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Sample records for quantitative tomography simulations

  1. Quantitative tomography simulations and reconstruction algorithms

    SciTech Connect

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

    2000-11-01

    X-ray, neutron and proton transmission radiography and computed tomography (CT) are important diagnostic tools that are at the heart of LLNLs effort to meet the goals of the DOE's Advanced Radiography Campaign. This campaign seeks to improve radiographic simulation and analysis so that radiography can be a useful quantitative diagnostic tool for stockpile stewardship. Current radiographic accuracy does not allow satisfactory separation of experimental effects from the true features of an object's tomographically reconstructed image. This can lead to difficult and sometimes incorrect interpretation of the results. By improving our ability to simulate the whole radiographic and CT system, it will be possible to examine the contribution of system components to various experimental effects, with the goal of removing or reducing them. In this project, we are merging this simulation capability with a maximum-likelihood (constrained-conjugate-gradient-CCG) reconstruction technique yielding a physics-based, forward-model image-reconstruction code. In addition, we seek to improve the accuracy of computed tomography from transmission radiographs by studying what physics is needed in the forward model. During FY 2000, an improved version of the LLNL ray-tracing code called HADES has been coupled with a recently developed LLNL CT algorithm known as CCG. The problem of image reconstruction is expressed as a large matrix equation relating a model for the object being reconstructed to its projections (radiographs). Using a constrained-conjugate-gradient search algorithm, a maximum likelihood solution is sought. This search continues until the difference between the input measured radiographs or projections and the simulated or calculated projections is satisfactorily small. We developed a 2D HADES-CCG CT code that uses full ray-tracing simulations from HADES as the projector. Often an object has axial symmetry and it is desirable to reconstruct into a 2D r-z mesh with a limited

  2. 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.

  3. 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

  4. 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

  5. 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.

  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. 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.

  8. Quantitative damage imaging using Lamb wave diffraction tomography

    NASA Astrophysics Data System (ADS)

    Zhang, Hai-Yan; Ruan, Min; Zhu, Wen-Fa; Chai, Xiao-Dong

    2016-12-01

    In this paper, we investigate the diffraction tomography for quantitative imaging damages of partly through-thickness holes with various shapes in isotropic plates by using converted and non-converted scattered Lamb waves generated numerically. Finite element simulations are carried out to provide the scattered wave data. The validity of the finite element model is confirmed by the comparison of scattering directivity pattern (SDP) of circle blind hole damage between the finite element simulations and the analytical results. The imaging method is based on a theoretical relation between the one-dimensional (1D) Fourier transform of the scattered projection and two-dimensional (2D) spatial Fourier transform of the scattering object. A quantitative image of the damage is obtained by carrying out the 2D inverse Fourier transform of the scattering object. The proposed approach employs a circle transducer network containing forward and backward projections, which lead to so-called transmission mode (TMDT) and reflection mode diffraction tomography (RMDT), respectively. The reconstructed results of the two projections for a non-converted S0 scattered mode are investigated to illuminate the influence of the scattering field data. The results show that Lamb wave diffraction tomography using the combination of TMDT and RMDT improves the imaging effect compared with by using only the TMDT or RMDT. The scattered data of the converted A0 mode are also used to assess the performance of the diffraction tomography method. It is found that the circle and elliptical shaped damages can still be reasonably identified from the reconstructed images while the reconstructed results of other complex shaped damages like crisscross rectangles and racecourse are relatively poor. Project supported by the National Natural Science Foundation of China (Grant Nos. 11474195, 11274226, 11674214, and 51478258).

  9. Weighted filtered backprojection for quantitative fluorescence optical projection tomography

    NASA Astrophysics Data System (ADS)

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

    2008-07-01

    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.

  10. Quantitative photoacoustic tomography based on the radiative transfer equation.

    PubMed

    Yao, Lei; Sun, Yao; Jiang, Huabei

    2009-06-15

    We describe a method for quantitative photoacoustic tomography (PAT) based on the radiative transfer equation (RTE) coupled with the Helmholtz photoacoustic wave equation. This RTE-based quantitative PAT allows for accurate recovery of absolute absorption coefficient images of heterogeneous media and provides significantly improved image reconstruction for the cases where the photon diffusion approximation may fail. The method and associated finite element reconstruction algorithm are validated using a series of tissuelike phantom experiments.

  11. Quantitative analysis in medicine using photoacoustic tomography.

    PubMed

    Haisch, Christoph

    2009-01-01

    Photoacoustic imaging, or photoacoustic tomography, is a 2D or 3D optical imaging method based on localized optical absorption of pulsed laser radiation. By a spatially resolved detection of the following thermoelastic expansion, the local distribution of the absorption can be determined. The technique has been proven to have significant potential for the imaging of human and animal organs and single blood vessels, combining high contrast with good spatial resolution. The contrast is based on the specific optical absorption of certain components in the visible and near-infrared spectral range, for most applications of blood. Generally, the images represent the local distribution of blood in a qualitative or semiquantitative way. Although photoacoustic imaging is capable of revealing absolute and spatially resolved concentrations of endogenous (such as oxyhemoglobin and deoxyhemoglobin) or artificial (such as tumor markers) chromophores, only a very limited number of publications have dealt with this demanding task. In this report, the problems involved and possible solutions are reviewed and summarized.

  12. Quantitative contrast-enhanced optical coherence tomography

    PubMed Central

    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. PMID:26869724

  13. 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.

  14. Quantitative contrast-enhanced optical coherence tomography

    SciTech Connect

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

    2016-01-11

    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.

  15. Quantitative coherent-scatter-computed tomography

    NASA Astrophysics Data System (ADS)

    Batchelar, Deidre L.; Westmore, Michael S.; Lai, Hao; Cunningham, Ian A.

    1998-07-01

    Conventional means of diagnosiing and assessing the progression of osteoporosis, including radiographic absorptiometry and quantitative CT, are directly or indirectly dependent upon bone density. This is, how ever, not always a reliable indicator of fracture risk. Changes in the trabecular structure and bone mineral content (BMC) are thought to provide a better indication of the change of spontaneous fractures occurring. Coherent-scatter CT (CSCT) is a technique which produces images based on the low angle (0 - 10 degrees) x-ray diffraction properties of tissue. Diffraction patterns from an object are acquired using first-generation CT geometry with a diagnostic x-ray image intensifier based system. These patterns are used to reconstruct a series of maps of the angle dependent coherent scatter cross section in a tomographic slice which are dependent upon the molecular structure of the scatterer. Hydroxyapatite has a very different cross section to that of soft tissue, and the CSCT method may, therefore, form the basis for a more direct measure of BMC. Our original CSCT images suffered from a 'cupping' artifact, resulting in increased intensities for pixels at the periphery of the object. This artifact, which is due to self-attenuation of scattered x rays, caused a systematic error of up to 20% in cross-sections measured from a CT image. This effect has been removed by monitoring the transmitted intensity using a photodiode mounted on the primary beam stop, and normalizing the scatter intensity to that of the transmitted beam for each projection. Images reconstructed from data normalized in this way do not exhibit observable attenuation artifacts. Elimination of this artifact enables the determination of accurate quantitative measures of BMC at each pixel in a tomograph.

  16. 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.

  17. HAADF-STEM atom counting in atom probe tomography specimens: Towards quantitative correlative microscopy.

    PubMed

    Lefebvre, W; Hernandez-Maldonado, D; Moyon, F; Cuvilly, F; Vaudolon, C; Shinde, D; Vurpillot, F

    2015-12-01

    The geometry of atom probe tomography tips strongly differs from standard scanning transmission electron microscopy foils. Whereas the later are rather flat and thin (<20 nm), tips display a curved surface and a significantly larger thickness. As far as a correlative approach aims at analysing the same specimen by both techniques, it is mandatory to explore the limits and advantages imposed by the particular geometry of atom probe tomography specimens. Based on simulations (electron probe propagation and image simulations), the possibility to apply quantitative high angle annular dark field scanning transmission electron microscopy to of atom probe tomography specimens has been tested. The influence of electron probe convergence and the benefice of deconvolution of electron probe point spread function electron have been established. Atom counting in atom probe tomography specimens is for the first time reported in this present work. It is demonstrated that, based on single projections of high angle annular dark field imaging, significant quantitative information can be used as additional input for refining the data obtained by correlative analysis of the specimen in APT, therefore opening new perspectives in the field of atomic scale tomography.

  18. 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.

  19. In vivo validation of quantitative frequency domain fluorescence tomography

    NASA Astrophysics Data System (ADS)

    Lin, Yuting; Ghijsen, Michael; Nalcioglu, Orhan; Gulsen, Gultekin

    2012-12-01

    We have developed a hybrid frequency domain fluorescence tomography and magnetic resonance imaging system (MRI) for small animal imaging. The main purpose of this system is to obtain quantitatively accurate fluorescence concentration and lifetime images using a multi-modality approach. In vivo experiments are undertaken to evaluate the system. We compare the recovered fluorescence parameters with and without MRI structural a priori information. In addition, we compare two optical background heterogeneity correction methods: Born normalization and utilizing diffuse optical tomography (DOT) functional a priori information. The results show that the concentration and lifetime of a 4.2-mm diameter indocyanine green inclusion located 15 mm deep inside a rat can be recovered with less than a 5% error when functional a priori information from DOT and structural a priori information from MRI are utilized.

  20. Shifted helical computed tomography to optimize cardiac positron emission tomography-computed tomography coregistration: quantitative improvement and limitations.

    PubMed

    Johnson, Nils P; Pan, Tinsu; Gould, K Lance

    2010-10-01

    Positron emission tomography-computed tomography (PET-CT) uses CT attenuation correction but suffers from misregistration artifacts. However, the quantitative accuracy of helical versus cine CT in the same patient after optimized coregistration by shifting both CT data as needed for each patient is unknown. We studied 293 patients undergoing cardiac perfusion PET-CT using helical CT attenuation correction for comparison to cine CT. Objective, quantitative criteria identified perfusion abnormalities that were associated visually with PET-CT misregistration. Custom software shifted CT data to optimize coregistration with quantitative artifact improvement. The majority (58.1%) of cases with both helical and shifted helical CT data (n  = 93) had artifacts that improved or resolved by software shifting helical CT data. Translation of shifted helical CT was greatest in the x-direction (8.8 ± 3.3 mm) and less in the y- and z-directions (approximately 3.5 mm). The magnitude of differences in quantitative end points was greatest for helical (p  =  .0001, n  =  177 studies), less for shifted helical but significant (p  =  .0001, n  =  93 studies), and least for cine (not significant, n  =  161 studies) CT compared to optimal attenuation correction for each patient. Frequent artifacts owing to attenuation-emission misregistration are substantially corrected by software shifting helical CT scans to achieve proper coregistration that, however, remains on average significantly inferior to cine CT attenuation quantitatively.

  1. 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

  2. Quantitative fluorescence tomography using a trimodality system: in vivo validation

    NASA Astrophysics Data System (ADS)

    Lin, Yuting; Barber, William C.; Iwanczyk, Jan S.; Roeck, Werner W.; Nalcioglu, Orhan; Gulsen, Gultekin

    2010-07-01

    A fully integrated trimodality fluorescence, diffuse optical, and x-ray computed tomography (FT/DOT/XCT) system for small animal imaging is reported in this work. The main purpose of this system is to obtain quantitatively accurate fluorescence concentration images using a multimodality approach. XCT offers anatomical information, while DOT provides the necessary background optical property map to improve FT image accuracy. The quantitative accuracy of this trimodality system is demonstrated in vivo. In particular, we show that a 2-mm-diam fluorescence inclusion located 8 mm deep in a nude mouse can only be localized when functional a priori information from DOT is available. However, the error in the recovered fluorophore concentration is nearly 87%. On the other hand, the fluorophore concentration can be accurately recovered within 2% error when both DOT functional and XCT structural a priori information are utilized together to guide and constrain the FT reconstruction algorithm.

  3. Seismic traveltime tomography: a simulated annealing approach

    NASA Astrophysics Data System (ADS)

    Wéber, Zoltán

    2000-04-01

    Seismic traveltime tomography involves finding a velocity model that minimizes the error energy between the measured and the theoretical traveltimes. When solving this nonlinear inverse problem, a local optimization technique can easily produce a solution for which the gradient of the error energy function vanishes, but the energy function itself does not take its global minimum. Other methods such as simulated annealing can be applied to such global optimization problems. The simulated annealing approach to seismic traveltime tomography described in this paper has been tested on synthetic as well as real seismic data. It is shown that unlike local methods, the convergence of the simulated annealing algorithm is independent of the initial model: even in cases of virtually no prior information, it is capable of producing reliable results. The method can provide a number of acceptable solutions. When prior information is sparse, the solution of the global optimization can be used as an input to a local optimization procedure, such as, e.g., simultaneous iterative reconstruction technique (SIRT), producing an even more accurate result.

  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 computed tomography imaging of airway remodeling in severe asthma

    PubMed Central

    Fetita, Catalin I.; Brillet, Pierre-Yves

    2016-01-01

    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

  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.

  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. Quantitative single-photon emission computed tomography/computed tomography for technetium pertechnetate thyroid uptake measurement

    PubMed Central

    Lee, Hyunjong; Kim, Ji Hyun; Kang, Yeon-koo; Moon, Jae Hoon; So, Young; Lee, Won Woo

    2016-01-01

    Abstract Objectives: Technetium pertechnetate (99mTcO4) is a radioactive tracer used to assess thyroid function by thyroid uptake system (TUS). However, the TUS often fails to deliver accurate measurements of the percent of thyroid uptake (%thyroid uptake) of 99mTcO4. Here, we investigated the usefulness of quantitative single-photon emission computed tomography/computed tomography (SPECT/CT) after injection of 99mTcO4 in detecting thyroid function abnormalities. Materials and methods: We retrospectively reviewed data from 50 patients (male:female = 15:35; age, 46.2 ± 16.3 years; 17 Graves disease, 13 thyroiditis, and 20 euthyroid). All patients underwent 99mTcO4 quantitative SPECT/CT (185 MBq = 5 mCi), which yielded %thyroid uptake and standardized uptake value (SUV). Twenty-one (10 Graves disease and 11 thyroiditis) of the 50 patients also underwent conventional %thyroid uptake measurements using a TUS. Results: Quantitative SPECT/CT parameters (%thyroid uptake, SUVmean, and SUVmax) were the highest in Graves disease, second highest in euthyroid, and lowest in thyroiditis (P < 0.0001, Kruskal–Wallis test). TUS significantly overestimated the %thyroid uptake compared with SPECT/CT (P < 0.0001, paired t test) because other 99mTcO4 sources in addition to thyroid, such as salivary glands and saliva, contributed to the %thyroid uptake result by TUS, whereas %thyroid uptake, SUVmean and SUVmax from the SPECT/CT were associated with the functional status of thyroid. Conclusions: Quantitative SPECT/CT is more accurate than conventional TUS for measuring 99mTcO4 %thyroid uptake. Quantitative measurements using SPECT/CT may facilitate more accurate assessment of thyroid tracer uptake. PMID:27399139

  9. Quantitative Cardiac Positron Emission Tomography: The Time Is Coming!

    PubMed Central

    Sciagrà, Roberto

    2012-01-01

    In the last 20 years, the use of positron emission tomography (PET) has grown dramatically because of its oncological applications, and PET facilities are now easily accessible. At the same time, various groups have explored the specific advantages of PET in heart disease and demonstrated the major diagnostic and prognostic role of quantitation in cardiac PET. Nowadays, different approaches for the measurement of myocardial blood flow (MBF) have been developed and implemented in user-friendly programs. There is large evidence that MBF at rest and under stress together with the calculation of coronary flow reserve are able to improve the detection and prognostication of coronary artery disease. Moreover, quantitative PET makes possible to assess the presence of microvascular dysfunction, which is involved in various cardiac diseases, including the early stages of coronary atherosclerosis, hypertrophic and dilated cardiomyopathy, and hypertensive heart disease. Therefore, it is probably time to consider the routine use of quantitative cardiac PET and to work for defining its place in the clinical scenario of modern cardiology. PMID:24278760

  10. Quantitative computed tomography imaging in chronic obstructive pulmonary disease

    PubMed Central

    Fernandes, Lalita; Fernandes, Yasmin; Mesquita, Anthony Menezes

    2016-01-01

    Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease having small airway inflammation, emphysema, and pulmonary hypertension. It is now clear that spirometry alone cannot differentiate each component. Quantitative computed tomography (QCT) is increasingly used to quantify the amount of emphysema and small airway involvement in COPD. Inspiratory CT guides in assessing emphysema while expiratory CT identifies areas of air trapping which is a surrogate of small airway inflammation. By constructing a three-dimensional model of airways, we can also measure the airway wall thickness of segmental and subsegmental airways. The aim of this review is to present the current knowledge and methodologies in QCT of the lung that aid in identifying discrete COPD phenotypes. PMID:27890994

  11. Towards quantitative analysis of retinal features in optical coherence tomography.

    PubMed

    Baroni, Maurizio; Fortunato, Pina; La Torre, Agostino

    2007-05-01

    The purpose of this paper was to propose a new computer method for quantitative evaluation of representative features of the retina using optical coherence tomography (OCT). A multi-step approach was devised and positively tested for segmentation of the three main retinal layers: the vitreo-retinal interface and the inner and outer retina. Following a preprocessing step, three regions of interest were delimited. Significant peaks corresponding to high and low intensity strips were located along the OCT A-scan lines and accurate boundaries between different layers were obtained by maximizing an edge likelihood function. For a quantitative description, thickness measurement, densitometry, texture and curvature analyses were performed. As a first application, the effect of intravitreal injection of triamcinolone acetonide (IVTA) for the treatment of vitreo-retinal interface syndrome was evaluated. Almost all the parameters, measured on a set of 16 pathologic OCT images, were statistically different before and after IVTA injection (p<0.05). Shape analysis of the internal limiting membrane confirmed the reduction of the pathological traction state. Other significant parameters, such as reflectivity and texture contrast, exhibited relevant changes both at the vitreo-retinal interface and in the inner retinal layers. Texture parameters in the inner and outer retinal layers significantly correlated with the visual acuity restoration. According to these findings an IVTA injection might be considered a possible alternative to surgery for selected patients. In conclusion, the proposed approach appeared to be a promising tool for the investigation of tissue changes produced by pathology and/or therapy.

  12. Quantitative characterization of developing collagen gels using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Levitz, David; Hinds, Monica T.; Choudhury, Niloy; Tran, Noi T.; Hanson, Stephen R.; Jacques, Steven L.

    2010-03-01

    Nondestructive optical imaging methods such as optical coherence tomography (OCT) have been proposed for characterizing engineered tissues such as collagen gels. In our study, OCT was used to image collagen gels with different seeding densities of smooth muscle cells (SMCs), including acellular gels, over a five-day period during which the gels contracted and became turbid with increased optical scattering. The gels were characterized quantitatively by their optical properties, specified by analysis of OCT data using a theoretical model. At 6 h, seeded cell density and scattering coefficient (μs) were correlated, with μs equal to 10.8 cm-1/(106 cells/mL). Seeded cell density and the scattering anisotropy (g) were uncorrelated. Over five days, the reflectivity in SMC gels gradually doubled with little change in optical attenuation, which indicated a decrease in g that increased backscatter, but only a small drop in μs. At five days, a subpopulation of sites on the gel showed substantially higher reflectivity (approximately a tenfold increase from the first 24 h). In summary, the increased turbidity of SMC gels that develops over time is due to a change in the structure of collagen, which affects g, and not simply due to a change in number density of collagen fibers due to contraction.

  13. 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.

  14. 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

  15. 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.

  16. Evaluation of static and dynamic perfusion cardiac computed tomography for quantitation and classification tasks.

    PubMed

    Bindschadler, Michael; Modgil, Dimple; Branch, Kelley R; La Riviere, Patrick J; Alessio, Adam M

    2016-04-01

    Cardiac computed tomography (CT) acquisitions for perfusion assessment can be performed in a dynamic or static mode. Either method may be used for a variety of clinical tasks, including (1) stratifying patients into categories of ischemia and (2) using a quantitative myocardial blood flow (MBF) estimate to evaluate disease severity. In this simulation study, we compare method performance on these classification and quantification tasks for matched radiation dose levels and for different flow states, patient sizes, and injected contrast levels. Under conditions simulated, the dynamic method has low bias in MBF estimates (0 to [Formula: see text]) compared to linearly interpreted static assessment (0.45 to [Formula: see text]), making it more suitable for quantitative estimation. At matched radiation dose levels, receiver operating characteristic analysis demonstrated that the static method, with its high bias but generally lower variance, had superior performance ([Formula: see text]) in stratifying patients, especially for larger patients and lower contrast doses [area under the curve [Formula: see text] to 96 versus 0.86]. We also demonstrate that static assessment with a correctly tuned exponential relationship between the apparent CT number and MBF has superior quantification performance to static assessment with a linear relationship and to dynamic assessment. However, tuning the exponential relationship to the patient and scan characteristics will likely prove challenging. This study demonstrates that the selection and optimization of static or dynamic acquisition modes should depend on the specific clinical task.

  17. 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.

  18. Quantitative assessment of impedance tomography for temperature measurements in hyperthermia.

    PubMed

    Blad, B; Persson, B; Lindström, K

    1992-01-01

    The objective of this study is a non-invasive assessment of the thermal dose in hyperthermia. Electrical impedance tomography (EIT) has previously been given a first trial as a temperature monitoring method together with microwave-induced hyperthermia treatment, but it has not been thoroughly investigated. In the present work we have examined this method in order to investigate the correlation in vitro between the true spatial temperature distribution and the corresponding measured relative resistivity changes. Different hyperthermia techniques, such as interstitial water tubings, microwave-induced, laser-induced and ferromagnetic seeds have been used. The results show that it is possible to find a correlation between the measured temperature values and the tomographically measured relative resistivity changes in tissue-equivalent phantoms. But the uncertainty of the temperature coefficients, which has been observed, shows that the method has to be improved before it can be applied to clinical in vivo applications.

  19. Quantitative photo-acoustic tomography with partial data

    NASA Astrophysics Data System (ADS)

    Chen, Jie; Yang, Yang

    2012-11-01

    Photo-acoustic tomography is a newly developed hybrid imaging modality that combines a high-resolution modality with a high-contrast modality. We analyze the reconstruction of diffusion and absorption parameters in an elliptic equation and extend an earlier result of Bal and Uhlmann (2010 Inverse Problems 26 085010) to the partial data case. We show that the reconstruction can be uniquely determined by the knowledge of four internal data based on well-chosen partial boundary conditions. Stability of this reconstruction is ensured if a convexity condition is satisfied. A similar stability result is obtained without this geometric constraint if 4n well chosen partial boundary conditions are available, where n is the spatial dimension. The set of well chosen boundary measurements is characterized by some complex geometric optics solutions vanishing on a part of the boundary.

  20. 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.

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

    SciTech Connect

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

    2016-01-28

    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.

  2. Quantitative analyses of maxillary sinus using computed tomography.

    PubMed

    Perella, Andréia; Rocha, Sara Dos Santos; Cavalcanti, Marcelo de Gusmão Paraiso

    2003-09-01

    The aim of this study was to evaluate the precision and accuracy of linear measurements of maxillary sinus made in tomographic films, by comparing with 3D reconstructed images. Linear measurements of both maxillary sinus in computed tomography CT of 17 patients, with or without lesion by two calibrated examiners independently, on two occasions, with a single manual caliper. A third examiner has done the same measurements electronically in 3D-CT reconstruction. The statistical analysis was performed using ANOVA (analyses of variance). Intra-observer percentage error was little in both cases, with and without lesion; it ranged from 1.14% to 1.82%. The inter-observer error was a little higher reaching a 2.08% value. The accuracy presented a higher value. The perceptual accuracy error was higher in samples, which had lesion compared to that which had not. CT had provided adequate precision and accuracy for maxillary sinus analyses. The precision in cases with lesion was considered inferior when compared to that without lesion, but it can't affect the method efficacy.

  3. 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

  4. Objective breast tissue image classification using Quantitative Transmission ultrasound tomography

    PubMed Central

    Malik, Bilal; Klock, John; Wiskin, James; Lenox, Mark

    2016-01-01

    Quantitative Transmission Ultrasound (QT) is a powerful and emerging imaging paradigm which has the potential to perform true three-dimensional image reconstruction of biological tissue. Breast imaging is an important application of QT and allows non-invasive, non-ionizing imaging of whole breasts in vivo. Here, we report the first demonstration of breast tissue image classification in QT imaging. We systematically assess the ability of the QT images’ features to differentiate between normal breast tissue types. The three QT features were used in Support Vector Machines (SVM) classifiers, and classification of breast tissue as either skin, fat, glands, ducts or connective tissue was demonstrated with an overall accuracy of greater than 90%. Finally, the classifier was validated on whole breast image volumes to provide a color-coded breast tissue volume. This study serves as a first step towards a computer-aided detection/diagnosis platform for QT. PMID:27934955

  5. Objective breast tissue image classification using Quantitative Transmission ultrasound tomography

    NASA Astrophysics Data System (ADS)

    Malik, Bilal; Klock, John; Wiskin, James; Lenox, Mark

    2016-12-01

    Quantitative Transmission Ultrasound (QT) is a powerful and emerging imaging paradigm which has the potential to perform true three-dimensional image reconstruction of biological tissue. Breast imaging is an important application of QT and allows non-invasive, non-ionizing imaging of whole breasts in vivo. Here, we report the first demonstration of breast tissue image classification in QT imaging. We systematically assess the ability of the QT images’ features to differentiate between normal breast tissue types. The three QT features were used in Support Vector Machines (SVM) classifiers, and classification of breast tissue as either skin, fat, glands, ducts or connective tissue was demonstrated with an overall accuracy of greater than 90%. Finally, the classifier was validated on whole breast image volumes to provide a color-coded breast tissue volume. This study serves as a first step towards a computer-aided detection/diagnosis platform for QT.

  6. Treatment modification of yttrium-90 radioembolization based on quantitative positron emission tomography/CT imaging.

    PubMed

    Chang, Ted T; Bourgeois, Austin C; Balius, Anastasia M; Pasciak, Alexander S

    2013-03-01

    Treatment activity for yttrium-90 ((90)Y) radioembolization when calculated by using the manufacturer-recommended technique is only partially patient-specific and may result in a subtumoricidal dose in some patients. The authors describe the use of quantitative (90)Y positron emission tomography/computed tomography as a tool to provide patient-specific optimization of treatment activity and evaluate this new method in a patient who previously received traditional (90)Y radioembolization. The modified treatment resulted in a 40-Gy increase in absorbed dose to tumor and complete resolution of disease in the treated area within 3 months.

  7. 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

  8. 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.

  9. Understanding Cellulose Through Molecular Simulation and Electron Tomography

    SciTech Connect

    Matthews, J.

    2013-01-01

    High-resolution cellulose crystal structures have been determined from diffraction experiments using large diameter microfibrils as the sample material. However, cellulose microfibrils in plants are much smaller in diameter, and are more difficult to directly examine experimentally. Molecular dynamics simulation combined with quantum chemical calculations can help to elucidate the structure and dynamics of small diameter cellulose microfibrils. These simulation techniques also aid in the interpretation of electron tomography volumetric structural data from maize cell walls, where pretreatment with dilute acid or ammonia reveals microfibril geometry.

  10. 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.

  11. 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.

  12. Simulation of computed tomography dose based on voxel phantom

    NASA Astrophysics Data System (ADS)

    Liu, Chunyu; Lv, Xiangbo; Li, Zhaojun

    2017-01-01

    Computed Tomography (CT) is one of the preferred and the most valuable imaging tool used in diagnostic radiology, which provides a high-quality cross-sectional image of the body. It still causes higher doses of radiation to patients comparing to the other radiological procedures. The Monte-Carlo method is appropriate for estimation of the radiation dose during the CT examinations. The simulation of the Computed Tomography Dose Index (CTDI) phantom was developed in this paper. Under a similar conditions used in physical measurements, dose profiles were calculated and compared against the measured values that were reported. The results demonstrate a good agreement between the calculated and the measured doses. From different CT exam simulations using the voxel phantom, the highest absorbed dose was recorded for the lung, the brain, the bone surface. A comparison between the different scan type shows that the effective dose for a chest scan is the highest one, whereas the effective dose values during abdomen and pelvis scan are very close, respectively. The lowest effective dose resulted from the head scan. Although, the dose in CT is related to various parameters, such as the tube current, exposure time, beam energy, slice thickness and patient size, this study demonstrates that the MC simulation is a useful tool to accurately estimate the dose delivered to any specific organs for patients undergoing the CT exams and can be also a valuable technique for the design and the optimization of the CT x-ray source.

  13. The transesophageal echocardiography simulator based on computed tomography images.

    PubMed

    Piórkowski, Adam; Kempny, Aleksander

    2013-02-01

    Simulators are a new tool in education in many fields, including medicine, where they greatly improve familiarity with medical procedures, reduce costs, and, importantly, cause no harm to patients. This is so in the case of transesophageal echocardiography (TEE), in which the use of a simulator facilitates spatial orientation and helps in case studies. The aim of the project described in this paper is to simulate an examination by TEE. This research makes use of available computed tomography data to simulate the corresponding echocardiographic view. This paper describes the essential characteristics that distinguish these two modalities and the key principles of the wave phenomena that should be considered in the simulation process, taking into account the conditions specific to the echocardiography. The construction of the CT2TEE (Web-based TEE simulator) is also presented. The considerations include ray-tracing and ray-casting techniques in the context of ultrasound beam and artifact simulation. An important aspect of the interaction with the user is raised.

  14. 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.

  15. [High resolution peripheral quantitative computed tomography for the assessment of morphological and mechanical bone parameters].

    PubMed

    Fuller, Henrique; Fuller, Ricardo; Pereira, Rosa Maria R

    2015-01-01

    High resolution peripheral quantitative computed tomography (HR-pQCT) is a new technology commercially available for less than 10 years that allows performing in vivo assessment of bone parameters. HR-pQCT assesses the trabecular thickness, trabecular separation, trabecular number and connectivity density and, in addition, cortical bone density and thickness and total bone volume and density in high-definition mode, which additionally allows obtaining digital constructs of bone microarchitecture. The application of mathematics to captured data, a method called finite element analysis (FEA), allows the estimation of the physical properties of the tissue, simulating supported loads in a non-invasive way. Thus, HR-pQCT simultaneously acquires data previously provided separately by dual energy x-ray absorptiometry (DXA), magnetic resonance imaging and histomorphometry, aggregating biomechanical estimates previously only possible in extracted tissues. This method has a satisfactory reproducibility, with coefficients of variation rarely exceeding 3%. Regarding accuracy, the method shows a fair to good agreement (r(2) = 0.37-0.97). The main clinical application of this method is in the quantification and monitoring of metabolic bone disorders, more fully evaluating bone strength and fracture risk. In rheumatoid arthritis patients, this allows gauging the number and size of erosions and cysts, in addition to joint space. In osteoarthritis, it is possible to characterize the bone marrow edema-like areas that show a correlation with cartilage breakdown. Given its high cost, HR-pQCT is still a research tool, but the high resolution and efficiency of this method reveal advantages over the methods currently used for bone assessment, with a potential to become an important tool in clinical practice.

  16. A framework of modeling detector systems for computed tomography simulations

    NASA Astrophysics Data System (ADS)

    Youn, H.; Kim, D.; Kim, S. H.; Kam, S.; Jeon, H.; Nam, J.; Kim, H. K.

    2016-01-01

    Ultimate development in computed tomography (CT) technology may be a system that can provide images with excellent lesion conspicuity with the patient dose as low as possible. Imaging simulation tools have been cost-effectively used for these developments and will continue. For a more accurate and realistic imaging simulation, the signal and noise propagation through a CT detector system has been modeled in this study using the cascaded linear-systems theory. The simulation results are validated in comparisons with the measured results using a laboratory flat-panel micro-CT system. Although the image noise obtained from the simulations at higher exposures is slightly smaller than that obtained from the measurements, the difference between them is reasonably acceptable. According to the simulation results for various exposure levels and additive electronic noise levels, x-ray quantum noise is more dominant than the additive electronic noise. The framework of modeling a CT detector system suggested in this study will be helpful for the development of an accurate and realistic projection simulation model.

  17. Simulation of Underground Muon Flux with Application to Muon Tomography

    NASA Astrophysics Data System (ADS)

    Yamaoka, J. A. K.; Bonneville, A.; Flygare, J.; Lintereur, A.; Kouzes, R.

    2015-12-01

    Muon tomography uses highly energetic muons, produced by cosmic rays interacting within the upper atmosphere, to image dense materials. Like x-rays, an image can be constructed from the negative of the absorbed (or scattered) muons. Unlike x-rays, these muons can penetrate thousands of meters of earth. Muon tomography has been shown to be useful across a wide range of applications (such as imaging of the interior of volcanoes and cargo containers). This work estimates the sensitivity of muon tomography for various underground applications. We use simulations to estimate the change in flux as well as the spatial resolution when imaging static objects, such as mine shafts, and dynamic objects, such as a CO2 reservoir filling over time. We present a framework where we import ground density data from other sources, such as wells, gravity and seismic data, to generate an expected muon flux distribution at specified underground locations. This information can further be fed into a detector simulation to estimate a final experimental sensitivity. There are many applications of this method. We explore its use to image underground nuclear test sites, both the deformation from the explosion as well as the supporting infrastructure (access tunnels and shafts). We also made estimates for imaging a CO2 sequestration site similar to Futuregen 2.0 in Illinois and for imaging magma chambers beneath the Cascade Range volcanoes. This work may also be useful to basic science, such as underground dark matter experiments, where increasing experimental sensitivity requires, amongst other factors, a precise knowledge of the muon background.

  18. Quantitative computed tomography assessment of lung structure and function in pulmonary emphysema.

    PubMed

    Madani, A; Keyzer, C; Gevenois, P A

    2001-10-01

    Accurate diagnosis and quantification of pulmonary emphysema during life is important to understand the natural history of the disease, to assess the extent of the disease, and to evaluate and follow-up therapeutic interventions. Since pulmonary emphysema is defined through pathological criteria, new methods of diagnosis and quantification should be validated by comparisons against histological references. Recent studies have addressed the capability of computed tomography (CT) to quantify pulmonary emphysema accurately. The studies reviewed in this article have been based on CT scans obtained after deep inspiration or expiration, on subjective visual grading and on objective measurements of attenuation values. Especially dedicated software was used for this purpose, which provided numerical data, on both two- and three-dimensional approaches, and compared CT data with pulmonary function tests. More recently, fractal and textural analyses were applied to computed tomography scans to assess the presence, the extent, and the types of emphysema. Quantitative computed tomography has already been used in patient selection for surgical treatment of pulmonary emphysema and in pharmacotherapeutical trials. However, despite numerous and extensive studies, this technique has not yet been standardized and important questions about how best to use computed tomography for the quantification of pulmonary emphysema are still unsolved.

  19. 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.

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

    PubMed

    Pang, Wei; Coghill, George M

    2015-05-01

    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.

  1. Quantitative computed tomography of the liver in juvenile green sea turtles (Chelonia mydas).

    PubMed

    Bonelli, Marília de Albuquerque; de Oliveira, Daniel Capucho; Costa, Lorena Adão Vescovi Séllos; Forattini, Jannine Garcia; Júnior, João Luiz Rossi; Leite, Flaviana Lima Guião; Costa, Fabiano Séllos

    2013-06-01

    Quantitative computed tomography (QCT) is a highly sensitive, applicable technique for determining the x-ray attenuation of organs. This technique reveals great precision in the detection of alterations in the x-ray attenuation of hepatic parenchyma, although the lack of studies establishing normal values limits its application in wild animals. The objective of this study was to establish mean hepatic attenuation values in four healthy juvenile sea turtles (Chelonia mydas) using QCT. Helical computed tomography scans were performed and regions of interest selected in the liver after multi-planar reconstruction images were obtained. The mean attenuation value for the hepatic parenchyma in these four turtles was 60.09 +/- 5.3 standard deviation Hounsfield units. Determining normal x-ray attenuation values of the liver increases knowledge of the computed tomographic anatomy of this species and may be useful in the investigation of hepatic diseases.

  2. Quantitative chemical-structure evaluation using atom probe tomography: Short-range order analysis of Fe-Al.

    PubMed

    Marceau, R K W; Ceguerra, A V; Breen, A J; Raabe, D; Ringer, S P

    2015-10-01

    Short-range-order (SRO) has been quantitatively evaluated in an Fe-18Al (at%) alloy using atom probe tomography (APT) data and by calculation of the generalised multicomponent short-range order (GM-SRO) parameters, which have been determined by shell-based analysis of the three-dimensional atomic positions. The accuracy of this method with respect to limited detector efficiency and spatial resolution is tested against simulated D03 ordered data. Whilst there is minimal adverse effect from limited atom probe instrument detector efficiency, the combination of this with imperfect spatial resolution has the effect of making the data appear more randomised. The value of lattice rectification of the experimental APT data prior to GM-SRO analysis is demonstrated through improved information sensitivity.

  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. Quantitative evaluation of registration methods for atlas-based diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Wu, Xue; Eggebrecht, Adam T.; Culver, Joseph P.; Zhan, Yuxuan; Basevi, Hector; Dehghani, Hamid

    2013-06-01

    In Diffuse Optical Tomography (DOT), an atlas-based model can be used as an alternative to a subject-specific anatomical model for recovery of brain activity. The main step of the generation of atlas-based subject model is the registration of atlas model to the subject head. The accuracy of the DOT then relies on the accuracy of registration method. In this work, 11 registration methods are quantitatively evaluated. The registration method with EEG 10/20 systems with 19 landmarks and non-iterative point to point algorithm provides approximately 1.4 mm surface error and is considered as the most efficient registration method.

  5. 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.

  6. 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.

  7. Monte Carlo Simulations of Arterial Imaging with Optical Coherence Tomography

    SciTech Connect

    Amendt, P.; Estabrook, K.; Everett, M.; London, R.A.; Maitland, D.; Zimmerman, G.; Colston, B.; da Silva, L.; Sathyam, U.

    2000-02-01

    The laser-tissue interaction code LATIS [London et al., Appl. Optics 36, 9068 ( 1998)] is used to analyze photon scattering histories representative of optical coherence tomography (OCT) experiment performed at Lawrence Livermore National Laboratory. Monte Carlo photonics with Henyey-Greenstein anisotropic scattering is implemented and used to simulate signal discrimination of intravascular structure. An analytic model is developed and used to obtain a scaling law relation for optimization of the OCT signal and to validate Monte Carlo photonics. The appropriateness of the Henyey-Greenstein phase function is studied by direct comparison with more detailed Mie scattering theory using an ensemble of spherical dielectric scatterers. Modest differences are found between the two prescriptions for describing photon angular scattering in tissue. In particular, the Mie scattering phase functions provide less overall reflectance signal but more signal contrast compared to the Henyey-Greenstein formulation.

  8. 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

  9. 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

  10. 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.

  11. Quantitative 3-D imaging of eukaryotic cells using soft X-ray tomography.

    PubMed

    Parkinson, Dilworth Y; McDermott, Gerry; Etkin, Laurence D; Le Gros, Mark A; Larabell, Carolyn A

    2008-06-01

    Imaging has long been one of the principal techniques used in biological and biomedical research. Indeed, the field of cell biology grew out of the first electron microscopy images of organelles in a cell. Since this landmark event, much work has been carried out to image and classify the organelles in eukaryotic cells using electron microscopy. Fluorescently labeled organelles can now be tracked in live cells, and recently, powerful light microscope techniques have pushed the limit of optical resolution to image single molecules. In this paper, we describe the use of soft X-ray tomography, a new tool for quantitative imaging of organelle structure and distribution in whole, fully hydrated eukaryotic Schizosaccharomyces pombe cells. In addition to imaging intact cells, soft X-ray tomography has the advantage of not requiring the use of any staining or fixation protocols--cells are simply transferred from their growth environment to a sample holder and immediately cryofixed. In this way the cells can be imaged in a near native state. Soft X-ray tomography is also capable of imaging relatively large numbers of cells in a short period of time, and is therefore a technique that has the potential to produce information on organelle morphology from statistically significant numbers of cells.

  12. 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

  13. 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

  14. Direct Estimation of Optical Parameters From Photoacoustic Time Series in Quantitative Photoacoustic Tomography.

    PubMed

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

    2016-11-01

    Estimation of optical absorption and scattering of a target is an inverse problem associated with quantitative photoacoustic tomography. Conventionally, the problem is expressed as two folded. First, images of initial pressure distribution created by absorption of a light pulse are formed based on acoustic boundary measurements. Then, the optical properties are determined based on these photoacoustic images. The optical stage of the inverse problem can thus suffer from, for example, artefacts caused by the acoustic stage. These could be caused by imperfections in the acoustic measurement setting, of which an example is a limited view acoustic measurement geometry. In this work, the forward model of quantitative photoacoustic tomography is treated as a coupled acoustic and optical model and the inverse problem is solved by using a Bayesian approach. Spatial distribution of the optical properties of the imaged target are estimated directly from the photoacoustic time series in varying acoustic detection and optical illumination configurations. It is numerically demonstrated, that estimation of optical properties of the imaged target is feasible in limited view acoustic detection setting.

  15. 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.

  16. A pilot characterization of quantitative time-domain fluorescence diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Li, Jiao; Gao, Feng; Yi, Xi; Wang, Xin; Wu, Linhui; Zhu, Pingping; Zhang, Limin; Zhao, Huijuan

    2011-02-01

    Quantitative measurements of fluorescent parameters have merited great interest lately for near-infrared fluorescence diffuse optical tomography - the efficient small animal imaging tool. We present a two-dimensional image reconstruction method for time-domain fluorescence diffuse optical tomography, which employs the analytical solution to the Laplace-transformed time-domain photon-diffusion equation to construct the inverse model and introduces a pair of real-domain transform-factors to effectively separate the fluorescent yield and lifetime parameters from the algebraic reconstruction technique solutions to the resultant linear inversions. By use of a specifically designed a multi-channel time-correlated single photon counting system and a normalized Born formulation for the inversion, the proposed scheme in a circular domain is experimentally validated using small-animal-sized cylindrical phantoms that embed several fluorescent targets made from 1%-Intralipid solution and differently contrasting fluorescent agents, where the time-resolved excitation and fluorescence signals are measured on the boundary. The results show that the approach retrieves the positions and shapes of the targets with a reasonable accuracy and simultaneously achieve quantitative reconstruction of the fluorescent yield and lifetime.

  17. Quantitative and Qualitative Imaging in Single Photon Emission Tomography for Nuclear Medicine Applications.

    NASA Astrophysics Data System (ADS)

    Masoomi, Mojtaba (Arash).

    Available from UMI in association with The British Library. An important goal of single photon emission tomography (SPECT) is the determination of absolute regional radionuclide concentration as a function of time. Quantitative and qualitative studies of SPECT with regard to clinical application is the object of this work. Three basic approaches for image reconstruction and factors which affect the choice of a reconstruction algorithm have been reviewed, discussed and the reconstruction techniques, GRADY and CBP evaluated, based on computer modelling. A sophisticated package of computational subroutines, RECLBL, for image reconstruction and for generation of phantoms, which was fully implemented on PRIME was used throughout this study. Two different systems, a rotating gamma-camera and a prototype scanning-rig have been used to carry out tomography experiments with different phantoms in emission and transmission mode. Performance assessment and reproducibility of the gamma-camera was tested prior to the experimental work. SPECT studies are generally hampered for a number of reasons, the most severe being attenuation and scattering. The effect of scattered photons on image quality was discussed, three distinct techniques were utilised to correct the images and results were compared. Determination of the depth of the source, Am-241 and Tc-99m in the attenuating media, water and TEMEX by analysing the spectroscopic data base on the SPR and spatial resolution was studied, results revealed that both techniques had the same range of depth sensitivity. A method of simultaneous emission and transmission tomography was developed to correct the images for attenuation. The reproducibility of the technique was examined. Results showed that the technique is able to present a promising and a practical approach to more accurate quantitative SPECT imaging. A procedure to evaluate images, under certain conditions has been defined, its properties were evaluated using computer

  18. Computed tomography-based quantitative assessment of lower extremity lymphedema following treatment for gynecologic cancer

    PubMed Central

    Chung, Seung Hyun; Kim, Young Jae; Kim, Kwang Gi; Hwang, Ji Hye

    2017-01-01

    Objective To develop an algorithmic quantitative skin and subcutaneous tissue volume measurement protocol for lower extremity lymphedema (LEL) patients using computed tomography (CT), to verify the usefulness of the measurement techniques in LEL patients, and to observe the structural characteristics of subcutaneous tissue according to the progression of LEL in gynecologic cancer. Methods A program for algorithmic quantitative analysis of lower extremity CT scans has been developed to measure the skin and subcutaneous volume, muscle compartment volume, and the extent of the peculiar trabecular area with a honeycombed pattern. The CT venographies of 50 lower extremities from 25 subjects were reviewed in two groups (acute and chronic lymphedema). Results A significant increase in the total volume, subcutaneous volume, and extent of peculiar trabecular area with a honeycombed pattern except quantitative muscle volume was identified in the more-affected limb. The correlation of CT-based total volume and subcutaneous volume measurements with volumetry measurement was strong (correlation coefficient: 0.747 and 0.749, respectively). The larger extent of peculiar trabecular area with a honeycombed pattern in the subcutaneous tissue was identified in the more-affected limb of chronic lymphedema group. Conclusion CT-based quantitative assessments could provide objective volume measurements and information about the structural characteristics of subcutaneous tissue in women with LEL following treatment for gynecologic cancer. PMID:28028991

  19. Simulation of emission tomography using grid middleware for distributed computing.

    PubMed

    Thomason, M G; Longton, R F; Gregor, J; Smith, G T; Hutson, R K

    2004-09-01

    SimSET is Monte Carlo simulation software for emission tomography. This paper describes a simple but effective scheme for parallel execution of SimSET using NetSolve, a client-server system for distributed computation. NetSolve (version 1.4.1) is "grid middleware" which enables a user (the client) to run specific computations remotely and simultaneously on a grid of networked computers (the servers). Since the servers do not have to be identical machines, computation may take place in a heterogeneous environment. To take advantage of diversity in machines and their workloads, a client-side scheduler was implemented for the Monte Carlo simulation. The scheduler partitions the total decay events by taking into account the inherent compute-speeds and recent average workloads, i.e., the scheduler assigns more decay events to processors expected to give faster service and fewer decay events to those expected to give slower service. When compute-speeds and sustained workloads are taken into account, the speed-up is essentially linear in the number of equivalent "maximum-service" processors. One modification in the SimSET code (version 2.6.2.3) was made to ensure that the total number of decay events specified by the user is maintained in the distributed simulation. No other modifications in the standard SimSET code were made. Each processor runs complete SimSET code for its assignment of decay events, independently of others running simultaneously. Empirical results are reported for simulation of a clinical-quality lung perfusion study.

  20. Simulation and the Development of Clinical Judgment: A Quantitative Study

    ERIC Educational Resources Information Center

    Holland, Susan

    2015-01-01

    The purpose of this quantitative pretest posttest quasi-experimental research study was to explore the effect of the NESD on clinical judgment in associate degree nursing students and compare the differences between groups when the Nursing Education Simulation Design (NESD) guided simulation in order to identify educational strategies promoting…

  1. A dual-frequency applied potential tomography technique: computer simulations.

    PubMed

    Griffiths, H; Ahmed, A

    1987-01-01

    Applied potential tomography has been discussed in relation to both static and dynamic imaging. We have investigated the feasibility of obtaining static images by measuring profiles at two frequencies of drive current to exploit the differing gradients of electrical conductivity with frequency for different tissues. This method has the advantages that no profile for the homogeneous medium is then needed, and the electrodes can be coupled directly to the skin. To demonstrate the principle, computer simulations have been carried out using published electrical parameters for mammalian tissues at frequencies of 100 and 150 kHz. The distribution of complex electric potentials was calculated by the successive over-relaxation method in two dimensions for an abdominal cross-section with 16 electrodes equally spaced around the surface. From the computed electrode potentials, images were reconstructed using a back-projection method (neglecting phase information). Liver and kidney appeared most distinctly on the image because of their comparatively large conductivity gradients. The perturbations in the electrode potential differences between the two frequencies had a mean value of 5%, requiring accurate measurement in a practical system, compared with 150% when the 100 kHz values were related to a simulation of homogeneous saline equal in conductivity to muscle. The perturbations could be increased by widening the separation of the frequencies. Static imaging using a dual-frequency technique appears to be feasible, but a more detailed consideration of the electrical properties of tissues is needed to determine the optimum choice of frequencies.

  2. Quantitative three-dimensional analysis of embryonic chick morphogenesis via microcomputed tomography.

    PubMed

    Kim, Jun Sup; Min, Jouha; Recknagel, Andrew K; Riccio, Mark; Butcher, Jonathan T

    2011-01-01

    Embryonic development is a remarkably complex and rapidly evolving morphogenetic process. Although many of the early patterning events have been well described, understanding the anatomical changes at later stages where clinically relevant malformations are more likely to be survivable has been limited by the lack of quantitative 3D imaging tools. Microcomputed tomography (Micro-CT) has emerged as a powerful tool for embryonic imaging, but a quantitative analysis of organ and tissue growth has not been conducted. In this study, we present a simple method for acquiring highly detailed, quantitative 3D datasets of embryonic chicks with Micro-CT. Embryos between 4 and 12 days (HH23 and HH40) were labeled with osmium tetroxide (OT), which revealed highly detailed soft tissue anatomy when scanned at 25 μm resolution. We demonstrate tissue boundary and inter-tissue contrast fidelity in virtual 2D sections are quantitatively and qualitatively similar to those of histological sections. We then establish mathematical relationships for the volumetric growth of heart, limb, eye, and brain during this period of development. We show that some organs exhibit constant exponential growth (eye and heart), whereas others contained multiple phases of growth (forebrain and limb). Furthermore, we show that cardiac myocardial volumetric growth differs in a time and chamber specific manner. These results demonstrate Micro-CT is a powerful technique for quantitative imaging of embryonic growth. The data presented here establish baselines from which to compare the effects of genetic or experimental perturbations. Quantifying subtle differences in morphogenesis is increasingly important as research focuses on localized and conditional effects.

  3. Quantitative imaging of I-124 using positron emission tomography with applications to radioimmunodiagnosis and radioimmunotherapy

    SciTech Connect

    Pentlow, K.S.; Graham, M.C.; Lambrecht, R.M.; Cheung, N.K.; Larson, S.M. )

    1991-05-01

    Positron emission tomography (PET) is potentially useful for the quantitative imaging of radiolabeled antibodies, leading in turn to improved dosimetry in radioimmunotherapy. Iodine-124 is a positron-emitting nuclide with appropriate chemical properties and half-life (4.2 days) for such studies since the radiolabeling of antibodies with iodine is well understood and the half-life permits measurements over several days. Unfortunately, I-124 has a complex decay scheme with many high-energy gamma rays and a positron abundance of only 25%. It has therefore been largely ignored as a PET-imaging nuclide. However, measurements made with phantoms and animals under realistic conditions using a BGO-based PET scanner have shown that satisfactory imaging and quantitation can be achieved. Investigations of spatial resolution, the linearity of regional observed count rate versus activity in the presence of other activity, and the visualization and quantitation of activity in spheres with different surrounding background activities were carried out with phantoms up to 22 cm in diameter. Compared with F-18, spatial resolution was only slightly degraded (13.5 mm FWHM vs 12 mm FWHM) while linearity was the same over a 10:1 activity range (0.015 to 0.15 MBq/ml for I-124). The visualization and quantitation of spheres was also slightly degraded when using similar imaging times. Increasing the imaging time for I-124 reduced the difference. To verify that the technique would work in vivo, measurements were made of human neuroblastoma tumors in rats which had been injected with I-124 labeled 3F8 antibody. Although the number of samples was small, good agreement was achieved between image-based measurements and direct measurements of excised 4-g tumors. Thus quantitative imaging of I-124 labeled antibodies appears to be possible under realistic conditions.

  4. 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

  5. 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

  6. Quantitative in vivo optical tomography of cancer progression & vasculature development in adult zebrafish

    PubMed Central

    Kumar, Sunil; Lockwood, Nicola; Ramel, Marie-Christine; Correia, Teresa; Ellis, Matthew; Alexandrov, Yuriy; Andrews, Natalie; Patel, Rachel; Bugeon, Laurence; Dallman, Margaret J.; Brandner, Sebastian; Arridge, Simon; Katan, Matilda; McGinty, James; Frankel, Paul; French, Paul M.W.

    2016-01-01

    We describe a novel approach to study tumour progression and vasculature development in vivo via global 3-D fluorescence imaging of live non-pigmented adult zebrafish utilising angularly multiplexed optical projection tomography with compressive sensing (CS-OPT). This “mesoscopic” imaging method bridges a gap between established ~μm resolution 3-D fluorescence microscopy techniques and ~mm-resolved whole body planar imaging and diffuse tomography. Implementing angular multiplexing with CS-OPT, we demonstrate the in vivo global imaging of an inducible fluorescently labelled genetic model of liver cancer in adult non-pigmented zebrafish that also present fluorescently labelled vasculature. In this disease model, addition of a chemical inducer (doxycycline) drives expression of eGFP tagged oncogenic K-RASV12 in the liver of immune competent animals. We show that our novel in vivo global imaging methodology enables non-invasive quantitative imaging of the development of tumour and vasculature throughout the progression of the disease, which we have validated against established methods of pathology including immunohistochemistry. We have also demonstrated its potential for longitudinal imaging through a study of vascular development in the same zebrafish from early embryo to adulthood. We believe that this instrument, together with its associated analysis and data management tools, constitute a new platform for in vivo cancer studies and drug discovery in zebrafish disease models. PMID:27259259

  7. Quantitative in vivo optical tomography of cancer progression & vasculature development in adult zebrafish.

    PubMed

    Kumar, Sunil; Lockwood, Nicola; Ramel, Marie-Christine; Correia, Teresa; Ellis, Matthew; Alexandrov, Yuriy; Andrews, Natalie; Patel, Rachel; Bugeon, Laurence; Dallman, Margaret J; Brandner, Sebastian; Arridge, Simon; Katan, Matilda; McGinty, James; Frankel, Paul; French, Paul M W

    2016-07-12

    We describe a novel approach to study tumour progression and vasculature development in vivo via global 3-D fluorescence imaging of live non-pigmented adult zebrafish utilising angularly multiplexed optical projection tomography with compressive sensing (CS-OPT). This "mesoscopic" imaging method bridges a gap between established ~μm resolution 3-D fluorescence microscopy techniques and ~mm-resolved whole body planar imaging and diffuse tomography. Implementing angular multiplexing with CS-OPT, we demonstrate the in vivo global imaging of an inducible fluorescently labelled genetic model of liver cancer in adult non-pigmented zebrafish that also present fluorescently labelled vasculature. In this disease model, addition of a chemical inducer (doxycycline) drives expression of eGFP tagged oncogenic K-RASV12 in the liver of immune competent animals. We show that our novel in vivo global imaging methodology enables non-invasive quantitative imaging of the development of tumour and vasculature throughout the progression of the disease, which we have validated against established methods of pathology including immunohistochemistry. We have also demonstrated its potential for longitudinal imaging through a study of vascular development in the same zebrafish from early embryo to adulthood. We believe that this instrument, together with its associated analysis and data management tools, constitute a new platform for in vivo cancer studies and drug discovery in zebrafish disease models.

  8. Cell death detection by quantitative three-dimensional single-cell tomography

    PubMed Central

    Cheng, Nai-Chia; Hsieh, Tsung-Hsun; Wang, Yu-Ta; Lai, Chien-Chih; Chang, Chia-Kai; Lin, Ming-Yi; Huang, Ding-Wei; Tjiu, Jeng-Wei; Huang, Sheng-Lung

    2012-01-01

    Ultrahigh-resolution optical coherence tomography (UR-OCT) has been used for the first time to our knowledge to study single-cell basal cell carcinoma (BCC) in vitro. This noninvasive, in situ, label-free technique with deep imaging depth enables three-dimensional analysis of scattering properties of single cells with cellular spatial resolution. From three-dimensional UR-OCT imaging, live and dead BCC cells can be easily identified based on morphological observation. We developed a novel method to automatically extract characteristic parameters of a single cell from data volume, and quantitative comparison and parametric analysis were performed. The results demonstrate the capability of UR-OCT to detect cell death at the cellular level. PMID:23024905

  9. Finite element analysis of the hip and spine based on quantitative computed tomography.

    PubMed

    Carpenter, R Dana

    2013-06-01

    Quantitative computed tomography (QCT) provides three-dimensional information about bone geometry and the spatial distribution of bone mineral. Images obtained with QCT can be used to create finite element models, which offer the ability to analyze bone strength and the distribution of mechanical stress and physical deformation. This approach can be used to investigate different mechanical loading scenarios (stance and fall configurations at the hip, for example) and to estimate whole bone strength and the relative mechanical contributions of the cortical and trabecular bone compartments. Finite element analyses based on QCT images of the hip and spine have been used to provide important insights into the biomechanical effects of factors such as age, sex, bone loss, pharmaceuticals, and mechanical loading at sites of high clinical importance. Thus, this analysis approach has become an important tool in the study of the etiology and treatment of osteoporosis at the hip and spine.

  10. A hybrid fluorescence tomography and x-ray CT system for quantitative molecular imaging

    NASA Astrophysics Data System (ADS)

    Lin, Yuting; Barber, William C.; Iwanczk, Jan S.; Roeck, Werner W.; Nalcioglu, Orhan; Gulsen, Gultekin

    2010-02-01

    A gantry-based hybrid fluorescence and x-ray computed tomography (FT/CT) system is developed for quantitative molecular imaging. The performance of the dual modality FT/CT system is evaluated using an irregular shaped phantom with an inclusion containing Indocyanine-Green (ICG). The anatomical data from CT provides structural a priori information for the FT inverse problem. Although a 4.2 mm diameter inclusion can be resolved in the reconstructed concentration image without any a priori information, ICG concentration in the inclusion is recovered with 75% error. On the other hand, the error in the recovered ICG concentration reduces to 15% when a priori information from CT is utilized. The results demonstrate that accurate fluorophore concentration can only be obtained when x-ray CT structural a priori information is available.

  11. Retina-simulating phantom for optical coherence tomography.

    PubMed

    Baxi, Jigesh; Calhoun, William; Sepah, Yasir Jamal; Hammer, Daniel X; Ilev, Ilko; Pfefer, T Joshua; Nguyen, Quan Dong; Agrawal, Anant

    2014-02-01

    Optical coherence tomography (OCT) is a rapidly growing imaging modality, particularly in the field of ophthalmology. Accurate early diagnosis of diseases requires consistent and validated imaging performance. In contrast to more well-established medical imaging modalities, no standardized test methods currently exist for OCT quality assurance. We developed a retinal phantom which mimics the thickness and near-infrared optical properties of each anatomical retinal layer as well as the surface topography of the foveal pit. The fabrication process involves layer-by-layer spin coating of nanoparticle-embedded silicone films followed by laser micro-etching to modify the surface topography. The thickness of each layer and dimensions of the foveal pit are measured with high precision. The phantom is embedded into a commercially available, water-filled model eye to simulate ocular dispersion and emmetropic refraction, and for ease of use with clinical OCT systems. The phantom was imaged with research and clinical OCT systems to assess image quality and software accuracy. Our results indicate that this phantom may serve as a useful tool to evaluate and standardize OCT performance.

  12. 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

  13. Comparison of peripheral quantitative computed tomography forearm bone density versus DXA in rheumatoid arthritis patients and controls.

    PubMed

    Juhász, B; Gulyás, K; Horváth, Á; Pethő, Z; Bhattoa, H P; Váncsa, A; Szekanecz, É; Horváth, C; Kocsis, J; Horváth, Z; Hodosi, K; Szántó, S; Szűcs, G; Szekanecz, Z

    2017-04-01

    Rheumatoid arthritis (RA) has been associated with osteoporosis. Quantitative computed tomography (QCT) is capable of assessing bone density and composition. We found lower bone density in RA compared to controls. Age and RA duration influenced bone density. QCT may be useful to assess bone metabolism in RA.

  14. 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).

  15. 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.

  16. 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

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

    PubMed

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

    2016-02-01

    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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Accuracy of high-resolution peripheral quantitative computed tomography for measurement of bone quality.

    PubMed

    MacNeil, Joshua A; Boyd, Steven K

    2007-12-01

    The introduction of three-dimensional high-resolution peripheral in vivo quantitative computed tomography (HR-pQCT) (XtremeCT, Scanco Medical, Switzerland; voxel size 82 microm) provides a new approach to monitor micro-architectural bone changes longitudinally. The accuracy of HR-pQCT for three important determinants of bone quality, including bone mineral density (BMD), architectural measurements and bone mechanics, was determined through a comparison with micro-computed tomography (microCT) and dual energy X-ray absorptiometry (DXA). Forty measurements from 10 cadaver radii with low bone mass were scanned using the three modalities, and image registration was used for 3D data to ensure identical regions were analyzed. The areal BMD of DXA correlated well with volumetric BMD by HR-pQCT despite differences in dimensionality (R(2) = 0.69), and the correlation improved when non-dimensional bone mineral content was assessed (R(2) = 0.80). Morphological parameters measured by HR-pQCT in a standard patient analysis, including bone volume ratio, trabecular number, derived trabecular thickness, derived trabecular separation, and cortical thickness correlated well with muCT measures (R(2) = 0.59-0.96). Additionally, some non-metric parameters such as connectivity density (R(2) = 0.90) performed well. The mechanical stiffness assessed by finite element analysis of HR-pQCT images was generally higher than for microCT data due to resolution differences, and correlated well at the continuum level (R(2) = 0.73). The validation here of HR-pQCT against gold-standards microCT and DXA provides insight into the accuracy of the system, and suggests that in addition to the standard patient protocol, additional indices of bone quality including connectivity density and mechanical stiffness may be appropriate to include as part of a standard patient analysis for clinical monitoring of bone quality.

  3. 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.

  4. In vitro atherosclerotic plaque and calcium quantitation by intravascular ultrasound and electron-beam computed tomography.

    PubMed

    Gutfinger, D E; Leung, C Y; Hiro, T; Maheswaran, B; Nakamura, S; Detrano, R; Kang, X; Tang, W; Tobis, J M

    1996-05-01

    The purpose of this investigation was to compare the accuracy of intravascular ultrasound (IVUS) and electron-beam computed tomography (EBCT) in quantitating human atherosclerotic plaque and calcium. In experiment 1, 12 human atherosclerotic arterial segments were obtained at autopsy and imaged by using IVUS and EBCT. The plaque from each arterial segment was dissected and a volume measurement of the dissected plaque was obtained by water displacement. The plaque from each arterial segment was ashed at 700 degrees F, and the weight of the remaining ashes was used as an estimate of the calcium mass. In experiment II, 11 calcified arterial segments were obtained at autopsy and imaged by using IVUS at one site along the artery. A corresponding histologic cross section stained with Masson's trichrome was prepared. In experiment I, the mean plaque volume measured by water displacement was 165.3 +/- 118.4 microliters. The mean plaque volume calculated by IVUS was 166.1 +/- 114.4 microliters and correlated closely with that by water displacement (r = 0.98, p < 0.0001). The mean calcium mass measured by ashing was 19.4 +/- 15.8 mg. The mean calculated calcium mass by EBCT was 19.9 mg and correlated closely with that by ashing (r=0.98, p<0.001). The mean calculated calcium volume by IVUS was 18.6 +/- 11.2 microliters and correlated linearly with the calcium mass by ashing (r = 0.87, p < 0.0003). In experiment II, the mean cross-sectional area of the calcified matrix was 1.71 +/- 0.66 mm2 by histologic examination compared with 1.44 +/- 0.66 mm2 by IVUS. There was a good correlation between the calcified cross-sectional area by histologic examination and IVUS (r = 0.76, p < 0.007); however, IVUS may underestimate the amount of calcium present depending on the intralesional calcium morphologic characteristics. In conclusion, IVUS accurately quantitates atherosclerotic plaque volume as well as the cross-sectional area and volume of intralesional calcium, especially if the

  5. 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.

  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. 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

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

    PubMed Central

    Yang, Yi; Wang, Tianheng; Brewer, Molly

    2012-01-01

    Abstract. 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. PMID:23085900

  9. Quantitative experimental monitoring of molecular diffusion in clay with positron emission tomography

    NASA Astrophysics Data System (ADS)

    Kulenkampff, Johannes; Zakhnini, Abdelhamid; Gründig, Marion; Lippmann-Pipke, Johanna

    2016-08-01

    Clay plays a prominent role as barrier material in the geosphere. The small particle sizes cause extremely small pore sizes and induce low permeability and high sorption capacity. Transport of dissolved species by molecular diffusion, driven only by a concentration gradient, is less sensitive to the pore size. Heterogeneous structures on the centimetre scale could cause heterogeneous effects, like preferential transport zones, which are difficult to assess. Laboratory measurements with diffusion cells yield limited information on heterogeneity, and pore space imaging methods have to consider scale effects. We established positron emission tomography (PET), applying a high-resolution PET scanner as a spatially resolved quantitative method for direct laboratory observation of the molecular diffusion process of a PET tracer on the prominent scale of 1-100 mm. Although PET is rather insensitive to bulk effects, quantification required significant improvements of the image reconstruction procedure with respect to Compton scatter and attenuation. The experiments were conducted with 22Na and 124I over periods of 100 and 25 days, respectively. From the images we derived trustable anisotropic diffusion coefficients and, in addition, we identified indications of preferential transport zones. We thus demonstrated the unique potential of the PET imaging modality for geoscientific process monitoring under conditions where other methods fail, taking advantage of the extremely high detection sensitivity that is typical of radiotracer applications.

  10. Quantitation in positron emission computed tomography: 4. Effect of accidental coincidences.

    PubMed

    Hoffman, E J; Huang, S C; Phelps, M E; Kuhl, D E

    1981-06-01

    Accidental coincidences (ACs) and methods of compensation for ACs were investigated in terms of their effect on quantitation in positron emission computed tomography (ECT). Formulations of basic expressions describing the physical factors, which cause true coincidences or ACs, are presented to provide a framework of contrasting the two phenomena. Correction of image data for attenuation of the annihilation radiation or nonuniformities in detector efficiency is shown to amplify errors caused by the presence of ACs in the data. It was shown that failure to compensate for ACs caused overestimates in measurements of isotope concentrations from image data and that in many cases the overestimate was significant for relatively modest percentages of ACs in the data. Three methods of compensation for ACs were evaluated as to their accuracy and effect on statistical noise in images. It was found that nonuniform detector efficiencies could cause prominent image artifacts if an inadequate method was employed in the determination and subtraction of ACs from image data. The additional statistical noise produced in images by subtraction of ACs from total coincidence data demonstrates the advisability of minimizing AC rates in spite of an ability to adequately measure and compensate for their presence in the data.

  11. 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.

  12. Quantitative computed tomography of humpback whale (Megaptera novaeangliae) mandibles: mechanical implications for rorqual lunge-feeding.

    PubMed

    Field, Daniel J; Campbell-Malone, Regina; Goldbogen, Jeremy A; Shadwick, Robert E

    2010-07-01

    Rorqual whales (Balaenopteridae) lunge at high speed with mouth open to nearly 90 degrees to engulf large volumes of prey-laden water. This feeding process is enabled by extremely large skulls and mandibles that increase mouth area, thereby facilitating the flux of water into the mouth. When these mandibles are lowered during lunge-feeding, they are exposed to high drag, and therefore, may be subject to significant bending forces. We hypothesized that these mandibles exhibited a mechanical design (shape and density distribution) that enables these bones to accommodate high loads during lunge-feeding without exceeding their breaking strength. We used quantitative computed tomography (QCT) to determine the three-dimensional geometry and density distribution of a pair of subadult humpback whale (Megaptera novaeangliae) mandibles (length = 2.10 m). QCT data indicated highest bone density and cross-sectional area, and therefore, high resistance to bending and deflection, from the coronoid process to the middle of the dentary, which then decreased towards the anterior end of the mandible. These results differ from the caudorostral trends of increasing mandibular bone density in mammals, such as humans and the right whale, Eubalaena glacialis, indicating that adaptive bone remodeling is a significant contributing factor in establishing mandibular bone density distributions in rorquals.

  13. 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.

  14. Assessing vertebral fracture risk on volumetric quantitative computed tomography by geometric characterization of trabecular bone structure

    NASA Astrophysics Data System (ADS)

    Checefsky, Walter A.; Abidin, Anas Z.; Nagarajan, Mahesh B.; Bauer, Jan S.; Baum, Thomas; Wismüller, Axel

    2016-03-01

    The current clinical standard for measuring Bone Mineral Density (BMD) is dual X-ray absorptiometry, however more recently BMD derived from volumetric quantitative computed tomography has been shown to demonstrate a high association with spinal fracture susceptibility. In this study, we propose a method of fracture risk assessment using structural properties of trabecular bone in spinal vertebrae. Experimental data was acquired via axial multi-detector CT (MDCT) from 12 spinal vertebrae specimens using a whole-body 256-row CT scanner with a dedicated calibration phantom. Common image processing methods were used to annotate the trabecular compartment in the vertebral slices creating a circular region of interest (ROI) that excluded cortical bone for each slice. The pixels inside the ROI were converted to values indicative of BMD. High dimensional geometrical features were derived using the scaling index method (SIM) at different radii and scaling factors (SF). The mean BMD values within the ROI were then extracted and used in conjunction with a support vector machine to predict the failure load of the specimens. Prediction performance was measured using the root-mean-square error (RMSE) metric and determined that SIM combined with mean BMD features (RMSE = 0.82 +/- 0.37) outperformed MDCT-measured mean BMD (RMSE = 1.11 +/- 0.33) (p < 10-4). These results demonstrate that biomechanical strength prediction in vertebrae can be significantly improved through the use of SIM-derived texture features from trabecular bone.

  15. Quantitative Three-Dimensional Imaging of Heterogeneous Materials by Thermal Tomography

    SciTech Connect

    Sun, J. G.

    2016-07-19

    Infrared thermal imaging based on active thermal excitations has been widely used for nondestructive evaluation ( NDE) of materials. While the experimental systems have remained essentially the same during the last few decades, development of advanced data-processing methods has significantly improved the capabilities of this technology. However, many limitations still exist. One fundamental limitation is the requirement, either explicitly or implicitly, of the tested material to be homogeneous such that detected thermal contrasts may be used to determine an average material property or attributed to flaws. In this paper, a new thermal tomography ( TT) method is introduced, which for the first time can evaluate heterogeneous materials by directly imaging their thermal-property variations with space. It utilizes one-sided flash thermal-imaging data to construct the three-dimensional ( 3D) distribution of thermal effusivity in the entire volume of a test sample. Theoretical analyses for single and multilayer material systems were conducted to validate its formulation and to demonstrate its performance. Experimental results for a ceramic composite plate and a thermal barrier coating ( TBC) sample are also presented. It was shown that thermal diffusion is the primary factor that degrades the spatial resolution with depth for TT; the spatial resolutions in the lateral and axial directions were quantitatively evaluated.

  16. 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

  17. Quantitative Assessment of Cervical Vertebral Maturation Using Cone Beam Computed Tomography in Korean Girls

    PubMed Central

    Byun, Bo-Ram; Kim, Yong-Il; Maki, Koutaro; Son, Woo-Sung

    2015-01-01

    This study was aimed to examine the correlation between skeletal maturation status and parameters from the odontoid process/body of the second vertebra and the bodies of third and fourth cervical vertebrae and simultaneously build multiple regression models to be able to estimate skeletal maturation status in Korean girls. Hand-wrist radiographs and cone beam computed tomography (CBCT) images were obtained from 74 Korean girls (6–18 years of age). CBCT-generated cervical vertebral maturation (CVM) was used to demarcate the odontoid process and the body of the second cervical vertebra, based on the dentocentral synchondrosis. Correlation coefficient analysis and multiple linear regression analysis were used for each parameter of the cervical vertebrae (P < 0.05). Forty-seven of 64 parameters from CBCT-generated CVM (independent variables) exhibited statistically significant correlations (P < 0.05). The multiple regression model with the greatest R2 had six parameters (PH2/W2, UW2/W2, (OH+AH2)/LW2, UW3/LW3, D3, and H4/W4) as independent variables with a variance inflation factor (VIF) of <2. CBCT-generated CVM was able to include parameters from the second cervical vertebral body and odontoid process, respectively, for the multiple regression models. This suggests that quantitative analysis might be used to estimate skeletal maturation status. PMID:25878721

  18. 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.

  19. 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.

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

    PubMed

    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.

  1. 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

  2. The effect of in situ/in vitro three-dimensional quantitative computed tomography image voxel size on the finite element model of human vertebral cancellous bone.

    PubMed

    Lu, Yongtao; Engelke, Klaus; Glueer, Claus-C; Morlock, Michael M; Huber, Gerd

    2014-11-01

    Quantitative computed tomography-based finite element modeling technique is a promising clinical tool for the prediction of bone strength. However, quantitative computed tomography-based finite element models were created from image datasets with different image voxel sizes. The aim of this study was to investigate whether there is an influence of image voxel size on the finite element models. In all 12 thoracolumbar vertebrae were scanned prior to autopsy (in situ) using two different quantitative computed tomography scan protocols, which resulted in image datasets with two different voxel sizes (0.29 × 0.29 × 1.3 mm(3) vs 0.18 × 0.18 × 0.6 mm(3)). Eight of them were scanned after autopsy (in vitro) and the datasets were reconstructed with two voxel sizes (0.32 × 0.32 × 0.6 mm(3) vs. 0.18 × 0.18 × 0.3 mm(3)). Finite element models with cuboid volume of interest extracted from the vertebral cancellous part were created and inhomogeneous bilinear bone properties were defined. Axial compression was simulated. No effect of voxel size was detected on the apparent bone mineral density for both the in situ and in vitro cases. However, the apparent modulus and yield strength showed significant differences in the two voxel size group pairs (in situ and in vitro). In conclusion, the image voxel size may have to be considered when the finite element voxel modeling technique is used in clinical applications.

  3. 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.

  4. 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.

  5. Quantitative surface evaluation by matching experimental and simulated ronchigram images

    NASA Astrophysics Data System (ADS)

    Kantún Montiel, Juana Rosaura; Cordero Dávila, Alberto; González García, Jorge

    2011-09-01

    To estimate qualitatively the surface errors with Ronchi test, the experimental and simulated ronchigrams are compared. Recently surface errors have been obtained quantitatively matching the intersection point coordinates of ronchigrama fringes with x-axis . In this case, gaussian fit must be done for each fringe, and interference orders are used in Malacara algorithm for the simulations. In order to evaluate surface errors, we added an error function in simulations, described with cubic splines, to the sagitta function of the ideal surface. We used the vectorial transversal aberration formula and a ruling with cosinusoidal transmittance, because these rulings reproduce better experimental ronchigram fringe profiles. Several error functions are tried until the whole experimental ronchigrama image is reproduced. The optimization process was done using genetic algorithms.

  6. Feasibility Study of Computational Fluid Dynamics Simulation of Coronary Computed Tomography Angiography Based on Dual-Source Computed Tomography

    PubMed Central

    Lu, Jing; Yu, Jie; Shi, Heshui

    2017-01-01

    Background Adding functional features to morphological features offers a new method for non-invasive assessment of myocardial perfusion. This study aimed to explore technical routes of assessing the left coronary artery pressure gradient, wall shear stress distribution and blood flow velocity distribution, combining three-dimensional coronary model which was based on high resolution dual-source computed tomography (CT) with computational fluid dynamics (CFD) simulation. Methods Three cases of no obvious stenosis, mild stenosis and severe stenosis in left anterior descending (LAD) were enrolled. Images acquired on dual-source CT were input into software Mimics, ICEMCFD and FLUENT to simulate pressure gradient, wall shear stress distribution and blood flow velocity distribution. Measuring coronary enhancement ratio of coronary artery was to compare with pressure gradient. Results Results conformed to theoretical values and showed difference between normal and abnormal samples. Conclusions The study verified essential parameters and basic techniques in blood flow numerical simulation preliminarily. It was proved feasible. PMID:27924174

  7. Quantification of lower leg arterial calcifications by high-resolution peripheral quantitative computed tomography.

    PubMed

    Patsch, Janina M; Zulliger, Martin A; Vilayphou, Nicolas; Samelson, Elizabeth J; Cejka, Daniel; Diarra, Danielle; Berzaczy, Gundula; Burghardt, Andrew J; Link, Thomas M; Weber, Michael; Loewe, Christian

    2014-01-01

    Vascular calcifications and bone health seem to be etiologically linked via common risk factors such as aging and subclinical chronic inflammation. Epidemiologic studies have shown significant associations between low bone mineral density (BMD), fragility fractures and calcifications of the coronary arteries and the abdominal aorta. In the last decade, high-resolution peripheral quantitative computed tomography (HR-pQCT) has emerged as in-vivo research tool for the assessment of peripheral bone geometry, density, and microarchitecture. Although vascular calcifications are frequently observed as incidental findings in HR-pQCT scans, they have not yet been incorporated into quantitative HR-pQCT analyses. We developed a semi-automated algorithm to quantify lower leg arterial calcifications (LLACs), captured by HR-pQCT. The objective of our study was to determine validity and reliability of the LLAC measure. HR-pQCT scans were downscaled to a voxel size of 250μm. After subtraction of bone volumes from the scans, LLACs were detected and contoured by a semi-automated, dual-threshold seed-point segmentation. LLAC mass (in mg hydroxyapatite; HA) was calculated as the product of voxel-based calcification volume (mm(3)) and mean calcification density (mgHA/cm(3))/1000. To determine validity, we compared LLACs to coronary artery calcifications (CACs), as quantified by multi-detector computed tomography (MDCT) and Agatston scoring in forty-six patients on chronic hemodialysis. Moreover, we investigated associations of LLACs with age, time on dialysis, type-2 diabetes mellitus, history of stroke, and myocardial infarction. In a second step, we determined intra- and inter-reader reliability of the LLAC measure. In the validity study, LLACs were present (>0mgHA) in 76% of patients, 78% of patients had CACs (>0mgHA). Median LLAC was 6.65 (0.08-24.40)mgHA and median CAC as expressed by Agatston score was 266.3 (15.88-1877.28). We found a significant positive correlation between

  8. 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

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

    PubMed

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

    2016-03-01

    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.

  10. Improved reproducibility of high-resolution peripheral quantitative computed tomography for measurement of bone quality.

    PubMed

    MacNeil, Joshua A; Boyd, Steven K

    2008-07-01

    A human high-resolution peripheral quantitative computed tomography scanner (HR-pQCT) (XtremeCT, Scanco Medical, Switzerland) capable of measuring three important indicators of bone quality (micro-architectural morphology, mineralization and mechanical stiffness) has been developed. The goal of this study was to evaluate the reproducibility of male and female HR-pQCT in vivo measurements, and elucidate the causes of error in these measurements through a comparison with in vitro measurements. The best possible short-term reproducibility was found using a set of 10 in vitro measurements without repositioning, and a set of 10 with repositioning. Subsequently, in vivo measurements were performed on 15 male and 15 female subjects at baseline and follow-ups of 1 week and 4 months to determine the short- and long-term reproducibility of the system. In addition to the 2D area matching method used in the standard evaluation protocol, a custom developed 3D registration method was used to find the common region between repeated scans. The best possible reproducibility without movement artifacts and repositioning error was less than 0.5%, while the reproducibility with repositioning error was less than 1.5%. The in vivo reproducibility of density (<1%), morphological (<4.5%) and stiffness (<3.5) measurements was consistently poorer than the reproducibility of cadaver measurements, presumably due to small movement artifacts and repositioning errors. Using 3D image registration, repositioning error was reduced on average by 23% and 8% for measurements of the radius and tibia sites, respectively. This study has provided bounds for the reproducibility of HR-pQCT to monitor bone quality longitudinally, and a basis for clinical study design to determine detectable changes.

  11. Assessment of Regional Bone Density in Fractured Vertebrae Using Quantitative Computed Tomography

    PubMed Central

    Soliman, Hany A.G.; Mac-Thiong, Jean-Marc; Levasseur, Annie; Parent, Stefan

    2017-01-01

    Study Design Cohort study. Purpose The aim of this study is to propose and evaluate a new technique to assess bone mineral density of fractured vertebrae using quantitative computed tomography (QCT). Overview of Literature There is no available technique to estimate bone mineral density (BMD) at the fractured vertebra because of the alterations in bony structures at the fracture site. Methods Forty patients with isolated fracture from T10 to L2 were analyzed from the vertebrae above and below the fracture level. Apparent density (AD) was measured based on the relationship between QCT images attenuation coefficients and the density of calibration objects. AD of 8 independent regions of interest (ROI) within the vertebral body and 2 ROI within the pedicles of vertebrae above and below the fractured vertebra were measured. At the level of the fractured vertebra, AD was measured at the pedicles, which are typically intact. AD of the fractured vertebral body was linearly interpolated, based on the assumption that AD at the fractured vertebra is equivalent to the average AD measured in vertebrae adjacent to the fracture. Estimated and measured AD of the pedicles at the fractured level were compared to verify our assumption of linear interpolation from adjacent vertebrae. Results The difference between the measured and the interpolated density of the pedicles at the fractured vertebra was 0.006 and 0.003 g/cm3 for right and left pedicle respectively. The highest mean AD located at the pedicles and the lowest mean AD was found at the anterior ROI of the vertebral body. Significant negative correlation exist between age and AD of ROI in the vertebral body. Conclusions This study suggests that the proposed technique is adequate to estimate the AD of a fractured vertebra from the density of adjacent vertebrae. PMID:28243370

  12. Quantitative carbon ion beam radiography and tomography with a flat-panel detector.

    PubMed

    Telsemeyer, Julia; Jäkel, Oliver; Martišíková, Mária

    2012-12-07

    High dose gradients are inherent to ion beam therapy. This results in high sensitivity to discrepancies between planned and delivered dose distributions. Therefore an accurate knowledge of the ion stopping power of the traversed tissue is critical. One proposed method to ensure high quality dose deposition is to measure the stopping power by ion radiography. Although the idea of imaging with highly energetic ions is more than forty years old, there is a lack of simple detectors suitable for this purpose. In this study the performance of an amorphous silicon flat-panel detector, originally designed for photon imaging, was investigated for quantitative carbon ion radiography and tomography. The flat-panel detector was exploited to measure the water equivalent thickness (WET) and water equivalent path length (WEPL) of a phantom at the Heidelberg Ion-Beam Therapy Center (HIT). To do so, the ambiguous correlation of detector signal to particle energy was overcome by active or passive variation of carbon ion beam energy and measurement of the signal-to-beam energy correlation. The active method enables one to determine the WET of the imaged object with an uncertainty of 0.5 mm WET. For tomographic WEPL measurements the passive method was exploited resulting in an accuracy of 0.01 WEPL. The developed imaging technique presents a method to measure the two-dimensional maps of WET and WEPL of phantoms with a simple and commercially available detector. High spatial resolution of 0.8 × 0.8 mm(2) is given by the detector design. In the future this powerful tool will be used to evaluate the performance of the treatment planning algorithm by studying WET uncertainties.

  13. 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

  14. Computational anatomy of the dens axis evaluated by quantitative computed tomography: Implications for anterior screw fixation.

    PubMed

    Gehweiler, Dominic; Wähnert, Dirk; Meier, Norbert; Spruit, Maarten; Raschke, Michael Johannes; Richards, Robert Geoff; Noser, Hansrudi; Kamer, Lukas

    2017-01-05

    The surgical fracture fixation of the odontoid process (dens) of the second cervical vertebra (C2/axis) is a challenging procedure, particularly in elderly patients affected by bone loss, and includes screw positioning close to vital structures. The aim of this study was to provide an extended anatomical knowledge of C2, the bone mass distribution and bone loss, and to understand the implications for anterior screw fixation. One hundred and twenty standard clinical quantitative computed tomography (QCT) scans of the intact cervical spine from 60 female and 60 male European patients, aged 18-90 years, were used to compute a three-dimensional statistical model and an averaged bone mass model of C2. Shape and size variability was assessed via principal component analysis (PCA), bone mass distribution by thresholding and via virtual core drilling, and the screw placement via virtual positioning of screw templates. Principal component analysis (PCA) revealed a highly variable anatomy of the dens with size as the predominant variation according to the first principal component (PC) whereas shape changes were primarily described by the remaining PCs. The bone mass distribution demonstrated a characteristic 3D pattern, and remained unchanged in the presence of bone loss. Virtual screw positioning of two 3.5 mm dens screws with a 1 mm safety zone was possible in 81.7% in a standard, parallel position and in additional 15.8% in a twisted position. The approach permitted a more detailed anatomical assessment of the dens axis. Combined with a preoperative QCT it may further improve the diagnostic procedure of odontoid fractures. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res.

  15. Geometric properties of distal radius and pathogenesis of Colles fracture: a peripheral quantitative computed tomography study.

    PubMed

    Nielsen, S P; Xie, X; Bärenholdt, O

    2001-01-01

    It is well known among clinicians that Colles fracture patients may have normal projected axial bone mineral density and that bone mass is not synonymous with bone strength. The aim of this work was to investigate whether cross-sectional properties of the distal radius in female patients with recent Colles fracture differ from those of a younger group of normal women without fracture. It was hypothesized that patients with Colles fracture had petite distal radii and that cortical thinning and reduced cortical and trabecular volumetric density are dominant features of this fracture type. We used a multilayer high-precision peripheral quantitative computed tomography (pQCT) device with a long-term precision error of 0.1% for a dedicated phantom during the measurement period (152 d). Clinical measurements were made at an ultradistal site rich in trabecular bone and a less ultradistal site rich in cortical bone. The results show that the following pQCT variables were significantly reduced in the nonfractured radius of the Colles fracture cases: mean ultradistal trabecular volumetric density, mean ultradistal and distal cortical volumetric density, mean ultradistal and distal cortical thickness (p < 0.001 for all differences). The outer cortical diameter, cross-sectional bone area, and cortical bending moment of inertia were not statistically different in the two groups. Thus, it would appear that Colles fracture cases did not have petite distal radii. The results suggest that the deforming force of Colles fracture has a transaxial direction (fall on outstretched arm), resulting in a crush fracture, and that it is not a bending force. We suggest that Colles fracture occurs as a result of the combined effect of a fall on the out-stretched arm, low trabecular and cortical volumetric bone density, and reduced cortical thickness.

  16. 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.

  17. 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

  18. 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

  19. Assessment of trabecular bone mineral density using quantitative computed tomography in normal cats.

    PubMed

    Cheon, Haengbok; Choi, Wooshin; Lee, Youngjae; Lee, Donghoon; Kim, Juhyung; Kang, Ji-Houn; Na, Kijeong; Chang, Jinhwa; Chang, Dongwoo

    2012-11-01

    The aim of this study was to assess age-related changes and anatomic variation in trabecular bone mineral density (tBMD) using quantitative computed tomography (QCT) in normal cats. Seventeen normal cats were included in this study and divided into the following 3 age groups:<6 months (n=4), 2-5 years (n=10) and >6 years (n=3). A computed tomographic scan of each vertebra from the 12th thoracic to the 7th lumbar spine and the pelvis was performed with a bone-density phantom (50, 100 and 150 mg/cm(3), calcium hydroxyapatite, CIRS phantom(®)). On the central transverse section, the elliptical region of interest (ROI) was drawn to measure the mean Hounsfield unit (HU) value. Those values were converted to equivalent tBMD (mg/cm(3)) by use of the bone-density phantom and linear regression analysis (r(2) >0.95). The mean tBMD value of the thoracic vertebrae (369.4 ± 31.8 mg/cm(3)) was significantly higher than that of the lumbar vertebrae (285 ± 58.1 mg/cm(3)). The maximum tBMD occurred at the T12, T13 and L1 levels in all age groups. There was a statistically significant difference in the mean tBMD value among the 3 age groups at the T12 (P<0.001), T13 (P<0.001) and L4 levels (P=0.013), respectively. The present study suggests that age-related changes and anatomic variation in tBMD values should be considered when assessing tBMD using QCT in cats with bone disorders.

  20. 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

  1. 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.

  2. Quantitative strain analysis in analogue modelling experiments: insights from X-ray computed tomography and tomographic image correlation

    NASA Astrophysics Data System (ADS)

    Adam, J.; Klinkmueller, M.; Schreurs, G.; Wieneke, B.

    2009-04-01

    The combination of scaled analogue modelling experiments, advanced research in analogue material mechanics (Lohrmann et al. 2003, Panien et al. 2006), X-ray computed tomography and new high-resolution deformation monitoring techniques (2D/3D Digital Image Correlation) is a new powerful tool not only to examine the evolution and interaction of faulting in analogue models, but also to evaluate relevant controlling factors such as mechanics, sedimentation, erosion and climate. This is of particular interest for applied problems in the energy sector (e.g., structurally complex reservoirs, LG & CO2 underground storage) because the results are essential for geological and seismic interpretation as well as for more realistically constrained fault/fracture simulations and reservoir characterisation. X-ray computed tomography (CT) analysis has been successfully applied to analogue models since the late 1980s. This technique permits visualisation of the interior of an analogue model without destroying it. Technological improvements have resulted in more powerful X-ray CT scanners that allow periodic acquisition of volumetric data sets thus making it possible to follow the 3-D evolution of the model structures with time (e.g. Schreurs et al., 2002, 2003). Optical strain monitoring (Digital Image Correlation, DIC) in analogue experiments (Adam et al., 2005) represents an important advance in quantitative physical modelling and in helping to understand non-linear rock deformation processes. Optical non-intrusive 2D/3D strain and surface flow analysis by DIC is a new methodology in physical modelling that enables the complete quantification of localised and distributed model deformation. The increase in spatial/temporal strain data resolution of several orders of magnitude makes physical modelling - used for decades to visualize the kinematic processes of geological deformation processes - a unique research tool to determine what fundamental physical processes control tectonic

  3. Quantitative Morphology Measures in Galaxies: Ground-Truthing from Simulations

    NASA Astrophysics Data System (ADS)

    Narayanan, Desika T.; Abruzzo, Matthew W.; Dave, Romeel; Thompson, Robert

    2017-01-01

    The process of galaxy assembly is a prevalent question in astronomy; there are a variety of potentially important effects, including baryonic accretion from the intergalactic medium, as well as major galaxy mergers. Recent years have ushered in the development of quantitative measures of morphology such as the Gini coefficient (G), the second-order moment of the brightest quintile of a galaxy’s light (M20), and the concentration (C), asymmetry (A), and clumpiness (S) of galaxies. To investigate the efficacy of these observational methods at identifying major mergers, we have run a series of very high resolution cosmological zoom simulations, and coupled these with 3D Monte Carlo dust radiative transfer. Our methodology is powerful in that it allows us to “observe” the simulation as an observer would, while maintaining detailed knowledge of the true merger history of the galaxy. In this presentation, we will present our main results from our analysis of these quantitative morphology measures, with a particular focus on high-redshift (z>2) systems.

  4. 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

  5. Quantitative micro-computed tomography: a non-invasive method to assess equivalent bone mineral density.

    PubMed

    Nazarian, Ara; Snyder, Brian D; Zurakowski, David; Müller, Ralph

    2008-08-01

    One of the many applications of micro computed tomography (microCT) is to accurately visualize and quantify cancellous bone microstructure. However, microCT based assessment of bone mineral density has yet to be thoroughly investigated. Specifically, the effects of varying imaging parameters, such as tube voltage (kVp), current (microA), integration time (ms), object to X-ray source distance (mm), projection number, detector array size and imaging media (surrounding the specimen), on the relationship between equivalent tissue density (rhoEQ) and its linear attenuation coefficient (micro) have received little attention. In this study, in house manufactured, hydrogen dipotassium phosphate liquid calibration phantoms (K2HPO4) were employed in addition to a resin embedded hydroxyapatite solid calibration phantoms supplied by Scanco Medical AG Company. Variations in current, integration time and projection number had no effect on the conversion relationship between micro and rhoEQ for the K2HPO4 and Scanco calibration phantoms [p>0.05 for all cases]. However, as expected, variations in scanning tube voltage, object to X-ray source distance, detector array size and imaging media (referring to the solution that surrounds the specimen in the imaging vial) significantly affected the conversion relationship between mu and rhoEQ for K2HPO4 and Scanco calibration phantoms [p<0.05 for all cases]. A multivariate linear regression approach was used to estimate rhoEQ based on attenuation coefficient, tube voltage, object to X-ray source distance, detector array size and imaging media for K2HPO4 liquid calibration phantoms, explaining 90% of the variation in rhoEQ. Furthermore, equivalent density values of bovine cortical bone (converted from attenuation coefficient to equivalent density using the K2HPO4 liquid calibration phantoms) samples highly correlated [R2=0.92] with the ash densities of the samples. In conclusion, Scanco calibration phantoms can be used to assess equivalent

  6. COMPARISON OF QUANTITATIVE COMPUTED TOMOGRAPHY-BASED MEASURES IN PREDICTING VERTEBRAL COMPRESSIVE STRENGTH

    PubMed Central

    Buckley, Jenni M.; Loo, Kenneth; Motherway, Julie

    2007-01-01

    Patient-specific measures derived from quantitative computed tomography (QCT) scans are currently being developed as a clinical tool for vertebral strength prediction. QCT-based measurement techniques vary greatly in structural complexity and generally fall into one of three categories: 1) bone mineral density (BMD), 2) “mechanics of solids” (MOS) models, such as minimum axial rigidity (the product of axial stiffness and vertebral height), or 3) three dimensional finite element (FE) models. There is no clear consensus as to the relative performance of these measures due to differences in experimental protocols, sample sizes and demographics, and outcome metrics. The goal of this study was to directly compare the performance of QCT-based assessment techniques of varying degrees of structural sophistication in predicting experimental vertebral compressive strength. Eighty-one human thoracic vertebrae (T6 – T10) from 44 donors cadavers (F = 32, M = 12; 85 + 8 y.o., max = 97 y.o., min = 54 y.o.) were QCT scanned and destructively tested in uniaxial compression. The QCT scans were processed to generate FE models and various BMD and MOS measures, including trabecular bone mineral density (tBMD), integral bone mineral density (iBMD), and axial rigidity. Bone mineral density was weakly to moderately predictive of compressive strength (R2 = 0.16 and 0.62 for tBMD and iBMD, respectively). Ex vivo vertebral strength was strongly correlated with both axial rigidity (R2 = 0.81) and FE strength measurements (R2 = 0.80), and the predictive capabilities of these two metrics were statistically equivalent (p > 0.05 for differences between FE and axial rigidity). The results of this study indicate that non-invasive predictive measures of vertebral strength should include some level of structural sophistication, specifically, gross geometric and material property distribution information. However, for uniaxial compression of isolated vertebrae, which is the current biomechanical

  7. 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

  8. Illumination pattern optimization for fluorescence tomography: theory and simulation studies.

    PubMed

    Dutta, Joyita; Ahn, Sangtae; Joshi, Anand A; Leahy, Richard M

    2010-05-21

    Fluorescence molecular tomography is a powerful tool for 3D visualization of molecular targets and pathways in vivo in small animals. Owing to the high degrees of absorption and scattering of light through tissue, the fluorescence tomographic inverse problem is inherently ill-posed. In order to improve source localization and the conditioning of the light propagation model, multiple sets of data are acquired by illuminating the animal surface with different spatial patterns of near-infrared light. However, the choice of these patterns in most experimental setups is ad hoc and suboptimal. This paper presents a systematic approach for designing efficient illumination patterns for fluorescence tomography. Our objective here is to determine how to optimally illuminate the animal surface so as to maximize the information content in the acquired data. We achieve this by improving the conditioning of the Fisher information matrix. We parameterize the spatial illumination patterns and formulate our problem as a constrained optimization problem that, for a fixed number of illumination patterns, yields the optimal set of patterns. For geometric insight, we used our method to generate a set of three optimal patterns for an optically homogeneous, regular geometrical shape and observed expected symmetries in the result. We also generated a set of six optimal patterns for an optically homogeneous cuboidal phantom set up in the transillumination mode. Finally, we computed optimal illumination patterns for an optically inhomogeneous realistically shaped mouse atlas for different given numbers of patterns. The regularized pseudoinverse matrix, generated using the singular value decomposition, was employed to reconstruct the point spread function for each set of patterns in the presence of a sample fluorescent point source deep inside the mouse atlas. We have evaluated the performance of our method by examining the singular value spectra as well as plots of average spatial

  9. Differentiating malignant from benign gastric mucosal lesions with quantitative analysis in dual energy spectral computed tomography

    PubMed Central

    Meng, Xiaoyan; Ni, Cheng; Shen, Yaqi; Hu, Xuemei; Chen, Xiao; Li, Zhen; Hu, Daoyu

    2017-01-01

    Abstract To investigate the value of quantitative analysis in dual energy spectral computed tomography (DESCT) for differentiating malignant gastric mucosal lesions from benign gastric mucosal lesions (including gastric inflammation [GI] and normal gastric mucosa [NGM]). This study was approved by the ethics committee, and all patients provided written informed consent. A total of 161 consecutive patients (63 with gastric cancer [GC], 48 with GI, and 50 with NGM) who underwent dual-phase contrast enhanced DESCT scans in the arterial phase (AP) and portal venous phase (PVP) were included in this study. Iodine concentration (IC) in lesions was derived from the iodine-based material-decomposition images and normalized to that in the aorta to obtain normalized IC (nIC). The ratios of IC and nIC between the AP and PVP were calculated. Diagnostic confidence for GC and GI was evaluated with reviewing the features including gastric wall thickness, focal, and eccentric on the conventional polychromatic images. All statistical analyses were performed by using statistical software SPSS 17.0 (SPSS, Chicago, IL). IC and nIC in GC differed significantly from those in GI and NGM, except for nICAP in comparing GC with GI. Mean nIC values of GC (0.18 ± 0.06 in AP and 0.62 ± 0.16 in PVP) were significantly higher than that of NGM (0.12 ± 0.03 in AP and 0.37 ± 0.08 in PVP) (all P < 0.05). There was also significant difference for IC values in GC, GI, and NGM (24.19 ± 8.27, 19.07 ± 5.82, and 13.61 ± 2.52 mg/mL, respectively, in AP and 28.00 ± 7.01, 24.66 ± 6.55, and 16.94 ± 3.06 mg/mL, respectively, in PVP). Based on Receiver Operating Characteristic Curve analysis, nIC and IC in PVP had high sensitivities of 88.89% and 90.48%, respectively, in differentiating GC from NGM, while the sensitivities were 71.43% and 88.89% during AP. Ratios IC and nIC ratios did not provide adequate diagnostic accuracy with their area under curves

  10. 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)

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

    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.

  12. Monte Carlo simulation of optical coherence tomography for turbid media with arbitrary spatial distributions.

    PubMed

    Malektaji, Siavash; Lima, Ivan T; Sherif, Sherif S

    2014-04-01

    We developed a Monte Carlo-based simulator of optical coherence tomography (OCT) imaging for turbid media with arbitrary spatial distributions. This simulator allows computation of both Class I diffusive reflectance due to ballistic and quasiballistic scattered photons and Class II diffusive reflectance due to multiple scattered photons. It was implemented using a tetrahedron-based mesh and importance sampling to significantly reduce computational time. Our simulation results were verified by comparing them with results from two previously validated OCT simulators for multilayered media. We present simulation results for OCT imaging of a sphere inside a background slab, which would not have been possible with earlier simulators. We also discuss three important aspects of our simulator: (1) resolution, (2) accuracy, and (3) computation time. Our simulator could be used to study important OCT phenomena and to design OCT systems with improved performance.

  13. TU-F-CAMPUS-J-05: Effect of Uncorrelated Noise Texture On Computed Tomography Quantitative Image Features

    SciTech Connect

    Oliver, J; Budzevich, M; Moros, E; Zhang, G; Hunt, D

    2015-06-15

    Purpose: To investigate the relationship between quantitative image features (i.e. radiomics) and statistical fluctuations (i.e. electronic noise) in clinical Computed Tomography (CT) using the standardized American College of Radiology (ACR) CT accreditation phantom and patient images. Methods: Three levels of uncorrelated Gaussian noise were added to CT images of phantom and patients (20) acquired in static mode and respiratory tracking mode. We calculated the noise-power spectrum (NPS) of the original CT images of the phantom, and of the phantom images with added Gaussian noise with means of 50, 80, and 120 HU. Concurrently, on patient images (original and noise-added images), image features were calculated: 14 shape, 19 intensity (1st order statistics from intensity volume histograms), 18 GLCM features (2nd order statistics from grey level co-occurrence matrices) and 11 RLM features (2nd order statistics from run-length matrices). These features provide the underlying structural information of the images. GLCM (size 128x128) was calculated with a step size of 1 voxel in 13 directions and averaged. RLM feature calculation was performed in 13 directions with grey levels binning into 128 levels. Results: Adding the electronic noise to the images modified the quality of the NPS, shifting the noise from mostly correlated to mostly uncorrelated voxels. The dramatic increase in noise texture did not affect image structure/contours significantly for patient images. However, it did affect the image features and textures significantly as demonstrated by GLCM differences. Conclusion: Image features are sensitive to acquisition factors (simulated by adding uncorrelated Gaussian noise). We speculate that image features will be more difficult to detect in the presence of electronic noise (an uncorrelated noise contributor) or, for that matter, any other highly correlated image noise. This work focuses on the effect of electronic, uncorrelated, noise and future work shall

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

    PubMed Central

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

    2016-01-01

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

  15. A realistic computed tomography simulator for small motion analysis of cerebral aneurysms.

    PubMed

    Sepehri, Shima; Zouaoui, Karim; Thiran, Jean-Philippe

    2013-01-01

    This paper describes a realistic simulator for the Computed Tomography (CT) scan process for motion analysis. In fact, we are currently developing a new framework to find small motion from the CT scan. In order to prove the fidelity of this framework, or potentially any other algorithm, we present in this paper a simulator to simulate the whole CT acquisition process with a priori known parameters. In other words, it is a digital phantom for the motion analysis that can be used to compare the results of any related algorithm with the ground-truth realistic analytical model. Such a simulator can be used by the community to test different algorithms in the biomedical imaging domain. The most important features of this simulator are its different considerations to simulate the best the real acquisition process and its generality.

  16. Quantitative exercise thallium-201 single photon emission computed tomography for the enhanced diagnosis of ischemic heart disease

    SciTech Connect

    Mahmarian, J.J.; Boyce, T.M.; Goldberg, R.K.; Cocanougher, M.K.; Roberts, R.; Verani, M.S. )

    1990-02-01

    The clinical utility of exercise thallium-201 single photon emission computed tomography was investigated in 360 consecutive patients who had concomitant coronary arteriography. Tomographic images were assessed visually and from computer-quantified polar maps. Sensitivity for detecting coronary artery disease was comparably high using quantitative and visual analysis, although specificity tended to improve using the former method (87% versus 76%, p = 0.09). Quantitative analysis was superior to the visual method for identifying left anterior descending (81% versus 68%, p less than 0.05) and circumflex coronary artery (77% versus 60%, p less than 0.05) stenoses and detected most patients (92%) with multivessel coronary artery disease. Multivessel involvement was correctly predicted in 65% of the patients with more than one critically stenosed vessel. Exercise variables in patients with significant coronary artery disease were similar whether the tomographic images were normal or abnormal. However, patients with coronary stenoses and normal versus abnormal tomograms had a trend toward more single vessel disease (79% versus 62%, p = 0.07) and moderate coronary stenosis (66% versus 28%, p less than 0.001), but had less proximal left anterior descending artery involvement (8% versus 34%, p = 0.05). Computer-quantified perfusion defect size was directly related to the extent of coronary artery disease. Intra- and interobserver agreement for quantifying defects were excellent (r = 0.98 and 0.97, respectively). In conclusion, quantitative thallium-201 tomography offers improved detection of coronary artery disease, localization of the anatomic site of coronary stenosis, prediction of multivessel involvement and accurate determination of perfusion defect size, while maintaining a high specificity.

  17. Quantitative evaluation of dental abfraction and attrition using a swept-source optical coherence tomography system.

    PubMed

    Marcauteanu, Corina; Bradu, Adrian; Sinescu, Cosmin; Topala, Florin Ionel; Negrutiu, Meda Lavinia; Podoleanu, Adrian Gh

    2014-02-01

    A fast swept-source optical coherence tomography (SS-OCT) system is employed to acquire volumes of dental tissue, in order to monitor the temporal evolution of dental wear. An imaging method is developed to evaluate the volume of tissue lost in ex vivo artificially induced abfractions and attritions. The minimal volume (measured in air) that our system could measure is 2352 μm3. A volume of 25,000 A-scans is collected in 2.5 s. All these recommend the SS-OCT method as a valuable tool for dynamic evaluation of the abfraction and attrition with remarkable potential for clinical use.

  18. Quantitative assessment on coronary computed tomography angiography (CCTA) image quality: comparisons between genders and different tube voltage settings

    PubMed Central

    Chian, Teo Chee; Nassir, Norziana Mat; Ibrahim, Mohd Izuan; Yusof, Ahmad Khairuddin Md

    2017-01-01

    Background This study was carried out to quantify and compare the quantitative image quality of coronary computed tomography angiography (CCTA) between genders as well as between different tube voltages scan protocols. Methods Fifty-five cases of CCTA were collected retrospectively and all images including reformatted axial images at systolic and diastolic phases as well as images with curved multi planar reformation (cMPR) were obtained. Quantitative image quality including signal intensity, image noise, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of right coronary artery (RCA), left anterior descending artery (LAD), left circumflex artery (LCx) and left main artery (LM) were quantified using Analyze 12.0 software. Results Six hundred and fifty-seven coronary arteries were evaluated. There were no significant differences in any quantitative image quality parameters between genders. 100 kilovoltage peak (kVp) scanning protocol produced images with significantly higher signal intensity compared to 120 kVp scanning protocol (P<0.001) in all coronary arteries in all types of images. Higher SNR was also observed in 100 kVp scan protocol in all coronary arteries except in LCx where 120 kVp showed better SNR than 100 kVp. Conclusions There were no significant differences in image quality of CCTA between genders and different tube voltages. Lower tube voltage (100 kVp) scanning protocol is recommended in clinical practice to reduce the radiation dose to patient. PMID:28275559

  19. Simulation of polarization-sensitive optical coherence tomography images by a Monte Carlo method.

    PubMed

    Meglinski, Igor; Kirillin, Mikhail; Kuzmin, Vladimir; Myllylä, Risto

    2008-07-15

    We introduce a new Monte Carlo (MC) method for simulating optical coherence tomography (OCT) images of complex multilayered turbid scattering media. We demonstrate, for the first time of our knowledge, the use of a MC technique to imitate two-dimensional polarization-sensitive OCT images with nonplanar boundaries of layers in the medium like a human skin. The simulation of polarized low-coherent optical radiation is based on the vector approach generalized from the iterative procedure of the solution of Bethe-Saltpeter equation. The performances of the developed method are demonstrated both for conventional and polarization-sensitive OCT modalities.

  20. Simulation of a fast diffuse optical tomography system based on radiative transfer equation

    NASA Astrophysics Data System (ADS)

    Motevalli, S. M.; Payani, A.

    2016-12-01

    Studies show that near-infrared (NIR) light (light with wavelength between 700nm and 1300nm) undergoes two interactions, absorption and scattering, when it penetrates a tissue. Since scattering is the predominant interaction, the calculation of light distribution in the tissue and the image reconstruction of absorption and scattering coefficients are very complicated. Some analytical and numerical methods, such as radiative transport equation and Monte Carlo method, have been used for the simulation of light penetration in tissue. Recently, some investigators in the world have tried to develop a diffuse optical tomography system. In these systems, NIR light penetrates the tissue and passes through the tissue. Then, light exiting the tissue is measured by NIR detectors placed around the tissue. These data are collected from all the detectors and transferred to the computational parts (including hardware and software), which make a cross-sectional image of the tissue after performing some computational processes. In this paper, the results of the simulation of an optical diffuse tomography system are presented. This simulation involves two stages: a) Simulation of the forward problem (or light penetration in the tissue), which is performed by solving the diffusion approximation equation in the stationary state using FEM. b) Simulation of the inverse problem (or image reconstruction), which is performed by the optimization algorithm called Broyden quasi-Newton. This method of image reconstruction is faster compared to the other Newton-based optimization algorithms, such as the Levenberg-Marquardt one.

  1. How do trees grow? Response from the graphical and quantitative analyses of computed tomography scanning data collected on stem sections.

    PubMed

    Dutilleul, Pierre; Han, Li Wen; Beaulieu, Jean

    2014-06-01

    Tree growth, as measured via the width of annual rings, is used for environmental impact assessment and climate back-forecasting. This fascinating natural process has been studied at various scales in the stem (from cell and fiber within a growth ring, to ring and entire stem) in one, two, and three dimensions. A new approach is presented to study tree growth in 3D from stem sections, at a scale sufficiently small to allow the delineation of reliable limits for annual rings and large enough to capture directional variation in growth rates. The technology applied is computed tomography scanning, which provides - for one stem section - millions of data (indirect measures of wood density) that can be mapped, together with a companion measure of dispersion and growth ring limits in filigree. Graphical and quantitative analyses are reported for white spruce trees with circular vs non-circular growth. Implications for dendroclimatological research are discussed.

  2. Quantitative evaluation of atherosclerotic plaques using cross-polarization optical coherence tomography, nonlinear, and atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Gubarkova, Ekaterina V.; Kirillin, Mikhail Yu.; Dudenkova, Varvara V.; Timashev, Peter S.; Kotova, Svetlana L.; Kiseleva, Elena B.; Timofeeva, Lidia B.; Belkova, Galina V.; Solovieva, Anna B.; Moiseev, Alexander A.; Gelikonov, Gregory V.; Fiks, Ilya I.; Feldchtein, Felix I.; Gladkova, Natalia D.

    2016-12-01

    A combination of approaches to the image analysis in cross-polarization optical coherence tomography (CP OCT) and high-resolution imaging by nonlinear microscopy and atomic force microscopy (AFM) at the different stages of atherosclerotic plaque development is studied. This combination allowed us to qualitatively and quantitatively assess the disorganization of collagen in the atherosclerotic arterial tissue (reduction and increase of CP backscatter), at the fiber (change of the geometric distribution of fibers in the second-harmonic generation microscopy images) and fibrillar (violation of packing and different nature of a basket-weave network of fibrils in the AFM images) organization levels. The calculated CP channel-related parameters are shown to have a statistically significant difference between stable and unstable (also called vulnerable) plaques, and hence, CP OCT could be a potentially powerful, minimally invasive method for vulnerable plaques detection.

  3. 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.

  4. Using stochastic borehole seismic velocity tomography and Bayesian simulation to estimate Ni, Cu and Co grades.

    NASA Astrophysics Data System (ADS)

    Perozzi, Lorenzo; Gloaguen, Erwan; Rondenay, Stephane; Leite, André; McDowell, Glenn; Wheeler, Robert

    2010-05-01

    In the mining industry, classic methods to build a grade model for ore deposits are based on kriging or cokriging of grades for targeted minerals measured in drill core in fertile geological units. As the complexity of the geological geometry increases, so does the complexity of grade estimations. For example, in layered mafic or ultramafic intrusions, it is necessary to know the layering geometry in order to perform kriging of grades in the most fertile zones. Without additional information on geological framwork, the definition of fertile zones is a low-precision exercise that requires extensive experience and good ability from the geologist. Recently, thanks to computer and geophysical tool improvements, seismic tomography became very attractive for many application fields. Indeed, this non-intrusive technique allows inferring the mechanical properties of the ground using travel times and amplitude analysis of the transmitted wavelet between two boreholes, hence provide additional information on the nature of the deposit. Commonly used crosshole seismic velocity tomography algorithms estimate 2D slowness models (inverse of velocity) in the plane between the boreholes using the measured direct wave travel times from the transmitter (located in one of the hole) to the receivers (located in the other hole). Furthermore, geophysical borehole logging can be used to constrain seismic tomography between drill holes. Finally, this project aims to estimate grade of economically worth mineral by integrating seismic tomography data with respectively drill core measured grades acquired by Vale Inco for one of their mine sites in operation. In this study, a new type algorithm that combines geostatistical simulation and tomography in the same process (namely stochastic tomography) has been used. The principle of the stochastic tomography is based on the straight ray approximation and use the linear relationship between travel time and slowness to estimate the slowness

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

    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.

  6. A methodology for finding the optimal iteration number of the SIRT algorithm for quantitative Electron Tomography.

    PubMed

    Okariz, Ana; Guraya, Teresa; Iturrondobeitia, Maider; Ibarretxe, Julen

    2017-02-01

    The SIRT (Simultaneous Iterative Reconstruction Technique) algorithm is commonly used in Electron Tomography to calculate the original volume of the sample from noisy images, but the results provided by this iterative procedure are strongly dependent on the specific implementation of the algorithm, as well as on the number of iterations employed for the reconstruction. In this work, a methodology for selecting the iteration number of the SIRT reconstruction that provides the most accurate segmentation is proposed. The methodology is based on the statistical analysis of the intensity profiles at the edge of the objects in the reconstructed volume. A phantom which resembles a a carbon black aggregate has been created to validate the methodology and the SIRT implementations of two free software packages (TOMOJ and TOMO3D) have been used.

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

    PubMed

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

    2014-09-01

    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.

  8. Noncontact three-dimensional quantitative profiling of fast aspheric lenses by optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Goud, Bujagouni Karthik; Udupa, Dinesh Venkatesh; Prathap, Chilakala; Shinde, Deepak Dilip; Rao, Kompalli Divakar; Sahoo, Naba Kishore

    2016-12-01

    The use of optical coherence tomography (OCT) for noncontact three-dimensional aspheric lens profiling and retrieval of aspheric surface parameters is demonstrated. Two commercially available aspheric lenses with different focal length-to-diameter ratio have been imaged using OCT, and the measured optical path length distribution has been least square fitted with the aspheric lens surface retrieving the radius of curvature, aspheric constant, and conic constants. The refractive index of these lenses has also been measured referencing with a standard Zerodur glass flat. The fitted aspheric surface coefficients of the lenses are in close agreement with the manufacturer's values, thus, envisaging the potential of OCT in rapid screening, testing of aspheric lenses, and other micro-optical components such as those used in illumination optics.

  9. 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.

  10. [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

  11. Quantitative optical tomography of sub-surface heterogeneities using spatially modulated structured light.

    PubMed

    Konecky, Soren D; Mazhar, Amaan; Cuccia, David; Durkin, Anthony J; Schotland, John C; Tromberg, Bruce J

    2009-08-17

    We present a wide-field method for obtaining three-dimensional images of turbid media. By projecting patterns of light of varying spatial frequencies on a sample, we reconstruct quantitative, depth resolved images of absorption contrast. Images are reconstructed using a fast analytic inversion formula and a novel correction to the diffusion approximation for increased accuracy near boundaries. The method provides more accurate quantification of optical absorption and higher resolution than standard diffuse reflectance measurements.

  12. 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.

  13. Non-contact type time-domain fluorescence diffuse optical tomography for quantitative analysis of fluorophores

    NASA Astrophysics Data System (ADS)

    Nishimura, Goro; Furukawa, Daisuke; Awasthi, Kamlesh

    2013-03-01

    A non-contact type time-domain system for the fluorescence diffuse optical tomography was designed. The system is evaluated by a phantom with a fluorescence target. The contamination of the non-specific scattering superimposed on the excitation profile but it could be reduced with closely locating the detection fiber to the surface (~1 mm). Next, we analyzed the contamination in the temporal profiles with an Intralipid solution phantom with a fluorescent target. The contamination to the excitation profile is not clearly observed but that to the fluorescence is strong with a short distance between the excitation source and detection. Finally, we have concluded that a larger distance of source and detector yields better fluorescence sensitivity because the background is limiting the fluorescence detection. On the other hand, the signal quality depends on the statistics and thus the optimum range of the distance comes around 30 mm. Finally, this research gives the idea for the design of the source and detection configuration.

  14. Quantitative measurement of regional lung gas volume by synchrotron radiation computed tomography

    NASA Astrophysics Data System (ADS)

    Monfraix, Sylvie; Bayat, Sam; Porra, Liisa; Berruyer, Gilles; Nemoz, Christian; Thomlinson, William; Suortti, Pekka; Sovijärvi, Anssi R. A.

    2005-01-01

    The aim of this study was to assess the feasibility of a novel respiration-gated spiral synchrotron radiation computed tomography (SRCT) technique for direct quantification of absolute regional lung volumes, using stable xenon (Xe) gas as an inhaled indicator. Spiral SRCT with K-edge subtraction using two monochromatic x-ray beams was used to visualize and directly quantify inhaled Xe concentrations and airspace volumes in three-dimensional (3D) reconstructed lung images. Volume measurements were validated using a hollow Xe-filled phantom. Spiral images spanning 49 mm in lung height were acquired following 60 breaths of an 80% Xe-20% O2 gas mixture, in two anaesthetized and mechanically ventilated rabbits at baseline and after histamine aerosol inhalation. Volumetric images of 20 mm lung sections were obtained at functional residual capacity (FRC) and at end-inspiration. 3D images showed large patchy filling defects in peripheral airways and alveoli following histamine provocation. Local specific lung compliance was calculated based on FRC/end-inspiration images in normal lung. This study demonstrates spiral SRCT as a new technique for direct determination of regional lung volume, offering possibilities for non-invasive investigation of regional lung function and mechanics, with a uniquely high spatial resolution. An example of non-uniform volume distribution in rabbit lung following histamine inhalation is presented.

  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. 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.

  17. 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.

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

    PubMed

    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.

  19. Quantitative Computed Tomography Features for Predicting Tumor Recurrence in Patients with Surgically Resected Adenocarcinoma of the Lung

    PubMed Central

    Shim, Woo Hyun; Xu, Hai; Choi, Chang-Min; Kim, Hyeong Ryul; Lee, Jung Bok

    2017-01-01

    Purpose The purpose of this study was to determine if preoperative quantitative computed tomography (CT) features including texture and histogram analysis measurements are associated with tumor recurrence in patients with surgically resected adenocarcinoma of the lung. Methods The study included 194 patients with surgically resected lung adenocarcinoma who underwent preoperative CT between January 2013 and December 2013. Quantitative CT feature analysis of the lung adenocarcinomas were performed using in-house software based on plug-in package for ImageJ. Ten quantitative features demonstrating the tumor size, attenuation, shape and texture were extracted. The CT parameters obtained from 1-mm and 5-mm data were compared using intraclass correlation coefficients. Univariate and multivariable logistic regression methods were used to investigate the association between tumor recurrence and preoperative CT findings. Results The 1-mm and 5-mm data were highly correlated in terms of diameter, perimeter, area, mean attenuation and entropy. Circularity and aspect ratio were moderately correlated. However, skewness and kurtosis were poorly correlated. Multivariable logistic regression analysis revealed that area (odds ratio [OR], 1.002 for each 1-mm2 increase; P = 0.003) and mean attenuation (OR, 1.005 for each 1.0-Hounsfield unit increase; P = 0.022) were independently associated with recurrence. The receiver operating curves using these two independent predictive factors showed high diagnostic performance in predicting recurrence (C-index = 0.81, respectively). Conclusion Tumor area and mean attenuation are independently associated with recurrence in patients with surgically resected adenocarcinoma of the lung. PMID:28068363

  20. 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.

  1. 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.

  2. Experimental investigation of target and transducer effects on quantitative image reconstruction in photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Gamelin, John K.; Aguirre, Andres C.; Huang, Fei; Maurudis, Anastasios; Castillo, Diego; Wang, Lihong V.; Zhu, Quing

    2007-02-01

    In principle, absorbed energy profiles can be exactly reconstructed from photoacoustic measurements on a closed surface. Clinical applications, however, involve compromises due to transducer focus, frequency characteristics, and incomplete measurement apertures. These tradeoffs introduce artifacts and errors in reconstructed absorption distributions that affect quantitative interpretations as well as qualitative contrast between features. The quantitative effects of target geometry, limited measurement surfaces, and bandpass transducer frequency response have been investigated using a ring transducer system designed for small animal imaging. The directionality of photoacoustic radiation is shown to increase with target aspect ratio, producing proportionate overestimates of absorption values for two-dimension apertures less than approximately 150 degrees. For all target geometries and orientations, mean absorption values approach the full view values for hemicircular measurement surfaces although the true spatial uniformity is recovered only with the complete surface. The bandpass transducer frequency spectrum produces a peaked amplitude response biased toward spatial features ranging from 1 to 8 times the system resolution. We discuss the implications of these results for design of clinical systems.

  3. 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.

  4. 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

  5. Evaluation of Quantitative Computed Tomography Cortical Hip Quadrant in a Clinical Trial With Rosiglitazone: A Potential New Study Endpoint.

    PubMed

    Miller, Colin G; Bogado, Cesar C; Nino, Antonio J; Northcutt, Allison R; Yu, Hui Jing; Lewiecki, E Michael; Paul, G; Cobitz, Alexander R; Wooddell, Margaret J; Bilezikian, John P; Fitzpatrick, Lorraine A

    2016-10-01

    Quantitative computed tomography (QCT) measurements have been used extensively to ascertain information about bone quality and density due to the 3-dimensional information provided and the ability to segment out trabecular and cortical bones. QCT imaging helps to improve our understanding of the role that each bone compartment plays in the pathogenesis and prognosis of fracture. This study was conducted to explore longitudinal changes in femoral neck (FN) cortical bone structure using both volumetric bone mineral density (vBMD) and cortical shell thickness assessments via QCT in a double-blind, randomized, multicenter clinical trial in postmenopausal women with type 2 diabetes mellitus. This study also examined whether treatment-associated changes in the cortical bone vBMD and thickness in femoral neck quadrants could be evaluated. Subjects were randomized to rosiglitazone (RSG) or metformin (MET) for 52 wk followed by 24 wk of open-label MET. A subset of 87 subjects underwent QCT scans of the hip at baseline, after 52 wk of double-blind treatment, and after 24 wk of treatment with MET using standard full-body computed tomography scanners. All scans were evaluated and analyzed centrally. Cortical vBMD at the FN was precisely segmented from trabecular bone and used to assess a possible therapeutic effect on this bone compartment. QCT analysis showed reductions in adjusted mean percentage change in vBMD and in absolute cortical thickness occurred with RSG treatment from baseline to week 52, whereas changes with MET were generally minimal. The reductions observed during RSG treatment for 1 yr appeared to partially reverse during the open-label MET phase from weeks 52 to 76. The femoral neck quadrant may provide utility as a potential endpoint in clinical trials for the understanding of the therapeutic effect of new entities on cortical bone vs trabecular bone; however, further clinical validation is needed.

  6. 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.

  7. 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

  8. Quantitative Object Reconstruction using Abel Transform X-ray Tomography and Mixed Variable Optimization

    DTIC Science & Technology

    2007-02-12

    Young University, Department of Mathematics, 292 TMCB, Provo, Utah 84602 USA, rachaelp@byu.net 1 Report Documentation Page Form ApprovedOMB No. 0704...and simulation utilize the same forward measurement operator P , allowing for the possibility of an exact solution, modulo the effects of data noise...solution, modulo the effects of data noise. 13 Table 4: Test Set 2: Object Configurations. Object Materials Edge Locations (cm) 2a [Fe, Teflon, Fe

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Quantitative analysis of rectal cancer by spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zhang, Q. Q.; Wu, X. J.; Tang, T.; Zhu, S. W.; Yao, Q.; Gao, Bruce Z.; Yuan, X. C.

    2012-08-01

    To quantify OCT images of rectal tissue for clinic diagnosis, the scattering coefficient of the tissue is extracted by curve fitting the OCT signals to a confocal single model. A total of 1000 measurements (half and half of normal and malignant tissues) were obtained from 16 recta. The normal rectal tissue has a larger scattering coefficient ranging from 1.09 to 5.41 mm-1 with a mean value of 2.29 mm-1 (std:±0.32), while the malignant group shows lower scattering property and the values ranging from 0.25 to 2.69 mm-1 with a mean value of 1.41 mm-1 (std:±0.18). The peri-cancer of recta has also been investigated to distinguish the difference between normal and malignant rectal tissue. The results demonstrate that the quantitative analysis of the rectal tissue can be used as a promising diagnostic criterion of early rectal cancer, which has great value for clinical medical applications.

  14. Ultrahigh resolution optical coherence tomography for quantitative topographic mapping of retinal and intraretinal architectural morphology

    NASA Astrophysics Data System (ADS)

    Ko, Tony H.; Hartl, Ingmar; Drexler, Wolfgang; Ghanta, Ravi K.; Fujimoto, James G.

    2002-06-01

    Quantitative, three-dimensional mapping of retinal architectural morphology was achieved using an ultrahigh resolution ophthalmic OCT system. This OCT system utilizes a broad bandwidth titanium-sapphire laser light source generating bandwidths of up to 300 nm near 800 nm center wavelength. The system enables real-time cross-sectional imaging of the retina with ~3 micrometers axial resolution. The macula and the papillomacular axis of a normal human subject were systematically mapped using a series of linear scans. Edge detection and segmentation algorithms were developed to quantify retinal and intraretinal thicknesses. Topographic mapping of the total retinal thickness and the total ganglion cell/inner plexiform layer thickness was achieved around the macula. A topographic mapping quantifying the progressive thickening of the nerve fiber layer (NFL) nasally approaching the optic disk was also demonstrated. The ability to create three-dimensional topographic mapping of retinal architectural morphology at ~3 micrometers axial resolution will be relevant for the diagnosis of many retinal diseases. The topographic quantification of these structures can serve as a powerful tool for developing algorithms and clinical scanning protocols for the screening and staging of ophthalmic diseases such as glaucoma.

  15. 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.

  16. 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.

  17. Quantitative Dual-Energy Computed Tomography Supports a Vascular Etiology of Smoking-induced Inflammatory Lung Disease

    PubMed Central

    Iyer, Krishna S.; Newell, John D.; Jin, Dakai; Fuld, Matthew K.; Saha, Punam K.; Hansdottir, Sif

    2016-01-01

    Rationale: Endothelial dysfunction is of interest in relation to smoking-associated emphysema, a component of chronic obstructive pulmonary disease (COPD). We previously demonstrated that computed tomography (CT)-derived pulmonary blood flow (PBF) heterogeneity is greater in smokers with normal pulmonary function tests (PFTs) but who have visual evidence of centriacinar emphysema (CAE) on CT. Objectives: We introduced dual-energy CT (DECT) perfused blood volume (PBV) as a PBF surrogate to evaluate whether the CAE-associated increased PBF heterogeneity is reversible with sildenafil. Methods: Seventeen PFT-normal current smokers were divided into CAE-susceptible (SS; n = 10) and nonsusceptible (NS; n = 7) smokers, based on the presence or absence of CT-detected CAE. DECT-PBV images were acquired before and 1 hour after administration of 20 mg oral sildenafil. Regional PBV and PBV coefficients of variation (CV), a measure of spatial blood flow heterogeneity, were determined, followed by quantitative assessment of the central arterial tree. Measurements and Main Results: After sildenafil administration, regional PBV-CV decreased in SS subjects but did not decrease in NS subjects (P < 0.05), after adjusting for age and pack-years. Quantitative evaluation of the central pulmonary arteries revealed higher arterial volume and greater cross-sectional area (CSA) in the lower lobes of SS smokers, which suggested arterial enlargement in response to increased peripheral resistance. After sildenafil, arterial CSA decreased in SS smokers but did not decrease in NS smokers (P < 0.01). Conclusions: These results demonstrate that sildenafil restores peripheral perfusion and reduces central arterial enlargement in normal SS subjects with little effect in NS subjects, highlighting DECT-PBV as a biomarker of reversible endothelial dysfunction in smokers with CAE. PMID:26569033

  18. [A quantitative evaluation of brain computerized tomography in children using color image analyzer].

    PubMed

    Yamatani, M; Naganuma, Y; Hongoh, K; Murakami, M; Konishi, T; Okada, T

    1989-11-01

    We attempted the quantitative analysis of brain computerized tomographic scans in children using Color Image Analyzer. A consecutive series of 167 computerized tomographic scans were reviewed. Areas of subarachnoid spaces, cavums, ventricles and cerebellums were measured on three slices: A slice is at the level of head of caudate nucleus, anterior horn of lateral ventricle and third ventricle. B slice is at the level of body of lateral ventricle. C slice is at the level of sella turcica and pons. We investigated these values compared with Evans ratio, Cella Media Index, cerebellar atrophy score and visually evaluations. Serial brain CT scans of eight patient with infantile spasms were also evaluated for the assessment of the brain shrinkage after ACTH therapy. 1) The ratios of the subarachnoid space/the intracranial area on A and B slices (SAS A%, SAS B%) were significantly higher in the patients of severe brain atrophy. 2) There were linear relationship between Evans ratio and SAS A% (r = 0.405, p less than 0.001), Cella Media Index and the ratio of the lateral ventricles/the intracranial areas on B slice (r = -0.501, p less than 0.001), and the cerebellar atrophy score by Une and SAS C% (r = 0.369, p less than 0.001). 3) In the normal patients, the values of SAS A% and SAS B% were much greater in less than 1.5 years old children. These results suggest that the trend of CT findings related to age may reflect physiological changes of the space between the skull and the brain with age. 4) Brain shrinkage after ACTH therapy was more pronounced in the subarachnoid space than the ventricle.(ABSTRACT TRUNCATED AT 250 WORDS)

  19. 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

  20. Dynamic imaging and quantitative analysis of cranial neural tube closure in the mouse embryo using optical coherence tomography

    PubMed Central

    Wang, Shang; Garcia, Monica D.; Lopez, Andrew L.; Overbeek, Paul A.; Larin, Kirill V.; Larina, Irina V.

    2016-01-01

    Neural tube closure is a critical feature of central nervous system morphogenesis during embryonic development. Failure of this process leads to neural tube defects, one of the most common forms of human congenital defects. Although molecular and genetic studies in model organisms have provided insights into the genes and proteins that are required for normal neural tube development, complications associated with live imaging of neural tube closure in mammals limit efficient morphological analyses. Here, we report the use of optical coherence tomography (OCT) for dynamic imaging and quantitative assessment of cranial neural tube closure in live mouse embryos in culture. Through time-lapse imaging, we captured two neural tube closure mechanisms in different cranial regions, zipper-like closure of the hindbrain region and button-like closure of the midbrain region. We also used OCT imaging for phenotypic characterization of a neural tube defect in a mouse mutant. These results suggest that the described approach is a useful tool for live dynamic analysis of normal neural tube closure and neural tube defects in the mouse model. PMID:28101427

  1. Quantitative computed tomography (QCT) as a radiology reporting tool by using optical character recognition (OCR) and macro program.

    PubMed

    Lee, Young Han; Song, Ho-Taek; Suh, Jin-Suck

    2012-12-01

    The objectives are (1) to introduce a new concept of making a quantitative computed tomography (QCT) reporting system by using optical character recognition (OCR) and macro program and (2) to illustrate the practical usages of the QCT reporting system in radiology reading environment. This reporting system was created as a development tool by using an open-source OCR software and an open-source macro program. The main module was designed for OCR to report QCT images in radiology reading process. The principal processes are as follows: (1) to save a QCT report as a graphic file, (2) to recognize the characters from an image as a text, (3) to extract the T scores from the text, (4) to perform error correction, (5) to reformat the values into QCT radiology reporting template, and (6) to paste the reports into the electronic medical record (EMR) or picture archiving and communicating system (PACS). The accuracy test of OCR was performed on randomly selected QCTs. QCT as a radiology reporting tool successfully acted as OCR of QCT. The diagnosis of normal, osteopenia, or osteoporosis is also determined. Error correction of OCR is done with AutoHotkey-coded module. The results of T scores of femoral neck and lumbar vertebrae had an accuracy of 100 and 95.4 %, respectively. A convenient QCT reporting system could be established by utilizing open-source OCR software and open-source macro program. This method can be easily adapted for other QCT applications and PACS/EMR.

  2. 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.

  3. [Cerebral blood flow and oxygen extraction in lacunar hemiplegia. Semi-quantitative study using oxygen 15 and emission tomography].

    PubMed

    Rougemont, D; Baron, J C; Lebrun-Grandie, P; Bousser, M G; Cabanis, E; Laplane, D

    1983-01-01

    The oxygen 15 non invasive continuous inhalation technique coupled with positron emission tomography (P.E.T.) allows the local study of cerebral blood flow and oxygen metabolism. Recent P.E.T. studies have demonstrated the frequent occurrence of widespread metabolic depression remote from the site of middle cerebral artery territory infarct per se, especially over the cortical mantle and thalamus ipsilaterally, and over the cerebellar hemisphere contralaterally. These phenomena have been taken as indicative of transneural depression (i.e. diaschisis). We thought it interesting to study the possible occurrence of such abnormalities in patients with lacunar syndromes. We have applied the (15)0 technique to six patients (2 with pure motor hemiplegia, 4 with ataxic hemiparesis) for whom no large causal ischemic lesion could be demonstrated on CT scans; in only one patient was a lacunar lesion, presumably responsible for the clinical deficit demonstrated. Compared to a set of 19 patients without brain disease, the semi-quantitative results (analyzed in terms of asymmetry indices between homologous brain regions) in our patients did not disclose any pathophysiologically significant abnormality. More specifically, no evidence of physiological dysfunction similar to that reported in internal carotid artery territory infarcts, was detected over the cerebral or cerebellar cortices. These findings are commented upon in view of the presumably small size and the uncertain topography of the causal lesion.

  4. Lung extraction, lobe segmentation and hierarchical region assessment for quantitative analysis on high resolution computed tomography images.

    PubMed

    Ross, James C; Estépar, Raúl San José; Díaz, Alejandro; Westin, Carl-Fredrik; Kikinis, Ron; Silverman, Edwin K; Washko, George R

    2009-01-01

    Regional assessment of lung disease (such as chronic obstructive pulmonary disease) is a critical component to accurate patient diagnosis. Software tools than enable such analysis are also important for clinical research studies. In this work, we present an image segmentation and data representation framework that enables quantitative analysis specific to different lung regions on high resolution computed tomography (HRCT) datasets. We present an offline, fully automatic image processing chain that generates airway, vessel, and lung mask segmentations in which the left and right lung are delineated. We describe a novel lung lobe segmentation tool that produces reproducible results with minimal user interaction. A usability study performed across twenty datasets (inspiratory and expiratory exams including a range of disease states) demonstrates the tool's ability to generate results within five to seven minutes on average. We also describe a data representation scheme that involves compact encoding of label maps such that both "regions" (such as lung lobes) and "types" (such as emphysematous parenchyma) can be simultaneously represented at a given location in the HRCT.

  5. 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

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

    PubMed Central

    Gurler, Bulent; Yildirim, Aydin; Goker, Hasan; Pehlevan, Hatice Seval

    2016-01-01

    Purpose. To evaluate the effect of hydroxychloroquine on retinal pigment epithelium- (RPE-) Bruch's membrane complex, photoreceptor outer segment, and macular ganglion cell-inner plexiform layer (GCIPL) thicknesses using spectral-domain optical coherence tomography (SD-OCT). Methods. In this prospective case-control study, 51 eyes of 51 hydroxychloroquine patients and 30 eyes of 30 healthy subjects were included. High-quality images were obtained using a Cirrus HD-OCT with 5-line raster mode; the photoreceptor inner segment (IS) and outer segment (OS), sum of the segments (IS + OS), and RPE-Bruch's membrane complex were analyzed. Results. The thicknesses of the IS + OS and OS layers were significantly lower in the hydroxychloroquine subjects compared to the control subjects (P < 0.05). RPE-Bruch's membrane complex thicknesses were significantly higher in the hydroxychloroquine subjects than for those of the control subjects (P < 0.05). The minimum and temporal-inferior macular GCIPL thicknesses were significantly different between the patients with hydroxychloroquine use and the control subjects (P = 0.04 and P = 0.03, resp.). Conclusions. The foveal photoreceptor OS thinning, loss of GCIPL, and RPE-Bruch's membrane thickening were detected in patients with hydroxychloroquine therapy. This quantitative approach using SD-OCT images may have important implications to use as an early indicator of retinal toxicity without any visible signs of hydroxychloroquine retinopathy. PMID:27656292

  7. Dynamic imaging and quantitative analysis of cranial neural tube closure in the mouse embryo using optical coherence tomography.

    PubMed

    Wang, Shang; Garcia, Monica D; Lopez, Andrew L; Overbeek, Paul A; Larin, Kirill V; Larina, Irina V

    2017-01-01

    Neural tube closure is a critical feature of central nervous system morphogenesis during embryonic development. Failure of this process leads to neural tube defects, one of the most common forms of human congenital defects. Although molecular and genetic studies in model organisms have provided insights into the genes and proteins that are required for normal neural tube development, complications associated with live imaging of neural tube closure in mammals limit efficient morphological analyses. Here, we report the use of optical coherence tomography (OCT) for dynamic imaging and quantitative assessment of cranial neural tube closure in live mouse embryos in culture. Through time-lapse imaging, we captured two neural tube closure mechanisms in different cranial regions, zipper-like closure of the hindbrain region and button-like closure of the midbrain region. We also used OCT imaging for phenotypic characterization of a neural tube defect in a mouse mutant. These results suggest that the described approach is a useful tool for live dynamic analysis of normal neural tube closure and neural tube defects in the mouse model.

  8. 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.

  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.

  10. Effect of specimen-specific anisotropic material properties in quantitative computed tomography-based finite element analysis of the vertebra.

    PubMed

    Unnikrishnan, Ginu U; Barest, Glenn D; Berry, David B; Hussein, Amira I; Morgan, Elise F

    2013-10-01

    Intra- and inter-specimen variations in trabecular anisotropy are often ignored in quantitative computed tomography (QCT)-based finite element (FE) models of the vertebra. The material properties are typically estimated solely from local variations in bone mineral density (BMD), and a fixed representation of elastic anisotropy ("generic anisotropy") is assumed. This study evaluated the effect of incorporating specimen-specific, trabecular anisotropy on QCT-based FE predictions of vertebral stiffness and deformation patterns. Orthotropic material properties estimated from microcomputed tomography data ("specimen-specific anisotropy"), were assigned to a large, columnar region of the L1 centrum (n = 12), and generic-anisotropic material properties were assigned to the remainder of the vertebral body. Results were compared to FE analyses in which generic-anisotropic properties were used throughout. FE analyses were also performed on only the columnar regions. For the columnar regions, the axial stiffnesses obtained from the two categories of material properties were uncorrelated with each other (p = 0.604), and the distributions of minimum principal strain were distinctly different (p ≤ 0.022). In contrast, for the whole vertebral bodies in both axial and flexural loading, the stiffnesses obtained using the two categories of material properties were highly correlated (R2 > 0.82, p < 0.001) with, and were no different (p > 0.359) from, each other. Only moderate variations in strain distributions were observed between the two categories of material properties. The contrasting results for the columns versus vertebrae indicate a large contribution of the peripheral regions of the vertebral body to the mechanical behavior of this bone. In companion analyses on the effect of the degree of anisotropy (DA), the axial stiffnesses of the trabecular column (p < 0.001) and vertebra (p = 0.007) increased with increasing DA. These findings

  11. Quantitative positron emission tomography imaging of angiogenesis in rats with forelimb ischemia using (68)Ga-NOTA-c(RGDyK).

    PubMed

    Kim, Joong Hyun; Kim, Young-Hwa; Kim, Young Joo; Yang, Bo Yeun; Jeong, Jae Min; Youn, Hyewon; Lee, Dong Soo; Lee, Jae Sung

    2013-10-01

    Gallium-68-labeled 1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA)-cyclic Arg-Gly-Asp-D-Tyr-Lys (c(RGDyK)) was developed for αvβ3 targeting, and is a promising agent for imaging of cancer and disorders related to angiogenesis. In this study, we performed kinetic analysis of (68)Ga-NOTA-c(RGDyK) in rats with surgically induced forelimb ischemia, and immunohistochemical analysis was also performed to assess αvβ3 immuno-staining level. Animal models were created by excision of the left brachial vessels, and a sham operation was performed on the right brachial region under 2 % isoflurane anesthesia. Using an animal positron emission tomography/computed tomography (PET/CT) scanner, a list mode PET scan (120 min) was started with the injection of (68)Ga-NOTA-c(RGDyK) via the tail vein at 3, 5 and 7 days after ischemic surgery. Volumes of interest were drawn on the left ventricle, sham operation, control, and ischemic regions. Compartmental and two graphical analyses (Logan and RE plots) were performed for kinetic parameter estimation. The immunohistochemical analysis was also performed after the last PET scan, and cell components were scored on a six point scale for quantification of immuno-staining level (0-negative to 5-very high). A 3-compartment model with reversible binding best described the tissue time-activity curves. The distribution volume of the ischemic region was significantly higher than that of the sham operation (P < 10(-6)) and control region (P < 10(-9)). Both the Logan and RE plots showed high correlation with compartmental analysis (R(2) = 0.96 and 0.95 for Logan and RE, respectively). The temporal changes in distribution volume and binding potential were not significant. The immuno-staining level of the ischemic region was significantly higher than that of sham operation (P < 10(-4)) and control region (P < 10(-8)). Kinetic modeling studies with dynamic (68)Ga-NOTA-c(RGDyK) PET scan are feasible based on an image-derived input function in a

  12. Monte-Carlo simulations and image reconstruction for novel imaging scenarios in emission tomography

    NASA Astrophysics Data System (ADS)

    Gillam, John E.; Rafecas, Magdalena

    2016-02-01

    Emission imaging incorporates both the development of dedicated devices for data acquisition as well as algorithms for recovering images from that data. Emission tomography is an indirect approach to imaging. The effect of device modification on the final image can be understood through both the way in which data are gathered, using simulation, and the way in which the image is formed from that data, or image reconstruction. When developing novel devices, systems and imaging tasks, accurate simulation and image reconstruction allow performance to be estimated, and in some cases optimized, using computational methods before or during the process of physical construction. However, there are a vast range of approaches, algorithms and pre-existing computational tools that can be exploited and the choices made will affect the accuracy of the in silico results and quality of the reconstructed images. On the one hand, should important physical effects be neglected in either the simulation or reconstruction steps, specific enhancements provided by novel devices may not be represented in the results. On the other hand, over-modeling of device characteristics in either step leads to large computational overheads that can confound timely results. Here, a range of simulation methodologies and toolkits are discussed, as well as reconstruction algorithms that may be employed in emission imaging. The relative advantages and disadvantages of a range of options are highlighted using specific examples from current research scenarios.

  13. Simulation, hardware characterization, analysis, and assembly of the fiber trackers for the proton computed tomography scanner

    NASA Astrophysics Data System (ADS)

    Gearhart, Andrew James

    Proton computed tomography (pCT) is a new method of tomography that will allow for accurate patient imaging and reduced total patient radiation dose when compared to conventional X-ray CT. Proton therapy currently relies on the conversion of attenuation coefficients from X-ray CT scans to material density for use in the proton therapy treatment plan. With a pCT scan, the material density is directly measured, reducing the range errors from attenuation coefficient conversion. Therefore a pCT scan of a patient undergoing proton therapy will also aid in maximizing radiation dose to the target volume, while minimizing radiation dose to surrounding tissue. The pCT scanner is currently under construction, and completed components are being tested with a proton beam. This paper will focus on many of the studies done with the pCT scanner. Specifically, detector simulation, hardware characterization and analysis, and assembly of the fiber trackers used for the pCT scanner will be discussed.

  14. Shallow Ocean Bottom BRDF Prediction, Modeling, and Inversion via Simulation with Surface/Volume Data Derived from X-ray Tomography

    DTIC Science & Technology

    2008-01-01

    Shallow Ocean Bottom BRDF Prediction, Modeling, and Inversion via Simulation with Surface/Volume Data Derived from X-ray Tomography G. C...Prediction, Modeling, and Inversion via Simulation with Surface/Volume Data Derived from X-ray Tomography 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...focus Xray Computerized Tomography (MXCT) instrument at NRL SSC. The MXCT instrument requires preparation of the sample by embedding it in an epoxy

  15. A Quantitative Study of Simulated Bicuspid Aortic Valves

    NASA Astrophysics Data System (ADS)

    Szeto, Kai; Nguyen, Tran; Rodriguez, Javier; Pastuszko, Peter; Nigam, Vishal; Lasheras, Juan

    2010-11-01

    Previous studies have shown that congentially bicuspid aortic valves develop degenerative diseases earlier than the standard trileaflet, but the causes are not well understood. It has been hypothesized that the asymmetrical flow patterns and turbulence found in the bileaflet valves together with abnormally high levels of strain may result in an early thickening and eventually calcification and stenosis. Central to this hypothesis is the need for a precise quantification of the differences in the strain rate levels between bileaflets and trileaflet valves. We present here some in-vitro dynamic measurements of the spatial variation of the strain rate in pig aortic vales conducted in a left ventricular heart flow simulator device. We measure the strain rate of each leaflet during the whole cardiac cycle using phase-locked stereoscopic three-dimensional image surface reconstruction techniques. The bicuspid case is simulated by surgically stitching two of the leaflets in a normal valve.

  16. 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.

  17. 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

  18. 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

  19. Bilateral Asymmetry of Radius and Tibia Bone Macroarchitecture and Microarchitecture: A High-Resolution Peripheral Quantitative Computed Tomography Study.

    PubMed

    Hildebrandt, Erin M; Manske, Sarah L; Hanley, David A; Boyd, Steven K

    2016-01-01

    Studies assessing bone health often select the dominant or nondominant limb to scan, but not both, for efficiency reasons. New scanning technology allows 3-dimensional (3D) visualization of the microarchitecture in bone, but it is not well understood whether there are differences between the dominant and nondominant limbs. Using 3D high-resolution peripheral quantitative computed tomography (HR-pQCT), the aim of this study is to investigate the effect of limb dominance on bone macroarchitecture and microarchitecture. Healthy male and female participants (N=100; 59 female, 41 male), mean age 30.7±12.1 years, were scanned at both radii and tibiae using HR-pQCT. Hand and foot dominance were determined by the participant's self-report. Most participants were right hand dominant (94.0%) and right foot dominant (91.0%). In the pooled cohort, the dominant radius had significantly greater cortical area (2.11%; p=0.002) and failure load (3.00%; p=0.001). At the tibia, the dominant foot had significantly lower bone mineral density (-0.77%; p=0.042), cortical area (-1.05%; p=0.031), and thickness (-1.51%; p=0.017). For females, there were no differences at the radius, but at the tibia, the dominant side had greater cross-sectional area (1.03%; p=0.044). Our data suggest that dominance has a small yet significant effect on macroarchitecture at both the ultradistal radius and tibia but not microarchitecture. This work emphasizes that it is important to be consistent in the selection of either dominant or nondominant limbs for HR-pQCT cohort studies; however, in the case where the opposite limb needs to be scanned, there would be small differences in macroarchitecture and no significant differences in microarchitecture anticipated.

  20. Quantitative measurement of attenuation coefficients of bladder biopsies using optical coherence tomography for grading urothelial carcinoma of the bladder

    NASA Astrophysics Data System (ADS)

    Cauberg, Evelyne C. C.; de Bruin, Daniël M.; Faber, Dirk J.; de Reijke, Theo M.; Visser, Mike; de La Rosette, Jean J. M. C. H.; van Leeuwen, Ton G.

    2010-11-01

    Real-time grading of bladder urothelial carcinoma (UC) is clinically important, but the current standard for grading (histopathology) cannot provide this information. Based on optical coherence tomography (OCT)-measured optical attenuation (μt), the grade of bladder UC could potentially be assessed in real time. We evaluate ex vivo whether μt differs between different grades of UC and benign bladder tissue. Human bladder tissue specimens are examined ex vivo by 850-nm OCT using dynamic focusing. Three observers independently determine the μt from the OCT images, and three pathologists independently review the corresponding histology slides. For both methods, a consensus diagnosis is made. We include 76 OCT scans from 54 bladder samples obtained in 20 procedures on 18 patients. The median (interquartile range) μt of benign tissue is 5.75 mm-1 (4.77 to 6.14) versus 5.52 mm-1 (3.47 to 5.90), 4.85 mm-1 (4.25 to 6.50), and 5.62 mm-1 (5.01 to 6.29) for grade 1, 2, and 3 UC, respectively (p = 0.732). Interobserver agreement of histopathology is ``substantial'' [Kappa 0.62, 95% confidence interval (IC) 0.54 to 0.70] compared to ``almost perfect'' [interclass correlation coefficient (ICC) 0.87, 95% CI 0.80 to 0.92] for OCT. Quantitative OCT analysis (by μt) does not detect morphological UC changes. This may be due to factors typical for an ex-vivo experimental setting.

  1. Quality control for bone quality parameters affected by subject motion in high-resolution peripheral quantitative computed tomography.

    PubMed

    Pauchard, Yves; Liphardt, Anna-Maria; Macdonald, Heather M; Hanley, David A; Boyd, Steven K

    2012-06-01

    Subject motion during high-resolution peripheral quantitative computed tomography (HR-pQCT) causes image artifacts that affect morphological analysis of bone quality. The aim of our study was to determine effectiveness of techniques for quality control in the presence of motion in vivo including automated and manual approaches. First, repeatability of manual grading was determined within and between laboratories. Given proper training using a standardized scale and training images (provided by the manufacturer), we found that manual grading is suitable for repeatable image quality grading within and across sites (ICC>0.7). Both a new automated technique providing motion measures based on projection moments, and traditional manual grading (1=best, 5=worst) were subsequently used to assess subject data for motion in N=137 image pairs (scan/re-scan) from the Canadian Multicentre Osteoporosis Study (CaMos) Calgary cohort. High quality image pairs were selected and measurement precision was estimated by calculating the coefficient of variation (CV). Consistent with previous data, density parameters (e.g. total bone mineral density) are more robust than structural (e.g. trabecular number) or finite element parameters (e.g. failure load). To obtain acceptable measurement precision, images should not exceed a manual grading of 3 (on a scale from 1 to 5) or an automatic (ε(T)) grading of 1.2. Automatic and manual grading provide comparable quality control, but the advantage of the automated technique is its ability to provide a motion value at scan time (providing a basis for real time decision regarding re-scan requirements), and the assessment is objective. Notably, automatic motion measurement can be performed retrospectively based on original scan data, and is therefore well suited for multi-center studies as well as any research where objective quality control is paramount.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Idiopathic juvenile osteoporosis: a cross-sectional single-centre experience with bone histomorphometry and quantitative computed tomography

    PubMed Central

    2013-01-01

    Background Idiopathic juvenile osteoporosis (IJO) is a rare condition of poorly understood etiology and pathophysiology that affects otherwise healthy children. This condition is characterized clinically by bone pain and vertebral fractures; spontaneous recovery is observed after puberty in the majority of cases. Although decreased trabecular bone turnover has been noted previously, cortical and trabecular bone characteristics as determined by quantitative computed tomography (QCT) and their relationship to bone histomorphometry are unknown. Methods All children with a clinical diagnosis of IJO who were followed in our center since 1995 and who had undergone at least one diagnostic bone biopsy were included in this cross-sectional analysis. Results Fifteen patients (11 males/4 females) with median ages of 5.8 and 10.2 years at first symptoms and at referral, respectively, were included in the analysis. Histomorphometric analysis demonstrated decreased trabecular bone turnover (BFR/BS) in the majority of patients with heterogeneous parameters of trabecular mineralization and volume. QCTresults demonstrated that bone mineral density (BMD) was reduced in both trabecular/lumbar and cortical/femoral bone: Z score: -2.1 (−3.6;–1.0) and −0.9 (−8.2;1.4)in the two compartments, respectively. In the eight patients who underwent both bone biopsy and QCT, cortical BMD was associated with trabecular separation and with trabecular bone formation rate (r = 0.898 and −0.881, respectively, both p < 0.05). Conclusions This series confirms that IJO is characterized by impaired trabecular architecture that can be detected by both bone biopsy and QCT. The association between bone biopsy and QCT results may have implications for diagnosis, treatment, and follow-up of these children. PMID:23418950

  7. 23.4% saline decreases brain tissue volume in severe hepatic encephalopathy as assessed by a quantitative computed tomography marker

    PubMed Central

    Liotta, Eric M; Lizza, Bryan D; Romanova, Anna L; Guth, James C; Berman, Michael D; Carroll, Timothy J; Francis, Brandon; Ganger, Daniel; Ladner, Daniela P; Maas, Matthew B; Naidech, Andrew M

    2016-01-01

    Objective Cerebral edema is common in severe hepatic encephalopathy and may be life-threatening. Bolus 23.4% hypertonic saline (HTS) improves surveillance neuromonitoring scores, although its mechanism of action is not clearly established. We investigated the hypothesis that bolus HTS decreases cerebral edema in severe hepatic encephalopathy utilizing a quantitative technique to measure brain and CSF volume changes. Design Retrospective analysis of serial computed tomography (CT) scans and clinical data for a case-control series was performed. Setting Intensive care units of a tertiary care hospital. Patients Patients with severe hepatic encephalopathy treated with 23.4% HTS and control patients who did not receive 23.4% HTS. Methods We used clinically obtained CT scans to measure volumes of the ventricles, intracranial CSF, and brain using a previously validated semi-automated technique (Analyze Direct; Overland Park, KS). Volumes before and after 23.4% HTS were compared with Wilcoxon signed-rank test. Associations between total CSF volume, ventricular volume, serum sodium, and Glasgow Coma Scale Scores were assessed using Spearman correlation. Results Eleven patients with 18 administrations of 23.4% HTS met inclusion criteria. Total CSF (median 47.6 [35.1–69.4] to 61.9 [47.7–87.0] mL, p<0.001) and ventricular volumes (median 8.0 [6.9–9.5] to 9.2 [7.8–11.9] mL, p=0.002) increased and Glasgow Coma Scale Scores improved (median 4 [3–6] to 7 [6–9], p=0.008) after 23.4% HTS. In contrast, total CSF and ventricular volumes decreased in untreated control patients. Serum sodium increase was associated with increase in total CSF volume (r=0.83, p<0.001) and change in total CSF volume was associated with ventricular volume change (r=0.86, p<0.001). Conclusions Total CSF and ventricular volumes increased after 23.4% HTS, consistent with a reduction in brain tissue volume. Total CSF and ventricular volume change may be useful quantitative measures to assess

  8. 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

  9. Quantitative Classification of Eyes with and without Intermediate Age-related Macular Degeneration Using Optical Coherence Tomography

    PubMed Central

    Farsiu, Sina; Chiu, Stephanie J.; O'Connell, Rachelle V.; Folgar, Francisco A.; Yuan, Eric; Izatt, Joseph A.; Toth, Cynthia A.

    2013-01-01

    Objective To define quantitative indicators for the presence of intermediate age-related macular degeneration (AMD) via spectral-domain optical coherence tomography (SD-OCT) imaging of older adults. Design Evaluation of diagnostic test and technology. Participants and Controls One eye from 115 elderly subjects without AMD and 269 subjects with intermediate AMD from the Age-Related Eye Disease Study 2 (AREDS2) Ancillary SD-OCT Study. Methods We semiautomatically delineated the retinal pigment epithelium (RPE) and RPE drusen complex (RPEDC, the axial distance from the apex of the drusen and RPE layer to Bruch's membrane) and total retina (TR, the axial distance between the inner limiting and Bruch's membranes) boundaries. We registered and averaged the thickness maps from control subjects to generate a map of “normal” non-AMD thickness. We considered RPEDC thicknesses larger or smaller than 3 standard deviations from the mean as abnormal, indicating drusen or geographic atrophy (GA), respectively. We measured TR volumes, RPEDC volumes, and abnormal RPEDC thickening and thinning volumes for each subject. By using different combinations of these 4 disease indicators, we designed 5 automated classifiers for the presence of AMD on the basis of the generalized linear model regression framework. We trained and evaluated the performance of these classifiers using the leave-one-out method. Main Outcome Measures The range and topographic distribution of the RPEDC and TR thicknesses in a 5-mm diameter cylinder centered at the fovea. Results The most efficient method for separating AMD and control eyes required all 4 disease indicators. The area under the curve (AUC) of the receiver operating characteristic (ROC) for this classifier was >0.99. Overall neurosensory retinal thickening in eyes with AMD versus control eyes in our study contrasts with previous smaller studies. Conclusions We identified and validated efficient biometrics to distinguish AMD from normal eyes by

  10. Signal attenuation and localization in optical coherence tomography studied by Monte Carlo simulation.

    PubMed

    Smithies, D J; Lindmo, T; Chen, Z; Nelson, J S; Milner, T E

    1998-10-01

    A Monte Carlo model has been developed for optical coherence tomography (OCT). A geometrical optics implementation of the OCT probe with low-coherence interferometric detection was combined with three-dimensional stochastic Monte Carlo modelling of photon propagation in the homogeneous sample medium. Optical properties of the sample were selected to simulate intralipid and blood, representing moderately (g = 0.7) and highly (g = 0.99) anisotropic scattering respectively. For shallow optical depths in simulated intralipid (<3 scattering mean free path (mfp) units), the number of detected backscattered photons followed the extinction-single-backscatter model, and OCT was found to detect only minimally scattered photons. Within this depth range the backscatter positions of detected photons corresponded well with the nominal focus position of the probe. For propagation to deeper positions in intralipid, localization of backscattering was quickly lost due to detection of stray photons, and the number of detected photons remained constant with increasing depth in the non-absorbing medium. For strongly forward-directed scattering in simulated blood, the number of detected photons approached the extinction-single-backscatter model only for very shallow depths (<2 mfp units). However, backscattering positions for detected photons correlated well with the nominal focus position of the probe even for optical depths greater than 40 mfp units.

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

    PubMed

    Schierz, Philipp; Zierenberg, Johannes; Janke, Wolfhard

    2015-10-07

    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.

  12. 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.

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

    DOE PAGES

    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. 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.

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. Injection blow moulding single stage process: Validation of the numerical simulation through tomography analysis

    NASA Astrophysics Data System (ADS)

    Biglione, Jordan; Béreaux, Yves; Charmeau, Jean-Yves

    2016-10-01

    The injection blow moulding single stage process has been made available on standard injection moulding machine. Both the injection moulding stage and the blow moulding stage are being taken care of in an injection mould. Thus the dimensions of this mould are those of a conventional injection moulding mould. The fact that the two stages are located in the same mould leads to a process more constrained than the conventional one. This process introduces temperature gradients, molecular orientation, high stretch rates and high cooling rates. These constraints lead to a small processing window. In practice, the preform has to remain sufficiently melted to be blown so that the process takes place between the melting temperature and the crystallization temperature. In our numerical approach, the polymer is supposed to be blown in its molten state. Hence we have identified the mechanical behaviour of the polymer in its molten state through dynamical rheology experiments. A viscous Cross model has been proved to be relevant to the problem. Thermal dependence is assumed by an Arrhenius law. The process is simulated through a finite element code (POLYFLOW software) in the Ansys Workbench framework. Thickness measurements using image analysis of tomography data are performed and comparisons with the simulation results show good agreements.

  2. Application of orthogonal sampling to incomplete data interferometric tomography: numerical simulation and experimental analysis.

    PubMed

    Hongbing, Yao; Yongkang, Zhang; Xia, Ye; Anzhi, He

    2008-05-01

    Orthogonal projection sampling mode was proposed to reconstruct the incomplete-data flow field in optical computerized tomography (OCT). With numerical simulation technique, a two-peak plane symmetric flow field was reconstructed in different sampling modes and discussed in simulated results is the reconstructive accuracy with error indexes, such as mean square error (MSE) and peak error (PE). The corresponding experiments were researched with a Fabry-Perot rotary interferometer. The results indicated that the errors were drastically reduced and the precision was improved when orthogonal projection sampling mode was adopted in the reconstruction of the incomplete data field. The MSE obtained with orthogonal sampling mode was decreased 72.81% from that of the sequential projection sampling mode (the difference between the MSE obtained with the orthogonal sampling mode and that with the sequential sampling mode divided by the MSE of the sequential sampling mode) and the PE was decreased by 73.97%. The precision obtained from the experimental results reached 10%, which showed the orthogonal projection sampling could be a practicable sampling mode for the incomplete data field reconstruction in OCT and could provide some guidance for the flow-field measurement and apparatus design in the practical situation.

  3. 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.

  4. 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

  5. Simulation study of magnetic resonance imaging-guided cortically constrained diffuse optical tomography of human brain function

    NASA Astrophysics Data System (ADS)

    Boas, David A.; Dale, Anders M.

    2005-04-01

    Diffuse optical imaging can measure brain activity noninvasively in humans through the scalp and skull by measuring the light intensity modulation arising from localized-activity-induced absorption changes within the cortex. Spatial resolution and localization accuracy are currently limited by measurement geometry to approximately 3 cm in the plane parallel to the scalp. Depth resolution is a more significant challenge owing to the limited angle tomography permitted by reflectance-only measurements. We combine previously established concepts for improving image quality and demonstrate, through simulation studies, their application for improving the image quality of adult human brain function. We show in a three-dimensional human head model that localization accuracy is significantly improved by the addition of measurements that provide overlapping samples of brain tissue. However, the reconstructed absorption contrast is significantly underestimated because its depth is underestimated. We show that the absorption contrast amplitude accuracy can be significantly improved by providing a cortical spatial constraint in the image reconstruction to obtain a better depth localization. The cortical constraint makes physiological sense since the brain-activity-induced absorption changes are occurring in the cortex and not in the scalp, skull, and cerebral spinal fluid. This spatial constraint is provided by segmentation of coregistered structural magnetic resonance imaging (MRI). However, the absorption contrast deep within the cortex is reconstructed superficially, resulting in an underestimation of the absorption contrast. The synthesis of techniques described here indicates that multimodality imaging of brain function with diffuse optical imaging and MRI has the potential to provide more quantitative estimates of the total and deoxyhemoglobin response to brain activation, which is currently not provided by either method independently. However, issues of depth resolution

  6. A new material mapping procedure for quantitative computed tomography-based, continuum finite element analyses of the vertebra.

    PubMed

    Unnikrishnan, Ginu U; Morgan, Elise F

    2011-07-01

    Inaccuracies in the estimation of material properties and errors in the assignment of these properties into finite element models limit the reliability, accuracy, and precision of quantitative computed tomography (QCT)-based finite element analyses of the vertebra. In this work, a new mesh-independent, material mapping procedure was developed to improve the quality of predictions of vertebral mechanical behavior from QCT-based finite element models. In this procedure, an intermediate step, called the material block model, was introduced to determine the distribution of material properties based on bone mineral density, and these properties were then mapped onto the finite element mesh. A sensitivity study was first conducted on a calibration phantom to understand the influence of the size of the material blocks on the computed bone mineral density. It was observed that varying the material block size produced only marginal changes in the predictions of mineral density. Finite element (FE) analyses were then conducted on a square column-shaped region of the vertebra and also on the entire vertebra in order to study the effect of material block size on the FE-derived outcomes. The predicted values of stiffness for the column and the vertebra decreased with decreasing block size. When these results were compared to those of a mesh convergence analysis, it was found that the influence of element size on vertebral stiffness was less than that of the material block size. This mapping procedure allows the material properties in a finite element study to be determined based on the block size required for an accurate representation of the material field, while the size of the finite elements can be selected independently and based on the required numerical accuracy of the finite element solution. The mesh-independent, material mapping procedure developed in this study could be particularly helpful in improving the accuracy of finite element analyses of vertebroplasty and

  7. Quantitative evaluation of bone development of the distal phalanx of the cow hind limb using computed tomography.

    PubMed

    Tsuka, T; Ooshita, K; Sugiyama, A; Osaki, T; Okamoto, Y; Minami, S; Imagawa, T

    2012-01-01

    Computed tomography (CT) was performed on 400 claws (200 inner and 200 outer claws) of 100 pairs of bovine hind limbs to investigate the etiological theory that an exacerbating factor for ulceration is exostosis of the tuberculum flexorium within the distal phalanx. A variety of morphological changes of the tuberculum flexorium of bovine hind limb claws was visualized by 3-dimensional CT, and the geometry of these claws suggested a growth pattern of bone development with respect to the assumed daily loading patterns. This growth occurs initially at the abaxial caudal aspect of the distal phalanx and is followed by horizontal progression toward the axial aspect. The length of downward bone development on the solar face of the distal phalanx was 2.73±1.32 mm in the outer claws, significantly greater than in the inner claws (2.38±0.96 mm). Ratios of downward (vertical) bone development to the thickness of the subcutis and the corium (VerBD ratios) did not differ between the outer and inner claws (36.7 vs. 38.3%, respectively). Ratios of horizontal bone development to the axial-to-abaxial line of the tuberculum flexorium (HorBD ratios) were approximately 60% for both outer and inner claws. These quantitative measures regarding horizontal and vertical bone development within the distal phalanx were positively correlated with age and VerBD ratios (r=0.53 and r=0.36 for the inner and outer claws, respectively). Correlations between claw width of the outer claw and length of vertical bone development (r=0.43), the HorBD ratio (r=0.51), and the VerBD ratio (r=0.42) suggested that the relative size difference between the inner and outer claws enhances bone development in the outer claw. Correlation coefficients between VerBD and HorBD ratios (r=0.52 and 0.63 for the inner and outer claws, respectively) suggested that horizontal and vertical bone development occurs as a synchronized process within the tuberculum flexorium. This age-related progress of bone development

  8. Bone mineral density obtained by peripheral quantitative computed tomography (pQCT) in middle-aged and elderly Japanese.

    PubMed

    Tsuzuku, S; Niino, N; Ando, F; Shimokata, H

    2000-04-01

    To clarify age-related changes in bone mineral density (BMD) by peripheral quantitative computed tomography (pQCT), 1,124 Japanese middle-aged and elderly community-dwelling people were examined. The BMD of the trabecular bone was assessed at the distal part of the radius (D50), and the BMD of the cortical bone was assessed at the diaphysis of the radius (P100). P100 during age 40 to 49 was significantly higher in females (1359.6 +/- 10.7 mg/cm3, mean +/- SE) than in males (1253.5 +/- 9.5 mg/cm3), while there was no difference in D50, 245.3 +/- 5.1 mg/cm3 in females and 293.0 +/- 5.5 mg/cm3 in males. Females and males aged 50 to 59 lost 8.09 +/- 2.08 (mean +/- SE) mg/cm3 and 3.80 +/- 1.77 mg/cm3 of D50 every year, respectively. As for P100, females lost 25.1 +/- 4.48 mg/cm3, and males lost 6.37 +/- 3.89 mg/cm3 every year. Because of these gender differences, both D50 and P100 were significantly higher in males than in females aged 50 and over. Assuming that the average BMD between ages 40 and 44 was the maximum bone mineral density (BMD max), the percentage change from the BMD max with age was examined. Females aged 60 to 69 whose BMD were under 70% of the BMD max made up 73.9% in D50 and 23.2% in P100. Only 21.1% of males aged 60 to 69 showed less than 70% of the BMD max in D50 and only 3.8% in P100. The percentage decrease in BMD by age was larger in D50 than in P100 in both males and females. The individual difference in BMD was larger in D50 than in P100. These results suggest that pQCT may be useful to independently assess aging effects on cortical and trabecular bone density.

  9. 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.

  10. 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.

  11. Semi-quantitative and simulation analyses of effects of γ rays on determination of calibration factors of PET scanners with point-like (22)Na sources.

    PubMed

    Hasegawa, Tomoyuki; Sato, Yasushi; Oda, Keiichi; Wada, Yasuhiro; Murayama, Hideo; Yamada, Takahiro

    2011-09-21

    The uncertainty of radioactivity concentrations measured with positron emission tomography (PET) scanners ultimately depends on the uncertainty of the calibration factors. A new practical calibration scheme using point-like (22)Na radioactive sources has been developed. The purpose of this study is to theoretically investigate the effects of the associated 1.275 MeV γ rays on the calibration factors. The physical processes affecting the coincidence data were categorized in order to derive approximate semi-quantitative formulae. Assuming the design parameters of some typical commercial PET scanners, the effects of the γ rays as relative deviations in the calibration factors were evaluated by semi-quantitative formulae and a Monte Carlo simulation. The relative deviations in the calibration factors were less than 4%, depending on the details of the PET scanners. The event losses due to rejecting multiple coincidence events of scattered γ rays had the strongest effect. The results from the semi-quantitative formulae and the Monte Carlo simulation were consistent and were useful in understanding the underlying mechanisms. The deviations are considered small enough to correct on the basis of precise Monte Carlo simulation. This study thus offers an important theoretical basis for the validity of the calibration method using point-like (22)Na radioactive sources.

  12. 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

    2011-04-07

    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.

  13. 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.

  14. 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

  15. Depth-dependent displacement sensitivity analysis and the influence of Doppler angle for quantitative assessment of mechanical properties using phase-sensitive spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Lynch, Gillian; Subhash, Hrebesh; Alexandrov, Sergey; Leahy, Martin

    2016-03-01

    Optical coherence elastography (OCE) asesses the mechanical properties of samples by applying a mechanical stimulation and detecting the resulting sample displacement using optical coherence tomography (OCT). OCE methods which utilise the phase of the OCT signal offer the potential to detect displacements on the sub-nanometre scale. However, the displacement sensitivity achieveable is directly related to the signal-to-noise ratio and phase stability of the underlying OCT system. Furthermore, the estimation of Doppler angle is imperative in accurately measuring the sample displacement. This work evaluates the contributions of each of these parameters for quantitative assessment of mechanical properties using phase-sensitive spectral domain OCT.

  16. Quantitative imaging of cochlear soft tissues in wild-type and hearing-impaired transgenic mice by spectral domain optical coherence tomography

    PubMed Central

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

    2011-01-01

    Human hearing loss often occurs as a result of damage or malformations to the functional soft tissues within the cochlea, but these changes are not appreciable with current medical imaging modalities. We sought to determine whether optical coherence tomography (OCT) could assess the soft tissue structures relevant to hearing using mouse models. We imaged excised cochleae with an altered tectorial membrane and during normal development. The soft tissue structures and expected anatomical variations were visible using OCT, and quantitative measurements confirmed the ability to detect critical changes relevant to hearing. PMID:21934905

  17. Quantitative imaging of cochlear soft tissues in wild-type and hearing-impaired transgenic mice by spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

    Human hearing loss often occurs as a result of damage or malformations to the functional soft tissues within the cochlea, but these changes are not appreciable with current medical imaging modalities. We sought to determine whether optical coherence tomography (OCT) could assess the soft tissue structures relevant to hearing using mouse models. We imaged excised cochleae with an altered tectorial membrane and during normal development. The soft tissue structures and expected anatomical variations were visible using OCT, and quantitative measurements confirmed the ability to detect critical changes relevant to hearing.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 3D dynamic rupture simulation and local tomography studies following the 2010 Haiti earthquake

    NASA Astrophysics Data System (ADS)

    Douilly, Roby

    The 2010 M7.0 Haiti earthquake was the first major earthquake in southern Haiti in 250 years. As this event could represent the beginning of a new period of active seismicity in the region, and in consideration of how vulnerable the population is to earthquake damage, it is important to understand the nature of this event and how it has influenced seismic hazards in the region. Most significantly, the 2010 earthquake occurred on the secondary Leogâne thrust fault (two fault segments), not the Enriquillo Fault, the major strike-slip fault in the region, despite it being only a few kilometers away. We first use a finite element model to simulate rupture along the Leogâne fault. We varied friction and background stress to investigate the conditions that best explain observed surface deformations and why the rupture did not to jump to the nearby Enriquillo fault. Our model successfully replicated rupture propagation along the two segments of the Leogâne fault, and indicated that a significant stress increase occurred on the top and to the west of the Enriquillo fault. We also investigated the potential ground shaking level in this region if a rupture similar to the Mw 7.0 2010 Haiti earthquake were to occur on the Enriquillo fault. We used a finite element method and assumptions on regional stress to simulate low frequency dynamic rupture propagation for the segment of the Enriquillo fault closer to the capital. The high-frequency ground motion components were calculated using the specific barrier model, and the hybrid synthetics were obtained by combining the low-frequencies ( 1Hz) from the stochastic simulation using matched filtering at a crossover frequency of 1 Hz. The average horizontal peak ground acceleration, computed at several sites of interest through Port-au-Prince (the capital), has a value of 0.35g. Finally, we investigated the 3D local tomography of this region. We considered 897 high-quality records from the earthquake catalog as recorded by

  4. 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.

  5. Quantitative computed tomography analysis of the airways in patients with cystic fibrosis using automated software: correlation with spirometry in the evaluation of severity*

    PubMed Central

    Santos, Marcel Koenigkam; Cruvinel, Danilo Lemos; de Menezes, Marcelo Bezerra; Teixeira, Sara Reis; Vianna, Elcio de Oliveira; Elias Júnior, Jorge; Martinez, José Antonio Baddini

    2016-01-01

    Objective To perform a quantitative analysis of the airways using automated software, in computed tomography images of patients with cystic fibrosis, correlating the results with spirometric findings. Materials and Methods Thirty-four patients with cystic fibrosis were studied-20 males and 14 females; mean age 18 ± 9 years-divided into two groups according to the spirometry findings: group I (n = 21), without severe airflow obstruction (forced expiratory volume in first second [FEV1] > 50% predicted), and group II (n = 13), with severe obstruction (FEV1 ≤ 50% predicted). The following tracheobronchial tree parameters were obtained automatically: bronchial diameter, area, thickness, and wall attenuation. Results On average, 52 bronchi per patient were studied. The number of bronchi analyzed was higher in group II. The correlation with spirometry findings, especially between the relative wall thickness of third to eighth bronchial generation and predicted FEV1, was better in group I. Conclusion Quantitative analysis of the airways by computed tomography can be useful for assessing disease severity in cystic fibrosis patients. In patients with severe airflow obstruction, the number of bronchi studied by the method is higher, indicating more bronchiectasis. In patients without severe obstruction, the relative bronchial wall thickness showed a good correlation with the predicted FEV1. PMID:28100929

  6. Quantitative thallium-201 single photon emission computed tomography after oral dipyridamole for assessing the presence, anatomic location and severity of coronary artery disease

    SciTech Connect

    Borges-Neto, S.; Mahmarian, J.J.; Jain, A.; Roberts, R.; Verani, M.S.

    1988-05-01

    The objective of this investigation was to determine whether analysis of thallium-201 images as detected by quantitative single photon emission computed tomography after a single high oral dose of dipyridamole (300 mg) would accurately detect the presence of coronary artery disease and the anatomic location of the individual stenosis. Analyses were performed on 100 patients who concomitantly underwent diagnostic coronary arteriography and myocardial imaging. Tomographic myocardial perfusion defects were quantified using computer-generated polar maps. Eighty-four patients had significant coronary artery disease defined as greater than 50% luminal diameter stenosis. The sensitivity for detecting patients with coronary disease was 92% overall, 89% in patients without previous myocardial infarction and 97% in those with prior infarction. The technique had a sensitivity of 80, 87 and 51% for localizing coronary artery stenosis of the left anterior descending, the right coronary and the left circumflex artery, respectively. The corresponding specificity was 84, 92 and 92%. Furthermore, the presence of severe (greater than or equal to 70%) multivessel disease was identified with a sensitivity of 79% and a specificity of 87%. In conclusion, quantitative thallium-201 single photon emission computed tomography after oral dipyridamole has high sensitivity and specificity for diagnosing the presence of coronary disease, ascertaining the location of stenosed vessels and identifying the presence of multivessel disease.

  7. Shallow Ocean Bottom BRDF Prediction, Modeling, and Inversion via Simulation With Surface/Volume Data Derived from X-ray Tomography

    DTIC Science & Technology

    2009-01-01

    and Inversion via Simulation With Surface/Volume Data Derived from X-ray Tomography G. C. Boynton Physics Dept, University of Miami, PO Box...and Inversion via Simulation With Surface/Volume Data Derived from X-ray Tomography 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...sediments) into the previously manufactured sample holders for analysis by both our optical BRDF instrument and the Micro-focus Xray Computerized

  8. Quantitative severity of stress thallium-201 myocardial perfusion single-photon emission computed tomography defects in one-vessel coronary artery disease.

    PubMed

    Matzer, L; Kiat, H; Van Train, K; Germano, G; Papanicolaou, M; Silagan, G; Eigler, N; Maddahi, J; Berman, D S

    1993-08-01

    The relation between the quantitative myocardial perfusion defect severity of exercise thallium-201 single-photon emission computed tomography (SPECT) and the quantitative degree of coronary stenosis was examined in 18 patients with 1-vessel disease (> or = 50% diameter stenosis), and abnormal thallium-201 SPECT. A total of 26 vessels were analyzed. Thallium-201 SPECT quantitative defect severity score was derived by summing the number of pixels in a coronary territory in which counts fell below the normal mean and multiplied by the number of SDs by which they fell below the normal mean. The thallium-201 defect severity score was significantly (p < 0.001) related to the maximal percent luminal diameter narrowing (r = 0.93), percent area narrowing (r = 0.89), absolute stenotic area (r = 0.79), and absolute stenotic diameter (r = 0.81). As expected, the strongest relation between thallium-201 defect severity and quantitative angiographic indexes was in the low and high ranges of coronary stenosis, with more variability and lower correlation coefficients (percent diameter: r = 0.75, p < 0.02, percent area stenosis: r = 0.63, p < 0.05) in the middle ranges (50 to 80% diameter stenosis). This observation is likely to be due to the complex flow characteristics across stenotic lesions. The findings suggest that in a select population, thallium-201 defect severity is potentially useful for noninvasive characterization of the functional severity of coronary artery stenosis and may complement coronary angiography in predicting functionally significant stenosis.

  9. 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

  10. 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.

  11. Quantitative analyses of spectral measurement error based on Monte-Carlo simulation

    NASA Astrophysics Data System (ADS)

    Jiang, Jingying; Ma, Congcong; Zhang, Qi; Lu, Junsheng; Xu, Kexin

    2015-03-01

    The spectral measurement error is controlled by the resolution and the sensitivity of the spectroscopic instrument and the instability of involved environment. In this talk, the spectral measurement error has been analyzed quantitatively by using the Monte Carlo (MC) simulation. Take the floating reference point measurement for example, unavoidably there is a deviation between the measuring position and the theoretical position due to various influence factors. In order to determine the error caused by the positioning accuracy of the measuring device, Monte Carlo simulation has been carried out at the wavelength of 1310nm, simulating Intralipid solution of 2%. MC simulation was performed with the number of 1010 photons and the sampling interval of the ring at 1μm. The data from MC simulation will be analyzed on the basis of thinning and calculating method (TCM) proposed in this talk. The results indicate that TCM could be used to quantitatively analyze the spectral measurement error brought by the positioning inaccuracy.

  12. Spectral Domain Optical Coherence Tomography in Glaucoma: Qualitative and Quantitative Analysis of the Optic Nerve Head and Retinal Nerve Fiber Layer (An AOS Thesis)

    PubMed Central

    Chen, Teresa C.

    2009-01-01

    Purpose: To demonstrate that video-rate spectral domain optical coherence tomography (SDOCT) can qualitatively and quantitatively evaluate optic nerve head (ONH) and retinal nerve fiber layer (RNFL) glaucomatous structural changes. To correlate quantitative SDOCT parameters with disc photography and visual fields. Methods: SDOCT images from 4 glaucoma eyes (4 patients) with varying stages of open-angle glaucoma (ie, early, moderate, late) were qualitatively contrasted with 2 age-matched normal eyes (2 patients). Of 61 other consecutive patients recruited in an institutional setting, 53 eyes (33 patients) met inclusion/exclusion criteria for quantitative studies. Images were obtained using two experimental SDOCT systems, one utilizing a superluminescent diode and the other a titanium:sapphire laser source, with axial resolutions of about 6 μm and 3 μm, respectively. Results: Classic glaucomatous ONH and RNFL structural changes were seen in SDOCT images. An SDOCT reference plane 139 μm above the retinal pigment epithelium yielded cup-disc ratios that best correlated with masked physician disc photography cup-disc ratio assessments. The minimum distance band, a novel SDOCT neuroretinal rim parameter, showed good correlation with physician cup-disc ratio assessments, visual field mean deviation, and pattern standard deviation (P values range, .0003–.024). RNFL and retinal thickness maps correlated well with disc photography and visual field testing. Conclusions: To our knowledge, this thesis presents the first comprehensive qualitative and quantitative evaluation of SDOCT images of the ONH and RNFL in glaucoma. This pilot study provides basis for developing more automated quantitative SDOCT-specific glaucoma algorithms needed for future prospective multicenter national trials. PMID:20126502

  13. 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.

  14. Importance sampling-based Monte Carlo simulation of time-domain optical coherence tomography with embedded objects.

    PubMed

    Periyasamy, Vijitha; Pramanik, Manojit

    2016-04-10

    Monte Carlo simulation for light propagation in biological tissue is widely used to study light-tissue interaction. Simulation for optical coherence tomography (OCT) studies requires handling of embedded objects of various shapes. In this work, time-domain OCT simulations for multilayered tissue with embedded objects (such as sphere, cylinder, ellipsoid, and cuboid) was done. Improved importance sampling (IS) was implemented for the proposed OCT simulation for faster speed. At first, IS was validated against standard and angular biased Monte Carlo methods for OCT. Both class I and class II photons were in agreement in all the three methods. However, the IS method had more than tenfold improvement in terms of simulation time. Next, B-scan images were obtained for four types of embedded objects. All the four shapes are clearly visible from the B-scan OCT images. With the improved IS B-scan OCT images of embedded objects can be obtained with reasonable simulation time using a standard desktop computer. User-friendly, C-based, Monte Carlo simulation for tissue layers with embedded objects for OCT (MCEO-OCT) will be very useful for time-domain OCT simulations in many biological applications.

  15. Quantitative evaluation of simulated functional brain networks in graph theoretical analysis.

    PubMed

    Lee, Won Hee; Bullmore, Ed; Frangou, Sophia

    2017-02-01

    There is increasing interest in the potential of whole-brain computational models to provide mechanistic insights into resting-state brain networks. It is therefore important to determine the degree to which computational models reproduce the topological features of empirical functional brain networks. We used empirical connectivity data derived from diffusion spectrum and resting-state functional magnetic resonance imaging data from healthy individuals. Empirical and simulated functional networks, constrained by structural connectivity, were defined based on 66 brain anatomical regions (nodes). Simulated functional data were generated using the Kuramoto model in which each anatomical region acts as a phase oscillator. Network topology was studied using graph theory in the empirical and simulated data. The difference (relative error) between graph theory measures derived from empirical and simulated data was then estimated. We found that simulated data can be used with confidence to model graph measures of global network organization at different dynamic states and highlight the sensitive dependence of the solutions obtained in simulated data on the specified connection densities. This study provides a method for the quantitative evaluation and external validation of graph theory metrics derived from simulated data that can be used to inform future study designs.

  16. 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

  17. Multi-spectral photoacoustic elasticity tomography

    PubMed Central

    Liu, Yubin; Yuan, Zhen

    2016-01-01

    The goal of this work was to develop and validate a spectrally resolved photoacoustic imaging method, namely multi-spectral photoacoustic elasticity tomography (PAET) for quantifying the physiological parameters and elastic modulus of biological tissues. We theoretically and experimentally examined the PAET imaging method using simulations and in vitro experimental tests. Our simulation and in vitro experimental results indicated that the reconstructions were quantitatively accurate in terms of sizes, the physiological and elastic properties of the targets. PMID:27699101

  18. Wave propagation simulation based on the Fourier diffraction integral for X-ray refraction contrast imaging-computed tomography

    NASA Astrophysics Data System (ADS)

    Chang, Won-Seok; Kim, Jong-Ki; Cho, Jin-Ho; Lim, Jae-Hong

    2016-09-01

    With the advent of coherent X-ray sources, X-ray refraction has begun to be utilized for X-ray imaging of unprecedented sensitivity. The aim of this study was to develop a wave propagation simulator that provides a map of X-ray refraction after passing through an object. We applied the Fresnel diffraction integral for calculating the propagated wave and then obtained the refraction map by differentiating the phase in the refraction-analyzing direction. The simulation was validated by comparing the computed tomography (CT) reconstruction of a virtual phantom with its map of refractive index: the deviations were below 0.7% for soft tissues under our test condition. The simulator can be used for testing and developing highly-sensitive X-ray imaging techniques based on X-ray refraction analysis prior to experimentation.

  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. Quantitative immuno-positron emission tomography imaging of HER2-positive tumor xenografts with an iodine-124 labeled anti-HER2 diabody.

    PubMed

    Robinson, Matthew K; Doss, Mohan; Shaller, Calvin; Narayanan, Deepa; Marks, James D; Adler, Lee P; González Trotter, Dinko E; Adams, Gregory P

    2005-02-15

    Positron emission tomography (PET) provides an effective means of both diagnosing/staging several types of cancer and evaluating efficacy of treatment. To date, the only U.S. Food and Drug Administration-approved radiotracer for oncologic PET is (18)F-fluoro-deoxyglucose, which measures glucose accumulation as a surrogate for malignant activity. Engineered antibody fragments have been developed with the appropriate targeting specificity and systemic elimination properties predicted to allow for effective imaging of cancer based on expression of tumor associated antigens. We evaluated a small engineered antibody fragment specific for the HER2 receptor tyrosine kinase (C6.5 diabody) for its ability to function as a PET radiotracer when labeled with iodine-124. Our studies revealed HER2-dependent imaging of mouse tumor xenografts with a time-dependent increase in tumor-to-background signal over the course of the experiments. Radioiodination via an indirect method attenuated uptake of radioiodine in tissues that express the Na/I symporter without affecting the ability to image the tumor xenografts. In addition, we validated a method for using a clinical PET/computed tomography scanner to quantify tumor uptake in small-animal model systems; quantitation of the tumor targeting by PET correlated with traditional necropsy-based analysis at all time points analyzed. Thus, diabodies may represent an effective molecular structure for development of novel PET radiotracers.

  1. 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.

  2. Peripheral quantitative computed tomography-derived muscle density and peripheral magnetic resonance imaging-derived muscle adiposity: precision and associations with fragility fractures in women

    PubMed Central

    Wong, A.K.O.; Beattie, K.A.; Min, K.K.H.; Gordon, C.; Pickard, L.; Papaioannou, A.; Adachi, J.D.

    2016-01-01

    Purpose To determine the degree to which muscle density and fractures are explained by inter and intramuscular fat (IMF). Methods Women ≥50 years of age (Hamilton, ON, Canada) had peripheral magnetic resonance imaging and peripheral quantitative computed tomography scans at 66% of the tibial length. Muscle on computed tomography images was segmented from subcutaneous fat and bone using fixed thresholds, computing muscle density. IMF was segmented from muscle within magnetic resonance images using a region-growing algorithm, computing IMF volume. Fracture history over the last 14 years was obtained. Odds ratios for fractures were determined for muscle density, adjusting for IMF volume, total hip BMD, age and body mass index. Results Women with a history of fractures were older (N=32, age:75.6±8.3 years) than those without (N=39, age: 67.0±5.2 years) (<0.01). IMF volume explained 49.3% of variance in muscle density (p<0.001). Odds for fractures were associated with lower muscle density even after adjusting for IMF volume but were attenuated after adjusting for age. Conclusions Muscle adiposity represents only 50% of the muscle density measurement. Properties of muscle beyond its adiposity may be related to fractures, but larger and prospective studies are needed to confirm these associations. PMID:25524965

  3. Three-Dimensional Quantitative Chemical Roughness Of Buried ZrO2/In2O3 Interfaces Via Energy-Filtered Electron Tomography

    SciTech Connect

    Zhong, X. Y.; Kabius, B.; Schreiber, Daniel K.; Eastman, J. A.; Fong, D. D.; Petford-Long, Amanda K.

    2012-04-26

    The protocol to calculate the chemical roughness from three-dimensional (3-D) data cube acquired by energy-filtered electron tomography has been developed and applied to analyze the 3-D Zr distribution at the arbitrarily shaped interfaces in the ZrO2/In2O3 multilayer films. The calculated root-mean-square roughness quantitatively revealed the chemical roughness at the buried ZrO2/In2O3 interfaces, which is the deviation of Zr distribution from the ideal flat interface. Knowledge of the chemistry and structure of oxide interfaces in 3-D provides information useful for understanding changes in the behavior of a model ZrO2/In2O3 heterostructure that has potential to exhibit mixed conduction behavior. VC 2012 American Institute of Physics.

  4. 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

  5. FIFTH SEMINAR IN MEMORY OF D.N. KLYSHKO: Simulation of quantum systems by the tomography Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Bogdanov, Yu I.

    2007-12-01

    A new method of statistical simulation of quantum systems is presented which is based on the generation of data by the Monte Carlo method and their purposeful tomography with the energy minimisation. The numerical solution of the problem is based on the optimisation of the target functional providing a compromise between the maximisation of the statistical likelihood function and the energy minimisation. The method does not involve complicated and ill-posed multidimensional computational procedures and can be used to calculate the wave functions and energies of the ground and excited stationary sates of complex quantum systems. The applications of the method are illustrated.

  6. 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 ...

  7. An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing.

    PubMed

    Wu, Zujian; Pang, Wei; Coghill, George M

    Both qualitative and quantitative model learning frameworks for biochemical systems have been studied in computational systems biology. In this research, after introducing two forms of pre-defined component patterns to represent biochemical models, we propose an integrative qualitative and quantitative modelling framework for inferring biochemical systems. In the proposed framework, interactions between reactants in the candidate models for a target biochemical system are evolved and eventually identified by the application of a qualitative model learning approach with an evolution strategy. Kinetic rates of the models generated from qualitative model learning are then further optimised by employing a quantitative approach with simulated annealing. Experimental results indicate that our proposed integrative framework is feasible to learn the relationships between biochemical reactants qualitatively and to make the model replicate the behaviours of the target system by optimising the kinetic rates quantitatively. Moreover, potential reactants of a target biochemical system can be discovered by hypothesising complex reactants in the synthetic models. Based on the biochemical models learned from the proposed framework, biologists can further perform experimental study in wet laboratory. In this way, natural biochemical systems can be better understood.

  8. 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.

  9. 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

  10. Relationship between Quantitative Adverse Plaque Features from Coronary CT Angiography and Downstream Impaired Myocardial Flow Reserve by 13N-Ammonia Positron Emission Tomography: A Pilot Study

    PubMed Central

    Dey, Damini; Zamudio, Mariana Diaz; Schuhbaeck, Annika; Orozco, Luis Eduardo Juarez; Otaki, Yuka; Gransar, Heidi; Li, Debiao; Germano, Guido; Achenbach, Stephan; Berman, Daniel S.; Meave, Aloha; Alexanderson, Erick; Slomka, Piotr J.

    2016-01-01

    Background We investigated the relationship of quantitative plaque features from coronary CT Angiography (CTA) and coronary vascular dysfunction by impaired myocardial flow reserve (MFR) by 13N-Ammonia Positron Emission Tomography (PET). Methods and Results Fifty-one patients (32 men, 62.4±9.5 years) underwent combined rest-stress 13N-ammonia PET and CTA scans by hybrid PET/CT. Regional MFR was measured from PET. From CTA, 153 arteries were evaluated by semi-automated software, computing arterial non-calcified plaque (NCP), low-density NCP (NCP<30 HU), calcified and total plaque volumes, and corresponding plaque burden (plaque volumex100%/vessel volume), stenosis, remodeling index, contrast density difference (maximum difference in luminal attenuation per unit area in the lesion), and plaque length. Quantitative stenosis, plaque burden and myocardial mass were combined by boosted ensemble machine-learning algorithm into a composite risk score to predict impaired MFR (MFR≤2.0) by PET, in each artery. Nineteen patients (37%) had impaired regional MFR in at least one territory, (41/153 vessels). Patients with impaired regional MFR had higher arterial NCP (32.4 vs.17.2 %), low-density NCP (7 vs 4 %) and total plaque burden (37 vs 19.3 %, p<0.02). In multivariable analysis with 10-fold cross-validation, NCP burden was the most significant predictor of impaired MFR (Odds Ratio 1.35, p=0.021). For prediction of impaired MFR with 10-fold cross-validation, receiver-operating-characteristics-area-under-the-curve for the composite score was 0.83 (95%CI:0.79–0.91), greater than for quantitative stenosis (0.66, 95%CI:0.57–0.76, p = 0.005). Conclusions Compared to stenosis, arterial NCP burden and a composite score combining quantitative stenosis and plaque burden from CTA significantly improves identification of downstream regional vascular dysfunction. PMID:26467104

  11. 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

  12. Quantitative assessment of groundwater vulnerability using index system and transport simulation, Huangshuihe catchment, China.

    PubMed

    Yu, Cheng; Yao, Yingying; Hayes, Gregory; Zhang, Baoxiang; Zheng, Chunmiao

    2010-11-15

    Groundwater vulnerability assessment has been an increasingly important environment management tool. The existing vulnerability assessment approaches are mostly index systems which have significant disadvantages. There need to be some quantitative studies on vulnerability indicators based on objective physical process study. In this study, we tried to do vulnerability assessment in Huangshuihe catchment in Shandong province of China using both contaminant transport simulations and index system approach. Transit time of 75% of hypothetical injected contaminant concentration was considered as the vulnerability indicator. First, we collected the field data of the Huangshuihe catchment and the catchment was divided into 34 sub areas that can each be treated as a transport sub model. Next, we constructed a Hydrus1D transport model of Huangshuihe catchment. Different sub areas had different input values. Thirdly, we used Monte-Carlo simulation to improve the collected data and did vulnerability assessment using the statistics of the contaminant transit time as a vulnerability indicator. Finally, to compare with the assessment result by transport simulation, we applied two index systems to Huangshuihe catchment. The first was DRASTIC system, and the other was a system we tentatively constructed examining the relationships between the transit time and the input parameters by simply changing the input values. The result of comparisons between the two index systems and transport simulation approach suggested partial validation to DRASTIC, and the construction of the new tentative index system was an attempt of building up index approaches based on physical process simulation.

  13. In vitro comparison of cone beam computed tomography with different voxel sizes for detection of simulated external root resorption.

    PubMed

    Neves, Frederico S; de Freitas, Deborah Q; Campos, Paulo S F; de Almeida, Solange M; Haiter-Neto, Francisco

    2012-09-01

    The present study compared the efficacy of cone beam computed tomography using different voxel sizes in the diagnosis of simulated external root resorption. The presence or absence of simulated defects on buccal, mesial and distal root surfaces of 20 premolars was evaluated. The defects were small (0.26 mm in diameter and 0.08 mm deep), medium (0.62 mm in diameter and 0.19 mm deep) and large (1.05 mm in diameter and 0.24 mm deep), equally distributed on each root surface. Images were obtained using Classic i-CAT cone beam computed tomography with different voxel sizes: 0.12, 0.20, 0.25 and 0.30 mm. Five oral radiologists evaluated the images. Accuracy, sensitivity, specificity, positive and negative predictive values were determined. The sensitivity decreased and specificity increased as voxel size increased. Accuracy values were the highest for the smallest voxel size (0.12 mm). The results for voxel sizes 0.20 mm and 0.25 mm were similar. Positive and negative predictive values were similar in all protocols, except with 0.30 mm, in which they were the lowest. In conclusion, external root resorption was more easily diagnosed when a smaller voxel size was used.

  14. A synchrotron-based local computed tomography combined with data-constrained modelling approach for quantitative analysis of anthracite coal microstructure.

    PubMed

    Chen, Wen Hao; Yang, Sam Y S; Xiao, Ti Qiao; Mayo, Sherry C; Wang, Yu Dan; Wang, Hai Peng

    2014-05-01

    Quantifying three-dimensional spatial distributions of pores and material compositions in samples is a key materials characterization challenge, particularly in samples where compositions are distributed across a range of length scales, and where such compositions have similar X-ray absorption properties, such as in coal. Consequently, obtaining detailed information within sub-regions of a multi-length-scale sample by conventional approaches may not provide the resolution and level of detail one might desire. Herein, an approach for quantitative high-definition determination of material compositions from X-ray local computed tomography combined with a data-constrained modelling method is proposed. The approach is capable of dramatically improving the spatial resolution and enabling finer details within a region of interest of a sample larger than the field of view to be revealed than by using conventional techniques. A coal sample containing distributions of porosity and several mineral compositions is employed to demonstrate the approach. The optimal experimental parameters are pre-analyzed. The quantitative results demonstrated that the approach can reveal significantly finer details of compositional distributions in the sample region of interest. The elevated spatial resolution is crucial for coal-bed methane reservoir evaluation and understanding the transformation of the minerals during coal processing. The method is generic and can be applied for three-dimensional compositional characterization of other materials.

  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. 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

    2015-01-01

    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.

  17. A synchrotron-based local computed tomography combined with data-constrained modelling approach for quantitative analysis of anthracite coal microstructure

    PubMed Central

    Chen, Wen Hao; Yang, Sam Y. S.; Xiao, Ti Qiao; Mayo, Sherry C.; Wang, Yu Dan; Wang, Hai Peng

    2014-01-01

    Quantifying three-dimensional spatial distributions of pores and material compositions in samples is a key materials characterization challenge, particularly in samples where compositions are distributed across a range of length scales, and where such compositions have similar X-ray absorption properties, such as in coal. Consequently, obtaining detailed information within sub-regions of a multi-length-scale sample by conventional approaches may not provide the resolution and level of detail one might desire. Herein, an approach for quantitative high-definition determination of material compositions from X-ray local computed tomography combined with a data-constrained modelling method is proposed. The approach is capable of dramatically improving the spatial resolution and enabling finer details within a region of interest of a sample larger than the field of view to be revealed than by using conventional techniques. A coal sample containing distributions of porosity and several mineral compositions is employed to demonstrate the approach. The optimal experimental parameters are pre-analyzed. The quantitative results demonstrated that the approach can reveal significantly finer details of compositional distributions in the sample region of interest. The elevated spatial resolution is crucial for coal-bed methane reservoir evaluation and understanding the transformation of the minerals during coal processing. The method is generic and can be applied for three-dimensional compositional characterization of other materials. PMID:24763649

  18. 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.

  19. SeqSIMLA2: simulating correlated quantitative traits accounting for shared environmental effects in user-specified pedigree structure.

    PubMed

    Chung, Ren-Hua; Tsai, Wei-Yun; Hsieh, Chang-Hsun; Hung, Kuan-Yi; Hsiung, Chao A; Hauser, Elizabeth R

    2015-01-01

    Simulation tools that simulate sequence data in unrelated cases and controls or in families with quantitative traits or disease status are important for genetic studies. The simulation tools can be used to evaluate the statistical power for detecting the causal variants when planning a genetic epidemiology study, or to evaluate the statistical properties for new methods. We previously developed SeqSIMLA version 1 (SeqSIMLA1), which simulates family or case-control data with a disease or quantitative trait model. SeqSIMLA1, and several other tools that simulate quantitative traits, do not specifically model the shared environmental effects among relatives on a trait. However, shared environmental effects are commonly observed for some traits in families, such as body mass index. SeqSIMLA1 simulates a fixed three-generation family structure. However, it would be ideal to simulate prespecified pedigree structures for studies involving large pedigrees. Thus, we extended SeqSIMLA1 to create SeqSIMLA2, which can simulate correlated traits and considers the shared environmental effects. SeqSIMLA2 can also simulate prespecified large pedigree structures. There are no restrictions on the number of individuals that can be simulated in a pedigree. We used a blood pressure example to demonstrate that SeqSIMLA2 can simulate realistic correlation structures between the systolic and diastolic blood pressure among relatives. We also showed that SeqSIMLA2 can simulate large pedigrees with large chromosomal regions in a reasonable time frame.

  20. 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.

  1. 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.

  2. 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

  3. Direct, quantitative, and noninvasive imaging of the transport of active agents through intact brain with Positron Emission Tomography

    PubMed Central

    Sirianni, Rachael W.; Zheng, Ming-Qiang; Saltzman, W. Mark; Huang, Yiyun; Carson, Richard E.

    2014-01-01

    Purpose Our goal was to use Positron Emission Tomography (PET) to analyze the movement of radiolabeled agents in tissue to enable direct measurement of drug delivery to the brain. Procedures A variety of 11C- and 18F-labeled compounds were delivered directly to an agarose phantom or rat striatum. Concentration profiles were extracted for analysis and fitted to diffusion models. Results Diffusion coefficients ranged from 0.075±0.0026 mm2/min ([18F]Fluoride, 18 Da) to 0.0016±0.0018 mm2/min ([18F]NPB4-avidin, 68 kDa) and matched well with predictions based on molecular weight (R2=0.965). The tortuosity of the brain extracellular space was estimated to be 1.56, with the tissue clearance halftime of each tracer in the brain varying from 19 to 41 minutes. Conclusions PET is an effective modality to directly quantify the movement of locally delivered drugs or drug-carriers. This continuous, non-invasive assessment of delivery will aid the design of better drug delivery methods. PMID:23624949

  4. Quantitative performance characterization of image quality and radiation dose for a CS 9300 dental cone beam computed tomography machine

    PubMed Central

    Abouei, Elham; Lee, Sierra; Ford, Nancy L.

    2015-01-01

    Abstract. This paper aims to characterize the radiation dose and image quality (IQ) performance of a dental cone beam computed tomography (CBCT) unit over a range of fields of view (FOV). IQ and dose were measured using a Carestream 9300 dental CBCT. Phantoms were positioned in the FOV to imitate clinical positioning. IQ was assessed by scanning a SEDENTEXCT IQ phantom, and images were analyzed in ImageJ. Dose index 1 was obtained using a thimble ionization chamber and SEDENTEXCT DI phantom. Mean gray values agreed within 93.5% to 99.7% across the images, with pixel-to-pixel fluctuations of 6% to 12.5%, with poorer uniformity and increased noise for child protocols. CNR was fairly constant across FOVs, with higher CNR for larger patient settings. The measured limiting spatial resolution agreed well with 10% MTF and bar pattern measurements. Dose was reduced for smaller patient settings within a given FOV; however, smaller FOVs obtained with different acquisition settings did not necessarily result in reduced dose. The use of patient-specific acquisition settings decreased the radiation dose for smaller patients, with minimal impact on the IQ. The full set of IQ and dose measurements is reported to allow dental professionals to compare the different FOV settings for clinical use. PMID:26587550

  5. An x-ray tomography facility for quantitative prediction of mechanical and transport properties in geological, biological, and synthetic systems

    NASA Astrophysics Data System (ADS)

    Sakellariou, Arthur; Senden, Tim J.; Sawkins, Tim J.; Knackstedt, Mark A.; Turner, Michael L.; Jones, Anthony C.; Saadatfar, Mohammad; Roberts, Ray J.; Limaye, Ajay; Arns, Christoph H.; Sheppard, Adrian P.; Sok, Rob M.

    2004-10-01

    A fully integrated X-ray tomography facility with the ability to generate tomograms with 20483 voxels at 2 micron spatial resolution was built to satisfy the requirements of a virtual materials testing laboratory. The instrument comprises of a continuously pumped micro-focus X-ray gun, a milli-degree rotation stage and a high resolution and large field X-ray camera, configured in a cone beam geometry with a circular trajectory. The purpose of this facility is to routinely analyse and investigate real world biological, geological and synthetic materials at a scale in which the traditional domains of physics, chemistry, biology and geology merge. During the first 2 years of operation, approximately 4 Terabytes of data have been collected, processed and analysed, both as static and in some cases as composite dynamic data sets. This incorporates over 300 tomograms with 10243 voxels and 50 tomograms with 20483 voxels for a wide range of research fields. Specimens analysed include sedimentary rocks, soils, bone, soft tissue, ceramics, fibre-reinforced composites, foams, wood, paper, fossils, sphere packs, bio-morphs and small animals. In this paper, the exibility of the facility is highlighted with some prime examples.

  6. Power Analysis of Artificial Selection Experiments Using Efficient Whole Genome Simulation of Quantitative Traits

    PubMed Central

    Kessner, Darren; Novembre, John

    2015-01-01

    Evolve and resequence studies combine artificial selection experiments with massively parallel sequencing technology to study the genetic basis for complex traits. In these experiments, individuals are selected for extreme values of a trait, causing alleles at quantitative trait loci (QTL) to increase or decrease in frequency in the experimental population. We present a new analysis of the power of artificial selection experiments to detect and localize quantitative trait loci. This analysis uses a simulation framework that explicitly models whole genomes of individuals, quantitative traits, and selection based on individual trait values. We find that explicitly modeling QTL provides qualitatively different insights than considering independent loci with constant selection coefficients. Specifically, we observe how interference between QTL under selection affects the trajectories and lengthens the fixation times of selected alleles. We also show that a substantial portion of the genetic variance of the trait (50–100%) can be explained by detected QTL in as little as 20 generations of selection, depending on the trait architecture and experimental design. Furthermore, we show that power depends crucially on the opportunity for recombination during the experiment. Finally, we show that an increase in power is obtained by leveraging founder haplotype information to obtain allele frequency estimates. PMID:25672748

  7. Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits.

    PubMed

    Kessner, Darren; Novembre, John

    2015-04-01

    Evolve and resequence studies combine artificial selection experiments with massively parallel sequencing technology to study the genetic basis for complex traits. In these experiments, individuals are selected for extreme values of a trait, causing alleles at quantitative trait loci (QTL) to increase or decrease in frequency in the experimental population. We present a new analysis of the power of artificial selection experiments to detect and localize quantitative trait loci. This analysis uses a simulation framework that explicitly models whole genomes of individuals, quantitative traits, and selection based on individual trait values. We find that explicitly modeling QTL provides qualitatively different insights than considering independent loci with constant selection coefficients. Specifically, we observe how interference between QTL under selection affects the trajectories and lengthens the fixation times of selected alleles. We also show that a substantial portion of the genetic variance of the trait (50-100%) can be explained by detected QTL in as little as 20 generations of selection, depending on the trait architecture and experimental design. Furthermore, we show that power depends crucially on the opportunity for recombination during the experiment. Finally, we show that an increase in power is obtained by leveraging founder haplotype information to obtain allele frequency estimates.

  8. Feasibility of an automated quantitative computed tomography angiography-derived risk score for risk stratification of patients with suspected coronary artery disease.

    PubMed

    de Graaf, Michiel A; Broersen, Alexander; Ahmed, Wehab; Kitslaar, Pieter H; Dijkstra, Jouke; Kroft, Lucia J; Delgado, Victoria; Bax, Jeroen J; Reiber, Johan H C; Scholte, Arthur J

    2014-06-15

    Coronary computed tomography angiography (CTA) has important prognostic value. Additionally, quantitative CTA (QCT) provides a more detailed accurate assessment of coronary artery disease (CAD) on CTA. Potentially, a risk score incorporating all quantitative stenosis parameters allows accurate risk stratification. Therefore, the purpose of this study was to determine if an automatic quantitative assessment of CAD using QCT combined into a CTA risk score allows risk stratification of patients. In 300 patients, QCT was performed to automatically detect and quantify all lesions in the coronary tree. Using QCT, a novel CTA risk score was calculated based on plaque extent, severity, composition, and location on a segment basis. During follow-up, the composite end point of all-cause mortality, revascularization, and nonfatal infarction was recorded. In total, 10% of patients experienced an event during a median follow-up of 2.14 years. The CTA risk score was significantly higher in patients with an event (12.5 [interquartile range 8.6 to 16.4] vs 1.7 [interquartile range 0 to 8.4], p <0.001). In 127 patients with obstructive CAD (≥50% stenosis), 27 events were recorded, all in patients with a high CTA risk score. In conclusion, the present study demonstrated that a fully automatic QCT analysis of CAD is feasible and can be applied for risk stratification of patients with suspected CAD. Furthermore, a novel CTA risk score incorporating location, severity, and composition of coronary lesion was developed. This score may improve risk stratification but needs to be confirmed in larger studies.

  9. A quantitative correlation of the effect of density distributions in roller-compacted ribbons on the mechanical properties of tablets using ultrasonics and X-ray tomography.

    PubMed

    Akseli, Ilgaz; Iyer, Srinivas; Lee, Hwahsiung P; Cuitiño, Alberto M

    2011-09-01

    Enabling the paradigm of quality by design requires the ability to quantitatively correlate material properties and process variables to measureable product performance attributes. In this study, we show how heterogeneities in compacted ribbon densities quantitatively correlate to tablet mechanical properties. These density variations, which have been purposely modulated by internal and external lubrications, are characterized longitudinally and transversally by nondestructive ultrasonic and X-ray micro-computed tomography measurements. Subsequently, different transversal regions of the compacted ribbon are milled under the same conditions, and granules with nominally the same particle size distribution are utilized to manufacture cylindrical tablets, whose mechanical properties are further analyzed by ultrasonic measurements. We consider three different ribbon conditions: no lubrication (case 1); lubricated powder (case 2); and lubricated tooling (hopper, side sealing plates, feed screws, and rolls) (case 3). This study quantitatively reveals that variation in local densities in ribbons (for case 1) and process conditions (i.e., internal case 2 and external lubrication case 3) during roller compaction significantly affect the mechanical properties of tablets even for granules with the same particle size distribution. For case 1, the mechanical properties of tablets depend on the spatial location where granules are produced. For cases 2 and 3, the ribbon density homogeneity was improved by the use of a lubricant. It is demonstrated that the mechanical performances of tablets are decreased due to applied lubricant and work-hardening phenomenon. Moreover, we extended our study to correlate the speed of sound to the tensile strength of the tablet. It is found that the speed of sound increases with the tensile strength for the tested tablets.

  10. 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.

  11. Quantitative binomial distribution analyses of nanoscale like-solute atom clustering and segregation in atom probe tomography data.

    PubMed

    Moody, Michael P; Stephenson, Leigh T; Ceguerra, Anna V; Ringer, Simon P

    2008-07-01

    The applicability of the binomial frequency distribution is outlined for the analysis of the evolution nanoscale atomic clustering of dilute solute in an alloy subject to thermal ageing in 3D atom probe data. The conventional chi(2) statistics and significance testing are demonstrated to be inappropriate for comparison of quantity of solute segregation present in two or more different sized system. Pearson coefficient, mu, is shown to normalize chi(2) with respect to sample size over an order of magnitude. A simple computer simulation is implemented to investigate the binomial analysis and infer meaning in the measured value of mu over a series of systems at different solute concentrations and degree of clustering. The simulations replicate the form of experimental data and demonstrate the effect of detector efficiency to significantly underestimate the measured segregation. The binomial analysis is applied to experimental atom probe data sets and complementary simulations are used to interpret the results.

  12. Simulation of realistic abnormal SPECT brain perfusion images: application in semi-quantitative analysis

    NASA Astrophysics Data System (ADS)

    Ward, T.; Fleming, J. S.; Hoffmann, S. M. A.; Kemp, P. M.

    2005-11-01

    Simulation is useful in the validation of functional image analysis methods, particularly when considering the number of analysis techniques currently available lacking thorough validation. Problems exist with current simulation methods due to long run times or unrealistic results making it problematic to generate complete datasets. A method is presented for simulating known abnormalities within normal brain SPECT images using a measured point spread function (PSF), and incorporating a stereotactic atlas of the brain for anatomical positioning. This allows for the simulation of realistic images through the use of prior information regarding disease progression. SPECT images of cerebral perfusion have been generated consisting of a control database and a group of simulated abnormal subjects that are to be used in a UK audit of analysis methods. The abnormality is defined in the stereotactic space, then transformed to the individual subject space, convolved with a measured PSF and removed from the normal subject image. The dataset was analysed using SPM99 (Wellcome Department of Imaging Neuroscience, University College, London) and the MarsBaR volume of interest (VOI) analysis toolbox. The results were evaluated by comparison with the known ground truth. The analysis showed improvement when using a smoothing kernel equal to system resolution over the slightly larger kernel used routinely. Significant correlation was found between effective volume of a simulated abnormality and the detected size using SPM99. Improvements in VOI analysis sensitivity were found when using the region median over the region mean. The method and dataset provide an efficient methodology for use in the comparison and cross validation of semi-quantitative analysis methods in brain SPECT, and allow the optimization of analysis parameters.

  13. Volumetric quantitative characterization of human patellar cartilage with topological and geometrical features on phase contrast x-ray computed tomography

    PubMed Central

    Nagarajan, Mahesh B.; Coan, Paola; Huber, Markus B.; Diemoz, Paul C.; Wismüller, Axel

    2015-01-01

    Phase contrast X-ray computed tomography (PCI-CT) has attracted significant interest in recent years for its ability to provide significantly improved image contrast in low absorbing materials such as soft biological tissue. In the research context of cartilage imaging, previous studies have demonstrated the ability of PCI-CT to visualize structural details of human patellar cartilage matrix and capture changes to chondrocyte organization induced by osteoarthritis. This study evaluates the use of geometrical and topological features for volumetric characterization of such chondrocyte patterns in the presence (or absence) of osteoarthritic damage. Geometrical features derived from the scaling index method (SIM) and topological features derived from Minkowski Functionals were extracted from 1392 volumes of interest (VOI) 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 VOIs as healthy or osteoarthritic; classification performance was evaluated using the area under the receiver-operating characteristic (ROC) curve (AUC). Our results show that the classification performance of SIM-derived geometrical features (AUC: 0.90 ± 0.09) significantly outperform Minkowski Functionals volume (AUC: 0.54 ± 0.02), surface (AUC: 0.72 ± 0.06), mean breadth (AUC: 0.74 ± 0.06) and Euler characteristic (AUC: 0.78 ± 0.04) (p < 10−4). These results suggest that such geometrical features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix in an automated manner, while also enabling classification of cartilage as healthy or osteoarthritic with high accuracy. Such features could potentially serve as diagnostic imaging markers for evaluating osteoarthritis progression and its response to different therapeutic intervention strategies. PMID:26142112

  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 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

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. Monte Carlo simulation of x-ray scattering for quantitative characterization of breast cancer.

    PubMed

    Elshemey, Wael M; Elsharkawy, Wafaa B

    2009-06-21

    In the last decade there has been growing interest in the possibility of characterizing breast cancer using differences in the coherent x-ray-scattering profiles of normal and malignant tissues. To a great extent, characterization has depended on the differences in the peak positions of both tissues in addition to the overall profile which exhibits a distinctive sharp adipose peak in the case of a normal breast. In many excised tissue samples, breast cancer samples may be mixed with a variable percentage of other tissues which affect the shape of the x-ray-scattering profile and consequently the ability to characterize the tissue. Moreover, fibroglandular tissue produces a scattering profile showing an extent of similarity to breast cancer. The present study introduces a Monte Carlo simulation code capable of tracing photon transport inside a mixed two-component sample. The code is utilized to simulate and best fit x-ray-scattering profiles of the measured samples. This provides reliable breast tissue characterization in addition to a quantitative estimate of the percentage of each component in a given sample. It is expected that the present simulation would potentially enhance the characterization of breast cancer using the x-ray-scattering technique.

  2. 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.

  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. 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.

  5. DOT tomography of the solar atmosphere. III. Observations and simulations of reversed granulation

    NASA Astrophysics Data System (ADS)

    Leenaarts, J.; Wedemeyer-Böhm, S.

    2005-02-01

    We compare high-quality image sequences from the Dutch Open Telescope (DOT) with synthetic image sequences obtained from 3D radiation-hydrodynamics simulations of the solar granulation. In particular, we study the subsonic brightness pattern observed in the wings of Ca II HK. The simulations reproduce the observed intensity contrast, time scales, and Fourier behaviour rather well. Most differences can be attributed to the resolution difference between the observations and the simulation and the small geometrical extent of the simulation. We conclude that magnetic fields play no major role in the formation of reversed granulation.

  6. A simulation-based study on the influence of beam hardening in X-ray computed tomography for dimensional metrology.

    PubMed

    Lifton, Joseph J; Malcolm, Andrew A; McBride, John W

    2015-01-01

    X-ray computed tomography (CT) is a radiographic scanning technique for visualising cross-sectional images of an object non-destructively. From these cross-sectional images it is possible to evaluate internal dimensional features of a workpiece which may otherwise be inaccessible to tactile and optical instruments. Beam hardening is a physical process that degrades the quality of CT images and has previously been suggested to influence dimensional measurements. Using a validated simulation tool, the influence of spectrum pre-filtration and beam hardening correction are evaluated for internal and external dimensional measurements. Beam hardening is shown to influence internal and external dimensions in opposition, and to have a greater influence on outer dimensions compared to inner dimensions. The results suggest the combination of spectrum pre-filtration and a local gradient-based surface determination method are able to greatly reduce the influence of beam hardening in X-ray CT for dimensional metrology.

  7. 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.

  8. 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.

  9. Simulation of cellular changes on Optical Coherence Tomography of human retina.

    PubMed

    Santos, Miriam; Araujo, Aderito; Barbeiro, Silvia; Caramelo, Francisco; Correia, Antonio; Marques, Maria Isabel; Pinto, Luis; Serranho, Pedro; Bernardes, Rui; Morgado, Miguel

    2015-08-01

    We present a methodology to assess cell level alterations on the human retina responsible for functional changes observable in the Optical Coherence Tomography data in healthy ageing and in disease conditions, in the absence of structural alterations. The methodology is based in a 3D multilayer Monte Carlo computational model of the human retina. The optical properties of each layer are obtained by solving the Maxwell's equations for 3D domains representative of small regions of those layers, using a Discontinuous Galerkin Finite Element Method (DG-FEM). Here we present the DG-FEM Maxwell 3D model and its validation against Mie's theory for spherical scatterers. We also present an application of our methodology to the assessment of cell level alterations responsible for the OCT data in Diabetic Macular Edema. It was possible to identify which alterations are responsible for the changes observed in the OCT scans of the diseased groups.

  10. Quantitative second harmonic generation imaging of the diseased state osteogenesis imperfecta: experiment and simulation.

    PubMed

    Lacomb, Ronald; Nadiarnykh, Oleg; Campagnola, Paul J

    2008-06-01

    We report the integrated use of 3D second harmonic generation (SHG) imaging microscopy and Monte Carlo simulation as a combined metric to quantifiably differentiate normal and diseased tissues based on the physical properties of the respective extracellular matrix. To achieve this, we have identified a set of parameters comprised of the SHG creation attributes and the bulk optical parameters, which are used collectively via comparative analysis. Monte Carlo simulations of the SHG axial directional and attenuation responses allow their decomposition into the underlying factors that are not readily obtainable through experimental techniques. Specifically, this approach allows for estimation of the SHG creation attributes (directionality and relative conversion efficiency) and separation of primary and secondary filter effects, collectively that form the observed SHG contrast. The quantitative metric is shown for the connective tissue disorder Osteogenesis Imperfecta (characterized by abnormal assembly of type I collagen) using a murine model that expresses the disease in the dermis layer of skin. Structural dissimilarities between the osteogenesis imperfecta mouse and wild-type tissues lead to significant differences in the SHG depth-dependent directionality and signal attenuation. The Monte Carlo simulations of these responses using measured bulk optical parameters reproduce the experimental data trends, and the extracted emission directionality and conversion efficiencies are consistent with independent determinations. The simulations also illustrate the dominance of primary filter affects on overall SHG generation and attenuation. Thus, the combined method of 3D SHG imaging and modeling forms an essential foundation for parametric description of the matrix properties that are not distinguishable by sole consideration of either bulk optical parameters or SHG alone. Moreover, due to the quasi-coherence of the SHG process in tissues, we submit that this approach

  11. 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.

  12. Challenges and Approaches to Quantitative Therapy Response Assessment in Glioblastoma Multiforme Using the Novel Apoptosis Positron Emission Tomography Tracer F-18 ML-10.

    PubMed

    Oborski, Matthew J; Laymon, Charles M; Qian, Yongxian; Lieberman, Frank S; Nelson, Arden D; Mountz, James M

    2014-02-01

    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.

  13. Peripheral quantitative computed tomography (pQCT) for the assessment of bone strength in most of bone affecting conditions in developmental age: a review.

    PubMed

    Stagi, Stefano; Cavalli, Loredana; Cavalli, Tiziana; de Martino, Maurizio; Brandi, Maria Luisa

    2016-09-26

    Peripheral quantitative computed tomography provides an automatical scan analysis of trabecular and cortical bone compartments, calculating not only their bone mineral density (BMD), but also bone geometrical parameters, such as marrow and cortical Cross-Sectional Area (CSA), Cortical Thickness (CoTh), both periosteal and endosteal circumference, as well as biomechanical parameters like Cross-Sectional Moment of Inertia (CSMI), a measure of bending, polar moment of inertia, indicating bone strength in torsion, and Strength Strain Index (SSI). Also CSA of muscle and fat can be extracted. Muscles, which are thought to stimulate bones to adapt their geometry and mineral content, are determinant to preserve or increase bone strength; thus, pQCT provides an evaluation of the functional 'muscle-bone unit', defined as BMC/muscle CSA ratio. This functional approach to bone densitometry can establish if bone strength is normally adapted to the muscle force, and if muscle force is adequate for body size, providing more detailed insights to targeted strategies for the prevention and treatment of bone fragility. The present paper offers an extensive review of technical features of pQCT and its possible clinical application in the diagnostic of bone status as well as in the monitoring of the skeleton's health follow-up.

  14. Bone mineral density in children and adolescents with juvenile diabetes: selective measurement of bone mineral density of trabecular and cortical bone using peripheral quantitative computed tomography.

    PubMed

    Lettgen, B; Hauffa, B; Möhlmann, C; Jeken, C; Reiners, C

    1995-01-01

    Bone mineral density (BMD) was studied in 21 children and adolescents with type I diabetes and in age- and sex-matched healthy controls. BMD was selectively measured in trabecular and total bone using peripheral quantitative computed tomography (pQCT). Cortical bone density was calculated. There was a decrease of trabecular bone density (-18.9%, p < 0.01), total bone density (-9.0%, NS) and cortical bone density (-5.1%, NS) in diabetes. Trabecular bone density was inversely correlated with the duration of diabetes and the concentration of glycosylated hemoglobin (HbA1) (r = -0.48, p = 0.027 and r = -0.63, p = 0.002, respectively). Total BMD correlated inversely with HbA1 (r = -0.52, p = 0.017). pQCT allows the selective measurement of metabolically active trabecular bone where changes of mineralization first occur. We conclude that pQCT is a useful method for investigating BMD in diabetes.

  15. Quantitative Analysis of Lens Nuclear Density Using Optical Coherence Tomography (OCT) with a Liquid Optics Interface: Correlation between OCT Images and LOCS III Grading

    PubMed Central

    Park, Jin Hyoung

    2016-01-01

    Purpose. To quantify whole lens and nuclear lens densities using anterior-segment optical coherence tomography (OCT) with a liquid optics interface and evaluate their correlation with Lens Opacities Classification System III (LOCS III) lens grading and corrected distance visual acuity (BCVA). Methods. OCT images of the whole lens and lens nucleus of eyes with age-related nuclear cataract were analyzed using ImageJ software. The lens grade and nuclear density were represented in pixel intensity units (PIU) and correlations between PIU, BCVA, and LOCS III were assessed. Results. Forty-seven eyes were analyzed. The mean whole lens and lens nuclear densities were 26.99 ± 5.23 and 19.43 ± 6.15 PIU, respectively. A positive linear correlation was observed between lens opacities (R2 = 0.187, p < 0.01) and nuclear density (R2 = 0.316, p < 0.01) obtained from OCT images and LOCS III. Preoperative BCVA and LOCS III were also positively correlated (R2 = 0.454, p < 0.01). Conclusions. Whole lens and lens nuclear densities obtained from OCT correlated with LOCS III. Nuclear density showed a higher positive correlation with LOCS III than whole lens density. OCT with a liquid optics interface is a potential quantitative method for lens grading and can aid in monitoring and managing age-related cataracts. PMID:27651952

  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

    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

    2014-10-08

    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.

  17. Non-invasive Assessment of Lower Limb Geometry and Strength Using Hip Structural Analysis and Peripheral Quantitative Computed Tomography: A Population-Based Comparison.

    PubMed

    Litwic, A E; Clynes, M; Denison, H J; Jameson, K A; Edwards, M H; Sayer, A A; Taylor, P; Cooper, C; Dennison, E M

    2016-02-01

    Hip fracture is the most significant complication of osteoporosis in terms of mortality, long-term disability and decreased quality of life. In the recent years, different techniques have been developed to assess lower limb strength and ultimately fracture risk. Here we examine relationships between two measures of lower limb bone geometry and strength; proximal femoral geometry and tibial peripheral quantitative computed tomography. We studied a sample of 431 women and 488 men aged in the range 59-71 years. The hip structural analysis (HSA) programme was employed to measure the structural geometry of the left hip for each DXA scan obtained using a Hologic QDR 4500 instrument while pQCT measurements of the tibia were obtained using a Stratec 2000 instrument in the same population. We observed strong sex differences in proximal femoral geometry at the narrow neck, intertrochanteric and femoral shaft regions. There were significant (p < 0.001) associations between pQCT-derived measures of bone geometry (tibial width; endocortical diameter and cortical thickness) and bone strength (strength strain index) with each corresponding HSA variable (all p < 0.001) in both men and women. These results demonstrate strong correlations between two different methods of assessment of lower limb bone strength: HSA and pQCT. Validation in prospective cohorts to study associations of each with incident fracture is now indicated.

  18. 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.

  19. Multi-scale, micro-computed tomography-based pore network models to simulate drainage in heterogeneous rocks

    NASA Astrophysics Data System (ADS)

    Bultreys, Tom; Van Hoorebeke, Luc; Cnudde, Veerle

    2015-04-01

    The multi-phase flow behavior of complex rocks with broad pore size distributions often digresses from classical relations. Pore-scale simulation methods can be a great tool to improve the understanding of this behavior. However, the broad range of pore sizes present makes it difficult to gather the experimental input data needed for these simulations and poses great computational challenges. We developed a novel micro-computed-tomography (micro-CT) based dual pore network model (DPNM), which takes microporosity into account in an upscaled fashion using symbolic network elements called micro-links, while treating the macroporosity as a traditional pore network model. The connectivity and conductivity of the microporosity is derived from local information measured on micro-CT scans. Microporous connectivity is allowed both in parallel and in series to the macropore network. We allow macropores to be drained as a consequence of their connection with microporosity, permitting simulations where the macropore network alone does not percolate. The validity of the method is shown by treating an artificial network and a network extracted from a micro-CT scan of Estaillades limestone.

  20. Atomically resolved tomography to directly inform simulations for structure-property relationships

    NASA Astrophysics Data System (ADS)

    Moody, Michael P.; Ceguerra, Anna V.; Breen, Andrew J.; Cui, Xiang Yuan; Gault, Baptiste; Stephenson, Leigh T.; Marceau, Ross K. W.; Powles, Rebecca C.; Ringer, Simon P.

    2014-11-01

    Microscopy encompasses a wide variety of forms and scales. So too does the array of simulation techniques developed that correlate to and build upon microstructural information. Nevertheless, a true nexus between microscopy and atomistic simulations is lacking. Atom probe has emerged as a potential means of achieving this goal. Atom probe generates three-dimensional atomistic images in a format almost identical to many atomistic simulations. However, this data is imperfect, preventing input into computational algorithms to predict material properties. Here we describe a methodology to overcome these limitations, based on a hybrid data format, blending atom probe and predictive Monte Carlo simulations. We create atomically complete and lattice-bound models of material specimens. This hybrid data can then be used as direct input into density functional theory simulations to calculate local energetics and elastic properties. This research demonstrates the role that atom probe combined with theoretical approaches can play in modern materials engineering.

  1. 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

  2. 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.

  3. Myocardial physiology measurements using contrast enhanced dynamic computed tomography: simulation of beam hardening effect

    NASA Astrophysics Data System (ADS)

    Cao, Minsong; Stantz, Keith M.; Liang, Yun

    2006-03-01

    Initial animal study for quantifying myocardial physiology through contrast-enhanced dynamic x-ray CT suggested that beam hardening is one of the limiting factors for accurate regional physiology measurement. In this study, a series of simulations were performed to investigate its deterioration effects and two correction algorithms were adapted to evaluate for their efficiency in improving the measurements. The simulation tool consists of a module simulating data acquisition of a real polyenergetic scanner system and a heart phantom consisting of simple geometric objects representing ventricles and myocardium. Each phantom component was modeled with time-varying attenuation coefficients determined by ideal iodine contrast dynamic curves obtained from experimental data or simulation. A compartment model was used to generate the ideal myocardium contrast curve using physiological parameters consistent with measured values. Projection data of the phantom were simulated and reconstructed to produce a sequence of simulated CT images. Simulated contrast dynamic curves were fitted to the compartmental model and the resultant physiological parameters were compared with ideal values to estimate the errors induced by beam hardening artifacts. The simulations yielded similar deterioration patterns of contrast dynamic curves as observed in the initial study. Significant underestimation of left ventricle curves and corruption of regional myocardium curves result in systematic errors of regional perfusion up to approximately 24% and overestimates of fractional blood volume (f iv) up to 13%. The correction algorithms lead to significant improvement with errors of perfusion reduced to 7% and errors of f iv within 2% which shows promise for more robust myocardial physiology measurement.

  4. 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

    2012-07-07

    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.

  5. Absolute electrical impedance tomography (aEIT) guided ventilation therapy in critical care patients: simulations and future trends.

    PubMed

    Denaï, Mouloud A; Mahfouf, Mahdi; Mohamad-Samuri, Suzani; Panoutsos, George; Brown, Brian H; Mills, Gary H

    2010-05-01

    Thoracic electrical impedance tomography (EIT) is a noninvasive, radiation-free monitoring technique whose aim is to reconstruct a cross-sectional image of the internal spatial distribution of conductivity from electrical measurements made by injecting small alternating currents via an electrode array placed on the surface of the thorax. The purpose of this paper is to discuss the fundamentals of EIT and demonstrate the principles of mechanical ventilation, lung recruitment, and EIT imaging on a comprehensive physiological model, which combines a model of respiratory mechanics, a model of the human lung absolute resistivity as a function of air content, and a 2-D finite-element mesh of the thorax to simulate EIT image reconstruction during mechanical ventilation. The overall model gives a good understanding of respiratory physiology and EIT monitoring techniques in mechanically ventilated patients. The model proposed here was able to reproduce consistent images of ventilation distribution in simulated acutely injured and collapsed lung conditions. A new advisory system architecture integrating a previously developed data-driven physiological model for continuous and noninvasive predictions of blood gas parameters with the regional lung function data/information generated from absolute EIT (aEIT) is proposed for monitoring and ventilator therapy management of critical care patients.

  6. Mixed quantitative/qualitative modeling and simulation of the cardiovascular system.

    PubMed

    Nebot, A; Cellier, F E; Vallverdú, M

    1998-02-01

    The cardiovascular system is composed of the hemodynamical system and the central nervous system (CNS) control. Whereas the structure and functioning of the hemodynamical system are well known and a number of quantitative models have already been developed that capture the behavior of the hemodynamical system fairly accurately, the CNS control is, at present, still not completely understood and no good deductive models exist that are able to describe the CNS control from physical and physiological principles. The use of qualitative methodologies may offer an interesting alternative to quantitative modeling approaches for inductively capturing the behavior of the CNS control. In this paper, a qualitative model of the CNS control of the cardiovascular system is developed by means of the fuzzy inductive reasoning (FIR) methodology. FIR is a fairly new modeling technique that is based on the general system problem solving (GSPS) methodology developed by G.J. Klir (Architecture of Systems Problem Solving, Plenum Press, New York, 1985). Previous investigations have demonstrated the applicability of this approach to modeling and simulating systems, the structure of which is partially or totally unknown. In this paper, five separate controller models for different control actuations are described that have been identified independently using the FIR methodology. Then the loop between the hemodynamical system, modeled by means of differential equations, and the CNS control, modeled in terms of five FIR models, is closed, in order to study the behavior of the cardiovascular system as a whole. The model described in this paper has been validated for a single patient only.

  7. Bone strength measured by peripheral quantitative computed tomography and the risk of nonvertebral fractures: the osteoporotic fractures in men (MrOS) study.

    PubMed

    Sheu, Yahtyng; Zmuda, Joseph M; Boudreau, Robert M; Petit, Moira A; Ensrud, Kristine E; Bauer, Douglas C; Gordon, Christopher L; Orwoll, Eric S; Cauley, Jane A

    2011-01-01

    Many fractures occur in individuals without osteoporosis defined by areal bone mineral density (aBMD). Inclusion of other aspects of skeletal strength may be useful in identifying at-risk subjects. We used surrogate measures of bone strength at the radius and tibia measured by peripheral quantitative computed tomography (pQCT) to evaluate their relationships with nonvertebral fracture risk. Femoral neck (FN) aBMD, measured by dual-energy X-ray absorptiometry (DXA), also was included. The study population consisted of 1143 white men aged 69+ years with pQCT measures at the radius and tibia from the Minneapolis and Pittsburgh centers of the Osteoporotic Fractures in Men (MrOS) study. Principal-components analysis and Cox proportional-hazards modeling were used to identify 21 of 58 pQCT variables with a major contribution to nonvertebral incident fractures. After a mean 2.9 years of follow-up, 39 fractures occurred. Men without incident fractures had significantly greater bone mineral content, cross-sectional area, and indices of bone strength than those with fractures by pQCT. Every SD decrease in the 18 of 21 pQCT parameters was significantly associated with increased fracture risk (hazard ration ranged from 1.4 to 2.2) independent of age, study site, body mass index (BMI), and FN aBMD. Using area under the receiver operation characteristics curve (AUC), the combination of FN aBMD and three radius strength parameters individually increased fracture prediction over FN aBMD alone (AUC increased from 0.73 to 0.80). Peripheral bone strength measures are associated with fracture risk and may improve our ability to identify older men at high risk of fracture.

  8. Quantitative assessment of electrical resistivity tomography for monitoring DNAPLs migration - Comparison with high-resolution light transmission visualization in laboratory sandbox

    NASA Astrophysics Data System (ADS)

    Deng, Yaping; Shi, Xiaoqing; Xu, Hongxia; Sun, Yuanyuan; Wu, Jichun; Revil, André

    2017-01-01

    Real-time monitoring of dense non-aqueous phase liquids (DNAPLs) migration and distribution is essential for the decision of an effective remediation strategy. Light transmission visualization (LTV) has shown its accuracy and efficiency for measuring DNAPLs saturation and water content in the laboratory, but it cannot be implemented in three dimensional sandbox or field-scale sites. Recently developed electrical resistivity tomography (ERT) has been applied in monitoring the migration and distribution of DNAPLs in bench- and field-scale studies. However, the evaluation of the ability of ERT for monitoring DNAPLs migration by a direct comparison of ERT with high-resolution techniques such as LTV within an experimental system is still lacking. Two sandbox experiments with different permeability conditions are conducted to quantitatively assess the capability of ERT for monitoring the DNAPLs migration. During the injections, LTV method is used to visualize the DNAPLs migration and provide high-resolution saturation data while ERT method is applied to capture the change of resistivity. The results from the comparison between LTV and ERT methods show that ERT is successful in detecting the accumulation and flow bypassing phenomenon around the low-permeability lenses, as well as the penetration through the high-permeability lenses. There is a fair correlation between the resistivity and saturation with overall correlation coefficients above 0.6, except at last stage. However, using classical regularization techniques (based on smoothness), the area of DNAPLs plume determined by ERT is commonly overestimated. Compared to the plume around the low-permeability lenses, the plume around the high-permeability lenses estimated by ERT is more extensive due to larger resistivity contrasts. In addition, ERT measurements indicate that the resistivity increase caused by the low-saturation DNAPLs is not apparent enough, which is likely to be covered up under the changing

  9. 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.

  10. 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 Central

    Edwards, MH; Robinson, DE; Ward, KA; Javaid, MK; Walker-Bone, K; Cooper, C; Dennison, EM

    2016-01-01

    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

  11. 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.

  12. 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.

  13. 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.

  14. Use of mechanistic simulations as a quantitative risk-ranking tool within the quality by design framework.

    PubMed

    Stocker, Elena; Toschkoff, Gregor; Sacher, Stephan; Khinast, Johannes G

    2014-11-20

    The purpose of this study is to evaluate the use of computer simulations for generating quantitative knowledge as a basis for risk ranking and mechanistic process understanding, as required by ICH Q9 on quality risk management systems. In this specific publication, the main focus is the demonstration of a risk assessment workflow, including a computer simulation for the generation of mechanistic understanding of active tablet coating in a pan coater. Process parameter screening studies are statistically planned under consideration of impacts on a potentially critical quality attribute, i.e., coating mass uniformity. Based on computer simulation data the process failure mode and effects analysis of the risk factors is performed. This results in a quantitative criticality assessment of process parameters and the risk priority evaluation of failure modes. The factor for a quantitative reassessment of the criticality and risk priority is the coefficient of variation, which represents the coating mass uniformity. The major conclusion drawn from this work is a successful demonstration of the integration of computer simulation in the risk management workflow leading to an objective and quantitative risk assessment.

  15. Patient-Specific Simulation of Cardiac Blood Flow From High-Resolution Computed Tomography.

    PubMed

    Lantz, Jonas; Henriksson, Lilian; Persson, Anders; Karlsson, Matts; Ebbers, Tino

    2016-12-01

    Cardiac hemodynamics can be computed from medical imaging data, and results could potentially aid in cardiac diagnosis and treatment optimization. However, simulations are often based on simplified geometries, ignoring features such as papillary muscles and trabeculae due to their complex shape, limitations in image acquisitions, and challenges in computational modeling. This severely hampers the use of computational fluid dynamics in clinical practice. The overall aim of this study was to develop a novel numerical framework that incorporated these geometrical features. The model included the left atrium, ventricle, ascending aorta, and heart valves. The framework used image registration to obtain patient-specific wall motion, automatic remeshing to handle topological changes due to the complex trabeculae motion, and a fast interpolation routine to obtain intermediate meshes during the simulations. Velocity fields and residence time were evaluated, and they indicated that papillary muscles and trabeculae strongly interacted with the blood, which could not be observed in a simplified model. The framework resulted in a model with outstanding geometrical detail, demonstrating the feasibility as well as the importance of a framework that is capable of simulating blood flow in physiologically realistic hearts.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. Optimization of beam quality for photon-counting spectral computed tomography in head imaging: simulation study

    PubMed Central

    Chen, Han; Xu, Cheng; Persson, Mats; Danielsson, Mats

    2015-01-01

    Abstract. 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 (5  mg/mL) were studied. Three parameters that affect beam quality were evaluated: kVp settings (50 to 130 kVp), filter materials (Z=13 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 (SDNR2/BD) and that normalized by skin dose (SDNR2/SD). For nonenhanced imaging, the results show that the use of the 120-kVp spectrum filtered by 2 HVL copper (Z=29) provides the best performance in both FOMs. When iodine is used in K-edge imaging, the optimal filter is 2 HVL iodine (Z=53) and the optimal kVps are 60 kVp in terms of SDNR2/BD and 75 kVp in terms of SDNR2/SD. A tradeoff of 65 kVp was proposed to lower the potential risk of skin injuries if a

  1. Computer tomography prototyping and virtual procedure simulation in difficult cases of hip replacement surgery.

    PubMed

    Parchi, Paolo Domenico; Ferrari, Vincenzo; Piolanti, Nicola; Andreani, Lorenzo; Condino, Sara; Evangelisti, Gisberto; Lisanti, Michele

    2013-09-01

    Each year approximately 1 million total hip replacements (THR) are performed worldwide. A percentage of failure due to surgical approach and imprecise implant placement still exists. These result in several serious complications. We propose an approach to plan, to simulate, and to assist prosthesis implantation for difficult cases of THR based on 3-D virtual models, generated by segmenting patients' CT images, 3-D solid models, obtained by rapid prototyping (RP), and virtual procedure simulation. We carried out 8 THR with the aid of 3-D reconstruction and RP. After each procedure a questionnaire was submitted to the surgeon to assess the perceived added value of the technology. In all cases, the surgeon evaluated the 3-D model as useful in order to perform the planning. The clinical results showed a mean increase in the Harris Hip Score of about 42.5 points. The mean time of prototyping was 7.3 hours, (min 3.5 hours, max 9.3 hours). The mean surgery time was 65 minutes (min 50 minutes, max 88 minutes). Our study suggests that meticulous preoperative planning is necessary in front of a great aberration of the joint and in absence of normal anatomical landmarks, CT scan is mandatory, and 3-D reconstruction with solid model is useful.

  2. 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

    2014-03-06

    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.

  3. 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.

  4. A multi-scale Lattice Boltzmann model for simulating solute transport in 3D X-ray micro-tomography images of aggregated porous materials

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoxian; Crawford, John W.; Flavel, Richard J.; Young, Iain M.

    2016-10-01

    The Lattice Boltzmann (LB) model and X-ray computed tomography (CT) have been increasingly used in combination over the past decade to simulate water flow and chemical transport at pore scale in porous materials. Because of its limitation in resolution and the hierarchical structure of most natural soils, the X-ray CT tomography can only identify pores that are greater than its resolution and treats other pores as solid. As a result, the so-called solid phase in X-ray images may in reality be a grey phase, containing substantial connected pores capable of conducing fluids and solute. Although modified LB models have been developed to simulate fluid flow in such media, models for solute transport are relatively limited. In this paper, we propose a LB model for simulating solute transport in binary soil images containing permeable solid phase. The model is based on the single-relaxation time approach and uses a modified partial bounce-back method to describe the resistance caused by the permeable solid phase to chemical transport. We derive the relationship between the diffusion coefficient and the parameter introduced in the partial bounce-back method, and test the model against analytical solution for movement of a pulse of tracer. We also validate it against classical finite volume method for solute diffusion in a simple 2D image, and then apply the model to a soil image acquired using X-ray tomography at resolution of 30 μm in attempts to analyse how the ability of the solid phase to diffuse solute at micron-scale affects the behaviour of the solute at macro-scale after a volumetric average. Based on the simulated results, we discuss briefly the danger in interpreting experimental results using the continuum model without fully understanding the pore-scale processes, as well as the potential of using pore-scale modelling and tomography to help improve the continuum models.

  5. A 19-week exercise program for people with chronic stroke enhances bone geometry at the tibia: a peripheral quantitative computed tomography study

    PubMed Central

    Pang, Marco YC; Ashe, Maureen C.; Eng, Janice J.; McKay, Heather A.; Dawson, Andrew S.

    2011-01-01

    Introduction and Hypothesis Regular skeletal-loading exercise is an effective intervention to improve bone health in older individuals. However, little is known about the bone responses to exercise in people with stroke. Following a stroke, muscle atrophy and bone loss occurs. Diminished areal bone mineral density combined with an increased number of falls substantially enhances the risk for a fragility fracture. We undertook a randomized controlled intervention trial to assess the impact of a 19-week comprehensive exercise program on lower extremity bone health in people with chronic stroke. Methods Sixty-three community-dwelling individuals with chronic stroke were randomly allocated to either an intervention group or a control group. The intervention group participated in a 19-week thrice-weekly exercise program consisting of skeletal-loading, aerobic, strengthening and balance exercises. The control group completed a seated upper extremity exercise program. We used peripheral quantitative computed tomography (pQCT) to measure bone geometry and volumetric bone mineral density at the distal 4% and midshaft 50% of the tibia before and after the intervention. Results Following the exercise program, the intervention group had significantly more percent gain in trabecular bone content at the 4% site on the paretic side than the control group (p=0.048). At the 50% site on the paretic side, the intervention group also had significantly greater percent gain in cortical thickness (p=0.026) but not the polar stress strain index (p-SSI) when compared with the control group. However, no significant between-group difference was found in trabecular bone density (4% site) and cortical bone density (50% site) percent gain on the paretic side. No significant changes were observed in any variables on the non-paretic side at the 4% or 50% site. Conclusions This study provided some evidence that the 19-week comprehensive exercise program could have a positive impact on bone

  6. A Critical Comparison Between Two Scanning Protocols of High-Resolution Peripheral Quantitative Computed Tomography at the Distal Radius in Adolescents.

    PubMed

    Cheuk, Ka-Yee; Tam, Elisa Man-Shan; Yu, Fiona Wai-Ping; Yip, Benjamin Hon-Kei; Hung, Vivian Wing-Yin; Wang, Xiaofang; Ghasem-Zadeh, Ali; Zhu, Tracy Y; Qin, Ling; Cheng, Jack Chun-Yiu; Lam, Tsz-Ping

    2016-01-01

    High-resolution peripheral quantitative computed tomography (HR-pQCT) is a unique technology for assessing bone mineral density and bone microarchitecture. Currently, no universally accepted protocol for selecting the region of interest (ROI) at the distal radius has been established for growing subjects. This study aimed (1) to investigate the differences in HR-pQCT measurements of 2 different ROI protocols applied to the distal radius of healthy adolescents and (2) to identify the least common area of ROI (the least common ROI) between the protocols. Twenty-six boys and 26 girls aged between 13 and 16 yr old were recruited. Nondominant distal radius was scanned by 2 HR-pQCT protocols, namely, the "5-mm protocol," where the distal end of ROI started at 5 mm proximal to a reference line, and the "4% protocol," where the ROI started at 4% of the ulnar length proximal to another reference line. The least common ROI between the 2 protocols was identified and the slice numbering within the common ROI was determined. Bland-Altman plots were used to check the agreement of the least common ROIs between the 2 protocols. Paired t-test and Wilcoxon signed-rank test were used for analysis. In boys, significant differences between protocols were found in most parameters with the maximum difference observed in the cortical area (25.0%, p < 0.001). In girls, differences were observed only for total volumetric bone mineral density (3.6%, p = 0.032). The number of slices in the least common ROI was 66 (60.0%) and 57 (51.8%) in boys and girls, respectively. Good agreements on all HR-pQCT parameters from the least common ROI between the 2 protocols were found. Significant differences in bone parameters were noted between the 2 protocols. When comparing the 2 protocols, observed gender differences could reflect the differences in skeletal growth at the peripubertal period between genders. Least common ROI could be useful for cross-center comparisons and when merging

  7. Quantitative myocardial perfusion SPECT.

    PubMed

    Tsui, B M; Frey, E C; LaCroix, K J; Lalush, D S; McCartney, W H; King, M A; Gullberg, G T

    1998-01-01

    In recent years, there has been much interest in the clinical application of attenuation compensation to myocardial perfusion single photon emission computed tomography (SPECT) with the promise that accurate quantitative images can be obtained to improve clinical diagnoses. The different attenuation compensation methods that are available create confusion and some misconceptions. Also, attenuation-compensated images reveal other image-degrading effects including collimator-detector blurring and scatter that are not apparent in uncompensated images. This article presents basic concepts of the major factors that degrade the quality and quantitative accuracy of myocardial perfusion SPECT images, and includes a discussion of the various image reconstruction and compensation methods and misconceptions and pitfalls in implementation. The differences between the various compensation methods and their performance are demonstrated. Particular emphasis is directed to an approach that promises to provide quantitative myocardial perfusion SPECT images by accurately compensating for the 3-dimensional (3-D) attenuation, collimator-detector response, and scatter effects. With advances in the computer hardware and optimized implementation techniques, quantitatively accurate and high-quality myocardial perfusion SPECT images can be obtained in clinically acceptable processing time. Examples from simulation, phantom, and patient studies are used to demonstrate the various aspects of the investigation. We conclude that quantitative myocardial perfusion SPECT, which holds great promise to improve clinical diagnosis, is an achievable goal in the near future.

  8. Comparison of retrieved noctilucent cloud particle properties from Odin tomography scans and model simulations

    NASA Astrophysics Data System (ADS)

    Megner, Linda; Christensen, Ole M.; Karlsson, Bodil; Benze, Susanne; Fomichev, Victor I.

    2016-12-01

    Mesospheric ice particles, known as noctilucent clouds or polar mesospheric clouds, have long been observed by rocket instruments, satellites and ground-based remote sensing, while models have been used to simulate ice particle growth and cloud properties. However, the fact that different measurement techniques are sensitive to different parts of the ice particle distribution makes it difficult to compare retrieved parameters such as ice particle radius or ice concentration from different experiments. In this work we investigate the accuracy of satellite retrieval based on scattered light and how this affects derived cloud properties. We apply the retrieval algorithm on spectral signals calculated from modelled cloud distributions and compare the results to the properties of the original distributions. We find that ice mass density is accurately retrieved whereas mean radius is often overestimated and high ice concentrations are generally underestimated. The reason is partly that measurements based on scattered light are insensitive to the smaller particles and partly that the retrieval algorithm assumes a Gaussian size distribution. Once we know the limits of the satellite retrieval we proceed to compare the properties retrieved from the modelled cloud distributions to those observed by the Optical, Spectroscopic, and Infrared Remote Imaging System (OSIRIS) instrument on the Odin satellite. We find that a model with a stationary atmosphere, as given by average atmospheric conditions, does not yield cloud properties that are in agreement with the observations, whereas a model with realistic temperature and vertical wind variations does. This indicates that average atmospheric conditions are insufficient to understand the process of noctilucent cloud growth and that a realistic atmospheric variability is crucial for cloud formation and growth. Further, the agreement between results from the model, when set up with a realistically variable atmosphere, and the

  9. Spectral simulation methods for enhancing qualitative and quantitative analyses based on infrared spectroscopy and quantitative calibration methods for passive infrared remote sensing of volatile organic compounds

    NASA Astrophysics Data System (ADS)

    Sulub, Yusuf Ismail

    Infrared spectroscopy (IR) has over the years found a myriad of applications including passive environmental remote sensing of toxic pollutants and the development of a blood glucose sensor. In this dissertation, capabilities of both these applications are further enhanced with data analysis strategies employing digital signal processing and novel simulation approaches. Both quantitative and qualitative determinations of volatile organic compounds are investigated in the passive IR remote sensing research described in this dissertation. In the quantitative work, partial least-squares (PLS) regression analysis is used to generate multivariate calibration models for passive Fourier transform IR remote sensing measurements of open-air generated vapors of ethanol in the presence methanol as an interfering species. A step-wise co-addition scheme coupled with a digital filtering approach is used to attenuate the effects of variation in optical path length or plume width. For the qualitative study, an IR imaging line scanner is used to acquire remote sensing data in both spatial and spectral domains. This technology is capable of not only identifying but also specifying the location of the sample under investigation. Successful implementation of this methodology is hampered by the huge costs incurred to conduct these experiments and the impracticality of acquiring large amounts of representative training data. To address this problem, a novel simulation approach is developed that generates training data based on synthetic analyte-active and measured analyte-inactive data. Subsequently, automated pattern classifiers are generated using piecewise linear discriminant analysis to predict the presence of the analyte signature in measured imaging data acquired in remote sensing applications. Near infrared glucose determinations based on the region of 5000--4000 cm-1 is the focus of the research in the latter part of this dissertation. A six-component aqueous matrix of glucose

  10. 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.

  11. Dual energy exposure control (DEEC) for computed tomography: Algorithm and simulation study

    SciTech Connect

    Stenner, Philip; Kachelriess, Marc

    2008-11-15

    DECT means acquiring the same object at two different energies, respectively two different tube voltages U{sub 1} and U{sub 2}. The raw data q{sub 1} and q{sub 2} undergo a decomposition process of type p=p(q{sub 1},q{sub 2}). The raw data p are reconstructed to obtain monochromatic images of the attenuation {mu}, of the object density {rho}, or of a specific material distribution. Recent advances in DECT focus on noise reduction techniques [S. Richard and J. H. Siewerdsen, Med. Phys. 35(2), 586-600 (2008)] and enable high performance DECT such as lung nodule detection [Shkumat et al., Med. Phys. 35(2), 629-632 (2008)]. Given p and a raw data-based projection-wise patient dose estimation D({alpha}) the authors determine the optimal tube current curves I{sub 1}({alpha}) and I{sub 2}({alpha}), with {alpha} being the view angle, which minimizes image noise for a given patient dose level. DEEC can perform online; I{sub 1}({alpha}) and I{sub 2}({alpha}) can be determined during the scan. Simulation studies using semianthropomorphic phantom data were carried out. In particular, functions p that generate {mu}-images and density images were evaluated. Image quality was compared to standard scans at U{sub 0}=120 kV (clinical CT) and U{sub 0}=45 kV (micro-CT) that were taken at the same dose level (D{sub 0}=D{sub 1}+D{sub 2}) and identical spatial resolution. Appropriate choice of p(q{sub 1},q{sub 2}) allows to obtain {mu}-images that show fewer artifacts and yield image noise levels comparable to the noise of the standard scan. The authors compared the standard scan to {mu}-images at 70 keV, which is the effective energy used in clinical CT, and found optimal results with {mu}-images at 25 keV for micro-CT. Nonoptimal choice of the decomposition function will, however, significantly increase image noise. In particular {mu}-images at 511 keV, as needed for PET/CT attenuation correction, exhibit more than twice as much image noise as the standard scan. With DEEC, which

  12. Quantitative risk assessment integrated with process simulator for a new technology of methanol production plant using recycled CO₂.

    PubMed

    Di Domenico, Julia; Vaz, Carlos André; de Souza, Maurício Bezerra

    2014-06-15

    The use of process simulators can contribute with quantitative risk assessment (QRA) by minimizing expert time and large volume of data, being mandatory in the case of a future plant. This work illustrates the advantages of this association by integrating UNISIM DESIGN simulation and QRA to investigate the acceptability of a new technology of a Methanol Production Plant in a region. The simulated process was based on the hydrogenation of chemically sequestered carbon dioxide, demanding stringent operational conditions (high pressures and temperatures) and involving the production of hazardous materials. The estimation of the consequences was performed using the PHAST software, version 6.51. QRA results were expressed in terms of individual and social risks. Compared to existing tolerance levels, the risks were considered tolerable in nominal conditions of operation of the plant. The use of the simulator in association with the QRA also allowed testing the risk in new operating conditions in order to delimit safe regions for the plant.

  13. NOTE: The use of molecular sieves to simulate hot lesions in 18F-fluorodeoxyglucose—positron emission tomography imaging

    NASA Astrophysics Data System (ADS)

    Matheoud, R.; Secco, C.; Ridone, S.; Inglese, E.; Brambilla, M.

    2008-04-01

    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 18F-fluorodeoxyglucose (18F-FDG) uptake of a group of 12 zeolites was studied as a function of their weight (120-1520 mg) and of the activity concentration of the 18F-FDG solution (1-37 MBq ml-1), using a multiple linear regression model. The reproducibility, homogeneity and stability over time of the 18F-FDG uptake were assessed. The fit of the regression model is good (r2 = 0.83). This relation allows the production of zeolites of a desired 18F-FDG activity using knowledge of the concentration of the soaking solution and the weight of the zeolite. The reproducibility of the 18F-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 18F-FDG uptake on zeolites is far from ideal. When placed in a saline solution the 'activated' zeolites release the 18F-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 18F-FDG. These features, together with their variable dimensions and shapes, make them ideal 18F-FDG sources with a fixed target-to-background ratio that can be placed anywhere in a phantom to study lesion detectability in PET imaging.

  14. Can a quantitative simulation of an Otto engine be accurately rendered by a simple Novikov model with heat leak?

    NASA Astrophysics Data System (ADS)

    Fischer, A.; Hoffmann, K.-H.

    2004-03-01

    In this case study a complex Otto engine simulation provides data including, but not limited to, effects from losses due to heat conduction, exhaust losses and frictional losses. This data is used as a benchmark to test whether the Novikov engine with heat leak, a simple endoreversible model, can reproduce the complex engine behavior quantitatively by an appropriate choice of model parameters. The reproduction obtained proves to be of high quality.

  15. Quantitative Modeling of Entangled Polymer Rheology: Experiments, Tube Models and Slip-Link Simulations

    NASA Astrophysics Data System (ADS)

    Desai, Priyanka Subhash

    Rheology properties are sensitive indicators of molecular structure and dynamics. The relationship between rheology and polymer dynamics is captured in the constitutive model, which, if accurate and robust, would greatly aid molecular design and polymer processing. This dissertation is thus focused on building accurate and quantitative constitutive models that can help predict linear and non-linear viscoelasticity. In this work, we have used a multi-pronged approach based on the tube theory, coarse-grained slip-link simulations, and advanced polymeric synthetic and characterization techniques, to confront some of the outstanding problems in entangled polymer rheology. First, we modified simple tube based constitutive equations in extensional rheology and developed functional forms to test the effect of Kuhn segment alignment on a) tube diameter enlargement and b) monomeric friction reduction between subchains. We, then, used these functional forms to model extensional viscosity data for polystyrene (PS) melts and solutions. We demonstrated that the idea of reduction in segmental friction due to Kuhn alignment is successful in explaining the qualitative difference between melts and solutions in extension as revealed by recent experiments on PS. Second, we compiled literature data and used it to develop a universal tube model parameter set and prescribed their values and uncertainties for 1,4-PBd by comparing linear viscoelastic G' and G" mastercurves for 1,4-PBds of various branching architectures. The high frequency transition region of the mastercurves superposed very well for all the 1,4-PBds irrespective of their molecular weight and architecture, indicating universality in high frequency behavior. Therefore, all three parameters of the tube model were extracted from this high frequency transition region alone. Third, we compared predictions of two versions of the tube model, Hierarchical model and BoB model against linear viscoelastic data of blends of 1,4-PBd

  16. 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.

  17. 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

  18. Three-dimensional noninvasive ultrasound Joule heat tomography based on the acousto-electric effect using unipolar pulses: a simulation study.

    PubMed

    Yang, Renhuan; Li, Xu; Song, Aiguo; He, Bin; Yan, Ruqiang

    2012-11-21

    Electrical properties of biological tissues are highly sensitive to their physiological and pathological status. Thus it is of importance to image electrical properties of biological tissues. However, spatial resolution of conventional electrical impedance tomography (EIT) is generally poor. Recently, hybrid imaging modalities combining electric conductivity contrast and ultrasonic resolution based on the acousto-electric effect has attracted considerable attention. In this study, we propose a novel three-dimensional (3D) noninvasive ultrasound Joule heat tomography (UJHT) approach based on the acousto-electric effect using unipolar ultrasound pulses. As the Joule heat density distribution is highly dependent on the conductivity distribution, an accurate and high-resolution mapping of the Joule heat density distribution is expected to give important information that is closely related to the conductivity contrast. The advantages of the proposed ultrasound Joule heat tomography using unipolar pulses include its simple inverse solution, better performance than UJHT using common bipolar pulses and its independence of a priori knowledge of the conductivity distribution of the imaging object. Computer simulation results show that using the proposed method, it is feasible to perform a high spatial resolution Joule heat imaging in an inhomogeneous conductive media. Application of this technique on tumor scanning is also investigated by a series of computer simulations.

  19. 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.

  20. Simulation of evaporation by an extension of the pseudopotential lattice Boltzmann method: a quantitative analysis.

    PubMed

    Márkus, Attila; Házi, Gábor

    2011-04-01

    An extension of the pseudopotential lattice Boltzmann method is introduced to simulate heat transfer problems involving phase transition. Using this model, evaporation through a plane interface and two-phase Poiseuille flow were simulated and the macroscopic jump conditions were utilized to evaluate the accuracy of the method. We have found that the simulation results are in very good agreement with the analytical solutions as far as we take into account the extent of the interface during the evaluation. Using the same model heterogeneous boiling was simulated taking into account the geometry of a cavity and the important features of the boiling process could be observed in the simulation results.

  1. 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.

  2. 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…

  3. 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…

  4. The development of a quantitative evaluation tool for simulations in nursing education.

    PubMed

    Todd, Martha; Manz, Julie A; Hawkins, Kim S; Parsons, Mary E; Hercinger, Maribeth

    2008-01-01

    In a complex healthcare environment, educating nursing students to safely care for clients is a challenging endeavor. As the use of high fidelity simulations increases, the ability to evaluate students is essential. A review of the literature identified a lack of tested simulation evaluation instruments to accurately measure student performance. A simulation evaluation tool was developed and tested with senior nursing students. Content validity was established from the literature and from the review of the tool by an expert panel. Reliability was established using sixteen simulation sessions, with two trained evaluators at each session. Percent agreement by evaluators ranged from 84.4% to 89.1%. Additional research needs to verify these results with different evaluators, varying levels of students, and additional scenarios. A valid, reliable tool to evaluate simulation experiences improves student assessment skills and ultimately clinical performance.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. A method of simulating polarization-sensitive optical coherence tomography based on a polarization-sensitive Monte Carlo program and a sphere cylinder birefringence model

    NASA Astrophysics Data System (ADS)

    Chen, Dongsheng; Zeng, Nan; Liu, Celong; Ma, Hui

    2012-12-01

    In this paper, we present a new method to simulate the signal of polarization-sensitive optical coherence tomography (for short, PS-OCT) by the use of the sphere cylinder birefringence Monte Carlo program developed by our laboratory. Using the program, we can simulate various turbid media based on different optical models and analyze the scattering and polarization information of the simulated media. The detecting area and angle range and the scattering times of the photons are three main conditions we can use to screen out the photons which contribute to the signal of PS-OCT, and in this paper, we study the effects of these three factors on simulation results using our program, and find that the scattering times of the photon is the main factor to affect the signal, and the detecting area and angle range are less important but necessary conditions. In order to test and verify the feasibility of our simulation, we use two methods as a reference. One is called Extended Huygens Fresnel (for short, EHF) method, which is based on electromagnetism theory and can describe the single scattering and multiple scattering of light. By comparison of the results obtained from EHF method and ours, we explore the screening regularities of the photons in the simulation. Meanwhile, we also compare our simulation with another polarization related simulation presented by a Russian group, and our experimental results. Both the comparisons find that our simulation is efficient for PS-OCT at the superficial depth range, and should be further corrected in order to simulate the signal of PS-OCT at deeper depth.

  10. Experimental determination of thermal profiles during laser spike annealing with quantitative comparison to 3-dimensional simulations

    SciTech Connect

    Iyengar, Krishna; Jung, Byungki; Willemann, Michael; Thompson, Michael O.; Clancy, Paulette

    2012-05-21

    Thin film platinum resistors were used to directly measure temperature profiles during laser spike annealing (LSA) with high spatial and temporal resolution. Observed resistance changes were calibrated to absolute temperatures using the melting points of the substrate silicon and thin gold films. Both the time-dependent temperature experienced by the sample during passage of the focussed laser beam and profiles across the spatially dependent laser intensity were obtained with sub-millisecond time resolution and 50 {mu}m spatial resolution. Full 3-dimensional simulations incorporating both optical and thermal variations of material parameters were compared with these results. Accounting properly for the specific material parameters, good agreement between experiments and simulations was achieved. Future temperature measurements in complex environments will permit critical evaluation of LSA simulations methodologies.

  11. 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.

  12. Incorporating Quantitative Single Photon Emission Computed Tomography into Radiation Therapy Treatment Planning for Lung Cancer: Impact of Attenuation and Scatter Correction on the Single Photon Emission Computed Tomography-Weighted Mean Dose and Functional Lung Segmentation

    SciTech Connect

    Yin Lingshu; Shcherbinin, Sergey; Celler, Anna

    2010-10-01

    Purpose: To assess the impact of attenuation and scatter corrections on the calculation of single photon emission computed tomography (SPECT)-weighted mean dose (SWMD) and functional volume segmentation as applied to radiation therapy treatment planning for lung cancer. Methods and Materials: Nine patients with lung cancer underwent a SPECT lung perfusion scan. For each scan, four image sets were reconstructed using the ordered subsets expectation maximization method with attenuation and scatter corrections ranging from none to a most comprehensive combination of attenuation corrections and direct scatter modeling. Functional volumes were segmented in each reconstructed image using 10%, 20%, ..., 90% of maximum SPECT intensity as a threshold. Systematic effects of SPECT reconstruction methods on treatment planning using functional volume were studied by calculating size and spatial agreements of functional volumes, and V{sub 20} for functional volume from actual treatment plans. The SWMD was calculated for radiation beams with a variety of possible gantry angles and field sizes. Results: Functional volume segmentation is sensitive to the particular method of SPECT reconstruction used. Large variations in functional volumes, as high as >50%, were observed in SPECT images reconstructed with different attenuation/scatter corrections. However, SWMD was less sensitive to the type of scatter corrections. SWMD was consistent within 2% for all reconstructions as long as computed tomography-based attenuation correction was used. Conclusion: When using perfusion SPECT images during treatment planning optimization/evaluation, the SWMD may be the preferred figure of merit, as it is less affected by reconstruction technique, compared with threshold-based functional volume segmentation.

  13. Quantitative assessment of touch-screen panel by nondestructive inspection with three-dimensional real-time display optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Cho, Nam Hyun; Park, Kibeom; Kim, Jae-Young; Jung, Yeongri; Kim, Jeehyun

    2015-05-01

    We investigated the use of optical coherence tomography (OCT) to measure several materials immersed in optical adhesives. The effects of variations in the concentration, physical characteristics, and thickness of the materials were studied, and these parameters were found to significantly affect the OCT measurement. The materials were selected for their distinct spectral properties in the infrared region. To ensure reliability, we acquired images using a scanning electron microscope after performing the semiconductor production process. We verified the feasibility of the application of OCT for defect inspection and product verification of touch-screen panels.

  14. 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

  15. 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

  16. 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

  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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. Quadrant Analysis of Quantitative Computed Tomography Scans of the Femoral Neck Reveals Superior Region-Specific Weakness in Young and Middle-Aged Men With Type 1 Diabetes Mellitus.

    PubMed

    Kuroda, Takuma; Ishikawa, Koji; Nagai, Takashi; Fukui, Tomoyasu; Hirano, Tsutomu; Inagaki, Katsunori

    2017-03-13

    We have previously shown that the intertrochanter of young and middle-aged patients with type 1 diabetes mellitus (T1DM) showed higher buckling ratio (an index of cortical instability) and lower volumetric bone mineral density (vBMD). However, we have not yet reported the detailed findings regarding the mechanical and density properties of the femoral neck. Therefore, we present a subanalysis of our previous study with the aim of further evaluating the middle third of the femoral neck via quadrant quantitative computed tomography in young and middle-aged patients with T1DM. Bone parameters in 4 anatomical quadrants (superoanterior [SA], inferoanterior [IA], inferoposterior [IP], and superoposterior [SP]) were cross-sectionally evaluated in 17 male T1DM patients and 18 sex-matched healthy controls aged between 18 and 49 yr using quadrant quantitative computed tomography analysis. Patients with T1DM had a thinner cortical thickness in the SP quadrant and a significantly lower cortical vBMD in the SA quadrant than the controls. The serum insulin-like growth factor-1 values in patients with T1DM were positively correlated with the average cortical thickness in the SA quadrant and the average trabecular vBMD in the SP quadrant of the femoral neck. The cortical thickness in controls was negatively correlated with age in the SP and IP quadrants. The cortical thickness in patients with T1DM showed no correlation with age in all quadrants. The fragility of the femoral neck was remarkable in the superior region of patients with T1DM. Insulin-like growth factor-1 may play an important role in superior cortical thinning and in lowering cortical vBMD. Furthermore, in young and middle-aged men with T1DM, the structure of the femoral neck exhibits similar changes as those observed with aging.

  3. Evaluation of fourier transform profilometry performance: quantitative waste volume determination under simulated Hanford waste tank conditions

    SciTech Connect

    Jang, Ping-Rey; Leone, Teresa; Long, Zhiling; Mott, Melissa A.; Perry Norton, O.; Okhuysen, Walter P.; Monts, David L.

    2007-07-01

    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 have completed a preliminary 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. Based on a Hanford C-200 series tank with camera access through a riser with significant offset relative to the centerline, we devised a testing methodology that encompassed a range of obstacles likely to be encountered 'in tank'. These test objects were inspected by use

  4. Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: quantitative correlation with experiment.

    PubMed

    Strockbine, Bentley; Rizzo, Robert C

    2007-05-15

    Peptides based on C-terminal regions of the human immunodeficiency virus (HIV) viral protein gp41 represent an important new class of antiviral therapeutics called peptide fusion inhibitors. In this study, computational methods were used to model the binding of six peptides that contain residues that pack into a conserved hydrophobic pocket on HIVgp41, an attractive target site for the development of small molecule inhibitors. Free energies of binding were computed using molecular mechanics Generalized Born surface area (MM-GBSA) methods from molecular dynamics (MD) simulations, which employed either explicit (TIP3P) or continuum Generalized Born (GB) water models and strong correlations between experimental and computational affinities were obtained in both cases. Energy decomposition of the TIP3P-MD results (r2 = 0.75) reveals that variation in experimental affinity is highly correlated with changes in intermolecular van der Waals energies (deltaE(vdw)) on both a local (residue-based, r2 = 0.94) and global (peptide-based, r2 = 0.84) scale. The results show that differential association of C-peptides with HIVgp41 is driven solely by changes within the conserved pocket supporting the hypothesis that this region is an important drug target site. Such strong agreement with experiment is notable given the large size of the ligands (34 amino-acids) relative to the small range of experimental affinities (2 kcal/mol) and demonstrates good sensitivity of this computational method for simulating peptide fusion inhibitors. Finally, inspection of simulation trajectories identified a highly populated pi-type hydrogen bond, which formed between Gln575 on the receptor and the aromatic ring of peptide ligand Phe631, which could have important implications for drug design.

  5. 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.

  6. 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

  7. 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.

  8. Quantitative model for the heterogeneity of atomic position fluctuations in proteins: A simulation study

    SciTech Connect

    Kneller, Gerald R.; Hinsen, Konrad

    2009-07-28

    We propose a simple analytical model for the elastic incoherent structure factor of proteins measured by neutron scattering, which allows extracting the distribution of atomic position fluctuations from a fit of the model to the experimental data. The method is validated by applying it to elastic incoherent structure factors of lysozyme which have been obtained by molecular dynamics simulation and by normal mode analysis, respectively, and for which distributions of the atomic position fluctuations can be generated numerically for direct comparison with the predictions of the model. The comparison shows a remarkable agreement, in particular, concerning the lower limit for the position fluctuations, which is pronounced in the numerical data.

  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. Classification of basal cell carcinoma in human skin using machine learning and quantitative features captured by polarization sensitive optical coherence tomography

    PubMed Central

    Marvdashti, Tahereh; Duan, Lian; Aasi, Sumaira Z.; Tang, Jean Y.; Ellerbee Bowden, Audrey K.

    2016-01-01

    We report the first fully automated detection of basal cell carcinoma (BCC), the most commonly occurring type of skin cancer, in human skin using polarization-sensitive optical coherence tomography (PS-OCT). Our proposed automated procedure entails building a machine-learning based classifier by extracting image features from the two complementary image contrasts offered by PS-OCT, intensity and phase retardation (PR), and selecting a subset of features that yields a classifier with the highest accuracy. Our classifier achieved 95.4% sensitivity and specificity, validated by leave-one-patient-out cross validation (LOPOCV), in detecting BCC in human skin samples collected from 42 patients. Moreover, we show the superiority of our classifier over the best possible classifier based on features extracted from intensity-only data, which demonstrates the significance of PR data in detecting BCC. PMID:27699133

  11. 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.

  12. Quantitative prediction of charge mobilities of π-stacked systems by first-principles simulation.

    PubMed

    Deng, Wei-Qiao; Sun, Lei; Huang, Jin-Dou; Chai, Shuo; Wen, Shu-Hao; Han, Ke-Li

    2015-04-01

    This protocol is intended to provide chemists and physicists with a tool for predicting the charge carrier mobilities of π-stacked systems such as organic semiconductors and the DNA double helix. An experimentally determined crystal structure is required as a starting point. The simulation involves the following operations: (i) searching the crystal structure; (ii) selecting molecular monomers and dimers from the crystal structure; (iii) using density function theory (DFT) calculations to determine electronic coupling for dimers; (iv) using DFT calculations to determine self-reorganization energy of monomers; and (v) using a numerical calculation to determine the charge carrier mobility. For a single crystal structure consisting of medium-sized molecules, this protocol can be completed in ∼4 h. We have selected two case studies (a rubrene crystal and a DNA segment) as examples of how this procedure can be used.

  13. 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.

  14. Quantitative Imaging of Turbulent Mixing Dynamics in High-Pressure Fuel Injection to Enable Predictive Simulations of Engine Combustion

    SciTech Connect

    Frank, Jonathan H.; Pickett, Lyle M.; Bisson, Scott E.; Patterson, Brian D.; Ruggles, Adam J.; Skeen, Scott A.; Manin, Julien Luc; Huang, Erxiong; Cicone, Dave J.; Sphicas, Panos

    2015-09-01

    In this LDRD project, we developed a capability for quantitative high - speed imaging measurements of high - pressure fuel injection dynamics to advance understanding of turbulent mixing in transcritical flows, ignition, and flame stabilization mechanisms, and to provide e ssential validation data for developing predictive tools for engine combustion simulations. Advanced, fuel - efficient engine technologies rely on fuel injection into a high - pressure, high - temperature environment for mixture preparation and com bustion. Howe ver, the dynamics of fuel injection are not well understood and pose significant experimental and modeling challenges. To address the need for quantitative high - speed measurements, we developed a Nd:YAG laser that provides a 5ms burst of pulses at 100 kHz o n a robust mobile platform . Using this laser, we demonstrated s patially and temporally resolved Rayleigh scattering imaging and particle image velocimetry measurements of turbulent mixing in high - pressure gas - phase flows and vaporizing sprays . Quantitativ e interpretation of high - pressure measurements was advanced by reducing and correcting interferences and imaging artifacts.

  15. Simulation of collaborative studies for real-time PCR-based quantitation methods for genetically modified crops.

    PubMed

    Watanabe, Satoshi; Sawada, Hiroshi; Naito, Shigehiro; Akiyama, Hiroshi; Teshima, Reiko; Furui, Satoshi; Kitta, Kazumi; Hino, Akihiro

    2013-01-01

    To study impacts of various random effects and parameters of collaborative studies on the precision of quantitation methods of genetically modified (GM) crops, we developed a set of random effects models for cycle time values of a standard curve-based relative real-time PCR that makes use of an endogenous gene sequence as the internal standard. The models and data from a published collaborative study for six GM lines at four concentration levels were used to simulate collaborative studies under various conditions. Results suggested that by reducing the numbers of well replications from three to two, and standard levels of endogenous sequence from five to three, the number of unknown samples analyzable on a 96-well PCR plate in routine analyses could be almost doubled, and still the acceptable repeatability RSD (RSDr < or = 25%) and the reproducibility RSD (RSDR < 35%) of the collaborative study could be met. Further, RSDr and RSD(R) were found most sensitive to random effects attributable to inhomogeneity among blind replicates, but they were little influenced by those attributable to DNA extractions. The proposed models are expected to be useful for optimizing standard curve-based relative quantitation methods for GM crops by real-time PCR and their collaborative studies.

  16. Quantitative Simulation of Granular Collapse Experiments with Visco-Plastic Models

    NASA Astrophysics Data System (ADS)

    Mangeney, A.; Ionescu, I. R.; Bouchut, F.; Roche, O.

    2014-12-01

    One of the key issues in landslide modeling is to define the appropriate rheological behavior of these natural granular flows. In particular the description of the static and of the flowing states of granular media is still an open issue. This plays a crucial role in erosion/deposition processes. A first step to address this issue is to derive models able to reproduce laboratory experiments of granular flows. We propose here a mechanical and numerical model of dry granular flows that quantitatively well reproduces granular column collapse over inclined planes, with rheological parameters directly derived from the laboratory experiments. We reformulate the so-called μ(I) rheology proposed by Jop et al. (2006) where I is the so-called inertial number in the framework of Drucker-Prager plasticity with yield stress and a viscosity η(||D||, p) depending on both the pressure p and the norm of the strain rate tensor ||D||. The resulting dynamic viscosity varies from very small values near the free surface and near the front to 1.5 Pa.s within the quasi-static zone. We show that taking into account a constant mean viscosity during the flow (η = 1 Pa.s here) provides results very similar to those obtained with the variable viscosity deduced from the μ(I) rheology, while significantly reducing the computational cost. This has important implication for application to real landslides and rock avalanches. The numerical results show that the flow is essentially located in a surface layer behind the front, while the whole granular material is flowing near the front where basal sliding occurs. The static/flowing interface changes as a function of space and time, in good agreement with experimental observations. Heterogeneities are observed within the flow with low and high pressure zones, localized small upward velocity zones and vortices near the transition between the flowing and static grains. These instabilities create 'sucking zones' and have some characteristics similar

  17. Flow visualization and quantitative velocity and pressure measurements in simulated single and double brush seals

    NASA Technical Reports Server (NTRS)

    Braun, M. J.; Canacci, V. A.; Hendricks, R. C.

    1991-01-01

    A method to visualize and characterize the complex flow fields in simulated single and double brush seals is presented. The brush seal configuration was tested in a gravity fed water tunnel and a pump driven pressurized oil tunnel. Visualization of the flow field revealed regions that are characteristically river jetting, vortical, crossflow and exist upstream, downstream or within the seal. Such flows are especially engendered by variations in fiber void that are spatial and temporal and affect changes in seal leakage and stability. While the effects of interface motion and cylindrical configuration have not been considered herein, it is believed that the observed flow fields and pressure drop patterns characterize flow phenomenology in brush seals. The axial pressure profiles upstream, across and downstream of the brush have been measured under a variety of inlet pressure conditions and the ensuing pressure maps are presented and discussed. Through the application of the Full Flow Field Tracking method developed by the authors, the flow patterns and the accompanying fluid velocities inside the brush were non-intrusively determined and graphically reconstructed.

  18. 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

  19. Development of a multi-wavelength diffuse optical tomography system for early diagnosis of rheumatoid arthritis: simulation, phantoms and healthy human studies

    PubMed Central

    Wu, Hao Yang; Filer, Andrew; Styles, Iain; Dehghani, Hamid

    2016-01-01

    A multi-wavelength diffuse optical tomography (DOT) system has been developed to directly extract physiological information, such as total haemoglobin concentration, from tissue in human hand joints. Novel methods for 3D surface imaging and spectrally constrained image reconstruction are introduced and their potential application to imaging of rheumatoid arthritis is discussed. Results are presented from simulation studies as well as experiments using phantoms and data from imaging of three healthy volunteers. The image features are recovered partially for phantom data using transmission measurements only. Images that reveal joint regions and surrounding features within the hand are shown to co-register with co–acquired ultrasound images which are shown to be related to total haemoglobin concentration. PMID:27896015

  20. 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

  1. Computer-Aided Diagnosis in Phase Contrast Imaging X-Ray Computed Tomography for Quantitative Characterization of ex vivo Human Patellar Cartilage

    PubMed Central

    Nagarajan, Mahesh B.; Coan, Paola; Huber, Markus B.; Diemoz, Paul C.; Glaser, Christian; Wismüller, Axel

    2014-01-01

    Visualization of ex vivo human patellar cartilage matrix through the phase contrast imaging X-ray computed tomography (PCI-CT) has been previously demonstrated. Such studies revealed osteoarthritis-induced changes to chondrocyte organization in the radial zone. This study investigates the application of texture analysis to characterizing such chondrocyte patterns in the presence and absence of osteoarthritic damage. Texture features derived from Minkowski functionals (MF) and gray-level co-occurrence matrices (GLCM) were extracted from 842 regions of interest (ROI) annotated on PCI-CT images of ex vivo human patellar cartilage specimens. These texture 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). The best classification performance was observed with the MF features perimeter (AUC: 0.94 ± 0.08) and “Euler characteristic” (AUC: 0.94 ± 0.07), and GLCM-derived feature “Correlation” (AUC: 0.93 ± 0.07). These results suggest that such texture features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix, enabling classification of cartilage as healthy or osteoarthritic with high accuracy. PMID:23744660

  2. Computer-aided diagnosis in phase contrast imaging X-ray computed tomography for quantitative characterization of ex vivo human patellar cartilage.

    PubMed

    Nagarajan, Mahesh B; Coan, Paola; Huber, Markus B; Diemoz, Paul C; Glaser, Christian; Wismuller, Axel

    2013-10-01

    Visualization of ex vivo human patellar cartilage matrix through the phase contrast imaging X-ray computed tomography (PCI-CT) has been previously demonstrated. Such studies revealed osteoarthritis-induced changes to chondrocyte organization in the radial zone. This study investigates the application of texture analysis to characterizing such chondrocyte patterns in the presence and absence of osteoarthritic damage. Texture features derived from Minkowski functionals (MF) and gray-level co-occurrence matrices (GLCM) were extracted from 842 regions of interest (ROI) annotated on PCI-CT images of ex vivo human patellar cartilage specimens. These texture 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). The best classification performance was observed with the MF features perimeter (AUC: 0.94 ±0.08 ) and "Euler characteristic" (AUC: 0.94 ±0.07 ), and GLCM-derived feature "Correlation" (AUC: 0.93 ±0.07). These results suggest that such texture features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix, enabling classification of cartilage as healthy or osteoarthritic with high accuracy.

  3. Quantitative estimation of infarct size by simultaneous dual radionuclide single photon emission computed tomography: comparison with peak serum creatine kinase activity

    SciTech Connect

    Kawaguchi, K.; Sone, T.; Tsuboi, H.; Sassa, H.; Okumura, K.; Hashimoto, H.; Ito, T.; Satake, T. )

    1991-05-01

    To test the hypothesis that simultaneous dual energy single photon emission computed tomography (SPECT) with technetium-99m (99mTc) pyrophosphate and thallium-201 (201TI) can provide an accurate estimate of the size of myocardial infarction and to assess the correlation between infarct size and peak serum creatine kinase activity, 165 patients with acute myocardial infarction underwent SPECT 3.2 +/- 1.3 (SD) days after the onset of acute myocardial infarction. In the present study, the difference in the intensity of 99mTc-pyrophosphate accumulation was assumed to be attributable to difference in the volume of infarcted myocardium, and the infarct volume was corrected by the ratio of the myocardial activity to the osseous activity to quantify the intensity of 99mTc-pyrophosphate accumulation. The correlation of measured infarct volume with peak serum creatine kinase activity was significant (r = 0.60, p less than 0.01). There was also a significant linear correlation between the corrected infarct volume and peak serum creatine kinase activity (r = 0.71, p less than 0.01). Subgroup analysis showed a high correlation between corrected volume and peak creatine kinase activity in patients with anterior infarctions (r = 0.75, p less than 0.01) but a poor correlation in patients with inferior or posterior infarctions (r = 0.50, p less than 0.01). In both the early reperfusion and the no reperfusion groups, a good correlation was found between corrected infarct volume and peak serum creatine kinase activity (r = 0.76 and r = 0.76, respectively; p less than 0.01).

  4. Volumetric quantitative characterization of human patellar cartilage with topological and geometrical features on phase-contrast X-ray computed tomography.

    PubMed

    Nagarajan, Mahesh B; Coan, Paola; Huber, Markus B; Diemoz, Paul C; Wismüller, Axel

    2015-11-01

    Phase-contrast X-ray computed tomography (PCI-CT) has attracted significant interest in recent years for its ability to provide significantly improved image contrast in low absorbing materials such as soft biological tissue. In the research context of cartilage imaging, previous studies have demonstrated the ability of PCI-CT to visualize structural details of human patellar cartilage matrix and capture changes to chondrocyte organization induced by osteoarthritis. This study evaluates the use of geometrical and topological features for volumetric characterization of such chondrocyte patterns in the presence (or absence) of osteoarthritic damage. Geometrical features derived from the scaling index method (SIM) and topological features derived from Minkowski Functionals were extracted from 1392 volumes of interest (VOI) 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 VOIs as healthy or osteoarthritic; classification performance was evaluated using the area under the receiver operating characteristic curve (AUC). Our results show that the classification performance of SIM-derived geometrical features (AUC: 0.90 ± 0.09) is significantly better than Minkowski Functionals volume (AUC: 0.54 ± 0.02), surface (AUC: 0.72 ± 0.06), mean breadth (AUC: 0.74 ± 0.06) and Euler characteristic (AUC: 0.78 ± 0.04) (p < 10(-4)). These results suggest that such geometrical features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix in an automated manner, while also enabling classification of cartilage as healthy or osteoarthritic with high accuracy. Such features could potentially serve as diagnostic imaging markers for evaluating osteoarthritis progression and its response to different therapeutic intervention strategies.

  5. Quantitative single photon emission computed thallium-201 tomography for detection and localization of coronary artery disease: Optimization and prospective validation of a new technique

    SciTech Connect

    Maddahi, J.; Van Train, K.; Prigent, F.; Garcia, E.V.; Friedman, J.; Ostrzega, E.; Berman, D. )

    1989-12-01

    One hundred eight-three men underwent stress-redistribution thallium-201 myocardial perfusion tomography. After evaluation of various preprocessing filters in a phantom study, the Butterworth filter with a frequency cutoff of 0.2 cycles/pixel, order 5 (which provided optimal filter power) was used in the back projection algorithm of the patient studies. All short-axis and apical portions of vertical long-axis images were quantified by dividing each myocardial slice into 60 equal sectors and displaying the maximal count per sector as a linear profile. In a pilot group consisting of 20 normal men (less than 5% likelihood of coronary artery disease) and 25 men with coronary artery disease (greater than or equal to 50% coronary stenosis by angiography), profiles representing the lowest observed value below the mean normal profiles provided the best threshold for defining normal limits. Abnormal portions of the patient profiles were plotted on a two-dimensional polar map. The polar map was divided into 102 sectors, and sectors with a probability of greater than or equal to 80% for disease of each one of the three major coronary arteries were clustered to represent specific coronary artery territories. Receiver operating characteristic curve analysis for defect size showed that the optimal threshold for defining a definite perfusion defect was 12% for the left anterior descending and left circumflex and 8% for the right coronary artery territories. These criteria were prospectively applied to an additional 92 patients with angiographic coronary artery disease, 18 patients with normal coronary arteriograms and 28 patients with less than 5% likelihood of coronary disease. Sensitivity, specificity and normalcy rate for overall detection of coronary disease were 96%, 56% and 86%, respectively.

  6. Quantitative evaluation of the relationship between dorsal wall length, sole thickness, and rotation of the distal phalanx in the bovine claw using computed tomography.

    PubMed

    Tsuka, T; Murahata, Y; Azuma, K; Osaki, T; Ito, N; Okamoto, Y; Imagawa, T

    2014-10-01

    Computed tomography (CT) was performed on 800 untrimmed claws (400 inner claws and 400 outer claws) of 200 pairs of bovine hindlimbs to investigate the relationships between dorsal wall length and sole thickness, and between dorsal wall length and the relative rotation angle of distal phalanx-to-sole surface (S-D angle). Sole thickness was 3.8 and 4.0 mm at the apex of the inner claws and outer claws, respectively, with dorsal wall lengths <70 mm. These sole thickness values were less than the critical limit of 5 mm, which is associated with a softer surface following thinning of the soles. A sole thickness of 5 mm at the apex was estimated to correlate with dorsal wall lengths of 72.1 and 72.7 mm for the inner and outer claws, respectively. Sole thickness was 6.1 and 6.4 mm at the apex of the inner and outer claws, respectively, with dorsal wall lengths of 75 mm. These sole thickness values were less than the recommended sole thickness of 7 mm based on the protective function of the soles. A sole thickness >7 mm at the apex was estimated to correlate with a dorsal wall length of 79.8 and 78.4mm for the inner and outer claws, respectively. The S-D angles were recorded as anteversions of 2.9° and 4.7° for the inner and outer claws, respectively, with a dorsal wall length of 75 mm. These values indicate that the distal phalanx is likely to have rotated naturally forward toward the sole surface. The distal phalanx rotated backward to the sole surface at 3.2° and 7.6° for inner claws with dorsal wall lengths of 90-99 and ≥100 mm, respectively; and at 3.5° for outer claws with a dorsal wall length ≥100 mm. Dorsal wall lengths of 85.7 and 97.2 mm were estimated to correlate with a parallel positional relationship of the distal phalanx to the sole surface in the inner and outer claws, respectively.

  7. Quantitative Positron Emission Tomography Imaging Detects Early Metabolic Remodeling in a Mouse Model of Pressure Overload Left Ventricular Hypertrophy in vivo

    PubMed Central

    Zhong, Min; Alonso, Clayton E.; Taegtmeyer, Heinrich; Kundu, Bijoy K.

    2013-01-01

    We proposed that metabolic remodeling in the form of increased myocardial glucose analogue 2-[18F] fluoro-2deoxy-D-glucose (FDG) uptake precedes and triggers the onset of severe contractile dysfunction in pressure overload left ventricular hypertrophy (LVH) in vivo. To test this hypothesis we used a mouse model of transverse aortic constriction (TAC) together with Positron Emission Tomography (PET) and assessed serial changes in cardiac metabolism and function over 7 days. Methods PET scans of 16 C57BL/6 male mice were performed using a microPET scanner under sevofluorane anesthesia. A 10-minute transmission scan was followed by a 60-minute dynamic FDG-PET scan with cardiac and respiratory gating. Blood glucose levels were measured before and after the emission scan. Transverse aortic constriction (TAC) and sham surgeries were performed after baseline imaging. Osmotic mini-pumps containing either propranolol (5 mg/kg/day) or vehicle alone were implanted subcutaneously at the end of surgery. Subsequent scans were taken at days 1 and 7 after surgery. A compartment model, in which the blood input function with spill-over and partial volume corrections and the metabolic rate constants in a 3-compartment model are simultaneously estimated, was used to determine the net myocardial FDG influx constant, Ki. The rate of myocardial glucose use, rMGU, was also computed. Estimations of the ejection fractions (EF) were based on the high resolution gated PET images Results Mice undergoing TAC surgery exhibited an increase in the Ki (580%) and glucose usage the day after surgery indicating early adaptive response. On day 7 the EF had decreased by 24% indicating a maladaptive response. Average Ki increases were not linearly associated with increases in rMGU. Ki exceeded rMGU by 29% in the TAC mice. TAC Mice treated with propranolol attenuated rate of FDG uptake, diminished mismatch between Ki and rMGU (9%) and rescued cardiac function. Conclusions Metabolic maladaptation precedes

  8. Quantitative Analysis of Outer Retinal Tubulation in Age-Related Macular Degeneration From Spectral-Domain Optical Coherence Tomography and Histology

    PubMed Central

    Litts, Katie M.; Ach, Thomas; Hammack, Kristen M.; Sloan, Kenneth R.; Zhang, Yuhua; Freund, K. Bailey; Curcio, Christine A.

    2016-01-01

    Purpose To assess outer retinal tubulation (ORT) morphology from spectral-domain optical coherence tomography (SD-OCT) volumes and donor eye histology, analyze ORT reflectivity, and estimate the number of cones surviving in ORT. Methods In SD-OCT volumes from nine patients with advanced AMD, ORT was analyzed en face and in B-scans. The hyperreflective ORT border in cross-section was delineated and surface area calculated. Reflectivity was compared between ORT types (Closed, Open, Forming, and Branching). A flatmount retina from a donor with neovascular AMD was labeled to visualize the external limiting membrane that delimits ORT and allow measurements of cross-sectional cone area, center-to-center cone spacing, and cone density. The number of cones surviving in ORT was estimated. Results By en face SD-OCT, ORT varies in complexity and shape. Outer retinal tubulation networks almost always contain Closed cross-sections. Spectral-domain OCT volumes containing almost exclusively Closed ORTs showed no significant direction-dependent differences in hyperreflective ORT border intensity. The surface areas of partial ORT assessed by SD-OCT volumes ranged from 0.16 to 1.76 mm2. From the flatmount retina, the average cross-sectional area of cone inner segments was 49.1 ± 7.9 μm2. The average cone spacing was 7.5 ± 0.6 μm. Outer retinal tubulation cone density was 20,351 cones/mm2. The estimated number of cones in ORT in a macula ranged from 26,399 to 186,833 cones, which is 6% to 44% of the cones present in a healthy macula. Conclusions These first estimates for cone density and number of cones surviving in ORT suggest that ORT formation considerably distorts the photoreceptor mosaic. Results provide additional insight into the reflectivity characteristics and number of ORT cones observable in living patients by SD-OCT, as cones persist and disease progresses. PMID:27177321

  9. In vivo quantitative imaging of photoassimilate transport dynamics and allocation in large plants using a commercial positron emission tomography (PET) scanner

    DOE PAGES

    Karve, Abhijit A.; Alexoff, David; Kim, Dohyun; ...

    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

  10. 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.; Cho, Michael H.; Hersh, Craig P.; Lange, Christoph; Wouters, Emiel; Casaburi, Richard H.; Coxson, Harvey O.; MacNee, William; Rennard, Stephen I.; Lomas, David A.; Agusti, Alvar; Celli, Bartolome R.; Black-Shinn, Jennifer L.; Kinney, Greg L.; Lutz, Sharon M.; Hokanson, John E.; Silverman, Edwin K.

    2014-01-01

    Rationale: Muscle wasting in chronic obstructive pulmonary disease (COPD) is associated with a poor prognosis and is not readily assessed by measures of body mass index (BMI). BMI does not discriminate between relative proportions of adipose tissue and lean muscle and may be insensitive to early pathologic changes in body composition. Computed tomography (CT)–based assessments of the pectoralis muscles may provide insight into the clinical significance of skeletal muscles in smokers. Objectives: We hypothesized that objective assessment of the pectoralis muscle area on chest CT scans provides information that is clinically relevant and independent of BMI. Methods: Data from the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) Study (n = 73) were used to assess the relationship between pectoralis muscle area and fat-free mass. We then used data in a subset (n = 966) of a larger cohort, the COPDGene (COPD Genetic Epidemiology) Study, to explore the relationship between pectoralis muscle area and COPD-related traits. Measurements and Main Results: We first investigated the correlation between pectoralis muscle area and fat-free mass, using data from a subset of participants in the ECLIPSE Study. We then further investigated pectoralis muscle area in COPDGene Study participants and found that higher pectoralis muscle area values were associated with greater height, male sex, and younger age. On subsequent clinical correlation, compared with BMI, pectoralis muscle area was more significantly associated with COPD-related traits, including spirometric measures, dyspnea, and 6-minute-walk distance (6MWD). For example, on average, each 10-cm2 increase in pectoralis muscle area was associated with a 0.8-unit decrease in the BODE (Body mass index, Obstruction, Dyspnea, Exercise) index (95% confidence interval, –1.0 to –0.6; P < 0.001). Furthermore, statistically significant associations between pectoralis muscle area and COPD

  11. 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

  12. 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

  13. Can simulations quantitatively predict peptide transfer free energies to urea solutions? Thermodynamic concepts and force field limitations.

    PubMed

    Horinek, Dominik; Netz, Roland R

    2011-06-16

    Many proteins denature when they are transferred to concentrated urea solutions. Three mechanisms for urea's denaturing ability have been proposed: (i) direct binding to polar parts of the protein surface, (ii) direct binding to nonpolar parts of the protein surface, and (iii) an indirect effect mediated by modifications of the bulk water properties. The disentanglement of these three processes has been the goal of many experimental and computational studies, yet there is no final agreement on the relative importance of the three contributions. The separation of the two direct mechanisms, albeit conceptually clear, is difficult in experimental studies and in simulations depends subtly on how the discrimination between polar and nonpolar groups is accomplished. Indirect effects, embodied in the change of solution activity as urea is added, are rarely monitored in urea/peptide simulations and thus have remained elusive in numerical studies. In this paper we establish a rigorous separation of all three contributions to the solvation thermodynamics of stretched peptide chains. We contrast this scenario with two commonly used model systems: the air/water interface and the interface between water and a hydrophobic alkane self-assembled monolayer. Together with bulk thermodynamic properties of urea/water mixed solvents, a complete thermodynamic description of the urea/water/peptide system is obtained: urea avoids the air/water interface but readily adsorbs at the oil-water interface and at hydrophobic as well as hydrophilic peptide chains, in accordance with experimental results. Simple thermodynamic arguments show that the indirect contribution to urea's denaturing capability is negligibly small, although urea strongly changes the water bulk properties as judged by the number of hydrogen bonds formed. Urea's tendency to bind to proteins is correctly reproduced with several force field combinations, but the quantitative binding strength as well as the relative importance

  14. A novel synthetic aperture technique for breast tomography with toroidal arrays

    SciTech Connect

    Huang, Lianjie; Simonetti, Francesco

    2009-01-01

    Ultrasound is commonly used as an adjunct to mammography for diagnostic evaluation of suspicions arising from breast cancer screening. As an alternative to conventional sonography that uses hand-held transducers, toroidal array probes that encircle the breast immersed in a water bath have been investigated for ultrasound tomography. This paper introduces a new method for three-dimensional synthetic aperture diffraction tomography that maximizes the resolution in the scanning direction and provides quantitative reconstructions of the acoustic properties of the object. The method is validated by means of numerical simulations.

  15. 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.

  16. 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.

  17. Insights into the Key Compounds of Durian (Durio zibethinus L. 'Monthong') Pulp Odor by Odorant Quantitation and Aroma Simulation Experiments.

    PubMed

    Li, Jia-Xiao; Schieberle, Peter; Steinhaus, Martin

    2017-01-25

    Sixteen compounds, previously identified as potent odorants by application of an aroma extract dilution analysis and the gas chromatography-olfactometry analysis of static headspace samples, were quantitated in the pulp of durians, variety Monthong, and odor activity values (OAVs) were calculated by dividing the concentrations obtained by the odor thresholds of the compounds in water. In combination with data recently reported for hydrogen sulfide and short-chain alkanethiols, OAVs > 1 were obtained for 19 compounds, among which ethyl (2S)-2-methylbutanoate (fruity; OAV 1700000), ethanethiol (rotten onion; OAV 480000), and 1-(ethylsulfanyl)ethane-1-thiol (roasted onion; OAV 250000) were the most potent, followed by methanethiol (rotten, cabbage; OAV 45000), ethane-1,1-dithiol (sulfury, durian; OAV 23000), and ethyl 2-methylpropanoate (fruity; OAV 22000). Aroma simulation and omission experiments revealed that the overall odor of durian pulp could be mimicked by only two compounds, namely, ethyl (2S)-2-methylbutanoate and 1-(ethylsulfanyl)ethane-1-thiol, when combined in their natural concentrations.

  18. Final Report (2010-2015) for the Topical Collaboration on Quantitative Jet and Electromagnetic Tomography (JET) of Extreme Phases of Matter in Heavy-ion Collisions

    SciTech Connect

    Gyulassy, Miklos; Romatschke, Paul; Bass, Steffen; Muller, Berndt; Strickland, Michael; Wang, Xin -Nian; Vogt, Ramona; Vitev, Ivan; Gale, Charles; Jeon, Sangyong; Heinz, Ulrich; Molnar, Denes; Fries, Rainer; Ko, Che -Ming; Majumder, Abhijit

    2015-08-31

    During the 5-year funding period (2010-2015), the JET Collaboration carried out a comprehensive research program with coordinated efforts involving all PI members and external associated members according to the plan and milestones outlined in the approved JET proposal. We identified important issues in the study of parton energy loss and made significant progress toward NLO calculations; advanced event-by-event hydrodynamic simulations of bulk matter evolution; developed Monte Carlo tools that combine different parton energy loss approaches, hydrodynamic models and parton recombination model for jet hadronization; and carried out the first comprehensive phenomenological study to extract the jet transport parameter.

  19. Validation of quantitation of regional myocardial blood flow in vivo with /sup 11/C-labeled human albumin microspheres and positron emission tomography. [Dogs

    SciTech Connect

    Wilson, R.A.; Shea, M.J.; De Landsheere, C.M.; Turton, D.; Brady, F.; Deanfield, J.E.; Selwyn, A.P.

    1984-10-01

    Use of radiolabeled microspheres is a standard method to measure regional myocardial perfusion in animals. Human albumin microspheres have been given safely to patients, but positron-emitting /sup 67/Ga-labeled human albumin microspheres are characterized by an unstable radiolabel. A new labeling procedure that covalently binds /sup 11/C to human albumin microspheres via /sup 11/CH/sub 3/I was developed. Seven open-chest and two closed-chest dogs were studied. Reference and /sup 11/C-labeled human albumin microspheres (2 to 25 mCi) were both injected into the left atrium. Positron tomographic images were obtained of the myocardial distribution of the /sup 11/C-labeled microspheres. Timed arterial withdrawal was used for both reference gamma-labeled microspheres and /sup 11/C-labeled human albumin microspheres. Regional myocardial perfusion calculated by this technique correlated well with values obtained with reference microspheres over a range of 0.2 to 3.5 ml/min/g. Thus, /sup 11/C human albumin microspheres are stable radiochemically and can be used as a quantitative measure of regional myocardial perfusion.

  20. Multi-institutional Quantitative Evaluation and Clinical Validation of Smart Probabilistic Image Contouring Engine (SPICE) Autosegmentation of Target Structures and Normal Tissues on Computer Tomography Images in the Head and Neck, Thorax, Liver, and Male Pelvis Areas

    SciTech Connect

    Zhu, Mingyao; Bzdusek, Karl; Brink, Carsten; Eriksen, Jesper Grau; Hansen, Olfred; Jensen, Helle Anita; Gay, Hiram A.; Thorstad, Wade; Widder, Joachim; Brouwer, Charlotte L.; Steenbakkers, Roel J.H.M.; Vanhauten, Hubertus A.M.; Cao, Jeffrey Q.; McBrayne, Gail; Patel, Salil H.; Cannon, Donald M.; Hardcastle, Nicholas; Tomé, Wolfgang A.; Guckenberg, Matthias; Parikh, Parag J.

    2013-11-15

    Purpose: Clinical validation and quantitative evaluation of computed tomography (CT) image autosegmentation using Smart Probabilistic Image Contouring Engine (SPICE). Methods and Materials: CT images of 125 treated patients (32 head and neck [HN], 40 thorax, 23 liver, and 30 prostate) in 7 independent institutions were autosegmented using SPICE and computational times were recorded. The number of structures autocontoured were 25 for the HN, 7 for the thorax, 3 for the liver, and 6 for the male pelvis regions. Using the clinical contours as reference, autocontours of 22 selected structures were quantitatively evaluated using Dice Similarity Coefficient (DSC) and Mean Slice-wise Hausdorff Distance (MSHD). All 40 autocontours were evaluated by a radiation oncologist from the institution that treated the patients. Results: The mean computational times to autosegment all the structures using SPICE were 3.1 to 11.1 minutes per patient. For the HN region, the mean DSC was >0.70 for all evaluated structures, and the MSHD ranged from 3.2 to 10.0 mm. For the thorax region, the mean DSC was 0.95 for the lungs and 0.90 for the heart, and the MSHD ranged from 2.8 to 12.8 mm. For the liver region, the mean DSC was >0.92 for all structures, and the MSHD ranged from 5.2 to 15.9 mm. For the male pelvis region, the mean DSC was >0.76 for all structures, and the MSHD ranged from 4.8 to 10.5 mm. Out of the 40 autocontoured structures reviews by experts, 25 were scored useful as autocontoured or with minor edits for at least 90% of the patients and 33 were scored useful autocontoured or with minor edits for at least 80% of the patients. Conclusions: Compared with manual contouring, autosegmentation using SPICE for the HN, thorax, liver, and male pelvis regions is efficient and shows significant promise for clinical utility.

  1. 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.

  2. Impaired exercise-related myocardial uptake of technetium-99m-tetrofosmin in relation to coronary narrowing and diabetic state: assessment with quantitative single photon emission computed tomography.

    PubMed

    Sasao, H; Nakata, T; Tsuchihashi, K; Wakabayashi, T; Nakaihara, N; Doi, A; Hashimoto, A; Kobayashi, H; Shimamoto, K

    2001-01-01

    Despite the diagnostic efficacy of stress myocardial perfusion imaging, the correlation between the actual perfusion tracer activity and diseased state of a coronary artery has not been studied in detail. We estimated exercise-related perfusion augmentation in relation to disease states of a coronary artery in diabetic and non-diabetic patients by a newly developed quantitative technetium (Tc)-99m-tetrofosmin myocardial imaging technique. Tc-99m-tetrofosmin tomographic imaging with an exercise-rest protocol was performed in 26 stable coronary patients and in 8 age-matched controls. Percent increase (%IR) in myocardial count during symptom-limited submaximal exercise-stress was calculated in 16 non-infarcted polar map segments and in each coronary territory by a subtraction technique with corrections for physical decay and injected tracer doses, and the results were compared with those of angiographically quantified coronary diameter stenosis (%DS). Percent IR and peak heart rate during exercise showed a positive linear correlation both in coronary territories with significant stenosis (%DS > or = 75%) and in control or nonstenotic (%DS < 75%) territories. The regression line in stenotic regions was, however. significantly (p < 0.01) shifted downward compared to that in non-stenotic regions. Percent IR in stenotic regions showed a significant inverse correlation with %DS. Coronary stenosis of 75% or more was identified by a %IR cutoff value of 40% with 77% sensitivity, 70% specificity, and an accuracy of 72%. In coronary territories with a %DS of less than 75%, %IR in diabetic patients was significantly lower (46+/-15%) than that in nondiabetic patients (61+/-25%). Thus, blunted exercise-related augmentation of myocardial uptake of Tc-99m-tetrofosmin correlates with the severity of coronary narrowing and diabetic state.

  3. Dynamic contrast enhanced magnetic resonance perfusion imaging in high-risk smokers and smoking-related COPD: correlations with pulmonary function tests and quantitative computed tomography.

    PubMed

    Xia, Yi; Guan, Yu; Fan, Li; Liu, Shi-Yuan; Yu, Hong; Zhao, Li-Ming; Li, Bing

    2014-09-01

    The study aimed to prospectively evaluate correlations between dynamic contrast-enhanced (DCE) MR perfusion imaging, pulmonary function tests (PFT) and volume quantitative CT in smokers with or without chronic obstructive pulmonary disease (COPD) and to determine the value of DCE-MR perfusion imaging and CT volumetric imaging on the assessment of smokers. According to the ATS/ERS guidelines, 51 male smokers were categorized into five groups: At risk for COPD (n = 8), mild COPD (n = 9), moderate COPD (n = 12), severe COPD (n = 10), and very severe COPD (n = 12). Maximum slope of increase (MSI), positive enhancement integral (PEI), etc. were obtained from MR perfusion data. The signal intensity ratio (RSI) of the PDs and normal lung was calculated (RSI = SIPD/SInormal). Total lung volume (TLV), total emphysema volume (TEV) and emphysema index (EI) were obtained from volumetric CT data. For "at risk for COPD," the positive rate of PDs on MR perfusion images was higher than that of abnormal changes on non-enhanced CT images (p < 0.05). Moderate-to-strong positive correlations were found between all the PFT parameters and SIPD, or RSI (r range 0.445∼0.683, p ≤ 0.001). TEV and EI were negatively correlated better with FEV1/FVC than other PFT parameters (r range -0.48 --0.63, p < 0.001). There were significant differences in RSI and SIPD between "at risk for COPD" and "very severe COPD," and between "mild COPD" and "very severe COPD". Thus, MR perfusion imaging may be a good approach to identify early evidence of COPD and may have potential to assist in classification of COPD.

  4. Quantitative three-dimensional analysis of poly (lactic-co-glycolic acid) microsphere using hard X-ray nano-tomography revealed correlation between structural parameters and drug burst release.

    PubMed

    Huang, Xiaozhou; Li, Na; Wang, Dajiang; Luo, Yuyan; Wu, Ziyu; Guo, Zhefei; Jin, Qixing; Liu, Zhuying; Huang, Yafei; Zhang, Yongming; Wu, Chuanbin

    2015-08-10

    The objective of this study was to investigate the use of transmission hard X-ray nano-computed-tomography (nano-CT) for characterization of the pore structure and drug distribution in poly (lactic-co-glycolic acid) (PLGA) microspheres encapsulating bovine serum albumin and to study the correlation between drug distribution and burst release. The PLGA microspheres were fabricated using a double-emulsion method. The results of pore structure analysis accessed with nano-CT were compared with those acquired by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). Surface pore interconnectivity and surface protein interconnectivity were obtained using combined nano-CT and pixel analysis. The correlation between surface protein interconnectivity with the initial burst release across various tested formulations was also analyzed. The size, shape, and distribution of the pores and protein could be clearly observed in the whole microsphere using nano-CT, whereas only the sectional information was observed using SEM or CLSM. Interconnected pores and surface connected pores could be clearly distinguished in nano-CT, which enables the quantitative analysis of surface pore interconnectivity and surface protein interconnectivity. The surface protein interconnectivity in different formulations correlated well with the burst release at 5-10h. Nano-CT provided a nondestructive, high-resolution, and three-dimensional analysis method to characterize the porous microsphere.

  5. Modeling pure methane hydrate dissociation using a numerical simulator from a novel combination of X-ray computed tomography and macroscopic data

    SciTech Connect

    Gupta, A.; Moridis, G.J.; Kneafsey, T.J.; Sloan, Jr., E.D.

    2009-08-15

    The numerical simulator TOUGH+HYDRATE (T+H) was used to predict the transient pure methane hydrate (no sediment) dissociation data. X-ray computed tomography (CT) was used to visualize the methane hydrate formation and dissociation processes. A methane hydrate sample was formed from granular ice in a cylindrical vessel, and slow depressurization combined with thermal stimulation was applied to dissociate the hydrate sample. CT images showed that the water produced from the hydrate dissociation accumulated at the bottom of the vessel and increased the hydrate dissociation rate there. CT images were obtained during hydrate dissociation to confirm the radial dissociation of the hydrate sample. This radial dissociation process has implications for dissociation of hydrates in pipelines, suggesting lower dissociation times than for longitudinal dissociation. These observations were also confirmed by the numerical simulator predictions, which were in good agreement with the measured thermal data during hydrate dissociation. System pressure and sample temperature measured at the sample center followed the CH{sub 4} hydrate L{sub w}+H+V equilibrium line during hydrate dissociation. The predicted cumulative methane gas production was within 5% of the measured data. Thus, this study validated our simulation approach and assumptions, which include stationary pure methane hydrate-skeleton, equilibrium hydrate-dissociation and heat- and mass-transfer in predicting hydrate dissociation in the absence of sediments. It should be noted that the application of T+H for the pure methane hydrate system (no sediment) is outside the general applicability limits of T+H.

  6. Ultrasonic Lamb wave tomography

    NASA Astrophysics Data System (ADS)

    Leonard, Kevin R.; Malyarenko, Eugene V.; Hinders, Mark K.

    2002-12-01

    Nondestructive evaluation (NDE) of aerospace structures using traditional methods is a complex, time-consuming process critical to maintaining mission readiness and flight safety. Limited access to corrosion-prone structure and the restricted applicability of available NDE techniques for the detection of hidden corrosion or other damage often compound the challenge. In this paper we discuss our recent work using ultrasonic Lamb wave tomography to address this pressing NDE technology need. Lamb waves are ultrasonic guided waves, which allow large sections of aircraft structures to be rapidly inspected for structural flaws such as disbonds, corrosion and delaminations. Because the velocity of Lamb waves depends on thickness, for example, the