytic power of enzymes. PMID:25285029

  5. Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy

    PubMed Central

    Voltz, Karine; Léonard, Jérémie; Touceda, Patricia Tourón; Conyard, Jamie; Chaker, Ziyad; Dejaegere, Annick; Godet, Julien; Mély, Yves; Haacke, Stefan; Stote, Roland H.

    2016-01-01

    Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies. PMID:26896800

  6. Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy.

    PubMed

    Voltz, Karine; Léonard, Jérémie; Touceda, Patricia Tourón; Conyard, Jamie; Chaker, Ziyad; Dejaegere, Annick; Godet, Julien; Mély, Yves; Haacke, Stefan; Stote, Roland H

    2016-04-20

    Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies. PMID:26896800

  7. Quantitative resonant soft x-ray reflectivity of ultrathin anisotropic organic layers: Simulation and experiment of PTCDA on Au.

    PubMed

    Capelli, R; Mahne, N; Koshmak, K; Giglia, A; Doyle, B P; Mukherjee, S; Nannarone, S; Pasquali, L

    2016-07-14

    Resonant soft X-ray reflectivity at the carbon K edge, with linearly polarized light, was used to derive quantitative information of film morphology, molecular arrangement, and electronic orbital anisotropies of an ultrathin 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) film on Au(111). The experimental spectra were simulated by computing the propagation of the electromagnetic field in a trilayer system (vacuum/PTCDA/Au), where the organic film was treated as an anisotropic medium. Optical constants were derived from the calculated (through density functional theory) absorption cross sections of the single molecule along the three principal molecular axes. These were used to construct the dielectric tensor of the film, assuming the molecules to be lying flat with respect to the substrate and with a herringbone arrangement parallel to the substrate plane. Resonant soft X-ray reflectivity proved to be extremely sensitive to film thickness, down to the single molecular layer. The best agreement between simulation and experiment was found for a film of 1.6 nm, with flat laying configuration of the molecules. The high sensitivity to experimental geometries in terms of beam incidence and light polarization was also clarified through simulations. The optical anisotropies of the organic film were experimentally determined and through the comparison with calculations, it was possible to relate them to the orbital symmetry of the empty electronic states. PMID:27421398

  8. Quantitative resonant soft x-ray reflectivity of ultrathin anisotropic organic layers: Simulation and experiment of PTCDA on Au

    NASA Astrophysics Data System (ADS)

    Capelli, R.; Mahne, N.; Koshmak, K.; Giglia, A.; Doyle, B. P.; Mukherjee, S.; Nannarone, S.; Pasquali, L.

    2016-07-01

    Resonant soft X-ray reflectivity at the carbon K edge, with linearly polarized light, was used to derive quantitative information of film morphology, molecular arrangement, and electronic orbital anisotropies of an ultrathin 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) film on Au(111). The experimental spectra were simulated by computing the propagation of the electromagnetic field in a trilayer system (vacuum/PTCDA/Au), where the organic film was treated as an anisotropic medium. Optical constants were derived from the calculated (through density functional theory) absorption cross sections of the single molecule along the three principal molecular axes. These were used to construct the dielectric tensor of the film, assuming the molecules to be lying flat with respect to the substrate and with a herringbone arrangement parallel to the substrate plane. Resonant soft X-ray reflectivity proved to be extremely sensitive to film thickness, down to the single molecular layer. The best agreement between simulation and experiment was found for a film of 1.6 nm, with flat laying configuration of the molecules. The high sensitivity to experimental geometries in terms of beam incidence and light polarization was also clarified through simulations. The optical anisotropies of the organic film were experimentally determined and through the comparison with calculations, it was possible to relate them to the orbital symmetry of the empty electronic states.

  9. Quantitative comparisons between experimentally measured 2-D carbon radiation and Monte Carlo impurity (MCI) code simulations

    SciTech Connect

    Evans, T.E.; Leonard, A.W.; West, W.P.; Finkenthal, D.F.; Fenstermacher, M.E.; Porter, G.D.

    1998-08-01

    Experimentally measured carbon line emissions and total radiated power distributions from the DIII-D divertor and Scrape-Off Layer (SOL) are compared to those calculated with the Monte Carlo Impurity (MCI) model. A UEDGE background plasma is used in MCI with the Roth and Garcia-Rosales (RG-R) chemical sputtering model and/or one of six physical sputtering models. While results from these simulations do not reproduce all of the features seen in the experimentally measured radiation patterns, the total radiated power calculated in MCI is in relatively good agreement with that measured by the DIII-D bolometric system when the Smith78 physical sputtering model is coupled to RG-R chemical sputtering in an unaltered UEDGE plasma. Alternatively, MCI simulations done with UEDGE background ion temperatures along the divertor target plates adjusted to better match those measured in the experiment resulted in three physical sputtering models which when coupled to the RG-R model gave a total radiated power that was within 10% of measured value.

  10. Enhancement of photoacoustic tomography in the tissue with speed-of-sound variance using ultrasound computed tomography

    NASA Astrophysics Data System (ADS)

    Cheng, Ren-Xiang; Chao, Tao; Xiao-Jun, Liu

    2015-11-01

    The speed-of-sound variance will decrease the imaging quality of photoacoustic tomography in acoustically inhomogeneous tissue. In this study, ultrasound computed tomography is combined with photoacoustic tomography to enhance the photoacoustic tomography in this situation. The speed-of-sound information is recovered by ultrasound computed tomography. Then, an improved delay-and-sum method is used to reconstruct the image from the photoacoustic signals. The simulation results validate that the proposed method can obtain a better photoacoustic tomography than the conventional method when the speed-of-sound variance is increased. In addition, the influences of the speed-of-sound variance and the fan-angle on the image quality are quantitatively explored to optimize the image scheme. The proposed method has a good performance even when the speed-of-sound variance reaches 14.2%. Furthermore, an optimized fan angle is revealed, which can keep the good image quality with a low cost of hardware. This study has a potential value in extending the biomedical application of photoacoustic tomography. Projection supported by the National Basic Research Program of China (Grant No. 2012CB921504), the National Natural Science Foundation of China (Grant Nos. 11422439, 11274167, and 11274171), and the Specialized Research Fund for the Doctoral Program of Higher Education, China (Grant No. 20120091110001).

  11. Feasibility of generating quantitative composition images in dual energy mammography: a simulation study

    NASA Astrophysics Data System (ADS)

    Lee, Donghoon; Kim, Ye-seul; Choi, Sunghoon; Lee, Haenghwa; Choi, Seungyeon; Kim, Hee-Joung

    2016-03-01

    Breast cancer is one of the most common malignancies in women. For years, mammography has been used as the gold standard for localizing breast cancer, despite its limitation in determining cancer composition. Therefore, the purpose of this simulation study is to confirm the feasibility of obtaining tumor composition using dual energy digital mammography. To generate X-ray sources for dual energy mammography, 26 kVp and 39 kVp voltages were generated for low and high energy beams, respectively. Additionally, the energy subtraction and inverse mapping functions were applied to provide compositional images. The resultant images showed that the breast composition obtained by the inverse mapping function with cubic fitting achieved the highest accuracy and least noise. Furthermore, breast density analysis with cubic fitting showed less than 10% error compare to true values. In conclusion, this study demonstrated the feasibility of creating individual compositional images and capability of analyzing breast density effectively.

  12. Combined EPMA, FIB and Monte Carlo simulation: a versatile tool for quantitative analysis of multilayered structures

    NASA Astrophysics Data System (ADS)

    Richter, S.; Pinard, P. T.

    2016-02-01

    Electron probe microanalysis and focussed ion beam milling are combined to improve the sensitivity and applicability of depth profiling quantification. With the nanoscale milling capabilities of the ion beam, very shallow bevels are milled by using a special preparation procedure to reduce any curtaining effect and minimize Ga ions implantation. A Ni/Cr multilayered specimen is used to evaluate the depth resolution. The best results are obtained by a well-focussed electron beam offered by a field-emission microprobe. A new evaluation algorithm is presented to quantify the structure in terms of mass thicknesses or if the density is known in terms of real thicknesses. The quantification procedure is based on Monte Carlo simulations where calculated k-ratios (calibrated X-ray intensities) are compared to the experimental ones to find the optimal structure. In comparison with an ion milled cross-section, the proposed bevel technique is more sensitive and provides more information about the material's structure.

  13. Quantitative microstructure characterization of a Ni-YSZ bi-layer coupled with simulated electrode polarisation

    NASA Astrophysics Data System (ADS)

    Usseglio-Viretta, F.; Laurencin, J.; Delette, G.; Villanova, J.; Cloetens, P.; Leguillon, D.

    2014-06-01

    Microstructure of a cermet Ni-YSZ bi-layer is analysed on the basis of three dimensional reconstructions obtained on both functional layer and cell support. Microstructural parameters of gas, ionic and electronic phases are determined in terms of phase connectivity, mean particles diameter, particles size distribution, specific surface area, tortuosity factor and density of TPBls. Microstructural properties are introduced in an SOEC cathode micro model that takes into account the specific configuration of the Ni-YSZ composite bi-layer. Simulations show that the extent of the electrochemical reaction in the support is very limited. Moreover, it is found that electrode apparent activation energy is a combination of effective ionic conduction and charge transfer in the active functional layer.

  14. Quantitative Estimations of Thermal Damage in Skin Tissue Using Monte Carlo Simulation of Polarized Light

    NASA Astrophysics Data System (ADS)

    Lee, G. W.; Kim, T. H.; Youn, J. I.

    2016-03-01

    Thermal treatment has been used for collagen tightening and tissue contour enhancement. It is important to monitor the condition of collagenous tissue during and immediately after thermal treatment. Collagen denaturation changes the optical properties such as scattering coefficient and anisotropy. In this study, Monte Carlo simulation of polarized light was used to calculate the degree of linear polarization (DOLP) of backscattered light from thermally damaged porcine skin, and the Mueller matrix was calculated to verify the result of DOLP. We observed a decrease in the DOLP and a significant change in the radial distribution of the Mueller matrix elements at temperatures ranging from 55 to 65°C. This could be attributed to the increase in scattering coefficient and decrease in anisotropy caused by thermal denaturation in the tissue. The DOLP method has a potential implementation as a real-time closed-loop feedback system for use in various thermal treatment methods through measuring changes in optical properties of target tissues.

  15. Quantitatively analyzing phonon spectral contribution of thermal conductivity based on nonequilibrium molecular dynamics simulations. II. From time Fourier transform

    NASA Astrophysics Data System (ADS)

    Zhou, Yanguang; Hu, Ming

    2015-11-01

    From a nanoscale heat transfer point of view, currently one of the most interesting and challenging tasks is to quantitatively analyze phonon mode specific transport properties in solid materials, which plays a vital role in many emerging and diverse technological applications. It has not been long that such information can be provided by the phonon spectral energy density (SED) or equivalently time domain normal mode analysis (TDNMA) methods in the framework of equilibrium molecular dynamics (EMD) simulations. However, few methods have been developed for nonequilibrium molecular dynamics (NEMD) simulations [Phys. Rev. B 91, 115426 (2015), 10.1103/PhysRevB.91.115426], the other widely used computational method for calculating thermal transport of materials in addition to EMD. In this work, a computational scheme based on time Fourier transform of atomistic heat current, called the frequency domain direct decomposed method (FDDDM), is proposed to analyze the contributions of frequency dependent thermal conductivity in NEMD simulations. The FDDDM results of Lennard-Jones argon and Stillinger-Weber Si are compared with the TDNMA method from EMD simulation. Similar trends are found for both cases, which confirm the validity of our FDDDM approach. Benefiting from the inherent nature of NEMD and the theoretical formula that does not require any temperature assumption, the FDDDM can be directly used to investigate the size and temperature effect. Moreover, the unique advantage of FDDDM prior to previous methods (such as SED and TDNMA) is that it can be straightforwardly used to characterize the phonon frequency dependent thermal conductivity of disordered systems, such as amorphous materials. The FDDDM approach can also be a good candidate to be used to understand the phonon behaviors and thus provides useful guidance for designing efficient structures for advanced thermal management.

  16. Cross-validation of interferometric synthetic aperture microscopy and optical coherence tomography.

    PubMed

    Ralston, Tyler S; Adie, Steven G; Marks, Daniel L; Boppart, Stephen A; Carney, P Scott

    2010-05-15

    Computationally reconstructed interferometric synthetic aperture microscopy is coregistered with optical coherence tomography (OCT) focal plane data to provide quantitative cross validation with OCT. This is accomplished through a qualitative comparison of images and a quantitative analysis of the width of the point-spread function in simulation and experiment. The width of the ISAM point-spread function is seen to be independent of depth, in contrast to OCT. PMID:20479849

  17. Quantitative and qualitative analyses of under-balcony acoustics with real and simulated arrays of multiple sources

    NASA Astrophysics Data System (ADS)

    Kwon, Youngmin

    The objective of this study was to quantitatively and qualitatively identify the acoustics of the under-balcony areas in music performance halls under realistic conditions that are close to an orchestral performance in consideration of multiple music instrumental sources and their diverse sound propagation patterns. The study executed monaural and binaural impulse response measurements with an array of sixteen directional sources (loudspeakers) for acoustical assessments. Actual measurements in a performance hall as well as computer simulations were conducted for the quantitative assessments. Psycho-acoustical listening tests were conducted for the qualitative assessments using the music signals binaurally recorded in the hall with the same source array. The results obtained from the multiple directional source tests were analyzed by comparing them to those obtained from the tests performed with a single omni-directional source. These two sets of results obtained in the under-balcony area were also compared to those obtained in the main orchestra area. The quantitative results showed that the use of a single source conforming to conventional measurement protocol seems to be competent for measurements of the room acoustical parameters such as EDTmid, RTmid, C80500-2k, IACCE3 and IACCL3. These quantitative measures, however, did not always agree with the results of the qualitative assessments. The primary reason is that, in many other acoustical analysis respects, the acoustical phenomena shown from the multiple source measurements were not similar to those shown from the single source measurements. Remarkable differences were observed in time-domain impulse responses, frequency content, spectral distribution, directional distribution of the early reflections, and in sound energy density over time. Therefore, the room acoustical parameters alone should not be the acoustical representative characterizing a performance hall or a specific area such as the under

  18. A quantitative analysis of head movement behaviour during visual acuity assessment under prosthetic vision simulation

    NASA Astrophysics Data System (ADS)

    Chen, S. C.; Hallum, L. E.; Suaning, G. J.; Lovell, N. H.

    2007-03-01

    In most current vision prosthesis designs, head movement is the sole director of visual gaze and scanning due to the head-mounted nature of the camera. Study of this unnatural behaviour may provide insight into improved prosthesis designs and rehabilitation procedures. In this paper, we conducted a psychophysical study to investigate the characteristics of head movements of normally sighted subjects undergoing a visual acuity task in simulated prosthetic vision (SPV). In 12 naïve, untrained subjects, we recorded spontaneous changes in the amount of head movements during SPV sessions compared to control (normal vision) sessions. The observed behaviour continued to be refined until five or six sessions of practice. Increased head movement velocity was shown to be correlated to improved visual acuity performance, up to 0.3 logMAR, an equivalent of detecting details at half the physical size compared to complete deprivation of head movements. We postulate that visual scanning can as much as double the spatial frequency information in prosthetic vision. Increased head movement velocity observed when subjects were attempting smaller test items and for low-pass filtering schemes with higher cut-off frequencies may be further evidence that higher frequency content may be available through visual scanning, unconsciously driving subjects to increase head movement velocity.

  19. Quantitative multiplexed simulated-cell identification by SERS in microfluidic devices

    NASA Astrophysics Data System (ADS)

    Hoonejani, M. R.; Pallaoro, A.; Braun, G. B.; Moskovits, M.; Meinhart, C. D.

    2015-10-01

    A reliable identification of cells on the basis of their surface markers is of great interest for diagnostic and therapeutic applications. We present a multiplexed labeling and detection strategy that is applied to four microparticle populations, each mimicking cellular or bacterial samples with varying surface concentrations of up to four epitopes, using four distinct biotags that are meant to be used in conjunction with surface enhanced Raman spectroscopy (SERS) instead of fluorescence, together with microfluidics. Four populations of 6 μm polystyrene beads were incubated with different mixtures, ``cocktails'' of four SERS biotags (SBTs), simulating the approach that one would follow when seeking to identify multiple biomarkers encountered in biological applications. Populations were flowed in a microfluidic flow-focusing device and the SERS signal from individual beads was acquired during continuous flow. The spectrally rich SERS spectra enabled us to separate confidently the populations by utilizing principal component analysis (PCA). Also, using classical least squares (CLS), we were able to calculate the contributions of each SBT to the overall signal in each of the populations, and showed that the relative SBT contributions are consistent with the nominal percentage of each marker originally designed into that bead population, by functionalizing it with a given SBT cocktail. Our results demonstrate the multiplexing capability of SBTs in potential applications such as immunophenotyping.A reliable identification of cells on the basis of their surface markers is of great interest for diagnostic and therapeutic applications. We present a multiplexed labeling and detection strategy that is applied to four microparticle populations, each mimicking cellular or bacterial samples with varying surface concentrations of up to four epitopes, using four distinct biotags that are meant to be used in conjunction with surface enhanced Raman spectroscopy (SERS) instead of

  20. Semi-quantitative predictions of hot tearing and cold cracking in aluminum DC casting using numerical process simulator

    NASA Astrophysics Data System (ADS)

    Subroto, T.; Miroux, A.; Mortensen, D.; M'Hamdi, M.; Eskin, D. G.; Katgerman, L.

    2012-07-01

    Cracking is one of the most critical defects that may occur during aluminum direct-chill (DC) casting. There are two types of cracking typical of DC casting: hot tearing and cold cracking. To study and predict such defects, currently we are using a process simulator, ALSIM. ALSIM is able to provide semi-quantitative predictions of hot tearing and cold cracking susceptibility. In this work, we performed benchmark tests using predictions of both types of cracks and experimental results of DC casting trials. The trials series resulted in billets with hot tearing as well as cold cracking. The model was also used to study the influence of several casting variables such as casting speed and inlet geometry with respect to the cracking susceptibility in the ingots. In this work, we found that the sump geometry was changed by the feeding scheme, which played an important role in hot tear occurrence. Moreover, increasing the casting speed also increased the hot tear and cold crack susceptibility. In addition, from the result of simulation, we also observed a phenomenon that supported the hypotheses of connection between hot tearing and cold cracking.

  1. Quantitative comparison of wavelength dependence on penetration depth and imaging contrast for ultrahigh-resolution optical coherence tomography using supercontinuum sources at five wavelength regions

    NASA Astrophysics Data System (ADS)

    Ishida, S.; Nishizawa, N.

    2012-01-01

    Optical coherence tomography (OCT) is a non invasive optical imaging technology for micron-scale cross-sectional imaging of biological tissue and materials. We have been investigating ultrahigh resolution optical coherence tomography (UHR-OCT) using fiber based supercontinuum sources. Although ultrahigh longitudinal resolution was achieved in several center wavelength regions, its low penetration depth is a serious limitation for other applications. To realize ultrahigh resolution and deep penetration depth simultaneously, it is necessary to choose the proper wavelength to maximize the light penetration and enhance the image contrast at deeper depths. Recently, we have demonstrated the wavelength dependence of penetration depth and imaging contrast for ultrahigh resolution OCT at 0.8 μm, 1.3 μm, and 1.7 μm wavelength ranges. In this paper, additionally we used SC sources at 1.06 μm and 1.55 μm, and we have investigated the wavelength dependence of UHR-OCT at five wavelength regions. The image contrast and penetration depth have been discussed in terms of the scattering coefficient and water absorption of samples. Almost the same optical characteristics in longitudinal and lateral resolution, sensitivity, and incident optical power at all wavelength regions were demonstrated. We confirmed the enhancement of image contrast and decreased ambiguity of deeper epithelioid structure at longer wavelength region.

  2. Investigation and optimization of a finite element simulation of transducer array systems for 3D ultrasound computer tomography with respect to electrical impedance characteristics

    NASA Astrophysics Data System (ADS)

    Kohout, B.; Pirinen, J.; Ruiter, N. V.

    2012-03-01

    The established standard screening method to detect breast cancer is X-ray mammography. However X-ray mammography often has low contrast for tumors located within glandular tissue. A new approach is 3D Ultrasound Computer Tomography (USCT), which is expected to detect small tumors at an early stage. This paper describes the development, improvement and the results of Finite Element Method (FEM) simulations of the Transducer Array System (TAS) used in our 3D USCT. The focus of this work is on researching the influence of meshing and material parameters on the electrical impedance curves. Thereafter, these findings are used to optimize the simulation model. The quality of the simulation was evaluated by comparing simulated impedance characteristics with measured data of the real TAS. The resulting FEM simulation model is a powerful tool to analyze and optimize transducer array systems applied for USCT. With this simulation model, the behavior of TAS for different geometry modifications was researched. It provides a means to understand the acoustical performances inside of any ultrasound transducer represented by its electrical impedance characteristic.

  3. Quantitative Assessment of Altered Rectal Mucosal Permeability Due to Rectally Applied Nonoxynol-9, Biopsy, and Simulated Intercourse

    PubMed Central

    Fuchs, Edward J.; Grohskopf, Lisa A.; Lee, Linda A.; Bakshi, Rahul P.; Hendrix, Craig W.

    2013-01-01

    Background. Microbicide toxicity may reduce the efficacy of topical preexposure prophylaxis for human immunodeficiency virus (HIV) transmission. Noninvasive quantitative measures of microbicide toxicity would usefully inform microbicide development. Methods. Ten subjects received 3 one-time interventions: 5 mL of Normosol-R fluid alone (negative control), 5 mL of 2% nonoxynol-9 (N-9) gel, and 5 mL of Normosol-R with coital simulation and sigmoidoscopic biopsy (CS + BX). Each dose of N-9 and Normosol-R contained 500 µCi of 99mtechnetium–diethylene triamine pentaacetic acid. Plasma and urine radioactivity was assessed over 24 hours. Results. The plasma radioisotope concentration peaked 1 hour after N-9 dosing. The mean maximum radioisotope concentration after N-9 receipt was 12.0 times (95% confidence interval [CI], 6.8–21.0) and 8.4 times (95% CI, 5.2–13.5) the mean concentration after Normosol-R control receipt and CS + BX receipt, respectively; paired differences persisted for 24 hours. After N-9 dosing, the urine isotope level was 3.6 times (95% CI, 1.1–11.4) the level observed 8 hours after Normosol-R control receipt and 4.0 times (95% CI, 1.4–11.4) the level observed 4 hours after CS + BX receipt. Permeability after CS + BX receipt was greater than that after Normosol-R control receipt in 0–2-hour urine specimens only (mean permeability, 2.4; 95% CI, 1.0–5.8) but was not greater in blood. Conclusions. Plasma sampling after rectal radioisotope administration provided quantitative estimates of altered mucosal permeability after chemical and mechanical stresses. Permeability testing may provide a useful noninvasive adjunct to assess the mucosal effects of candidate microbicides. Clinical Trials Registration. NCT00389311. PMID:23325915

  4. Understanding Atom Probe Tomography of Oxide-Supported Metal Nanoparticles by Correlation with Atomic Resolution Electron Microscopy and Field Evaporation Simulation

    SciTech Connect

    Devaraj, Arun; Colby, Robert J.; Vurpillot, F.; Thevuthasan, Suntharampillai

    2014-03-26

    Metal-dielectric composite materials, specifically metal nanoparticles supported on or embedded in metal oxides, are widely used in catalysis. The accurate optimization of such nanostructures warrants the need for detailed three-dimensional characterization. Atom probe tomography is uniquely capable of generating sub-nanometer structural and compositional data with part-per-million mass sensitivity, but there are reconstruction artifacts for composites containing materials with strongly differing fields of evaporation, as for oxide-supported metal nanoparticles. By correlating atom probe tomography with scanning transmission electron microscopy for Au nanoparticles embedded in an MgO support, deviations from an ideal topography during evaporation are demonstrated directly, and correlated with compositional errors in the reconstructed data. Finite element simulations of the field evaporation process confirm that protruding Au nanoparticles will evolve on the tip surface, and that evaporation field variations lead to an inaccurate assessment of the local composition, effectively lowering the spatial resolution of the final reconstructed dataset. Cross-correlating the experimental data with simulations results in a more detailed understanding of local evaporation aberrations during APT analysis of metal-oxide composites, paving the way towards a more accurate three-dimensional characterization of this technologically important class of materials.

  5. Analysis of calvarial bone defects in rats using microcomputed tomography: potential for a novel composite material and a new quantitative measurement.

    PubMed

    Efeoglu, Candan; Burke, Julie L; Parsons, Andrew J; Aitchison, Graham A; Scotchford, Colin; Rudd, Chris; Vikram, Aditya; Fisher, Sheila E

    2009-12-01

    Reconstruction of craniomaxillofacial defects is a challenge for surgeons and has psychological and functional burdens for patients. Undoubtedly, there is a need for improved biomaterials and techniques for craniomaxillofacial reconstruction. We assessed the potential regeneration of bone using three modifications of a novel composite and explored the validity of a new measurement using microcomputed tomography (micro-CT). We placed three different composite samples in calvarial defects in rats and analysed healing with micro-CT. The results showed that polycaprolactone (PCL) with phosphate glass fibre is promising for non-load bearing applications in the craniomaxillofacial region. Also, the new micro-CT measurement of the temporal characterisation of the mineralisation of bone (TCBM) has the potential to evolve into a reliable predictor of bony healing and its quality. PMID:19395133

  6. Review of tissue simulating phantoms with controllable optical, mechanical and structural properties for use in optical coherence tomography

    PubMed Central

    Lamouche, Guy; Kennedy, Brendan F.; Kennedy, Kelsey M.; Bisaillon, Charles-Etienne; Curatolo, Andrea; Campbell, Gord; Pazos, Valérie; Sampson, David D.

    2012-01-01

    We review the development of phantoms for optical coherence tomography (OCT) designed to replicate the optical, mechanical and structural properties of a range of tissues. Such phantoms are a key requirement for the continued development of OCT techniques and applications. We focus on phantoms based on silicone, fibrin and poly(vinyl alcohol) cryogels (PVA-C), as we believe these materials hold the most promise for durable and accurate replication of tissue properties. PMID:22741083

  7. Imaging pitfalls, normal anatomy, and anatomical variants that can simulate disease on cardiac imaging as demonstrated on multidetector computed tomography

    PubMed Central

    White, Charles S

    2015-01-01

    Advances in computed tomography have led to continuous improvement in cardiac imaging. Dedicated postprocessing capabilities, faster scan times, and cardiac gating methods reveal details of normal cardiac anatomy and anatomic variants that can mimic pathologic conditions. This article will review normal cardiac anatomy and variants that can mimic disease. Radiologists should be familiar with normal cardiac anatomy and anatomic variants to avoid misinterpretation of normal findings for pathologic processes. PMID:25610617

  8. A quantitative assessment of volumetric and anatomic changes of the parotid gland during intensity-modulated radiotherapy for head and neck cancer using serial computed tomography

    SciTech Connect

    Ajani, Abdallah A.; Qureshi, Muhammad M.; Kovalchuk, Nataliya; Orlina, Lawrence; Sakai, Osamu; Truong, Minh Tam

    2013-10-01

    To evaluate the change in volume and movement of the parotid gland measured by serial contrast-enhanced computed tomography scans in patients with head and neck cancer treated with parotid-sparing intensity-modulated radiotherapy (IMRT). A prospective study was performed on 13 patients with head and neck cancer undergoing dose-painted IMRT to 69.96 Gy in 33 fractions. Serial computed tomography scans were performed at baseline, weeks 2, 4, and 6 of radiotherapy (RT), and at 6 weeks post-RT. The parotid volume was contoured at each scan, and the movement of the medial and lateral borders was measured. The patient's body weight was recorded at each corresponding week during RT. Regression analyses were performed to ascertain the rate of change during treatment as a percent change per fraction in parotid volume and distance relative to baseline. The mean parotid volume decreased by 37.3% from baseline to week 6 of RT. The overall rate of change in parotid volume during RT was−1.30% per fraction (−1.67% and−0.91% per fraction in≥31 Gy and<31 Gy mean planned parotid dose groups, respectively, p = 0.0004). The movement of parotid borders was greater in the≥31 Gy mean parotid dose group compared with the<31 Gy group (0.22% per fraction and 0.14% per fraction for the lateral border and 0.19% per fraction and 0.06% per fraction for the medial border, respectively). The median change in body weight was−7.4% (range, 0.75% to−17.5%) during RT. A positive correlation was noted between change in body weight and parotid volume during the course of RT (Spearman correlation coefficient, r = 0.66, p<0.01). Head and neck IMRT results in a volume loss of the parotid gland, which is related to the planned parotid dose, and the patient's weight loss during RT.

  9. A quantitative assessment of volumetric and anatomic changes of the parotid gland during intensity-modulated radiotherapy for head and neck cancer using serial computed tomography.

    PubMed

    Ajani, Abdallah A; Qureshi, Muhammad M; Kovalchuk, Nataliya; Orlina, Lawrence; Sakai, Osamu; Truong, Minh Tam

    2013-01-01

    To evaluate the change in volume and movement of the parotid gland measured by serial contrast-enhanced computed tomography scans in patients with head and neck cancer treated with parotid-sparing intensity-modulated radiotherapy (IMRT). A prospective study was performed on 13 patients with head and neck cancer undergoing dose-painted IMRT to 69.96Gy in 33 fractions. Serial computed tomography scans were performed at baseline, weeks 2, 4, and 6 of radiotherapy (RT), and at 6 weeks post-RT. The parotid volume was contoured at each scan, and the movement of the medial and lateral borders was measured. The patient's body weight was recorded at each corresponding week during RT. Regression analyses were performed to ascertain the rate of change during treatment as a percent change per fraction in parotid volume and distance relative to baseline. The mean parotid volume decreased by 37.3% from baseline to week 6 of RT. The overall rate of change in parotid volume during RT was-1.30% per fraction (-1.67% and-0.91% per fraction in≥31Gy and<31Gy mean planned parotid dose groups, respectively, p = 0.0004). The movement of parotid borders was greater in the≥31Gy mean parotid dose group compared with the<31Gy group (0.22% per fraction and 0.14% per fraction for the lateral border and 0.19% per fraction and 0.06% per fraction for the medial border, respectively). The median change in body weight was-7.4% (range, 0.75% to-17.5%) during RT. A positive correlation was noted between change in body weight and parotid volume during the course of RT (Spearman correlation coefficient, r = 0.66, p<0.01). Head and neck IMRT results in a volume loss of the parotid gland, which is related to the planned parotid dose, and the patient's weight loss during RT. PMID:23558146

  10. Quantitative assessment of volcanic ash hazards for health and infrastructure at Mt. Etna (Italy) by numerical simulation

    NASA Astrophysics Data System (ADS)

    Barsotti, S.; Andronico, D.; Neri, A.; Del Carlo, P.; Baxter, P. J.; Aspinall, W. P.; Hincks, T.

    2010-04-01

    We performed a quantitative hazard assessment to determine the potential impacts of volcanic tephra fall on human health and infrastructure in the vicinity of Mt. Etna (Italy). Using the numerical model VOL-CALPUFF, we explored the dynamics of long-lasting weak plume eruptions and their effects on the surrounding region. Input data are based on credible estimates of the main parameters characterising the expected events as derived from the historically observed and reconstructed explosive record of Mt. Etna. Monte Carlo techniques are used to capture the effects on estimates of finer ash concentration and total ground deposition due to volcanological uncertainties and meteorological variability. Numerical simulations compute the likelihoods of experiencing critical 10-μm volcanic particle (VP 10) concentrations in ambient air and tephra ground deposition at various populated locations around the volcano, including the city of Catania, and at key infrastructure, such as airports and main roads. Results show how the towns and infrastructure on the east side of the volcano are significantly more exposed to ash-related hazards than those on the west side, in accordance with wind statistics. Simulation outcomes also illustrate how, at the sites analysed, the amount of deposited particulate matter is proportional to the intensity (i.e. mass flow rate) of the event whereas predicted values of VP 10 concentrations are significantly larger for smaller events due to the reduced dispersal of low altitude plumes. The use of a simple re-mobilization model highlights the fact that particle re-suspension needs to be considered in the estimation of VP 10 values. Our findings can be used to inform civil protection agencies responsible for mitigating tephra fall impacts to human health, road transport and aviation safety.

  11. Validation of a Monte Carlo model used for simulating tube current modulation in computed tomography over a wide range of phantom conditions/challenges

    SciTech Connect

    Bostani, Maryam McMillan, Kyle; Cagnon, Chris H.; McNitt-Gray, Michael F.; DeMarco, John J.

    2014-11-01

    Purpose: Monte Carlo (MC) simulation methods have been widely used in patient dosimetry in computed tomography (CT), including estimating patient organ doses. However, most simulation methods have undergone a limited set of validations, often using homogeneous phantoms with simple geometries. As clinical scanning has become more complex and the use of tube current modulation (TCM) has become pervasive in the clinic, MC simulations should include these techniques in their methodologies and therefore should also be validated using a variety of phantoms with different shapes and material compositions to result in a variety of differently modulated tube current profiles. The purpose of this work is to perform the measurements and simulations to validate a Monte Carlo model under a variety of test conditions where fixed tube current (FTC) and TCM were used. Methods: A previously developed MC model for estimating dose from CT scans that models TCM, built using the platform of MCNPX, was used for CT dose quantification. In order to validate the suitability of this model to accurately simulate patient dose from FTC and TCM CT scan, measurements and simulations were compared over a wide range of conditions. Phantoms used for testing range from simple geometries with homogeneous composition (16 and 32 cm computed tomography dose index phantoms) to more complex phantoms including a rectangular homogeneous water equivalent phantom, an elliptical shaped phantom with three sections (where each section was a homogeneous, but different material), and a heterogeneous, complex geometry anthropomorphic phantom. Each phantom requires varying levels of x-, y- and z-modulation. Each phantom was scanned on a multidetector row CT (Sensation 64) scanner under the conditions of both FTC and TCM. Dose measurements were made at various surface and depth positions within each phantom. Simulations using each phantom were performed for FTC, detailed x–y–z TCM, and z-axis-only TCM to obtain

  12. Quantitative Evaluation of the Dispersion of Graphene Sheets With and Without Functional Groups Using Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Cha, JinHyeok; Kyoung, Woomin; Song, Kyonghwa; Park, Sangbaek; Lim, Taewon; Lee, Jongkook; Kang, Hyunmin

    2016-03-01

    Nanofluids with enhanced thermal properties are candidates for thermal management in automotive systems, with scope for improving energy efficiency. In particular, many studies have reported on dispersions of nanoparticles with long-term stability in the base fluid, with qualitative evaluations of the dispersion stability via either the naked eye or optical instruments. Additives such as surfactants can be used to enhance the dispersion of nanoparticles; however, this may diminish their intrinsic thermal properties. Here, we describe molecular dynamics simulations of nanofluids containing graphene sheets dispersed in ethylene glycol and water. We go on to suggest a quantitative evaluation method for the degree of dispersion, based on the ratio of the total number of nanoparticles to the number of clustered nanoparticles. Moreover, we investigate the effects of functional groups on the surface of graphene, which are expected to improve the dispersion without requiring additives such as surfactants due to steric hindrance and chemical affinity for the surrounding fluid. We find that, for pure graphene, the degree of dispersion decreased as the quantity of graphene sheets increased, which is attributed to an increased probability of aggregation at higher loadings; however, the presence of functional groups inhibited the graphene sheets from forming aggregates.

  13. Quantitative Evaluation of the Dispersion of Graphene Sheets With and Without Functional Groups Using Molecular Dynamics Simulations.

    PubMed

    Cha, JinHyeok; Kyoung, Woomin; Song, Kyonghwa; Park, Sangbaek; Lim, Taewon; Lee, Jongkook; Kang, Hyunmin

    2016-12-01

    Nanofluids with enhanced thermal properties are candidates for thermal management in automotive systems, with scope for improving energy efficiency. In particular, many studies have reported on dispersions of nanoparticles with long-term stability in the base fluid, with qualitative evaluations of the dispersion stability via either the naked eye or optical instruments. Additives such as surfactants can be used to enhance the dispersion of nanoparticles; however, this may diminish their intrinsic thermal properties. Here, we describe molecular dynamics simulations of nanofluids containing graphene sheets dispersed in ethylene glycol and water. We go on to suggest a quantitative evaluation method for the degree of dispersion, based on the ratio of the total number of nanoparticles to the number of clustered nanoparticles. Moreover, we investigate the effects of functional groups on the surface of graphene, which are expected to improve the dispersion without requiring additives such as surfactants due to steric hindrance and chemical affinity for the surrounding fluid. We find that, for pure graphene, the degree of dispersion decreased as the quantity of graphene sheets increased, which is attributed to an increased probability of aggregation at higher loadings; however, the presence of functional groups inhibited the graphene sheets from forming aggregates. PMID:26964558

  14. High-resolution quantitative precipitation forecasts and simulations by the Cloud-Resolving Storm Simulator (CReSS) for Typhoon Morakot (2009)

    NASA Astrophysics Data System (ADS)

    Wang, Chung-Chieh; Kuo, Hung-Chi; Yeh, Tien-Chiang; Chung, Chao-Hsuan; Chen, Yu-Han; Huang, Shin-Yi; Wang, Yi-Wen; Liu, Ching-Hwang

    2013-12-01

    SummaryTyphoon Morakot (2009) struck Taiwan during 7-9 August 2009, and brought extreme rainfall up to 2855 mm and the worst damages in the past 50 years. The operational models showed deficiency and serious under-prediction in rainfall amount at real time. This study demonstrates that the Cloud-Resolving Storm Simulator (CReSS), a state-of-the-art, high-resolution model, at a grid size of 3 km and starting as early as 0000 UTC 4 August, can successfully simulate and reproduce the event with high accuracy, including the distribution and timing of heavy rainfall in Taiwan. In the simulation starting at 0000 UTC 6 August, for example, the threat scores for 24-h rainfall for 8 August (with extreme amounts >1450 mm) reach 0.8-0.4 even at thresholds of 100-500 mm. This result is only possible due to small track error and the phase-locking mechanism of the Taiwan topography to heavy rainfall. Furthermore, real-time forecast and hindcast integrations of the CReSS model show that high-quality quantitative precipitation forecasts (QPFs) with peak total amount 67-80% of the true value are also obtained from initial conditions at 0000 UTC 6 August, which is about 2 days prior to the beginning of the heaviest rainfall in southern Taiwan. In these integrations, typhoon track errors in the global model forecasts used as boundary conditions are the major error source that prevent more ideal QPF results before and at 1200 UTC 5 August. When properly configured, it is believed that other similar cloud-resolving models can achieve comparable performance. Thus, the importance of and potential benefits from deterministic high-resolution forecasts is stressed, which may give an extended lead-time when the track error is small. With potentially longer time window for emergency action just prior to extreme rainfall events when it matters the most, such forecasts may ultimately lead to reduced losses in lives and properties.

  15. Hybrid quantitative simulation on the in-line phase-contrast x-ray imaging of three dimensional samples under actual clinic imaging parameters

    SciTech Connect

    Yu Hong; Han Shensheng; Ding Jianhui; Jiang Zhaoxia; Peng Weijun

    2009-07-06

    A hybrid model combining Monte Carlo method with diffraction theory of wave optics has been developed and applied to quantitatively simulate the in-line diffractive phase-contrast x-ray imaging of three dimensional tissue samples under actual clinic imaging parameters. The primary microcosmic interactions of medical-energy x-ray within matter including photoabsorption, Compton scattering, and coherent scattering, have been taken into account in the Monte Carlo simulation. A diffraction processing based on Fresnel diffraction theory is carried out to simulate the macroscopic diffraction effect. A comparison with experiment results has also been performed.

  16. Computer-aided diagnosis for phase-contrast X-ray computed tomography: quantitative characterization of human patellar cartilage with high-dimensional geometric features.

    PubMed

    Nagarajan, Mahesh B; Coan, Paola; Huber, Markus B; Diemoz, Paul C; Glaser, Christian; Wismüller, Axel

    2014-02-01

    Phase-contrast computed tomography (PCI-CT) has shown tremendous potential as an imaging modality for visualizing human cartilage with high spatial resolution. Previous studies have demonstrated the ability of PCI-CT to visualize (1) structural details of the human patellar cartilage matrix and (2) changes to chondrocyte organization induced by osteoarthritis. This study investigates the use of high-dimensional geometric features in characterizing such chondrocyte patterns in the presence or absence of osteoarthritic damage. Geometrical features derived from the scaling index method (SIM) and statistical features derived from gray-level co-occurrence matrices were extracted from 842 regions of interest (ROI) annotated on PCI-CT images of ex vivo human patellar cartilage specimens. These features were subsequently used in a machine learning task with support vector regression to classify ROIs as healthy or osteoarthritic; classification performance was evaluated using the area under the receiver-operating characteristic curve (AUC). SIM-derived geometrical features exhibited the best classification performance (AUC, 0.95 ± 0.06) and were most robust to changes in ROI size. These results suggest that such geometrical features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix in an automated and non-subjective manner, while also enabling classification of cartilage as healthy or osteoarthritic with high accuracy. Such features could potentially serve as imaging markers for evaluating osteoarthritis progression and its response to different therapeutic intervention strategies. PMID:24043594

  17. Characterization of the image-derived carotid artery input function using independent component analysis for the quantitation of [18F] fluorodeoxyglucose positron emission tomography images

    NASA Astrophysics Data System (ADS)

    Chen, K.; Chen, X.; Renaut, R.; Alexander, G. E.; Bandy, D.; Guo, H.; Reiman, E. M.

    2007-12-01

    We previously developed a noninvasive technique for the quantification of fluorodeoxyglucose (FDG) positron emission tomography (PET) images using an image-derived input function obtained from a manually drawn carotid artery region. Here, we investigate the use of independent component analysis (ICA) for more objective identification of the carotid artery and surrounding tissue regions. Using FDG PET data from 22 subjects, ICA was applied to an easily defined cubical region including the carotid artery and neighboring tissue. Carotid artery and tissue time activity curves and three venous samples were used to generate spillover and partial volume-corrected input functions and to calculate the parametric images of the cerebral metabolic rate for glucose (CMRgl). Different from a blood-sampling-free ICA approach, the results from our ICA approach are numerically well matched to those based on the arterial blood sampled input function. In fact, the ICA-derived input functions and CMRgl measurements were not only highly correlated (correlation coefficients >0.99) to, but also highly comparable (regression slopes between 0.92 and 1.09), with those generated using arterial blood sampling. Moreover, the reliability of the ICA-derived input function remained high despite variations in the location and size of the cubical region. The ICA procedure makes it possible to quantify FDG PET images in an objective and reproducible manner. Image-derived input function by ICA for FDG-PET.

  18. A model for quantitative correction of coronary calcium scores on multidetector, dual source, and electron beam computed tomography for influences of linear motion, calcification density, and temporal resolution: A cardiac phantom study

    SciTech Connect

    Greuter, M. J. W.; Groen, J. M.; Nicolai, L. J.; Dijkstra, H.; Oudkerk, M.

    2009-11-15

    Purpose: The objective of this study is to quantify the influence of linear motion, calcification density, and temporal resolution on coronary calcium determination using multidetector computed tomography (MDCT), dual source CT (DSCT), and electron beam tomography (EBT) and to find a quantitative method which corrects for the influences of these parameters using a linear moving cardiac phantom. Methods: On a robotic arm with artificial arteries with four calcifications of increasing density, a linear movement was applied between 0 and 120 mm/s (step of 10 mm/s). The phantom was scanned five times on 64-slice MDCT, DSCT, and EBT using a standard acquisition protocol. The average Agatston, volume, and mass scores were determined for each velocity, calcification, and scanner. Susceptibility to motion was quantified using a cardiac motion susceptibility (CMS) index. Resemblance to EBT and physical volume and mass was quantified using a {Delta} index. Results: Increasing motion artifacts were observed at increasing velocities on all scanners, with increasing severity from EBT to DSCT to 64-slice MDCT. The calcium score showed a linear dependency on motion from which a correction factor could be derived. This correction factor showed a linear dependency on the mean calcification density with a good fit for all three scoring methods and all three scanners (0.73{<=}R{sup 2}{<=}0.95). The slope and offset of this correction factor showed a linear dependency on temporal resolution with a good fit for all three scoring methods and all three scanners (0.83{<=}R{sup 2}{<=}0.98). CMS was minimal for EBT and increasing values were observed for DSCT and highest values for 64-slice MDCT. CMS was minimal for mass score and increasing values were observed for volume score and highest values for Agatston score. For all densities and scoring methods DSCT showed on average the closest resemblance to EBT calcium scores. When using the correction factor, CMS index decreased on average by

  19. Quantitative radiology: automated measurement of polyp volume in computed tomography colonography using Hessian matrix-based shape extraction and volume growing

    PubMed Central

    Epstein, Mark L.; Obara, Piotr R.; Chen, Yisong; Liu, Junchi; Zarshenas, Amin; Makkinejad, Nazanin; Dachman, Abraham H.

    2015-01-01

    Background Current measurement of the single longest dimension of a polyp is subjective and has variations among radiologists. Our purpose was to develop a computerized measurement of polyp volume in computed tomography colonography (CTC). Methods We developed a 3D automated scheme for measuring polyp volume at CTC. Our scheme consisted of segmentation of colon wall to confine polyp segmentation to the colon wall, extraction of a highly polyp-like seed region based on the Hessian matrix, a 3D volume growing technique under the minimum surface expansion criterion for segmentation of polyps, and sub-voxel refinement and surface smoothing for obtaining a smooth polyp surface. Our database consisted of 30 polyp views (15 polyps) in CTC scans from 13 patients. Each patient was scanned in the supine and prone positions. Polyp sizes measured in optical colonoscopy (OC) ranged from 6-18 mm with a mean of 10 mm. A radiologist outlined polyps in each slice and calculated volumes by summation of volumes in each slice. The measurement study was repeated 3 times at least 1 week apart for minimizing a memory effect bias. We used the mean volume of the three studies as “gold standard”. Results Our measurement scheme yielded a mean polyp volume of 0.38 cc (range, 0.15-1.24 cc), whereas a mean “gold standard” manual volume was 0.40 cc (range, 0.15-1.08 cc). The “gold-standard” manual and computer volumetric reached excellent agreement (intra-class correlation coefficient =0.80), with no statistically significant difference [P (F≤f) =0.42]. Conclusions We developed an automated scheme for measuring polyp volume at CTC based on Hessian matrix-based shape extraction and volume growing. Polyp volumes obtained by our automated scheme agreed excellently with “gold standard” manual volumes. Our fully automated scheme can efficiently provide accurate polyp volumes for radiologists; thus, it would help radiologists improve the accuracy and efficiency of polyp volume

  20. In vivo quantitative imaging of photoassimilate transport dynamics and allocation in large plants using a commercial positron emission tomography (PET) scanner

    SciTech Connect

    Karve, Abhijit A.; Alexoff, David; Kim, Dohyun; Schueller, Michael J.; Ferrieri, Richard A.; Babst, Benjamin A.

    2015-11-09

    Although important aspects of whole-plant carbon allocation in crop plants (e.g., to grain) occur late in development when the plants are large, techniques to study carbon transport and allocation processes have not been adapted for large plants. Positron emission tomography (PET), developed for dynamic imaging in medicine, has been applied in plant studies to measure the transport and allocation patterns of carbohydrates, nutrients, and phytohormones labeled with positron-emitting radioisotopes. However, the cost of PET and its limitation to smaller plants has restricted its use in plant biology. Here we describe the adaptation and optimization of a commercial clinical PET scanner to measure transport dynamics and allocation patterns of 11C-photoassimilates in large crops. Based on measurements of a phantom, we optimized instrument settings, including use of 3-D mode and attenuation correction to maximize the accuracy of measurements. To demonstrate the utility of PET, we measured 11C-photoassimilate transport and allocation in Sorghum bicolor, an important staple crop, at vegetative and reproductive stages (40 and 70 days after planting; DAP). The 11C-photoassimilate transport speed did not change over the two developmental stages. However, within a stem, transport speeds were reduced across nodes, likely due to higher 11C-photoassimilate unloading in the nodes. Photosynthesis in leaves and the amount of 11C that was exported to the rest of the plant decreased as plants matured. In young plants, exported 11C was allocated mostly (88 %) to the roots and stem, but in flowering plants (70 DAP) the majority of the exported 11C (64 %) was allocated to the apex. Our results show that commercial PET scanners can be used reliably to measure whole-plant C-allocation in large plants nondestructively including, importantly, allocation to roots in soil. This capability revealed extreme changes in

  1. In vivo quantitative imaging of photoassimilate transport dynamics and allocation in large plants using a commercial positron emission tomography (PET) scanner

    DOE PAGESBeta

    Karve, Abhijit A.; Alexoff, David; Kim, Dohyun; Schueller, Michael J.; Ferrieri, Richard A.; Babst, Benjamin A.

    2015-11-09

    Although important aspects of whole-plant carbon allocation in crop plants (e.g., to grain) occur late in development when the plants are large, techniques to study carbon transport and allocation processes have not been adapted for large plants. Positron emission tomography (PET), developed for dynamic imaging in medicine, has been applied in plant studies to measure the transport and allocation patterns of carbohydrates, nutrients, and phytohormones labeled with positron-emitting radioisotopes. However, the cost of PET and its limitation to smaller plants has restricted its use in plant biology. Here we describe the adaptation and optimization of a commercial clinical PET scannermore » to measure transport dynamics and allocation patterns of 11C-photoassimilates in large crops. Based on measurements of a phantom, we optimized instrument settings, including use of 3-D mode and attenuation correction to maximize the accuracy of measurements. To demonstrate the utility of PET, we measured 11C-photoassimilate transport and allocation in Sorghum bicolor, an important staple crop, at vegetative and reproductive stages (40 and 70 days after planting; DAP). The 11C-photoassimilate transport speed did not change over the two developmental stages. However, within a stem, transport speeds were reduced across nodes, likely due to higher 11C-photoassimilate unloading in the nodes. Photosynthesis in leaves and the amount of 11C that was exported to the rest of the plant decreased as plants matured. In young plants, exported 11C was allocated mostly (88 %) to the roots and stem, but in flowering plants (70 DAP) the majority of the exported 11C (64 %) was allocated to the apex. Our results show that commercial PET scanners can be used reliably to measure whole-plant C-allocation in large plants nondestructively including, importantly, allocation to roots in soil. This capability revealed extreme changes in carbon allocation in sorghum plants, as they advanced to maturity

  2. Quantitative Computed Tomography Measures of Pectoralis Muscle Area and Disease Severity in Chronic Obstructive Pulmonary Disease. A Cross-Sectional Study

    PubMed Central

    McDonald, Merry-Lynn N.; Diaz, Alejandro A.; Ross, James C.; San Jose Estepar, Raul; Zhou, Linfu; Regan, Elizabeth A.; Eckbo, Eric; Muralidhar, Nina; Come, Carolyn E.;